Index (adams-spectral-base-pom 25.9.0-SNAPSHOT API)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
All Classes All Packages

A

absdiffTipText() - Method in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: Returns the tip text for this property.
absoluteTipText() - Method in class adams.data.spectrumfilter.Covariance: Returns the tip text for this property.
absoluteTipText() - Method in class adams.data.spectrumfilter.LRCoeff: Returns the tip text for this property.
absoluteTipText() - Method in class adams.flow.transformer.SpectrumDiff: Returns the tip text for this property.
ABSORBANCE - adams.data.io.input.SoilCaresScannerSpectrumReader.AmplitudeType
ABSORBANCE - Static variable in class adams.data.io.input.SoilCaresScannerSpectrumReader: the column name for the wavelengths.
AbstractAmplitudeTransformer - Class in adams.data.spectrumfilter.amplitudetransform: Ancestor for amplitude transformation schemes.
AbstractAmplitudeTransformer() - Constructor for class adams.data.spectrumfilter.amplitudetransform.AbstractAmplitudeTransformer
AbstractBinaryFormatsBasedMultiSpectrumFilter - Class in adams.data.multifilter: Ancestor for formats-based filters that require exactly two spectra.
AbstractBinaryFormatsBasedMultiSpectrumFilter() - Constructor for class adams.data.multifilter.AbstractBinaryFormatsBasedMultiSpectrumFilter
AbstractCleaner - Class in adams.data.cleaner.instance: Abstract base class for cleaners handling weka.core.Instance objects.
AbstractCleaner - Class in adams.data.cleaner.spectrum: Abstract base class for cleaners handling Spectrum objects.
AbstractCleaner() - Constructor for class adams.data.cleaner.instance.AbstractCleaner
AbstractCleaner() - Constructor for class adams.data.cleaner.spectrum.AbstractCleaner
AbstractDatabaseConnectionCleaner - Class in adams.data.cleaner.instance: Ancestor for cleaners that require a database connection.
AbstractDatabaseConnectionCleaner - Class in adams.data.cleaner.spectrum: Ancestor for cleaners that require a database connection.
AbstractDatabaseConnectionCleaner() - Constructor for class adams.data.cleaner.instance.AbstractDatabaseConnectionCleaner
AbstractDatabaseConnectionCleaner() - Constructor for class adams.data.cleaner.spectrum.AbstractDatabaseConnectionCleaner
AbstractDatabaseFilter - Class in adams.data.spectrumfilter: Abstract superclass for filters that operate on the database.
AbstractDatabaseFilter() - Constructor for class adams.data.spectrumfilter.AbstractDatabaseFilter
AbstractDetrend - Class in adams.data.spectrumfilter.detrend: Ancestor for schemes that perform detrend.
AbstractDetrend() - Constructor for class adams.data.spectrumfilter.detrend.AbstractDetrend
AbstractEvaluator - Class in adams.data.evaluator.instance: Abstract base class for evaluator handling weka.core.Instance objects.
AbstractEvaluator() - Constructor for class adams.data.evaluator.instance.AbstractEvaluator
AbstractFieldInstanceGenerator - Class in adams.data.instances: Abstract base class for schemes that turn spectra into weka.core.Instance objects.
AbstractFieldInstanceGenerator() - Constructor for class adams.data.instances.AbstractFieldInstanceGenerator
AbstractFieldInstanceGeneratorWithClass - Class in adams.data.instances: Ancestor for generators that use fields and a target to generate the instance.
AbstractFieldInstanceGeneratorWithClass() - Constructor for class adams.data.instances.AbstractFieldInstanceGeneratorWithClass
AbstractFormatsBasedMultiSpectrumFilter - Class in adams.data.multifilter: Ancestor for filters that require the user to specify the formats of the spectra to use for the filtering process.
AbstractFormatsBasedMultiSpectrumFilter() - Constructor for class adams.data.multifilter.AbstractFormatsBasedMultiSpectrumFilter
AbstractIDProviderPanel - Class in adams.gui.tools.idprovider: Panel that generates IDs.
AbstractIDProviderPanel(IDConsumer) - Constructor for class adams.gui.tools.idprovider.AbstractIDProviderPanel: Initializes the panel with the owner.
AbstractInPlaceSpectrumTransformer - Class in adams.flow.transformer: Ancestor for spectrum transformers that allow the processing to happen in-place, rather than on a copy of the data.
AbstractInPlaceSpectrumTransformer() - Constructor for class adams.flow.transformer.AbstractInPlaceSpectrumTransformer
AbstractJCampSpectrumReader - Class in adams.data.io.input: Ancestor for JCamp spectrum formats.
AbstractJCampSpectrumReader() - Constructor for class adams.data.io.input.AbstractJCampSpectrumReader
AbstractMultiPageMenuItem - Class in adams.gui.visualization.threewaydata.heatmapviewer.multipageaction: Ancestor for menu item generators for the 3way data heatmap viewer's multi-page pane.
AbstractMultiPageMenuItem() - Constructor for class adams.gui.visualization.threewaydata.heatmapviewer.multipageaction.AbstractMultiPageMenuItem
AbstractMultiplicativeScatterCorrection - Class in adams.data.spectrumfilter.multiplicativescattercorrection: Ancestor for schemes that perform multiplicative scatter correction.
AbstractMultiplicativeScatterCorrection() - Constructor for class adams.data.spectrumfilter.multiplicativescattercorrection.AbstractMultiplicativeScatterCorrection
AbstractMultiSpectrumFilter - Class in adams.data.multifilter: Abstract base class for multi-spectrum filters.
AbstractMultiSpectrumFilter() - Constructor for class adams.data.multifilter.AbstractMultiSpectrumFilter
AbstractMultiSpectrumOperation - Class in adams.data.multispectrumoperation: Ancestor for multi-spectrum operations.
AbstractMultiSpectrumOperation() - Constructor for class adams.data.multispectrumoperation.AbstractMultiSpectrumOperation
AbstractMultiSpectrumReportFilter - Class in adams.data.multireportfilter: Abstract base class for multi-spectrum report filters.
AbstractMultiSpectrumReportFilter() - Constructor for class adams.data.multireportfilter.AbstractMultiSpectrumReportFilter
AbstractNearestNeighborBasedEvaluator - Class in adams.data.evaluator.instance: Ancestor for evaluators that use a nearest neighbor search.
AbstractNearestNeighborBasedEvaluator() - Constructor for class adams.data.evaluator.instance.AbstractNearestNeighborBasedEvaluator
AbstractOutlierRemoval - Class in adams.data.multispectrumoperation.outlierremoval: Ancestor for outlier removal schemes that work on multiple spectra.
AbstractOutlierRemoval() - Constructor for class adams.data.multispectrumoperation.outlierremoval.AbstractOutlierRemoval
AbstractParser(SPCSpectrumReader.AbstractParser, byte[], int) - Constructor for class adams.data.io.input.SPCSpectrumReader.AbstractParser: Initializes the parser.
AbstractPlotUpdater - Class in adams.flow.sink.spectrumdisplay: Ancestor for classes that determine when to update the spectrum display, i.e., repaint all of it.
AbstractPlotUpdater() - Constructor for class adams.flow.sink.spectrumdisplay.AbstractPlotUpdater
AbstractPositionableThreeWayDataOverlay - Class in adams.gui.visualization.threewaydata.heatmapviewer.overlay: Ancestor for overlays that can be positioned on the 3-way data panel.
AbstractPositionableThreeWayDataOverlay() - Constructor for class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlay
AbstractPositionableThreeWayDataOverlayWithDimensions - Class in adams.gui.visualization.threewaydata.heatmapviewer.overlay: Ancestor for overlays that can be positioned on the heatmap panel and support dimensions.
AbstractPositionableThreeWayDataOverlayWithDimensions() - Constructor for class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlayWithDimensions
AbstractPostProcessor - Class in adams.data.postprocessor.instances: Abstract base class for postprocessing weka.core.Instances objects.
AbstractPostProcessor() - Constructor for class adams.data.postprocessor.instances.AbstractPostProcessor
AbstractPredictionCheck - Class in adams.flow.transformer.predictioncheck: Ancestor for prediction checks.
AbstractPredictionCheck() - Constructor for class adams.flow.transformer.predictioncheck.AbstractPredictionCheck
AbstractSampleDataReader - Class in adams.data.io.input: Ancestor for sample data readers.
AbstractSampleDataReader() - Constructor for class adams.data.io.input.AbstractSampleDataReader
AbstractSampleIDExtraction - Class in adams.data.io.input.sampleidextraction: Ancestor for schemes that extract the sample ID from the filename.
AbstractSampleIDExtraction() - Constructor for class adams.data.io.input.sampleidextraction.AbstractSampleIDExtraction
AbstractSerializableCleaner - Class in adams.data.cleaner.instance: Abstract cleaner that can serialize its setup to disk and also load it from there.
AbstractSerializableCleaner - Class in adams.data.cleaner.spectrum: Abstract cleaner that can serialize its setup to disk and also load it from there.
AbstractSerializableCleaner() - Constructor for class adams.data.cleaner.instance.AbstractSerializableCleaner
AbstractSerializableCleaner() - Constructor for class adams.data.cleaner.spectrum.AbstractSerializableCleaner
AbstractSerializableEvaluator - Class in adams.data.evaluator.instance: Abstract evaluator that can serialize its setup to disk and also load it from there.
AbstractSerializableEvaluator() - Constructor for class adams.data.evaluator.instance.AbstractSerializableEvaluator
AbstractSerializableFilter - Class in adams.data.spectrumfilter: Abstract cleaner that can serialize its setup to disk and also load it from there.
AbstractSerializableFilter() - Constructor for class adams.data.spectrumfilter.AbstractSerializableFilter
AbstractSerializablePostProcessor - Class in adams.data.postprocessor.instances: Abstract postprocessor that can serialize its setup to disk and also load it from there.
AbstractSerializablePostProcessor() - Constructor for class adams.data.postprocessor.instances.AbstractSerializablePostProcessor
AbstractSpectralDbBackend - Class in adams.db: Ancestor for classes that provide a spectral DB backend.
AbstractSpectralDbBackend() - Constructor for class adams.db.AbstractSpectralDbBackend
AbstractSpectrumAnalysis - Class in adams.data.spectrumanalysis: Ancestor for spectrum-based data analysis schemes.
AbstractSpectrumAnalysis() - Constructor for class adams.data.spectrumanalysis.AbstractSpectrumAnalysis
AbstractSpectrumBasedInstanceGenerator - Class in adams.data.instances: Abstract base class for schemes that turn spectra/sample data into weka.core.Instance objects.
AbstractSpectrumBasedInstanceGenerator() - Constructor for class adams.data.instances.AbstractSpectrumBasedInstanceGenerator
AbstractSpectrumComparator - Class in adams.data.spectrum: Ancestor for spectrum comparators.
AbstractSpectrumComparator() - Constructor for class adams.data.spectrum.AbstractSpectrumComparator: The default constructor uses comparison in ascending manner.
AbstractSpectrumConditions - Class in adams.db: Ancestor for spectrum conditions.
AbstractSpectrumConditions() - Constructor for class adams.db.AbstractSpectrumConditions
AbstractSpectrumFeatureGenerator - Class in adams.data.spectrum: Abstract base class for Spectrum feature generation.
AbstractSpectrumFeatureGenerator() - Constructor for class adams.data.spectrum.AbstractSpectrumFeatureGenerator
AbstractSpectrumHandler - Class in adams.gui.tools.previewbrowser: Ancestor for spectrum handlers.
AbstractSpectrumHandler() - Constructor for class adams.gui.tools.previewbrowser.AbstractSpectrumHandler
AbstractSpectrumImageGenerator - Class in adams.data.spectrumimage: Ancestor for image generators from spectra.
AbstractSpectrumImageGenerator() - Constructor for class adams.data.spectrumimage.AbstractSpectrumImageGenerator
AbstractSpectrumImageGeneratorWithRange - Class in adams.data.spectrumimage: Ancestor for spectrum image generators that limit the amplitude ranges.
AbstractSpectrumImageGeneratorWithRange() - Constructor for class adams.data.spectrumimage.AbstractSpectrumImageGeneratorWithRange
AbstractSpectrumInstanceGenerator - Class in adams.data.instances: Abstract base class for schemes that turn spectra/sample data into weka.core.Instance objects (spectra is included).
AbstractSpectrumInstanceGenerator() - Constructor for class adams.data.instances.AbstractSpectrumInstanceGenerator
AbstractSpectrumInstanceGeneratorWithClass - Class in adams.data.instances: Abstract base class for schemes that turn spectra/sample data into weka.core.Instance objects (spectra is included).
AbstractSpectrumInstanceGeneratorWithClass() - Constructor for class adams.data.instances.AbstractSpectrumInstanceGeneratorWithClass
AbstractSpectrumPaintlet - Class in adams.gui.visualization.spectrum: A specialized paintlet for sequence panels.
AbstractSpectrumPaintlet() - Constructor for class adams.gui.visualization.spectrum.AbstractSpectrumPaintlet
AbstractSpectrumPanelScriptlet - Class in adams.gui.scripting: Ancestor for scriptlets that require a SpectrumPanel.
AbstractSpectrumPanelScriptlet() - Constructor for class adams.gui.scripting.AbstractSpectrumPanelScriptlet
AbstractSpectrumReader - Class in adams.data.io.input: Abstract ancestor for readers that read files in various formats and turn them into spectrums.
AbstractSpectrumReader() - Constructor for class adams.data.io.input.AbstractSpectrumReader
AbstractSpectrumWriter - Class in adams.data.io.output: Abstract ancestor for writers that write spectra to files in various formats.
AbstractSpectrumWriter() - Constructor for class adams.data.io.output.AbstractSpectrumWriter
AbstractSpreadSheetRowGenerator - Class in adams.data.spreadsheetrowgenerator: Abstract base class for schemes that turn spectra into spreadsheet row objects.
AbstractSpreadSheetRowGenerator() - Constructor for class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator
AbstractStandardiseFilter - Class in adams.data.spectrumfilter: Ancestor for filters that standardize by interpolation.
AbstractStandardiseFilter() - Constructor for class adams.data.spectrumfilter.AbstractStandardiseFilter
AbstractThreeWayDataFeatureGenerator - Class in adams.data.threewayfeatures: Abstract base class for ThreeWayData feature generation.
AbstractThreeWayDataFeatureGenerator() - Constructor for class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator
AbstractThreeWayDataMerge - Class in adams.flow.transformer.threewaydatamerge: Ancestor for merge schemes.
AbstractThreeWayDataMerge() - Constructor for class adams.flow.transformer.threewaydatamerge.AbstractThreeWayDataMerge
AbstractThreeWayDataOverlay - Class in adams.gui.visualization.threewaydata.heatmapviewer.overlay: Ancestor for 3-way data image overlays.
AbstractThreeWayDataOverlay() - Constructor for class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractThreeWayDataOverlay
AbstractThreeWayDataReader - Class in adams.data.io.input: Abstract ancestor for readers that read files in various formats and turn them into three way data structures.
AbstractThreeWayDataReader() - Constructor for class adams.data.io.input.AbstractThreeWayDataReader
AbstractThreeWayDataTrainPostProcessor - Class in adams.flow.transformer.threewaydatatrain: Ancestor for post-processors of a model generated by ThreeWayDataTrain.
AbstractThreeWayDataTrainPostProcessor() - Constructor for class adams.flow.transformer.threewaydatatrain.AbstractThreeWayDataTrainPostProcessor
AbstractThreeWayDataWriter - Class in adams.data.io.output: Ancestor for writers for 3-way data.
AbstractThreeWayDataWriter() - Constructor for class adams.data.io.output.AbstractThreeWayDataWriter
AbstractWekaSpectrumAnalysis - Class in adams.data.spectrumanalysis: Ancestor for Weka-based analysis schemes, i.e., ones that use Instances as basis.
AbstractWekaSpectrumAnalysis() - Constructor for class adams.data.spectrumanalysis.AbstractWekaSpectrumAnalysis
accepts() - Method in class adams.data.compare.SpectrumCorrelation: Returns the classes that it can handle.
accepts() - Method in class adams.data.compare.SpectrumCosineSimilarity: Returns the classes that it can handle.
accepts() - Method in class adams.data.conversion.ArrayToSpectrum: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.JsonToSpectrum: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.MultiSpectrumToSpectra: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.PostProcessingContainerToWekaInstanceContainer: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.ReportToSampleData: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.SampleDataArrayToMap: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.SpectraToMultiSpectrum: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.SpectrumToArray: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.SpectrumToBufferedImage: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.SpectrumToJson: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.SpectrumToSpreadSheet: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.SpectrumToWave: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.SpreadSheetColumnsToSampleData: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.SpreadSheetRowsToSampleData: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.SpreadSheetTo2DTensor: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.SpreadSheetTo3DTensor: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.SpreadSheetToSpectrum: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.SpreadSheetToThreeWayData: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.TensorToSpreadSheet: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.TensorToThreeWayData: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.ThreeWayDataToHeatmap: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.ThreeWayDataToSpreadSheet: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.ThreeWayDataToTensor: Returns the class that is accepted as input.
accepts() - Method in class adams.data.conversion.WekaPredictionContainerToEvaluationContainer: Returns the class that is accepted as input.
accepts() - Method in class adams.data.multispectrumoperation.Remove: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.condition.bool.HasSpectrum: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.control.InstanceCleaner: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.control.SpectrumCleaner: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.sink.SampleDataDisplay: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.sink.SpectrumDisplay: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.sink.SpectrumImageWriter: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: Returns the type of data that gets accepted.
accepts() - Method in class adams.flow.standalone.rats.LoadSpectrumFileOutput: Returns the type of data that gets accepted.
accepts() - Method in class adams.flow.standalone.rats.SaveMultiSpectrumFileOutput: Returns the type of data that gets accepted.
accepts() - Method in class adams.flow.standalone.rats.SaveSpectrumFileOutput: Returns the type of data that gets accepted.
accepts() - Method in class adams.flow.transformer.AbstractInPlaceSpectrumTransformer: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.BulkSpectrumDbWriter: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.Cleaner: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.DeleteSampleDataValue: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.DeleteSampleDataValueByExpression: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.DeleteSpectrum: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.Evaluator: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.GetSampleDataValue: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.GetSpectrumAmplitude: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.InstanceGenerator: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.InstanceToSpectrum: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.MergeSampleDataFromMap: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.MultiSpectrumAdd: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.MultiSpectrumFilter: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.MultiSpectrumOperation: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.MultiSpectrumOutlierDetector: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.MultiSpectrumRemove: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.MultiSpectrumReportFilter: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.PostProcessor: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.PredictionCheck: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.SampleDataDbReader: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.SampleDataDbWriter: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.SampleDataFileWriter: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.SampleDataValueDbWriter: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.SetEvaluationMetaData: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.SetSampleDataValue: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.SpectralAngleMapper: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.SpectrumDbReader: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.SpectrumDbWriter: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.SpectrumDiff: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.SpectrumFeatureGenerator: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.SpectrumFileWriter: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.SpectrumInfo: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.SpectrumMinMax: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.SpreadSheetRowGenerator: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.ThreeWayDataFeatureGenerator: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.ThreeWayDataLoadingMatrix: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.ThreeWayDataMerge: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.transformer.ThreeWayDataTrain: Returns the class that the consumer accepts.
accepts() - Method in class adams.flow.webservice.multispectrum.MultiUpload: Returns the classes that are accepted input.
accepts() - Method in class adams.flow.webservice.Put: Returns the classes that are accepted input.
accepts() - Method in class adams.flow.webservice.spectrum.Upload: Returns the classes that are accepted input.
accepts() - Method in class adams.flow.webservice.Transform: Returns the classes that are accepted input.
accessoryNameTipText() - Method in class adams.data.io.output.ASCSpectrumWriter: Returns the tip text for this property.
action - Variable in class nz.ac.waikato.adams.webservice.spectral.transform.TransformRequest
ACTION - Static variable in class adams.gui.scripting.SelectWaveNumber: the action to execute.
ACTION - Static variable in class adams.gui.scripting.WriteSpectrum: the action to execute.
actionTipText() - Method in class adams.flow.webservice.Transform: Description of this option.
adams.core.discovery.genetic - package adams.core.discovery.genetic
adams.data.cleaner - package adams.data.cleaner
adams.data.cleaner.instance - package adams.data.cleaner.instance
adams.data.cleaner.spectrum - package adams.data.cleaner.spectrum
adams.data.columnfinder - package adams.data.columnfinder
adams.data.compare - package adams.data.compare
adams.data.container - package adams.data.container
adams.data.conversion - package adams.data.conversion
adams.data.evaluator.instance - package adams.data.evaluator.instance
adams.data.instances - package adams.data.instances
adams.data.io.input - package adams.data.io.input
adams.data.io.input.foss - package adams.data.io.input.foss
adams.data.io.input.opus - package adams.data.io.input.opus
adams.data.io.input.sampleidextraction - package adams.data.io.input.sampleidextraction
adams.data.io.output - package adams.data.io.output
adams.data.io.output.foss - package adams.data.io.output.foss
adams.data.multifilter - package adams.data.multifilter
adams.data.multireportfilter - package adams.data.multireportfilter
adams.data.multispectrumoperation - package adams.data.multispectrumoperation
adams.data.multispectrumoperation.outlierremoval - package adams.data.multispectrumoperation.outlierremoval
adams.data.postprocessor - package adams.data.postprocessor
adams.data.postprocessor.instances - package adams.data.postprocessor.instances
adams.data.sampledata - package adams.data.sampledata
adams.data.spectrum - package adams.data.spectrum
adams.data.spectrumanalysis - package adams.data.spectrumanalysis
adams.data.spectrumbaseline - package adams.data.spectrumbaseline
adams.data.spectrumfilter - package adams.data.spectrumfilter
adams.data.spectrumfilter.amplitudetransform - package adams.data.spectrumfilter.amplitudetransform
adams.data.spectrumfilter.detrend - package adams.data.spectrumfilter.detrend
adams.data.spectrumfilter.multiplicativescattercorrection - package adams.data.spectrumfilter.multiplicativescattercorrection
adams.data.spectrumimage - package adams.data.spectrumimage
adams.data.spectrumoutlier - package adams.data.spectrumoutlier
adams.data.spectrumsmoothing - package adams.data.spectrumsmoothing
adams.data.spreadsheetrowgenerator - package adams.data.spreadsheetrowgenerator
adams.data.statistics - package adams.data.statistics
adams.data.threeway - package adams.data.threeway
adams.data.threewayfeatures - package adams.data.threewayfeatures
adams.data.threewayfilter - package adams.data.threewayfilter
adams.data.threewayoutlier - package adams.data.threewayoutlier
adams.data.threewayreport - package adams.data.threewayreport
adams.db - package adams.db
adams.db.autodetect - package adams.db.autodetect
adams.db.generic - package adams.db.generic
adams.db.h2 - package adams.db.h2
adams.db.mirrored - package adams.db.mirrored
adams.db.mssql - package adams.db.mssql
adams.db.mysql - package adams.db.mysql
adams.db.postgresql - package adams.db.postgresql
adams.db.sqlite - package adams.db.sqlite
adams.env - package adams.env
adams.flow.condition.bool - package adams.flow.condition.bool
adams.flow.container - package adams.flow.container
adams.flow.control - package adams.flow.control
adams.flow.core - package adams.flow.core
adams.flow.rest - package adams.flow.rest
adams.flow.sink - package adams.flow.sink
adams.flow.sink.spectrumdisplay - package adams.flow.sink.spectrumdisplay
adams.flow.source - package adams.flow.source
adams.flow.standalone.rats - package adams.flow.standalone.rats
adams.flow.transformer - package adams.flow.transformer
adams.flow.transformer.datacontainer - package adams.flow.transformer.datacontainer
adams.flow.transformer.predictioncheck - package adams.flow.transformer.predictioncheck
adams.flow.transformer.report - package adams.flow.transformer.report
adams.flow.transformer.threewaydatamerge - package adams.flow.transformer.threewaydatamerge
adams.flow.transformer.threewaydatatrain - package adams.flow.transformer.threewaydatatrain
adams.flow.webservice - package adams.flow.webservice
adams.flow.webservice.multispectrum - package adams.flow.webservice.multispectrum
adams.flow.webservice.spectrum - package adams.flow.webservice.spectrum
adams.gui.chooser - package adams.gui.chooser
adams.gui.core.spreadsheettable - package adams.gui.core.spreadsheettable
adams.gui.menu - package adams.gui.menu
adams.gui.scripting - package adams.gui.scripting
adams.gui.selection - package adams.gui.selection
adams.gui.tools - package adams.gui.tools
adams.gui.tools.idprovider - package adams.gui.tools.idprovider
adams.gui.tools.previewbrowser - package adams.gui.tools.previewbrowser
adams.gui.visualization.debug.objectexport - package adams.gui.visualization.debug.objectexport
adams.gui.visualization.debug.objectrenderer - package adams.gui.visualization.debug.objectrenderer
adams.gui.visualization.instances.instancestable - package adams.gui.visualization.instances.instancestable
adams.gui.visualization.spectrum - package adams.gui.visualization.spectrum
adams.gui.visualization.spectrum.containerlistpopup - package adams.gui.visualization.spectrum.containerlistpopup
adams.gui.visualization.spectrum.plotpopup - package adams.gui.visualization.spectrum.plotpopup
adams.gui.visualization.threewaydata.heatmapviewer - package adams.gui.visualization.threewaydata.heatmapviewer
adams.gui.visualization.threewaydata.heatmapviewer.multipageaction - package adams.gui.visualization.threewaydata.heatmapviewer.multipageaction
adams.gui.visualization.threewaydata.heatmapviewer.overlay - package adams.gui.visualization.threewaydata.heatmapviewer.overlay
adams.opt.genetic - package adams.opt.genetic
add(double, double) - Method in class adams.data.threeway.L1Point: Add a L2Point.
add(Spectrum) - Method in class adams.db.generic.SpectrumT: Adds a spectrum to the database.
add(Spectrum) - Method in class adams.db.mirrored.SpectrumT: Adds a spectrum to the database.
add(Spectrum) - Method in class adams.db.SpectrumF: Adds a spectrum to the database.
add(Spectrum) - Method in interface adams.db.SpectrumIntf: Adds a spectrum to the database.
add(Spectrum, boolean) - Method in class adams.db.generic.SpectrumT: Adds a spectrum to the database.
add(Spectrum, boolean) - Method in class adams.db.mirrored.SpectrumT: Adds a spectrum to the database.
add(Spectrum, boolean) - Method in class adams.db.SpectrumF: Adds a spectrum to the database.
add(Spectrum, boolean) - Method in interface adams.db.SpectrumIntf: Adds a spectrum to the database.
add(Spectrum, boolean) - Method in class adams.db.sqlite.SpectrumT: Adds a spectrum to the database.
add(ArrayHistogram, Spectrum) - Method in class adams.gui.visualization.spectrum.HistogramFactory.Dialog: Adds a plot of the given spectrum.
add(ArrayHistogram, Spectrum) - Method in class adams.gui.visualization.spectrum.HistogramFactory.Panel: Adds a plot of the given spectrum.
add(ArrayHistogram, Spectrum, String) - Method in class adams.gui.visualization.spectrum.HistogramFactory.Dialog: Adds a plot of the given spectrum.
add(ArrayHistogram, Spectrum, String) - Method in class adams.gui.visualization.spectrum.HistogramFactory.Panel: Adds a plot of the given spectrum.
add(DataProvider, Spectrum) - Method in class adams.flow.transformer.SpectrumDbWriter: Adds the container to the database.
add(String, String, String, String, float[], float[]) - Method in class adams.data.io.input.TrinamixSpectrumReader: Adds the spectrum.
add(Hashtable<Float, SpectrumPoint>, Spectrum) - Static method in class adams.data.spectrum.SpectrumUtils: Merges the given spectrum with the current data pool.
Add - Class in adams.data.multifilter: Adds the amplitudes of first spectrum to the amplitudes of the second.
Add() - Constructor for class adams.data.multifilter.Add
addCommandLinesTipText() - Method in class adams.data.io.input.OpusSpectrumReaderExt: Returns the tip text for this property.
addDatabaseIDTipText() - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Returns the tip text for this property.
addDatabaseIDTipText() - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Returns the tip text for this property.
addField(Field) - Method in class adams.data.instances.AbstractSpectrumInstanceGenerator: Adds the specified field to the output format.
addIDTipText() - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Returns the tip text for this property.
ADDITIONALDATA_AVERAGE - Static variable in class adams.data.spectrumfilter.MultiplicativeScatterCorrection
additionalFieldsTipText() - Method in class adams.data.instances.AbstractSpectrumInstanceGenerator: Returns the tip text for this property.
addLogTipText() - Method in class adams.data.io.input.OpusSpectrumReaderExt: Returns the tip text for this property.
addOverlay(AbstractThreeWayDataOverlay) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Adds the heatmap overlay.
addQuery(Spectrum, boolean) - Method in class adams.db.generic.SpectrumT: Generates the query string for adding a spectrum.
addRawMetaDataTipText() - Method in class adams.data.io.input.JCampDX2SpectrumReader: Returns the tip text for this property.
addRawMetaDataTipText() - Method in class adams.data.io.input.JCampDXSpectrumReader: Returns the tip text for this property.
addReportValue(SampleData, String, DataType, Object) - Method in class adams.data.io.input.OpusSpectrumReaderExt: Adds the field to the report.
addSampleIDTipText() - Method in class adams.data.instances.AbstractSpectrumBasedInstanceGenerator: Returns the tip text for this property.
addSampleIDTipText() - Method in interface adams.data.instances.InstanceGeneratorWithSampleID: Returns the tip text for this property.
addSampleIDTipText() - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Returns the tip text for this property.
addTraceToReportTipText() - Method in class adams.data.io.input.OpusSpectrumReader: Returns the tip text for this property.
addUndoPoint(String) - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Adds an undo point with the given comment.
addWaveNumberTipText() - Method in class adams.data.instances.SimpleInstanceGenerator: Returns the tip text for this property.
addWaveNumberTipText() - Method in class adams.data.instances.SimpleSpectralInstanceGenerator: Returns the tip text for this property.
addWaveNumberTipText() - Method in class adams.data.spectrum.Amplitudes: Returns the tip text for this property.
Adjust - Class in adams.gui.visualization.spectrum.plotpopup: Whether to adjust the plot to the loaded or visible data.
Adjust() - Constructor for class adams.gui.visualization.spectrum.plotpopup.Adjust
adjustArrays(int) - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Adjusts the arrays to the new length.
algorithmTipText() - Method in class adams.data.spectrumfilter.PLS: Tip text for this property.
algorithmTipText() - Method in class adams.flow.transformer.SpectrumFeatureGenerator: Returns the tip text for this property.
algorithmTipText() - Method in class adams.flow.transformer.ThreeWayDataFeatureGenerator: Returns the tip text for this property.
algorithmTipText() - Method in class adams.flow.transformer.ThreeWayDataMerge: Returns the tip text for this property.
algorithmTipText() - Method in class adams.flow.transformer.ThreeWayDataTrain: Returns the tip text for this property.
allowAccessToFullInputFormat() - Method in class weka.filters.unsupervised.attribute.BestBySLR
allowAccessToFullInputFormat() - Method in class weka.filters.unsupervised.attribute.RangeBasedSavitzkyGolay
allowAccessToFullInputFormat() - Method in class weka.filters.unsupervised.attribute.SegmentedDownSample
allowAccessToFullInputFormat() - Method in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay
allSpectraTipText() - Method in class adams.data.io.input.OpusSpectrumReaderExt: Returns the tip text for this property.
alwaysShowMarkersTipText() - Method in class adams.gui.visualization.spectrum.SpectrumPaintlet: Returns the tip text for this property.
amplitude - Variable in class nz.ac.waikato.adams.webservice.rats.multispectrum.Wave
amplitude - Variable in class nz.ac.waikato.adams.webservice.rats.spectrum.Wave
amplitude - Variable in class nz.ac.waikato.adams.webservice.spectral.get.Wave
amplitude - Variable in class nz.ac.waikato.adams.webservice.spectral.put.Wave
amplitude - Variable in class nz.ac.waikato.adams.webservice.spectral.transform.Wave
AMPLITUDE - adams.data.conversion.SpectrumToArray.DataType
AmplitudeExpression - Class in adams.data.spectrumfilter: Applies the specified mathematical expression to each amplitude.
The following symbols are available:
- A: the current amplitude
- W: the current wave number
- I: the 0-based index of the wave number/amplitude
- S: the number of wave numbers in the current spectrum

The following grammar is used for the expressions:

expr_list ::= '=' expr_list expr_part | expr_part ;
expr_part ::= expr ;

expr ::= ( expr )

# data types
| number
| string
| boolean
| date

# constants
| true
| false
| pi
| e
| now()
| today()

# negating numeric value
| -expr

# comparisons
| expr < expr
| expr <= expr
| expr > expr
| expr >= expr
| expr = expr
| expr !
AmplitudeExpression() - Constructor for class adams.data.spectrumfilter.AmplitudeExpression
AmplitudeFinder - Class in adams.data.columnfinder: Selects all the attributes that start with AmplitudeFinder.PREFIX_AMPLITUDE.
AmplitudeFinder() - Constructor for class adams.data.columnfinder.AmplitudeFinder
amplitudePrefixTipText() - Method in class adams.data.instances.AbstractSpectrumInstanceGenerator: Returns the tip text for this property.
amplitudePrefixTipText() - Method in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: Returns the tip text for this property.
AmplitudeRange - Class in adams.data.spectrumoutlier: For each wave number in the training data the range (min/max) is calculated.
After training, if a spectrum falls outside these ranges, it gets flagged as an outlier.
NB: Assumes the spectra (training and subsequent) have the same wave numbers.
AmplitudeRange() - Constructor for class adams.data.spectrumoutlier.AmplitudeRange
AmplitudeRatio - Class in adams.data.spectrumimage: Generates a square image (width is number of wave numbers) with the pixels being the ratio for each possible amplitude pair.
AmplitudeRatio() - Constructor for class adams.data.spectrumimage.AmplitudeRatio
amplitudeRowsTipText() - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Returns the tip text for this property.
Amplitudes - Class in adams.data.spectrum: Simple feature generator that just outputs all the amplitudes of a spectrum.
Amplitudes() - Constructor for class adams.data.spectrum.Amplitudes
amplitudeTipText() - Method in class adams.flow.transformer.SetSpectrumAmplitude: Returns the tip text for this property.
AmplitudeTransform - Class in adams.data.spectrumfilter: Applies the specified transformer to the spectrum.
AmplitudeTransform() - Constructor for class adams.data.spectrumfilter.AmplitudeTransform
amplitudeTypeTipText() - Method in class adams.data.io.input.SoilCaresScannerSpectrumReader: Returns the tip text for this property.
AndrewsCurves - Class in adams.data.spectrumfilter: Generates Andrews Curves from array data.
César Ignacio García Osorio, Colin Fyfe (2003).
AndrewsCurves() - Constructor for class adams.data.spectrumfilter.AndrewsCurves
AniMLSpectrumReader - Class in adams.data.io.input: Reads spectra in AniML (Analytical Information Markup Language) format.

For more information see:
http://animl.sourceforge.net/

Valid options are:
AniMLSpectrumReader() - Constructor for class adams.data.io.input.AniMLSpectrumReader
antiAliasingEnabledTipText() - Method in class adams.gui.visualization.spectrum.SimpleSpectrumPaintlet: Returns the tip text for this property.
antiAliasingEnabledTipText() - Method in class adams.gui.visualization.spectrum.SpectrumPaintlet: Returns the tip text for this property.
APF - Static variable in class adams.data.io.input.opus.OpusBlockHelper: the APF character sequence.
append(Spectrum, Spectrum) - Method in class adams.flow.transformer.SpectrumAppend: Appends the current data container to the stored one.
apply() - Method in class adams.gui.tools.UpdateSampleDataPanel: Updates the selected spectra.
apply(MultiSpectrum, MessageCollection) - Method in class adams.data.multispectrumoperation.AbstractMultiSpectrumOperation: Performs the operation.
ApplyMultiplicativeScatterCorrection - Class in adams.data.spectrumfilter.amplitudetransform: Applies multiplicative scatter correction using the intercept and slope values stores in the report (using prefixes Intercept. and Slope.).
ApplyMultiplicativeScatterCorrection() - Constructor for class adams.data.spectrumfilter.amplitudetransform.ApplyMultiplicativeScatterCorrection
applyTipText() - Method in class adams.data.spectrumfilter.LRCoeff: Returns the tip text for this property.
APT - Static variable in class adams.data.io.input.opus.OpusBlockHelper: the APT character sequence.
AQM - Static variable in class adams.data.io.input.opus.OpusBlockHelper: the AQM character sequence.
ArffUtils - Class in adams.data.instances: A helper class for turning spectrum data into ARFF files and vice versa.
ArffUtils() - Constructor for class adams.data.instances.ArffUtils
arrayToDouble(Object, int) - Method in class adams.data.io.input.FitsLibsReader: Turns the array value into a double.
ArrayToSpectrum - Class in adams.data.conversion: Converts a float array representing amplitudes into a spectrum.
ArrayToSpectrum() - Constructor for class adams.data.conversion.ArrayToSpectrum
ascendingTipText() - Method in class adams.data.spectrum.AbstractSpectrumComparator: Returns the tip text for this property.
ASCIIXYSpectrumHandler - Class in adams.gui.tools.previewbrowser: Displays the following spectrum types: txt

Valid options are:
ASCIIXYSpectrumHandler() - Constructor for class adams.gui.tools.previewbrowser.ASCIIXYSpectrumHandler
ASCIIXYSpectrumReader - Class in adams.data.io.input: Reads spectra in ASCII XY format.
ASCIIXYSpectrumReader() - Constructor for class adams.data.io.input.ASCIIXYSpectrumReader
ASCIIXYSpectrumWriter - Class in adams.data.io.output: Writer that stores spectra in ASCII XY format.
ASCIIXYSpectrumWriter() - Constructor for class adams.data.io.output.ASCIIXYSpectrumWriter
ASCSpectrumHandler - Class in adams.gui.tools.previewbrowser: Displays the following spectrum types: asc

Valid options are:
ASCSpectrumHandler() - Constructor for class adams.gui.tools.previewbrowser.ASCSpectrumHandler
ASCSpectrumReader - Class in adams.data.io.input: Reads spectra in BLGG ASC format.
ASCSpectrumReader() - Constructor for class adams.data.io.input.ASCSpectrumReader
ASCSpectrumReader.ParsedFile - Class in adams.data.io.input: Class for parsing an ASC file.
ASCSpectrumWriter - Class in adams.data.io.output: Writer that stores spectrums in the BLGG ASC format.
ASCSpectrumWriter() - Constructor for class adams.data.io.output.ASCSpectrumWriter
assembleFields() - Method in class adams.flow.transformer.SampleDataValueDbWriter: Method for assembling the fields to overwrite.
assign(DataContainer<Spectrum>) - Method in class adams.data.spectrum.MultiSpectrum: Obtains the stored variables from the other data point, but not the actual data points.
assign(DataContainer<SpectrumPoint>) - Method in class adams.data.spectrum.Spectrum: Obtains the stored variables from the other data point, but not the actual data points.
assign(DataContainer<L1Point>) - Method in class adams.data.threeway.ThreeWayData: Obtains the stored variables from the other data point, but not the actual data points.
assign(DataContainer<L2Point>) - Method in class adams.data.threeway.L1Point: Obtains the stored variables from the other data point, but not the actual data points.
assign(DataPoint) - Method in class adams.data.spectrum.MultiSpectrum: Obtains the stored variables from the other data point.
assign(DataPoint) - Method in class adams.data.spectrum.Spectrum: Obtains the stored variables from the other data point.
assign(DataPoint) - Method in class adams.data.spectrum.SpectrumPoint: Obtains the stored variables from the other data point.
assign(DataPoint) - Method in class adams.data.threeway.L1Point: Obtains the stored variables from the other data point.
assign(DataPoint) - Method in class adams.data.threeway.L2Point: Obtains the stored variables from the other data point.
assign(AbstractContainer) - Method in class adams.gui.visualization.spectrum.SpectrumContainer: Updates itself with the values from given container (the manager is excluded!).
Atan2 - Class in adams.data.multifilter: Computes the atan2, with the first format representing 'y' and the second format 'x'.
Atan2() - Constructor for class adams.data.multifilter.Atan2
atomicMoveTipText() - Method in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: Returns the tip text for this property.
atomicMoveTipText() - Method in class adams.flow.standalone.rats.LoadSpectrumFileOutput: Returns the tip text for this property.
attributeNameTipText() - Method in class adams.data.cleaner.instance.MinMax: Returns the tip text for this property.
attributeRangeTipText() - Method in class adams.data.cleaner.instance.IQRCleaner: Returns the tip text for this property.
attributeRangeTipText() - Method in class adams.data.spectrumanalysis.FastICA: Returns the tip text for this property.
autoCommitTipText() - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Returns the tip text for this property.
autoCommitTipText() - Method in class adams.flow.transformer.BulkSpectrumDbWriter: Returns the tip text for this property.
Autocorrelation - Class in adams.data.spectrumfilter: Performs autocorrelation on the spectrum.
Autocorrelation() - Constructor for class adams.data.spectrumfilter.Autocorrelation
Average - Class in adams.data.multifilter: Averages spectra into a single one.
Average() - Constructor for class adams.data.multifilter.Average

B

BACK - adams.data.io.input.SoilCaresScannerSpectrumReader.SpectrumType
BACKEND_AUTODETECT - Static variable in class adams.db.AbstractSpectralDbBackend
BACKEND_MYSQL - Static variable in class adams.db.AbstractSpectralDbBackend
backendsTipText() - Method in class adams.db.mirrored.SpectralDbBackend: Returns the tip text for this property.
BACKUP_ACTUALCLEANER - Static variable in class adams.flow.transformer.Cleaner: the key for storing the current evaluator in the backup.
BACKUP_ACTUALEVALUATOR - Static variable in class adams.flow.transformer.Evaluator: the key for storing the current evaluator in the backup.
BACKUP_ACTUALMODEL - Static variable in class adams.flow.transformer.ThreeWayDataModelFilter: the key for storing the current model in the backup.
BACKUP_ACTUALPOSTPROCESSOR - Static variable in class adams.flow.transformer.PostProcessor: the key for storing the current postprocessor in the backup.
BACKUP_ALGORITHM - Static variable in class adams.flow.transformer.SpectrumFeatureGenerator: the key for storing the current algorithm in the backup.
BACKUP_ALGORITHM - Static variable in class adams.flow.transformer.ThreeWayDataFeatureGenerator: the key for storing the current algorithm in the backup.
BACKUP_CALLABLEACTOR - Static variable in class adams.flow.transformer.MultiSpectrumAdd: the key for backing up the callable actor.
BACKUP_CONFIGURED - Static variable in class adams.flow.transformer.MultiSpectrumAdd: the key for backing up the configured state.
BACKUP_CURRENT - Static variable in class adams.flow.transformer.SpectrumMinMax: the key for storing the current counter in the backup.
BACKUP_MAX - Static variable in class adams.flow.transformer.SpectrumMinMax: the key for storing the max spectrum in the backup.
BACKUP_MIN - Static variable in class adams.flow.transformer.SpectrumMinMax: the key for storing the min spectrum in the backup.
BACKUP_QUEUE - Static variable in class adams.flow.transformer.SpectrumFeatureGenerator: the key for storing the current objects in the backup.
BACKUP_QUEUE - Static variable in class adams.flow.transformer.ThreeWayDataFeatureGenerator: the key for storing the current objects in the backup.
backupState() - Method in class adams.flow.transformer.Cleaner: Backs up the current state of the actor before update the variables.
backupState() - Method in class adams.flow.transformer.Evaluator: Backs up the current state of the actor before update the variables.
backupState() - Method in class adams.flow.transformer.MultiSpectrumAdd: Backs up the current state of the actor before update the variables.
backupState() - Method in class adams.flow.transformer.PostProcessor: Backs up the current state of the actor before update the variables.
backupState() - Method in class adams.flow.transformer.SpectrumFeatureGenerator: Backs up the current state of the actor before update the variables.
backupState() - Method in class adams.flow.transformer.SpectrumMinMax: Backs up the current state of the actor before update the variables.
backupState() - Method in class adams.flow.transformer.ThreeWayDataFeatureGenerator: Backs up the current state of the actor before update the variables.
backupState() - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Backs up the current state of the actor before update the variables.
baseFilterTipText() - Method in class adams.data.multifilter.FilteredMultiSpectrumFilter: Returns the tip text for this property.
baseTipText() - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Returns the tip text for this property.
batchFilter(Spectrum[]) - Method in class adams.data.spectrumfilter.MultiplicativeScatterCorrection: Batch filters the data.
batchFilterTipText() - Method in class adams.data.spectrumfilter.KennardStone: Description for this property
batchSizeTipText() - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Returns the tip text for this property.
batchSizeTipText() - Method in class adams.flow.transformer.BulkSpectrumDbWriter: Returns the tip text for this property.
belowCountThresholdTipText() - Method in class adams.data.multispectrumoperation.outlierremoval.CorrelationBasedThreshold: Returns the tip text for this property.
belowCountThresholdTipText() - Method in class adams.data.multispectrumoperation.outlierremoval.CosineSimilarityBasedThreshold: Returns the tip text for this property.
BestBySLR - Class in weka.filters.unsupervised.attribute: Chooses a random subset of attributes, either an absolute number or a percentage.
BestBySLR() - Constructor for class weka.filters.unsupervised.attribute.BestBySLR
BL_400 - adams.data.io.output.foss.FossOutputHelper.InstrumentHeader.InstrumentType
BL_500 - adams.data.io.output.foss.FossOutputHelper.InstrumentHeader.InstrumentType
Block(byte[], int, int, int, int) - Constructor for class adams.data.io.input.opus.OpusBlockHelper.Block: Initializes the block.
BLOCK_DEFINITION_LENGTH - Static variable in class adams.data.io.input.opus.OpusBlockHelper: the block definition length (type, length, offset).
BLOCK_OFFSET - Static variable in class adams.data.io.input.opus.OpusBlockHelper: the offset for block definitions in the header.
BlockDefinition() - Constructor for class adams.data.io.input.opus.OpusBlockHelper.BlockDefinition
BLOCKS_OFFSET - Static variable in class adams.data.io.input.OpusSpectrumReader
BLOCKTYPE_DUMMY - Static variable in class adams.data.io.input.opus.OpusBlockHelper: the dummy block type (???).
BLOCKTYPE_INCREMENT_DATA_TO_DPF - Static variable in class adams.data.io.input.opus.OpusBlockHelper: increment from data to DPF block type.
BLOCKTYPE_MAIN_MASK - Static variable in class adams.data.io.input.opus.OpusBlockHelper: the mask for the block type of the main spectrum.
BLOCKTYPE_SPEC_MASK - Static variable in class adams.data.io.input.opus.OpusBlockHelper: the mask for the block type of the main spectrum.
BLOCKTYPE_TEXT - Static variable in class adams.data.io.input.opus.OpusBlockHelper: the text block type.
BOOLEAN - nz.ac.waikato.adams.webservice.rats.multispectrum.DataType
BOOLEAN - nz.ac.waikato.adams.webservice.rats.spectrum.DataType
BOOLEAN - nz.ac.waikato.adams.webservice.spectral.get.DataType
BOOLEAN - nz.ac.waikato.adams.webservice.spectral.put.DataType
BOOLEAN - nz.ac.waikato.adams.webservice.spectral.transform.DataType
BOX - adams.gui.visualization.spectrum.SpectrumPaintlet.MarkerShape: a square box.
bufferSizeTipText() - Method in class adams.data.io.input.ZippedSpectrumReader: Returns the tip text for this property.
build(Instances) - Method in class adams.data.evaluator.instance.AbstractEvaluator: Performs the check.
build(Instances) - Method in interface adams.data.evaluator.instance.Evaluator: Performs the check.
buildClassifier(Instances) - Method in class weka.classifiers.meta.SpectrumClassifier: Build the classifier on the filtered data.
buildClusterer(Instances) - Method in class weka.clusterers.SpectrumClusterer: Build the clusterer on the filtered data.
buildWaitTipText() - Method in class adams.data.evaluator.instance.FakeEvaluator: Returns the tip text for this property.
bulkAdd(Spectrum[], boolean, int, boolean, boolean) - Method in class adams.db.generic.SpectrumT: Stores the spectra in the database.
bulkAdd(Spectrum[], boolean, int, boolean, boolean) - Method in class adams.db.mirrored.SpectrumT: Stores the spectra in the database.
bulkAdd(Spectrum[], boolean, int, boolean, boolean) - Method in class adams.db.SpectrumF: Stores the spectra in the database.
bulkAdd(Spectrum[], boolean, int, boolean, boolean) - Method in interface adams.db.SpectrumIntf: Stores the spectra in the database.
BulkSampleDataDbWriter - Class in adams.flow.transformer: Writes sample data to the database and outputs whether the operation was successful.
BulkSampleDataDbWriter() - Constructor for class adams.flow.transformer.BulkSampleDataDbWriter
BulkSpectrumDbWriter - Class in adams.flow.transformer: Writes spectra to the database and outputs whether the operation was successful.
BulkSpectrumDbWriter() - Constructor for class adams.flow.transformer.BulkSpectrumDbWriter
bulkStore(SampleData[], DataType[], String, int, boolean, boolean) - Method in class adams.db.generic.SampleDataT: Stores the records.
bulkStore(SampleData[], DataType[], String, int, boolean, boolean) - Method in class adams.db.mirrored.SampleDataT: Stores the records.
bulkStore(SampleData[], DataType[], String, int, boolean, boolean) - Method in class adams.db.SampleDataF: Stores the records.
byte2UByte(byte) - Method in class adams.data.io.input.foss.FossHelper: Convert byte to unsigned byte.
byte2UByte(byte) - Method in class adams.data.io.input.foss.FossStdise: Convert byte to unsigned byte.
byte2UByte(byte) - Method in class adams.data.io.input.OpusSpectrumReader: Convert byte to unsigned byte.
byte2UByte(byte) - Static method in class adams.data.io.output.foss.FossOutputHelper: Convert byte to unsigned byte.
byteToUnsignedByte(byte) - Static method in class adams.data.io.input.opus.OpusBlockHelper: Convert byte to unsigned byte.

C

cacheTipText() - Method in class adams.flow.transformer.SpectralAngleMapper: Gets the tip-text for the cache option.
calcNewFitness() - Method in class adams.opt.genetic.RonWeasley.RonWeasleyJob: Calculates the new fitness.
calculate() - Method in class adams.data.statistics.L1PointStatistic: calculates the statistics.
calculate() - Method in class adams.data.statistics.SpectrumStatistic: calculates the statistics.
calculate() - Method in class adams.data.statistics.ThreeWayDataStatistic: calculates the statistics.
calculateDistance(Spectrum, Spectrum) - Method in class adams.data.spectrumfilter.KennardStone: Calculate the distance between any two spectra.
calculateSpectralAngles(Spectrum, Spectrum[]) - Method in class adams.flow.transformer.SpectralAngleMapper: Performs the calculation of spectral angles between the input spectrum and each reference spectrum.
callableNameTipText() - Method in class adams.flow.transformer.MultiSpectrumAdd: Returns the tip text for this property.
CALSpectrumHandler - Class in adams.gui.tools.previewbrowser: Displays the following spectrum types: cal

Valid options are:
CALSpectrumHandler() - Constructor for class adams.gui.tools.previewbrowser.CALSpectrumHandler
CALSpectrumLoader - Class in weka.core.converters: Loads a CAL file.
CALSpectrumLoader() - Constructor for class weka.core.converters.CALSpectrumLoader
CALSpectrumReader - Class in adams.data.io.input: Reads spectra in BLGG ASC format.
CALSpectrumReader() - Constructor for class adams.data.io.input.CALSpectrumReader
CALSpectrumWriter - Class in adams.data.io.output: Write spectra to .CAL file.
CALSpectrumWriter() - Constructor for class adams.data.io.output.CALSpectrumWriter
canAbstain() - Method in class weka.classifiers.meta.SpectrumClassifier: Whether abstaining is possible, e.g., used in meta-classifiers.
canHandle(AbstractAlgorithm) - Method in class adams.flow.transformer.threewaydatatrain.AbstractThreeWayDataTrainPostProcessor: Returns whether the algorithm can be handle.
canHandle(AbstractAlgorithm) - Method in class adams.flow.transformer.threewaydatatrain.ParafacLossHistory: Returns whether the algorithm can be handle.
canHandle(AbstractAlgorithm) - Method in class adams.flow.transformer.threewaydatatrain.PassThrough: Returns whether the algorithm can be handle.
canMirror(AbstractDatabaseConnection) - Method in class adams.db.mirrored.SpectralDbBackend: Checks whether connection can be mirrored.
canNotify(SpectrumPanel, SpectrumContainer) - Method in class adams.flow.sink.spectrumdisplay.SimplePlotUpdater: Checks whether all conditions are met to notify the listeners for changes in the plot.
canPaint(Graphics) - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Returns true if the paintlets can be executed.
canRenderCached(Object, JPanel) - Method in class adams.gui.visualization.debug.objectrenderer.SpectrumRenderer: Checks whether the renderer can use a cached setup to render an object.
canRenderCached(Object, JPanel) - Method in class adams.gui.visualization.debug.objectrenderer.ThreeWayDataHeatmapRenderer: Checks whether the renderer can use a cached setup to render an object.
canWriteMultiple() - Method in class adams.data.io.output.AbstractSpectrumWriter: Returns whether writing of multiple containers is supported.
canWriteMultiple() - Method in class adams.data.io.output.JsonSpectrumWriter: Returns whether writing of multiple containers is supported.
canWriteMultiple() - Method in class adams.data.io.output.NIRSpectrumWriter: Returns whether writing of multiple containers is supported.
canWriteMultiple() - Method in class adams.data.io.output.SimpleEEMWriter: Returns whether writing of multiple containers is supported.
canWriteMultiple() - Method in class adams.data.io.output.SimpleSpectrumWriter: Returns whether writing of multiple containers is supported.
canWriteMultiple() - Method in class adams.data.io.output.SimpleXYZWriter: Returns whether writing of multiple containers is supported.
canWriteMultiple() - Method in class adams.data.io.output.SpreadSheetSpectrumWriter: Returns whether writing of multiple containers is supported.
canWriteMultiple() - Method in class adams.data.io.output.TrinamixSpectrumWriter: Returns whether writing of multiple containers is supported.
CenterBurst - Class in adams.data.spectrumfilter: Locates the highest burst (negative or positive) in the spectrum and then retrieves these points from the spectrum:
(numPoints / 2 - 1), burst, (numPoints / 2)
CenterBurst() - Constructor for class adams.data.spectrumfilter.CenterBurst
ChangeFormat - Class in adams.data.spectrumfilter: A filter that uses the sample ID to retrieve different formats from the database.
ChangeFormat() - Constructor for class adams.data.spectrumfilter.ChangeFormat
check() - Method in class adams.db.AbstractSpectrumConditions: Checks the correctness of the provided values.
check(MultiSpectrum) - Method in class adams.data.multispectrumoperation.AbstractMultiSpectrumOperation: Hook method for checking the data before applying the operation.
check(MultiSpectrum) - Method in class adams.data.multispectrumoperation.outlierremoval.AbstractOutlierRemoval: Hook method for checking the data before performing outlier removal.
check(Spectrum) - Method in class adams.data.cleaner.spectrum.AbstractCleaner: Performs the check.
check(Spectrum) - Method in class adams.data.spectrumimage.AbstractSpectrumImageGenerator: Hook method for checks before generating the image.
check(Spectrum) - Method in class adams.data.spectrumimage.AbstractSpectrumImageGeneratorWithRange: Hook method for checks before generating the image.
check(Spectrum) - Method in class adams.data.spectrumimage.Spectrogram: Hook method for checks before generating the image.
check(ThreeWayData[]) - Method in class adams.flow.transformer.threewaydatamerge.AbstractThreeWayDataMerge: Hook method for checks before attempting to merge.
check(EvaluationContainer) - Method in class adams.flow.transformer.predictioncheck.AbstractPredictionCheck: Hook method for checks.
check(EvaluationContainer) - Method in class adams.flow.transformer.predictioncheck.MinProbability: Hook method for checks.
check(EvaluationContainer) - Method in class adams.flow.transformer.predictioncheck.Range: Hook method for checks.
check(ThreeWayDataModelContainer) - Method in class adams.flow.transformer.threewaydatatrain.AbstractThreeWayDataTrainPostProcessor: Hook method for checking container before post-processing it.
check(File, Spectrum) - Method in class adams.data.io.input.sampleidextraction.AbstractSampleIDExtraction: Performs checks before the actual extraction.
check(List<Spectrum>) - Method in class adams.data.spectrumanalysis.AbstractSpectrumAnalysis: Hook method for checks.
check(Instance) - Method in class adams.data.cleaner.instance.AbstractCleaner: Performs the check.
check(Instances) - Method in class adams.data.spectrumanalysis.AbstractWekaSpectrumAnalysis: Hook method for checks.
check(Instances) - Method in class adams.data.spectrumanalysis.FastICA: Hook method for checks.
checkData() - Method in class adams.data.conversion.ThreeWayDataToHeatmap: Checks whether the data can be processed.
checkData() - Method in class adams.data.io.input.AbstractSpectrumReader: Hook method for checking the data.
checkData() - Method in class adams.data.io.input.AbstractThreeWayDataReader: Hook method for checking the data.
checkData() - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Performs some checks on the provided cols/rows.
checkData() - Method in class adams.data.io.input.FilteredSpectrumReader: Hook method for checking the data.
checkData(MultiSpectrum) - Method in class adams.data.multifilter.AbstractBinaryFormatsBasedMultiSpectrumFilter: The default implementation only checks whether there is any data set.
checkData(MultiSpectrum) - Method in class adams.data.multifilter.AbstractMultiSpectrumFilter: The default implementation only checks whether there is any data set.
checkData(MultiSpectrum) - Method in class adams.data.multifilter.Fusion: Makes sure that the wave number starts/step sizes have the same length as the format array.
checkData(MultiSpectrum) - Method in class adams.data.multireportfilter.AbstractMultiSpectrumReportFilter: The default implementation only checks whether there is any data set.
checkData(Spectrum) - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Optional checks of the spectrum.
checkData(Spectrum) - Method in class adams.data.spectrumfilter.AbstractSerializableFilter: Loads the serialized data on demand in addition to the checks.
checkData(Spectrum) - Method in class adams.data.spectrumfilter.LRCoeff: The default implementation only checks whether there is any data set.
checkData(Spectrum) - Method in class adams.data.spectrumfilter.MultiplicativeScatterCorrection: The default implementation only checks whether there is any data set.
checkData(ThreeWayData) - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Optional checks of the data.
checkData(List<Spectrum>) - Method in class adams.data.io.output.ASCSpectrumWriter: Writer can only write single spectra.
checkData(List<Spectrum>) - Method in class adams.data.io.output.DPTSpectrumWriter: Writer can only write single chromatograms.
checkData(List<Spectrum>) - Method in class adams.data.io.output.FilteredSpectrumWriter: Performs checks on the data.
checkData(List<Spectrum>) - Method in class adams.data.io.output.JCampDX2SpectrumWriter: Writer can only write single chromatograms.
checkHeader(Spectrum) - Method in class adams.data.instances.AbstractFieldInstanceGenerator: Checks whether the number of waves are the same.
checkHeader(Spectrum) - Method in class adams.data.instances.AbstractFieldInstanceGeneratorWithClass: Checks whether the number of waves are the same.
checkHeader(Spectrum) - Method in class adams.data.instances.AbstractSpectrumInstanceGenerator: Checks whether the number of waves are the same.
checkHeader(Spectrum) - Method in class adams.data.instances.AbstractSpectrumInstanceGeneratorWithClass: Checks whether the number of waves are the same.
checkHeader(Spectrum) - Method in class adams.data.instances.SimpleInstanceGenerator: Checks whether the number of waves are the same.
checkHeader(Spectrum) - Method in class adams.data.instances.SimpleSpectralInstanceGenerator: Checks whether the number of waves are the same.
checkHeader(Spectrum) - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Checks whether the number of waves are the same.
checkHeader(Spectrum) - Method in class adams.data.spreadsheetrowgenerator.SampleDataOnlyRowGenerator: Checks whether the number of waves are the same.
checkHeader(Spectrum) - Method in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: Checks whether the number of waves are the same.
checkInput(Spectrum) - Method in class adams.data.instances.AbstractSpectrumBasedInstanceGenerator: Checks the input spectrum.
checkInput(Spectrum) - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Checks the input spectrum.
checkInput(Spectrum) - Method in class adams.flow.transformer.SpectralAngleMapper: Checks the input spectrum for validity.
checkInputVersusReferences(Spectrum, Spectrum[]) - Method in class adams.flow.transformer.SpectralAngleMapper: Checks that the input and the references are able to be angle-mapped.
checkPrediction(EvaluationContainer) - Method in class adams.flow.transformer.predictioncheck.AbstractPredictionCheck: Performs checks on the prediction.
checkReferences(Spectrum[]) - Method in class adams.flow.transformer.SpectralAngleMapper: Checks the reference spectra for validity.
checkRequirement(Class) - Method in class adams.gui.scripting.SpectralCommandProcessor: Checks the following requirement.
checkSetup() - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Checks whether the setup is consistent.
checkSpectrum(Spectrum) - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Checks the spectrum, whether all of its values (amplitudes + fields) are within the boundaries.
checkTipText() - Method in class adams.flow.transformer.PredictionCheck: Returns the tip text for this property.
checkValue(InterPercentileRangeCleaner.InterPercentileRange, double) - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Checks the specified value against the inter-percentile setup whether it is valid or not.
checkWaveNumberAlignment(Spectrum, Spectrum[]) - Method in class adams.flow.transformer.SpectralAngleMapper: Checks that the input and reference spectra have the same wave-number profile.
checkWaveNumberAlignmentTipText() - Method in class adams.flow.transformer.SpectralAngleMapper: Gets the tip-text for the checkWaveNumberAlignment option.
chooseColor(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>, List<SpectrumContainer>) - Method in class adams.gui.visualization.spectrum.plotpopup.Viewport: Allows the user to choose the color for all the spectra.
chunk() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader.ChunkedSheetIterator: Reads the next chunk if necessary.
ChunkedSheetIterator(ChunkedSpreadSheetReader, File) - Constructor for class adams.data.io.input.RowWiseSpreadSheetSpectrumReader.ChunkedSheetIterator: Initializes the iterator.
chunkSizeTipText() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Returns the tip text for this property.
CIRCLE - adams.gui.visualization.spectrum.SpectrumPaintlet.MarkerShape: a circle.
classifierFirstTipText() - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Returns the tip text for this property.
classifierNoneTipText() - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Returns the tip text for this property.
classifierSecondTipText() - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Returns the tip text for this property.
classifiersTipText() - Method in class adams.data.evaluator.instance.EnsembleEvaluator: Returns the tip text for this property.
classifiersTipText() - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Returns the tip text for this property.
classifiersTipText() - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Returns the tip text for this property.
classifierTipText() - Method in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: Returns the tip text for this property.
classifierTipText() - Method in class adams.data.cleaner.instance.RemoveOutliers: Returns the tip text for this property.
classifierTipText() - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Returns the tip text for this property.
classifierTipText() - Method in class adams.data.evaluator.instance.CrossValidatedPrediction: Returns the tip text for this property.
classifierTipText() - Method in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: Returns the tip text for this property.
classifierTipText() - Method in interface adams.data.evaluator.instance.WekaClassifierBasedEvaluator: Returns the tip text for this property.
classLabelsTipText() - Method in class adams.data.instances.AbstractFieldInstanceGeneratorWithClass: Returns the tip text for this property.
classLabelsTipText() - Method in class adams.data.instances.AbstractSpectrumInstanceGeneratorWithClass: Returns the tip text for this property.
classLabelsTipText() - Method in interface adams.data.instances.InstanceGeneratorWithClassLabels: Returns the tip text for this property.
clean(Instances) - Method in class adams.data.cleaner.instance.AbstractCleaner: Performs the clean.
cleanAfterBuildTipText() - Method in class adams.flow.transformer.Evaluator: Returns the tip text for this property.
cleanData(Instances, int, Classifier, int, int, long, double) - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Cleans the data using the specified classifier and parameters.
Cleaner - Class in adams.flow.transformer: In case of Instances objects, 'unclean' Instance objects get removed.
Cleaner() - Constructor for class adams.flow.transformer.Cleaner
Cleaner.CleanJob - Class in adams.flow.transformer
CleanerDetails<T> - Interface in adams.data.cleaner: Interface for cleaners that provide details about their internals after they have been built.
cleanerDetailsOutputTipText() - Method in class adams.flow.transformer.Cleaner: Returns the tip text for this property.
CleanerDetailsViewer - Class in adams.gui.tools.previewbrowser: Viewer for details of a cleaner.
CleanerDetailsViewer() - Constructor for class adams.gui.tools.previewbrowser.CleanerDetailsViewer
CleanerModelLoader - Class in adams.flow.core: Model loader for AbstractCleaner objects.
CleanerModelLoader() - Constructor for class adams.flow.core.CleanerModelLoader
cleanerTipText() - Method in class adams.flow.control.InstanceCleaner: Returns the tip text for this property.
cleanerTipText() - Method in class adams.flow.control.SpectrumCleaner: Returns the tip text for this property.
cleanerTipText() - Method in class adams.flow.transformer.Cleaner: Returns the tip text for this property.
CleaningContainer - Class in adams.flow.container: Container used by cleaners.
CleaningContainer() - Constructor for class adams.flow.container.CleaningContainer: Default constructor.
CleaningContainer(Instance) - Constructor for class adams.flow.container.CleaningContainer: Initializes the container with the WEKA instance.
CleaningContainer(Instance, SpreadSheet) - Constructor for class adams.flow.container.CleaningContainer: Initializes the container with the WEKA instance.
CleaningContainer(Instances) - Constructor for class adams.flow.container.CleaningContainer: Initializes the container with the WEKA instances.
CleanJob(AbstractCleaner, Instances) - Constructor for class adams.flow.transformer.Cleaner.CleanJob: Initializes the job.
cleanUp() - Method in class adams.data.evaluator.instance.AbstractNearestNeighborBasedEvaluator: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.data.evaluator.instance.DistanceToClosest
cleanUp() - Method in class adams.data.evaluator.instance.EnsembleEvaluator: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.data.evaluator.instance.FakeEvaluator: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Clean up training instances.
cleanUp() - Method in class adams.data.evaluator.instance.NullEvaluator: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.data.multifilter.AbstractMultiSpectrumFilter: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.data.multireportfilter.AbstractMultiSpectrumReportFilter: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.data.postprocessor.instances.AbstractSerializablePostProcessor: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.data.postprocessor.instances.WekaFilter: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.data.statistics.L1PointStatistic: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.data.statistics.SpectrumStatistic: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.data.statistics.ThreeWayDataStatistic: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.flow.sink.SpectrumDisplay.DisplayPanel
cleanUp() - Method in class adams.flow.standalone.rats.WSMultiSpectrumReception: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.flow.standalone.rats.WSSpectrumReception: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.flow.transformer.Cleaner.CleanJob: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.flow.transformer.Evaluator.EvaluateJob: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.flow.webservice.Get: Cleans up the client.
cleanUp() - Method in class adams.flow.webservice.Put: Cleans up the client.
cleanUp() - Method in class adams.flow.webservice.Transform: Cleans up the client.
cleanUp() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.gui.visualization.spectrum.SpectrumPointHitDetector: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.gui.visualization.spectrum.WaveNumberHitDetector: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Cleans up data structures, frees up memory.
cleanUp() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Cleans up data structures, frees up memory.
cleanUpOptions() - Method in class adams.data.spectrum.AbstractSpectrumComparator: Cleans up the options.
clear() - Method in class adams.gui.selection.SelectSpectrumPanel.TableModel: Clears the internal model.
clear() - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: Clears the container list.
clearData() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Removes all the data.
clearImageCache() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Clears the image cache.
clearPanel() - Method in class adams.flow.sink.SpectrumDisplay: Clears the content of the panel.
clearPanel() - Method in class adams.flow.sink.SpectrumDisplay.DisplayPanel
clearPanel() - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Clears the content of the panel.
clientTipText() - Method in class adams.data.io.output.NIRSpectrumWriter: Returns the tip text for this property.
cloneContent() - Method in class adams.data.container.TensorContainer: Returns a clone of the content.
close() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: closes the dialog/frame.
close() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: closes the dialog/frame.
closeAll() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Removes all the data.
closeCurrent() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Removes the current tab.
closest(long, L1Point, L1Point) - Static method in class adams.data.threeway.L1PointUtils: Returns a level 1 point with the level 2 data of the closest of the two level 1 points.
closeTab() - Method in class adams.gui.visualization.spectrum.MultiSpectrumPanel: Closes the current tab.
closeWindow() - Method in class adams.gui.visualization.spectrum.MultiSpectrumPanel: Closes the frame/window.
clusterPriors() - Method in class weka.clusterers.SpectrumClusterer: Returns the prior probability of each cluster.
CMLSpectrumHandler - Class in adams.gui.tools.previewbrowser: Displays the following spectrum types: cal

Valid options are:
CMLSpectrumHandler() - Constructor for class adams.gui.tools.previewbrowser.CMLSpectrumHandler
CMLSpectrumReader - Class in adams.data.io.input: Reads spectra in CML (Chemical Markup Language) format.

For more information see:
http://www.xml-cml.org/

Valid options are:
CMLSpectrumReader() - Constructor for class adams.data.io.input.CMLSpectrumReader
CNM - Static variable in class adams.data.io.input.opus.OpusBlockHelper: the CNM character sequence.
COL_DBID - Static variable in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator
COL_SAMPLEID - Static variable in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator
CollapseX - Class in adams.flow.transformer.threewaydatamerge: Calculates the mean/median/stdev data across the X layers.
CollapseX() - Constructor for class adams.flow.transformer.threewaydatamerge.CollapseX
CollapseX.StatisticType - Enum in adams.flow.transformer.threewaydatamerge: the statistic to calculate from the data values.
collect() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.DataCollector: Starts the collection of the data.
collectChunk(int, int) - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.DataCollector: Collects a single chunk.
collectChunks() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.DataCollector: Collects the data in chunks and computes the ranges based on that (picks the median).
colorFieldTipText() - Method in class adams.gui.visualization.spectrum.ReportColorSpectrumPaintlet: Returns the tip text for this property.
colorGeneratorTipText() - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Returns the tip text for this property.
colorProviderTipText() - Method in class adams.flow.sink.SpectrumDisplay: Returns the tip text for this property.
colorProviderTipText() - Method in class adams.gui.visualization.spectrum.SpectrumPaintletStringField: Returns the tip text for this property.
colorTipText() - Method in class adams.gui.visualization.spectrum.SelectedWaveNumberPaintlet: Returns the tip text for this property.
colSampleDataNamesTipText() - Method in class adams.data.conversion.SpreadSheetColumnsToSampleData: Returns the tip text for this property.
colSampleDataNamesTipText() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Returns the tip text for this property.
colsSampleDataValuesTipText() - Method in class adams.data.conversion.SpreadSheetColumnsToSampleData: Returns the tip text for this property.
columnAmplitudeTipText() - Method in class adams.data.conversion.SpreadSheetToSpectrum: Returns the tip text for this property.
columnDataTipText() - Method in class adams.data.conversion.SpreadSheetTo3DTensor: Returns the tip text for this property.
columnDataTipText() - Method in class adams.data.conversion.SpreadSheetToThreeWayData: Returns the tip text for this property.
columnIDTipText() - Method in class adams.data.conversion.SpreadSheetRowsToSampleData: Returns the tip text for this property.
columnIDTipText() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns the tip text for this property.
columnMeasurementNameTipText() - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Returns the tip text for this property.
columnMeasurementValueTipText() - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Returns the tip text for this property.
columnSampleIDTipText() - Method in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: Returns the tip text for this property.
columnSampleIDTipText() - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Returns the tip text for this property.
columnSampleTypeTipText() - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Returns the tip text for this property.
columnsAmplitudeTipText() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Returns the tip text for this property.
columnsAmplitudeTipText() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns the tip text for this property.
columnsBooleanTipText() - Method in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: Returns the tip text for this property.
columnsNumericTipText() - Method in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: Returns the tip text for this property.
columnsSampleDataTipText() - Method in class adams.data.conversion.SpreadSheetRowsToSampleData: Returns the tip text for this property.
columnsSampleDataTipText() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns the tip text for this property.
columnsSampleDataTipText() - Method in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: Returns the tip text for this property.
columnsTipText() - Method in class adams.data.conversion.SpreadSheetTo2DTensor: Returns the tip text for this property.
columnWaveNumberTipText() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Returns the tip text for this property.
columnWaveNumberTipText() - Method in class adams.data.conversion.SpreadSheetToSpectrum: Returns the tip text for this property.
ColumnWiseSpreadSheetSpectrumReader - Class in adams.data.io.input: Reads spectra from columns in a spreadsheet obtained with the specified spreadsheet reader.
ColumnWiseSpreadSheetSpectrumReader() - Constructor for class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader
ColumnWiseSpreadSheetSpectrumReader.SampleIDLocation - Enum in adams.data.io.input: Determines whether the sample ID is located.
columnXTipText() - Method in class adams.data.conversion.SpreadSheetTo3DTensor: Returns the tip text for this property.
columnXTipText() - Method in class adams.data.conversion.SpreadSheetToThreeWayData: Returns the tip text for this property.
columnYTipText() - Method in class adams.data.conversion.SpreadSheetTo3DTensor: Returns the tip text for this property.
columnYTipText() - Method in class adams.data.conversion.SpreadSheetToThreeWayData: Returns the tip text for this property.
columnZTipText() - Method in class adams.data.conversion.SpreadSheetTo3DTensor: Returns the tip text for this property.
columnZTipText() - Method in class adams.data.conversion.SpreadSheetToThreeWayData: Returns the tip text for this property.
CommandlineData(String) - Constructor for class adams.data.io.input.opus.OpusBlockHelper.CommandlineData: Initializes the object.
COMMENT - Static variable in class adams.data.io.output.JCampDX2SpectrumWriter: the comments.
compare(SpectrumPoint, SpectrumPoint) - Method in class adams.data.spectrum.SpectrumPointComparator: Compares its two arguments for order.
compare(Spectrum, Spectrum) - Method in class adams.data.spectrum.SpectrumComparator: Compares its two arguments for order.
compare(Spectrum, Spectrum) - Method in class adams.data.spectrum.SpectrumComparatorByReportValue: Compares its two arguments for order.
compare(L1Point, L1Point) - Method in class adams.data.threeway.L1PointComparator: Compares its two arguments for order.
compare(L2Point, L2Point) - Method in class adams.data.threeway.L2PointComparator: Compares its two arguments for order.
compareTo(AbstractMultiPageMenuItem) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.multipageaction.AbstractMultiPageMenuItem: Returns a comparison based on the name of the menu items.
compareTo(Object) - Method in class adams.data.cleaner.instance.AbstractCleaner: Compares this object with the specified object for order.
compareTo(Object) - Method in class adams.data.cleaner.spectrum.AbstractCleaner: Compares this object with the specified object for order.
compareTo(Object) - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.InterPercentileRange: Compares itself with the specified object.
compareTo(Object) - Method in class adams.data.evaluator.instance.AbstractEvaluator: Compares this object with the specified object for order.
compareTo(Object) - Method in class adams.data.multifilter.AbstractMultiSpectrumFilter: Compares this object with the specified object for order.
compareTo(Object) - Method in class adams.data.multireportfilter.AbstractMultiSpectrumReportFilter: Compares this object with the specified object for order.
compareTo(Object) - Method in class adams.data.postprocessor.instances.AbstractPostProcessor: Compares this object with the specified object for order.
compareTo(Object) - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Compares this object with the specified object for order.
compareTo(Object) - Method in class adams.data.spectrum.SpectrumPoint: Compares this object with the specified object for order.
compareTo(Object) - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Compares this object with the specified object for order.
compareTo(Object) - Method in class adams.data.threeway.L2Point: Compares this object with the specified object for order.
compareTo(Object) - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Compares this object with the specified object for order.
compareToHeader(Object) - Method in class adams.data.spectrum.Spectrum: Compares this object with the specified object for order.
compareToHeader(Object) - Method in class adams.data.threeway.L1Point: Compares this object with the specified object for order.
compareToHeader(Object) - Method in class adams.data.threeway.ThreeWayData: Compares this object with the specified object for order.
COMPONENTS - Static variable in class adams.gui.menu.ExportValidationSets
componentTipText() - Method in class adams.data.conversion.WekaPredictionContainerToEvaluationContainer: Returns the tip text for this property.
componentTipText() - Method in class adams.flow.transformer.Evaluator: Returns the tip text for this property.
ConditionalReportField - Class in adams.data.spectrumfilter: Sets the 'success' value for the specified field if the condition evaluates to 'true', otherwise the 'failure' value.
ConditionalReportField() - Constructor for class adams.data.spectrumfilter.ConditionalReportField
conditionBooleanTipText() - Method in class adams.data.multifilter.PickByReportValue: Returns the tip text for this property.
conditionNumericMaxTipText() - Method in class adams.data.multifilter.PickByReportValue: Returns the tip text for this property.
conditionNumericMinTipText() - Method in class adams.data.multifilter.PickByReportValue: Returns the tip text for this property.
conditionsTipText() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Returns the tip text for this property.
conditionsTipText() - Method in class adams.data.spectrumfilter.Covariance: Returns the tip text for this property.
conditionsTipText() - Method in class adams.data.spectrumfilter.LRCoeff: Returns the tip text for this property.
conditionsTipText() - Method in class adams.flow.source.OrphanedSampleDataIdSupplier: Returns the tip text for this property.
conditionsToFields() - Method in class adams.gui.tools.idprovider.DatabaseSearchPanel: Transfers the conditions to the fields.
conditionStringTipText() - Method in class adams.data.multifilter.PickByReportValue: Returns the tip text for this property.
conditionTipText() - Method in class adams.data.spectrumfilter.ConditionalReportField: Returns the tip text for this property.
confidenceLevelTipText() - Method in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: Returns the tip text for this property.
constituentsFieldsTipText() - Method in class adams.data.io.output.CALSpectrumWriter: Returns the tip text for this property.
ConstituentValues() - Constructor for class adams.data.io.output.foss.FossOutputHelper.ConstituentValues
containers(MouseEvent) - Method in class adams.gui.visualization.spectrum.SpectrumPointHitDetector: Detects hits and associates them with the containers.
containersInViewport(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>) - Method in class adams.gui.visualization.spectrum.plotpopup.Viewport: Locates the visible spectra that are on display in the current viewport.
conversionTipText() - Method in class adams.data.spectrumfilter.ReportFieldFromStringValue: Returns the tip text for this property.
conversionTipText() - Method in class adams.flow.transformer.SetEvaluationMetaData: Returns the tip text for this property.
convert(double[]) - Method in class adams.data.conversion.TensorToSpreadSheet: Converts the 1-D tensor data.
convert(double[]) - Method in class adams.data.conversion.TensorToThreeWayData: Converts the 1-D tensor data.
convert(double[][]) - Method in class adams.data.conversion.TensorToSpreadSheet: Converts the 2-D tensor data.
convert(double[][]) - Method in class adams.data.conversion.TensorToThreeWayData: Converts the 2-D tensor data.
convert(double[][][]) - Method in class adams.data.conversion.TensorToSpreadSheet: Converts the 3-D tensor data.
convert(double[][][]) - Method in class adams.data.conversion.TensorToThreeWayData: Converts the 3-D tensor data.
convert(DataPoint) - Method in class adams.data.spectrumfilter.LOWESS: Returns the X/Y values of the DataPoint as Point2D.
convert8ToDouble(byte[], int) - Method in class adams.data.io.input.OpusSpectrumReader: Convert 8 bytes to long.
converterTipText() - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Returns the tip text for this property.
converterTipText() - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Returns the tip text for this property.
convertToLong(byte[], int) - Method in class adams.data.io.input.foss.FossHelper: Convert 4 bytes to long.
convertToLong(byte[], int) - Method in class adams.data.io.input.foss.FossStdise: Convert 4 bytes to long.
convertToLong(byte[], int) - Method in class adams.data.io.input.OpusSpectrumReader: Convert 4 bytes to long.
copy(int, List<DataPoint>) - Method in class adams.data.threewayfilter.DownSample: Creates a copy of the data point.
copyBytes(int, int) - Method in class adams.data.io.input.SPCSpectrumReader.AbstractParser: Copies the bytes into a new array.
CORR - adams.data.io.input.SoilCaresScannerSpectrumReader.SpectrumType
correct(Spectrum) - Method in class adams.data.spectrumfilter.detrend.AbstractDetrend: Corrects the spectrum.
correct(Spectrum) - Method in class adams.data.spectrumfilter.detrend.Mean: Corrects the spectrum.
correct(Spectrum) - Method in class adams.data.spectrumfilter.detrend.RangeBased: Corrects the spectrum.
correct(Spectrum, Spectrum) - Method in class adams.data.spectrumfilter.multiplicativescattercorrection.AbstractMultiplicativeScatterCorrection: Corrects the spectrum.
correct(Spectrum, Spectrum) - Method in class adams.data.spectrumfilter.multiplicativescattercorrection.RangeBased: Corrects the spectrum.
correctData(Spectrum, double[]) - Method in class adams.data.spectrumbaseline.LinearRegressionBased: Corrects the data with the given coefficients.
correctionTipText() - Method in class adams.data.spectrumfilter.Detrend: Returns the tip text for this property.
correctionTipText() - Method in class adams.data.spectrumfilter.MultiplicativeScatterCorrection: Returns the tip text for this property.
CorrelationBasedThreshold - Class in adams.data.multispectrumoperation.outlierremoval: Applies the pre-filter and then computes the correlation coefficients between the spectra.
CorrelationBasedThreshold() - Constructor for class adams.data.multispectrumoperation.outlierremoval.CorrelationBasedThreshold
CosineSimilarityBasedThreshold - Class in adams.data.multispectrumoperation.outlierremoval: Applies the pre-filter and then computes the cosine similarity between the spectra.
CosineSimilarityBasedThreshold() - Constructor for class adams.data.multispectrumoperation.outlierremoval.CosineSimilarityBasedThreshold
count - Variable in class adams.data.io.input.foss.FossHelper.FossFields: row number in file.
count_offset - Static variable in class adams.data.io.input.foss.FossHelper: number of Rows in this file.
countDeleted() - Method in class adams.data.io.input.foss.FossHelper: How many deleted rows?
countRegions(List<SpectrumPoint>, long, long, boolean) - Static method in class adams.data.spectrum.SpectrumUtils: Counts the positive or negative regions between the given points (incl.
countSignChanges(List<SpectrumPoint>, long, long) - Static method in class adams.data.spectrum.SpectrumUtils: Counts the sign changes in the given data between the given points (incl.
countVisible() - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: Returns the number of visible containers.
Covariance - Class in adams.data.spectrumfilter: Plot covariance against Reference.
Covariance() - Constructor for class adams.data.spectrumfilter.Covariance
createContainerList() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Returns the container list.
createDisplayPanel(Token) - Method in class adams.flow.sink.SpectrumDisplay: Creates a new display panel for the token.
createDisplayPanel(Token) - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Creates a new display panel for the token.
createDummy(String, Date, String) - Static method in class adams.data.sampledata.SampleData: Creates a dummy report.
createDummy(String, Date, String) - Static method in class adams.data.threewayreport.ThreeWayReport: Creates a dummy report.
createDummyReport(Spectrum) - Method in class adams.data.io.input.AbstractSpectrumReader: Creates a dummy report.
createDummyReport(ThreeWayData) - Method in class adams.data.io.input.AbstractThreeWayDataReader: Creates a dummy report.
createGetRequest() - Method in class nz.ac.waikato.adams.webservice.spectral.get.ObjectFactory: Create an instance of GetRequest
createGetRequest(GetRequest) - Method in class nz.ac.waikato.adams.webservice.spectral.get.ObjectFactory: Create an instance of JAXBElement<GetRequest>
createGetResponse() - Method in class nz.ac.waikato.adams.webservice.spectral.get.ObjectFactory: Create an instance of GetResponse
createGetResponse(GetResponse) - Method in class nz.ac.waikato.adams.webservice.spectral.get.ObjectFactory: Create an instance of JAXBElement<GetResponse>
createGOE() - Method in class adams.gui.visualization.spectrum.SpectrumDatasetExportDialog: Creates the GOE panel to use.
createGOE() - Method in class adams.gui.visualization.spectrum.SpectrumExportDialog: Creates the GOE panel to use.
createHeader(Spectrum) - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Creates the header from a template spectrum.
createHeader(Spectrum) - Method in class adams.data.spectrum.Amplitudes: Creates the header from a template spectrum.
createHeader(ThreeWayData) - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Creates the header from template data.
createHeader(ThreeWayData) - Method in class adams.data.threewayfeatures.Flatten: Creates the header from template data.
createHeader(ThreeWayData) - Method in class adams.data.threewayfeatures.Histogram: Creates the header from template data.
createHeader(ThreeWayData) - Method in class adams.data.threewayfeatures.Max: Creates the header from template data.
createHeader(ThreeWayData) - Method in class adams.data.threewayfeatures.Mean: Creates the header from template data.
createHeader(ThreeWayData) - Method in class adams.data.threewayfeatures.Median: Creates the header from template data.
createHeader(ThreeWayData) - Method in class adams.data.threewayfeatures.Min: Creates the header from template data.
createHeader(ThreeWayData) - Method in class adams.data.threewayfeatures.MultiThreeWayDataFeatureGenerator: Creates the header from template data.
createHeader(ThreeWayData) - Method in class adams.data.threewayfeatures.StdDev: Creates the header from template data.
createHeader(Instances, Instances) - Method in class weka.filters.unsupervised.attribute.SpectrumFilter: Creates a new header based on the input data and the transformed spectral part.
createModel(SpectrumContainerManager) - Method in class adams.gui.visualization.spectrum.SpectrumContainerList: Creates a new model.
createMultiSpectrum() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.ObjectFactory: Create an instance of MultiSpectrum
createPopup(MouseEvent) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerMultiPagePane: Generates the right-click menu for the JList.
createPopupMenu(MouseEvent) - Method in class adams.gui.tools.DeleteSampleDataPanel: Creates the popup menu for the table.
createPrefix(int) - Method in class adams.data.threewayfeatures.MultiThreeWayDataFeatureGenerator: Generates the prefix for the specified flattener.
createPreview(File) - Method in class adams.gui.tools.previewbrowser.AbstractSpectrumHandler: Creates the actual view.
createPreview(File) - Method in class adams.gui.tools.previewbrowser.ThreeWayEEMHandler: Creates the actual preview.
createPreview(File) - Method in class adams.gui.tools.previewbrowser.ThreeWayXYZHandler: Creates the actual preview.
createPreview(File[]) - Method in class adams.gui.tools.previewbrowser.AbstractSpectrumHandler: Creates the actual view.
createPreview(Object) - Method in class adams.gui.tools.previewbrowser.CleanerDetailsViewer: Creates a PreviewPanel for the given object.
createProperties() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.ObjectFactory: Create an instance of Properties
createProperties() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.ObjectFactory: Create an instance of Properties
createProperties() - Method in class nz.ac.waikato.adams.webservice.spectral.get.ObjectFactory: Create an instance of Properties
createProperties() - Method in class nz.ac.waikato.adams.webservice.spectral.put.ObjectFactory: Create an instance of Properties
createProperties() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.ObjectFactory: Create an instance of Properties
createProperty() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.ObjectFactory: Create an instance of Property
createProperty() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.ObjectFactory: Create an instance of Property
createProperty() - Method in class nz.ac.waikato.adams.webservice.spectral.get.ObjectFactory: Create an instance of Property
createProperty() - Method in class nz.ac.waikato.adams.webservice.spectral.put.ObjectFactory: Create an instance of Property
createProperty() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.ObjectFactory: Create an instance of Property
createPutRequest() - Method in class nz.ac.waikato.adams.webservice.spectral.put.ObjectFactory: Create an instance of PutRequest
createPutRequest(PutRequest) - Method in class nz.ac.waikato.adams.webservice.spectral.put.ObjectFactory: Create an instance of JAXBElement<PutRequest>
createPutResponse() - Method in class nz.ac.waikato.adams.webservice.spectral.put.ObjectFactory: Create an instance of PutResponse
createPutResponse(PutResponse) - Method in class nz.ac.waikato.adams.webservice.spectral.put.ObjectFactory: Create an instance of JAXBElement<PutResponse>
createSpectrum() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.ObjectFactory: Create an instance of Spectrum
createSpectrum() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.ObjectFactory: Create an instance of Spectrum
createSpectrum() - Method in class nz.ac.waikato.adams.webservice.spectral.get.ObjectFactory: Create an instance of Spectrum
createSpectrum() - Method in class nz.ac.waikato.adams.webservice.spectral.put.ObjectFactory: Create an instance of Spectrum
createSpectrum() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.ObjectFactory: Create an instance of Spectrum
createTable() - Method in class adams.gui.visualization.spectrum.SpectrumContainerList: Creates a new table.
createTransformRequest() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.ObjectFactory: Create an instance of TransformRequest
createTransformRequest(TransformRequest) - Method in class nz.ac.waikato.adams.webservice.spectral.transform.ObjectFactory: Create an instance of JAXBElement<TransformRequest>
createTransformResponse() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.ObjectFactory: Create an instance of TransformResponse
createTransformResponse(TransformResponse) - Method in class nz.ac.waikato.adams.webservice.spectral.transform.ObjectFactory: Create an instance of JAXBElement<TransformResponse>
createUploadRequest() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.ObjectFactory: Create an instance of UploadRequest
createUploadRequest() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.ObjectFactory: Create an instance of UploadRequest
createUploadRequest(UploadRequest) - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.ObjectFactory: Create an instance of JAXBElement<UploadRequest>
createUploadRequest(UploadRequest) - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.ObjectFactory: Create an instance of JAXBElement<UploadRequest>
createUploadResponse() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.ObjectFactory: Create an instance of UploadResponse
createUploadResponse() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.ObjectFactory: Create an instance of UploadResponse
createUploadResponse(UploadResponse) - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.ObjectFactory: Create an instance of JAXBElement<UploadResponse>
createUploadResponse(UploadResponse) - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.ObjectFactory: Create an instance of JAXBElement<UploadResponse>
createWave() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.ObjectFactory: Create an instance of Wave
createWave() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.ObjectFactory: Create an instance of Wave
createWave() - Method in class nz.ac.waikato.adams.webservice.spectral.get.ObjectFactory: Create an instance of Wave
createWave() - Method in class nz.ac.waikato.adams.webservice.spectral.put.ObjectFactory: Create an instance of Wave
createWave() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.ObjectFactory: Create an instance of Wave
createWaves() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.ObjectFactory: Create an instance of Waves
createWaves() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.ObjectFactory: Create an instance of Waves
createWaves() - Method in class nz.ac.waikato.adams.webservice.spectral.get.ObjectFactory: Create an instance of Waves
createWaves() - Method in class nz.ac.waikato.adams.webservice.spectral.put.ObjectFactory: Create an instance of Waves
createWaves() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.ObjectFactory: Create an instance of Waves
Crop - Class in adams.data.threewayfilter
Crop() - Constructor for class adams.data.threewayfilter.Crop
CrossHair - Class in adams.gui.visualization.spectrum.plotpopup: Allows to enable/disable the cross-hairs tracker.
CrossHair() - Constructor for class adams.gui.visualization.spectrum.plotpopup.CrossHair
crossValidate(Instances, int) - Method in class adams.data.cleaner.instance.RemoveOutliers: Cross-validates the classifier on the given data.
CrossValidatedNeighborHood - Class in adams.data.evaluator.instance: Evaluator that cross-validates the specified classifier on the neighborhood determined for the instance under evaluation.
CrossValidatedNeighborHood() - Constructor for class adams.data.evaluator.instance.CrossValidatedNeighborHood
CrossValidatedPrediction - Class in adams.data.evaluator.instance: Evaluator that (kind of) cross-validates the specified classifier on the neighborhood determined for the instance under evaluation.
A classifier is built on each of the training sets that is generated for the cross-validation.
CrossValidatedPrediction() - Constructor for class adams.data.evaluator.instance.CrossValidatedPrediction
CrossValidatedPrediction.StatisticType - Enum in adams.data.evaluator.instance: The type of statistic to return.
CSF - Static variable in class adams.data.io.input.opus.OpusBlockHelper: the CSF character sequence.
currentInput() - Method in class adams.flow.control.InstanceCleaner: Returns the current input token, if any.
currentInput() - Method in class adams.flow.control.SpectrumCleaner: Returns the current input token, if any.
customComparatorTipText() - Method in class adams.data.conversion.SpectraToMultiSpectrum: Returns the tip text for this property.
customComparatorTipText() - Method in class adams.flow.transformer.SpectrumFileReader: Returns the tip text for this property.
customize(AbstractContainerListPopupCustomizer.Context<Spectrum, SpectrumContainerManager, SpectrumContainer>, JPopupMenu) - Method in class adams.gui.visualization.spectrum.containerlistpopup.Information: Returns a popup menu for the table of the container list.
customize(AbstractContainerListPopupCustomizer.Context<Spectrum, SpectrumContainerManager, SpectrumContainer>, JPopupMenu) - Method in class adams.gui.visualization.spectrum.containerlistpopup.SampleData: Returns a popup menu for the table of the container list.
customize(AbstractContainerListPopupCustomizer.Context<Spectrum, SpectrumContainerManager, SpectrumContainer>, JPopupMenu) - Method in class adams.gui.visualization.spectrum.containerlistpopup.SpectralData: Returns a popup menu for the table of the container list.
customize(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>, MouseEvent, JPopupMenu) - Method in class adams.gui.visualization.spectrum.plotpopup.Adjust: Returns a popup menu for the table of the container list.
customize(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>, MouseEvent, JPopupMenu) - Method in class adams.gui.visualization.spectrum.plotpopup.CrossHair: Returns a popup menu for the table of the container list.
customize(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>, MouseEvent, JPopupMenu) - Method in class adams.gui.visualization.spectrum.plotpopup.ExportVisible: Returns a popup menu for the table of the container list.
customize(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>, MouseEvent, JPopupMenu) - Method in class adams.gui.visualization.spectrum.plotpopup.GotoWaveNumber: Returns a popup menu for the table of the container list.
customize(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>, MouseEvent, JPopupMenu) - Method in class adams.gui.visualization.spectrum.plotpopup.Histogram: Returns a popup menu for the table of the container list.
customize(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>, MouseEvent, JPopupMenu) - Method in class adams.gui.visualization.spectrum.plotpopup.Hits: Returns a popup menu for the table of the container list.
customize(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>, MouseEvent, JPopupMenu) - Method in class adams.gui.visualization.spectrum.plotpopup.SaveVisible: Returns a popup menu for the table of the container list.
customize(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>, MouseEvent, JPopupMenu) - Method in class adams.gui.visualization.spectrum.plotpopup.Statistics: Returns a popup menu for the table of the container list.
customize(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>, MouseEvent, JPopupMenu) - Method in class adams.gui.visualization.spectrum.plotpopup.Viewport: Returns a popup menu for the table of the container list.

D

DATABASE_ID - Static variable in class adams.data.statistics.SpectrumStatistic
databaseConnectionStateChanged(DatabaseConnectionChangeEvent) - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: A change in the database connection occurred.
databaseConnectionStateChanged(DatabaseConnectionChangeEvent) - Method in class adams.gui.visualization.spectrum.SpectrumPanel: A change in the database connection occurred.
databaseDisconnected() - Method in class adams.gui.selection.SelectSpectrumPanel: Gets called when the database connection gets disconnected.
DatabaseSearchPanel - Class in adams.gui.tools.idprovider: Panel for obtaining IDs from the database.
DatabaseSearchPanel(IDConsumer) - Constructor for class adams.gui.tools.idprovider.DatabaseSearchPanel: Initializes the panel with the owner.
DataBlock() - Constructor for class adams.data.io.output.foss.FossOutputHelper.DataBlock
dataChanged(DataChangeEvent) - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Gets called if the data of the spectrum panel has changed.
DataCollector(AbstractDatabaseConnection, List<Integer>, double, double, int) - Constructor for class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.DataCollector: Initializes the data collector.
datapoint_offset - Static variable in class adams.data.io.input.foss.FossHelper: number of nir wavelengths.
datapoint_offset - Static variable in class adams.data.io.input.foss.FossStdise: number of wavelengths.
dataPointsTipText() - Method in class adams.data.io.output.ASCSpectrumWriter: Returns the tip text for this property.
DataType - Enum in nz.ac.waikato.adams.webservice.rats.multispectrum: Java class for DataType.
DataType - Enum in nz.ac.waikato.adams.webservice.rats.spectrum: Java class for DataType.
DataType - Enum in nz.ac.waikato.adams.webservice.spectral.get: Java class for DataType.
DataType - Enum in nz.ac.waikato.adams.webservice.spectral.put: Java class for DataType.
DataType - Enum in nz.ac.waikato.adams.webservice.spectral.transform: Java class for DataType.
dataTypesTipText() - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Returns the tip text for this property.
DATEFORMAT_TIME_MEASURED - Static variable in class adams.data.io.input.MPSSpectrumReader
dateFormatTipText() - Method in class adams.data.io.input.MPSSpectrumReader: Returns the tip text for this property.
DB_ID - adams.flow.transformer.SpectrumInfo.InfoType: the database ID.
DEFAULT_DERIVATIVE_ORDER - Static variable in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: the default for the derivative order.
DEFAULT_EXCLUDE - Static variable in class weka.filters.unsupervised.attribute.SegmentedDownSample: the default for the exclude expression.
DEFAULT_EXCLUDE - Static variable in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: the default for the exclude expression.
DEFAULT_FORMAT - Static variable in class adams.data.sampledata.SampleData: the default data type.
DEFAULT_FORMAT - Static variable in class adams.data.threewayreport.ThreeWayReport: the default data type.
DEFAULT_INSTRUMENT - Static variable in class adams.data.sampledata.SampleData: the default instrument ('unknown').
DEFAULT_INSTRUMENT - Static variable in class adams.data.threewayreport.ThreeWayReport: the default instrument ('unknown').
DEFAULT_METRIC - Static variable in class adams.data.evaluator.instance.AbstractEvaluator: the default metric.
DEFAULT_NTH_POINT - Static variable in class weka.filters.unsupervised.attribute.SegmentedDownSample: the default for the nth point.
DEFAULT_NUM_POINTS - Static variable in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: the default for the number of points.
DEFAULT_POLYNOMIAL_ORDER - Static variable in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: the default for the polynomial order.
DEFAULT_REGEXP - Static variable in class adams.gui.visualization.spectrum.SpectrumPaintletStringField: the default regular expression.
DEFAULT_WAVENO_REGEXP - Static variable in class adams.data.conversion.SpreadSheetColumnsToSpectra
DEFAULT_WAVENO_REGEXP - Static variable in class adams.data.conversion.SpreadSheetRowsToSpectra
defaultClassifierString() - Method in class weka.classifiers.meta.SpectrumClassifier: String describing default classifier.
defaultColorTipText() - Method in class adams.gui.visualization.spectrum.ReportColorSpectrumPaintlet: Returns the tip text for this property.
defaultColorTipText() - Method in class adams.gui.visualization.spectrum.SpectrumPaintletNumericField: Returns the tip text for this property.
defaultColorTipText() - Method in class adams.gui.visualization.spectrum.SpectrumPaintletStringField: Returns the tip text for this property.
defineOptions() - Method in class adams.data.cleaner.instance.AbstractCleaner: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.cleaner.instance.AbstractSerializableCleaner: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.cleaner.instance.IQRCleaner: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.cleaner.instance.MinMax: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.cleaner.instance.RemoveOutliers: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.cleaner.spectrum.AbstractCleaner: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.cleaner.spectrum.AbstractSerializableCleaner: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.cleaner.spectrum.MinMax: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.compare.SpectrumCorrelation: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.compare.SpectrumCosineSimilarity: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.conversion.ArrayToSpectrum: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.conversion.MultiSpectrumToSpectra: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.conversion.SpectraToMultiSpectrum: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.conversion.SpectrumToArray: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.conversion.SpectrumToBufferedImage: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.conversion.SpectrumToJson: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.conversion.SpreadSheetColumnsToSampleData: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.conversion.SpreadSheetRowsToSampleData: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.conversion.SpreadSheetTo2DTensor: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.conversion.SpreadSheetTo3DTensor: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.conversion.SpreadSheetToSpectrum: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.conversion.SpreadSheetToThreeWayData: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.conversion.ThreeWayDataToHeatmap: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.conversion.WekaPredictionContainerToEvaluationContainer: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.evaluator.instance.AbstractEvaluator: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.evaluator.instance.AbstractNearestNeighborBasedEvaluator: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.evaluator.instance.AbstractSerializableEvaluator: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.evaluator.instance.CrossValidatedPrediction: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.evaluator.instance.DistanceToCenter: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.evaluator.instance.DistanceToClosest: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.evaluator.instance.EnsembleEvaluator: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.evaluator.instance.FakeEvaluator: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.instances.AbstractFieldInstanceGenerator: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.instances.AbstractFieldInstanceGeneratorWithClass: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.instances.AbstractSpectrumBasedInstanceGenerator: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.instances.AbstractSpectrumInstanceGenerator: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.instances.AbstractSpectrumInstanceGeneratorWithClass: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.instances.FieldInstanceGenerator: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.instances.SimpleInstanceGenerator: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.instances.SimpleSpectralInstanceGenerator: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.AbstractJCampSpectrumReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.AbstractSampleDataReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.AbstractSpectrumReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.AbstractThreeWayDataReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.ASCIIXYSpectrumReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.ASCSpectrumReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.CALSpectrumReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.DPTSpectrumReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.ExtractIdAndTypeSpectrumReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.ExtractIdAndTypeThreeWayDataReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.FilteredSpectrumReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.FitsLibsReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.JCampDX2SpectrumReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.JCampDXSpectrumReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.MPSSpectrumReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.OpusSpectrumReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.OpusSpectrumReaderExt: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.RelabSpectrumReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.sampleidextraction.RegExp: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.ScioLabExportSpectrumReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.SimpleEEMReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.SimpleXYZReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.SoilCaresScannerSpectrumReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.SpecLibSpectrumReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.ThreeWayHeatmapReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.input.ZippedSpectrumReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.output.ASCIIXYSpectrumWriter: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.output.ASCSpectrumWriter: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.output.CALSpectrumWriter: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.output.DPTSpectrumWriter: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.output.FilteredSpectrumWriter: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.output.JCampDX2SpectrumWriter: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.output.JsonSpectrumWriter: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.output.NIRSpectrumWriter: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.output.SimpleSpectrumWriter: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.output.SimpleXYZWriter: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.output.SpectrumImageWriter: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.output.SpreadSheetSpectrumWriter: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.io.output.TrinamixSpectrumWriter: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.multifilter.AbstractFormatsBasedMultiSpectrumFilter: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.multifilter.AbstractMultiSpectrumFilter: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.multifilter.Average: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.multifilter.FilteredMultiSpectrumFilter: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.multifilter.Fusion: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.multifilter.PickByIndex: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.multifilter.PickByReportValue: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.multireportfilter.PullUpFields: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.multispectrumoperation.outlierremoval.CorrelationBasedThreshold: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.multispectrumoperation.outlierremoval.CosineSimilarityBasedThreshold: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.multispectrumoperation.OutlierRemoval: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.multispectrumoperation.outlierremoval.MeanSpectrumCosineSimilarityBasedThreshold: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.multispectrumoperation.Remove: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.postprocessor.instances.AbstractSerializablePostProcessor: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.postprocessor.instances.PredictionErrorIQR
defineOptions() - Method in class adams.data.postprocessor.instances.WekaFilter: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.sampledata.SignalToNoiseRatio: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrum.AbstractSpectrumComparator: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrum.Amplitudes: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrum.SpectrumComparatorByReportValue: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumanalysis.AbstractWekaSpectrumAnalysis: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumanalysis.FastICA: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumanalysis.PCA: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumanalysis.PLS: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.AbstractDatabaseFilter: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.AbstractSerializableFilter: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.AbstractStandardiseFilter: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.AmplitudeExpression: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.AmplitudeTransform: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.amplitudetransform.Triangle: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.AndrewsCurves: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.CenterBurst: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.ChangeFormat: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.ConditionalReportField: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.Covariance: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.Detrend: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.detrend.RangeBased: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.KennardStone
defineOptions() - Method in class adams.data.spectrumfilter.LogTransform: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.LRCoeff: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.MultiFilter: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.multiplicativescattercorrection.AbstractMultiplicativeScatterCorrection: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.MultiplicativeScatterCorrection: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.multiplicativescattercorrection.RangeBased: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.PadPower2: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.PCA: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.PLS: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.Rebase: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.Remove: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.ReportFieldFromStringValue: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.ReportFieldFromStringValueWithLookup: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.Scale: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.StandardiseByInterpolation: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.SubRange: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.SubtractSpectrum: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.WaveNumberExpression: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumfilter.WekaFilterToReport: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumimage.AbstractSpectrumImageGenerator: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumimage.AbstractSpectrumImageGeneratorWithRange: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumimage.Intensity: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumimage.Spectrogram: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumoutlier.MaxWaves: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumoutlier.MinMax: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumoutlier.MinWaves: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumoutlier.Oscillation: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumoutlier.StringMatcher: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spectrumoutlier.Swapped: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spreadsheetrowgenerator.SampleDataOnlyRowGenerator: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.threewayfeatures.Flatten: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.threewayfeatures.Histogram: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.threewayfeatures.MultiThreeWayDataFeatureGenerator: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.threewayfilter.Crop: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.threewayfilter.MultiFilter: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.threewayfilter.Shift: Adds options to the internal list of options.
defineOptions() - Method in class adams.data.threewayoutlier.ValueRange: Adds options to the internal list of options.
defineOptions() - Method in class adams.db.AbstractSpectrumConditions: Adds options to the internal list of options.
defineOptions() - Method in class adams.db.mirrored.SpectralDbBackend: Adds options to the internal list of options.
defineOptions() - Method in class adams.db.OrphanedSampleDataConditions: Adds options to the internal list of options.
defineOptions() - Method in class adams.db.SpectrumConditionsMulti: Adds options to the internal list of options.
defineOptions() - Method in class adams.db.SpectrumConditionsSingle: Adds options to the internal list of options.
defineOptions() - Method in class adams.db.SpectrumIDConditions: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.condition.bool.HasSpectrum: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.control.InstanceCleaner: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.control.SpectrumCleaner: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.rest.TransformSpectrum: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.sink.SpectrumDisplay: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.sink.spectrumdisplay.SimplePlotUpdater: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.source.NewSpectrum: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.source.OrphanedSampleDataIdSupplier: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.source.SpectrumIdSupplier: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.standalone.rats.LoadSpectrumFileOutput: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.standalone.rats.SaveMultiSpectrumFileOutput: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.standalone.rats.SaveSpectrumFileOutput: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.standalone.rats.WSMultiSpectrumReception: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.standalone.rats.WSSpectrumReception: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.AbstractInPlaceSpectrumTransformer: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.BulkSpectrumDbWriter: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.Cleaner: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.datacontainer.LoadSampleData: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.DeleteSpectrum: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.Evaluator: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.GetSpectrumAmplitude: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.InstanceGenerator: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.InstanceToSpectrum: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.MergeSampleDataFromMap: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.MultiSpectrumAdd: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.MultiSpectrumFilter: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.MultiSpectrumOperation: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.MultiSpectrumOutlierDetector: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.MultiSpectrumRemove: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.MultiSpectrumReportFilter: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.PostProcessor: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.PredictionCheck: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.predictioncheck.MinProbability: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.predictioncheck.Range: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.report.UpdateDatabaseID: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.SetEvaluationMetaData: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.SetSpectrumAmplitude: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.SpectralAngleMapper: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.SpectrumDbReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.SpectrumDbWriter: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.SpectrumDiff: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.SpectrumFeatureGenerator: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.SpectrumFileReader: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.SpectrumFileWriter: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.SpectrumInfo: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.SpectrumMinMax: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.SpreadSheetRowGenerator: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.ThreeWayDataFeatureGenerator: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.ThreeWayDataLoadingMatrix: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.threewaydatamerge.CollapseX: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.ThreeWayDataMerge: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.transformer.ThreeWayDataTrain: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.webservice.Get: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.webservice.multispectrum.RatsMultiSpectrumServiceWS: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.webservice.SpectralGetServiceWS: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.webservice.SpectralPutServiceWS: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.webservice.SpectralTransformServiceWS: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.webservice.spectrum.RatsSpectrumServiceWS: Adds options to the internal list of options.
defineOptions() - Method in class adams.flow.webservice.Transform: Adds options to the internal list of options.
defineOptions() - Method in class adams.gui.visualization.spectrum.ReportColorSpectrumPaintlet: Adds options to the internal list of options.
defineOptions() - Method in class adams.gui.visualization.spectrum.SelectedWaveNumberPaintlet: Adds options to the internal list of options.
defineOptions() - Method in class adams.gui.visualization.spectrum.SimpleSpectrumPaintlet: Adds options to the internal list of options.
defineOptions() - Method in class adams.gui.visualization.spectrum.SpectrumPaintlet: Adds options to the internal list of options.
defineOptions() - Method in class adams.gui.visualization.spectrum.SpectrumPaintletNumericField: Adds options to the internal list of options.
defineOptions() - Method in class adams.gui.visualization.spectrum.SpectrumPaintletStringField: Adds options to the internal list of options.
defineOptions() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlay: Adds options to the internal list of options.
defineOptions() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlayWithDimensions: Adds options to the internal list of options.
defineOptions() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Adds options to the internal list of options.
defineOptions() - Method in class adams.opt.genetic.RonWeasley: Adds options to the internal list of options.
defineOptions() - Method in class weka.filters.unsupervised.attribute.SavitzkyGolayRange: Adds options to the internal list of options.
delete() - Method in class adams.gui.tools.DeleteSampleDataPanel: Updates the selected spectra.
delete() - Method in class adams.gui.tools.DeleteSpectrumPanel: Removes the listed spectra.
delete(String, String) - Method in class adams.flow.rest.DeleteSpectrum: Deletes the specified spectrum.
deleted - Variable in class adams.data.io.input.foss.FossHelper.FossFields: is this a deleted row?
deleted_offset - Static variable in class adams.data.io.input.foss.FossHelper: number of Rows in this file.
DeleteDbSampleDataValue - Class in adams.flow.transformer: Deletes the specified values from the sampledata table.
DeleteDbSampleDataValue() - Constructor for class adams.flow.transformer.DeleteDbSampleDataValue
DeleteSampleData - Class in adams.gui.menu: Displays the dialog for deleting sample data values from selected spectra.
DeleteSampleData() - Constructor for class adams.gui.menu.DeleteSampleData: Initializes the menu item.
DeleteSampleData(AbstractApplicationFrame) - Constructor for class adams.gui.menu.DeleteSampleData: Initializes the menu item.
DeleteSampleDataPanel - Class in adams.gui.tools: Allows the user to delete sample data values from selected spectra.
DeleteSampleDataPanel() - Constructor for class adams.gui.tools.DeleteSampleDataPanel
DeleteSampleDataValue - Class in adams.flow.transformer: Deletes values from sample data.
DeleteSampleDataValue() - Constructor for class adams.flow.transformer.DeleteSampleDataValue
DeleteSampleDataValueByExpression - Class in adams.flow.transformer
DeleteSampleDataValueByExpression() - Constructor for class adams.flow.transformer.DeleteSampleDataValueByExpression
DeleteSpectra - Class in adams.gui.menu: Displays the dialog for deleting spectra.
DeleteSpectra() - Constructor for class adams.gui.menu.DeleteSpectra: Initializes the menu item.
DeleteSpectra(AbstractApplicationFrame) - Constructor for class adams.gui.menu.DeleteSpectra: Initializes the menu item.
DeleteSpectrum - Class in adams.flow.rest: REST plugin for deleting spectra.
DeleteSpectrum - Class in adams.flow.transformer: Removes the spectrum identified by database ID or sample ID.
DeleteSpectrum() - Constructor for class adams.flow.rest.DeleteSpectrum
DeleteSpectrum() - Constructor for class adams.flow.transformer.DeleteSpectrum
DeleteSpectrumPanel - Class in adams.gui.tools: A panel for deleting spectra.
DeleteSpectrumPanel() - Constructor for class adams.gui.tools.DeleteSpectrumPanel
delta_offset_1segment - Static variable in class adams.data.io.input.foss.FossStdise
delta_offset_2segments - Static variable in class adams.data.io.input.foss.FossStdise: start of intercepts.
denormalizeTipText() - Method in class adams.data.io.input.SimpleEEMReader: Returns the tip text for this property.
Derivative - Class in adams.data.spectrumfilter: A filter for generating derivatives of spectra.
Derivative() - Constructor for class adams.data.spectrumfilter.Derivative
derivativeOrderTipText() - Method in class weka.filters.unsupervised.attribute.SavitzkyGolayRange: Returns the tip text for this property.
derivativeOrderTipText() - Method in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: Returns the tip text for this property.
descendingTipText() - Method in class adams.data.io.output.ASCSpectrumWriter: Returns the tip text for this property.
descendingTipText() - Method in class adams.data.io.output.DPTSpectrumWriter: Returns the tip text for this property.
deserializeFile(MessageCollection) - Method in class adams.flow.core.CleanerModelLoader: Deserializes the model file.
deserializeFile(MessageCollection) - Method in class adams.flow.core.EvaluatorModelLoader: Deserializes the model file.
deserializeFile(MessageCollection) - Method in class adams.flow.core.PostProcessorModelLoader: Deserializes the model file.
deserializeFile(MessageCollection) - Method in class adams.flow.core.ThreeWayDataModelFilterLoader: Deserializes the model file.
destroy() - Method in class adams.data.cleaner.instance.AbstractSerializableCleaner: Frees up memory in a "destructive" non-reversible way.
destroy() - Method in class adams.data.cleaner.spectrum.AbstractSerializableCleaner: Frees up memory in a "destructive" non-reversible way.
destroy() - Method in class adams.data.evaluator.instance.AbstractSerializableEvaluator: Frees up memory in a "destructive" non-reversible way.
destroy() - Method in class adams.data.multifilter.AbstractMultiSpectrumFilter: Frees up memory in a "destructive" non-reversible way.
destroy() - Method in class adams.data.multireportfilter.AbstractMultiSpectrumReportFilter: Frees up memory in a "destructive" non-reversible way.
destroy() - Method in class adams.data.postprocessor.instances.AbstractSerializablePostProcessor: Frees up memory in a "destructive" non-reversible way.
destroy() - Method in class adams.data.spectrum.AbstractSpectrumComparator: Frees up memory in a "destructive" non-reversible way.
destroy() - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Frees up memory in a "destructive" non-reversible way.
destroy() - Method in class adams.data.spectrumfilter.AbstractSerializableFilter: Frees up memory in a "destructive" non-reversible way.
destroy() - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Frees up memory in a "destructive" non-reversible way.
destroy() - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Frees up memory in a "destructive" non-reversible way.
detectorTipText() - Method in class adams.data.cleaner.instance.RemoveOutliers: Returns the tip text for this property.
detectorTipText() - Method in class adams.flow.transformer.MultiSpectrumOutlierDetector: Returns the tip text for this property.
determineExperimentType(byte) - Method in class adams.data.io.input.SPCSpectrumReader.FileParser: Determines the experiment type.
determineLabelType(byte, char) - Method in class adams.data.io.input.SPCSpectrumReader.FileParser: Determines the label type.
determineOutputFormat(Instances) - Method in class weka.filters.unsupervised.attribute.BestBySLR: Determines the output format based on the input format and returns this.
determineOutputFormat(Instances) - Method in class weka.filters.unsupervised.attribute.RangeBasedSavitzkyGolay: Determines the output format based on the input format and returns this.
determineOutputFormat(Instances) - Method in class weka.filters.unsupervised.attribute.SegmentedDownSample: Determines the output format based on the input format and returns this.
determineOutputFormat(Instances) - Method in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: Determines the output format based on the input format and returns this.
determineOutputFormat(Instances) - Method in class weka.filters.unsupervised.attribute.SpectrumFilter: Determines the output format based on the input format and returns this.
determineParentID(Report) - Method in class adams.data.io.input.AbstractSampleDataReader: Tries to determine the parent ID for the current report.
determineSpectralRange(List<String>, Map<String, Range>) - Method in class adams.data.io.input.UnscramblerSpectrumReader: Determines the range(s) that most likely contains the spectra.
Detrend - Class in adams.data.spectrumfilter: Performs Detrend corrections.
Detrend() - Constructor for class adams.data.spectrumfilter.Detrend
Dialog(Dialog, Dialog.ModalityType) - Constructor for class adams.gui.visualization.spectrum.HistogramFactory.Dialog: Initializes the dialog.
Dialog(Dialog, Dialog.ModalityType) - Constructor for class adams.gui.visualization.spectrum.SampleDataFactory.Dialog: Initializes the dialog.
Dialog(Frame, boolean) - Constructor for class adams.gui.visualization.spectrum.HistogramFactory.Dialog: Initializes the dialog.
Dialog(Frame, boolean) - Constructor for class adams.gui.visualization.spectrum.SampleDataFactory.Dialog: Initializes the dialog.
diff(Spectrum, Spectrum, Spectrum, boolean) - Static method in class adams.data.spectrum.SpectrumUtils: Computes the difference between two spectra.
disambiguateAttributeName(String, HashSet<String>) - Method in class weka.filters.unsupervised.attribute.SpectrumFilter: Disambiguates the attribute.
display() - Method in class adams.gui.tools.ListSampleDataPanel: Updates the selected spectra.
display(AbstractSpectrumReader, File) - Method in class adams.gui.visualization.spectrum.SpectrumPanelWithSampleData: Displays the spectrum.
display(Spectrum) - Method in class adams.gui.visualization.spectrum.SpectrumPanelWithSampleData: Displays the spectrum.
display(Token) - Method in class adams.flow.sink.SpectrumDisplay: Displays the token (the panel and dialog have already been created at this stage).
display(Token) - Method in class adams.flow.sink.SpectrumDisplay.DisplayPanel
display(Token) - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Displays the token (the panel and dialog have already been created at this stage).
display(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>, List<SpectrumContainer>) - Method in class adams.gui.visualization.spectrum.plotpopup.Viewport: Displays the IDs etc of the spectra.
DisplayPanel(String) - Constructor for class adams.flow.sink.SpectrumDisplay.DisplayPanel
displayPanelRequiresScrollPane() - Method in class adams.flow.sink.SpectrumDisplay: Returns whether the created display panel requires a scroll pane or not.
displayPanelRequiresScrollPane() - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Returns whether the created display panel requires a scroll pane or not.
disposeComponent() - Method in class adams.flow.sink.SpectrumImageWriter: Disposes the generated component again.
DistanceToCenter - Class in adams.data.evaluator.instance: Uses the specified nearest neighbor search to determine a neighborhood.
DistanceToCenter() - Constructor for class adams.data.evaluator.instance.DistanceToCenter
DistanceToClosest - Class in adams.data.evaluator.instance: Uses the specified nearest neighbor search to locate the closest instance in the training data and returns the distance to it.
DistanceToClosest() - Constructor for class adams.data.evaluator.instance.DistanceToClosest
DistributeSampleData - Class in adams.data.multireportfilter: Distributes the sample data among all the sub-spectra, never overwrites already existing values.
DistributeSampleData() - Constructor for class adams.data.multireportfilter.DistributeSampleData
distributionForInstance(Instance) - Method in class weka.classifiers.meta.SpectrumClassifier: Classifies a given instance after filtering.
distributionForInstance(Instance) - Method in class weka.clusterers.SpectrumClusterer: Clusters a given instance after filtering.
distributionsForInstances(Instances) - Method in class weka.classifiers.meta.SpectrumClassifier: Batch scoring method
Divide - Class in adams.data.multifilter: Divides the amplitudes of first spectrum with the amplitudes of the second.
Divide() - Constructor for class adams.data.multifilter.Divide
doAnalyze(List<Spectrum>) - Method in class adams.data.spectrumanalysis.AbstractWekaSpectrumAnalysis: Performs the actual analysis.
doAnalyze(Instances) - Method in class adams.data.spectrumanalysis.AbstractWekaSpectrumAnalysis: Performs the actual analysis.
doAnalyze(Instances) - Method in class adams.data.spectrumanalysis.FastICA: Performs the actual analysis.
doAnalyze(Instances) - Method in class adams.data.spectrumanalysis.PCA: Performs the actual analysis.
doAnalyze(Instances) - Method in class adams.data.spectrumanalysis.PLS: Performs the actual analysis.
doApply(MultiSpectrum, MessageCollection) - Method in class adams.data.multispectrumoperation.AbstractMultiSpectrumOperation: Performs the actual operation.
doApply(MultiSpectrum, MessageCollection) - Method in class adams.data.multispectrumoperation.OutlierRemoval: Performs the actual filtering.
doApply(MultiSpectrum, MessageCollection) - Method in class adams.data.multispectrumoperation.PassThrough: Performs the actual operation.
doApply(MultiSpectrum, MessageCollection) - Method in class adams.data.multispectrumoperation.Remove: Executes the flow item.
doCheckPrediction(EvaluationContainer) - Method in class adams.flow.transformer.predictioncheck.AbstractPredictionCheck: Performs the actual checks on the prediction.
doCheckPrediction(EvaluationContainer) - Method in class adams.flow.transformer.predictioncheck.MinProbability: Performs the actual checks on the prediction.
doCheckPrediction(EvaluationContainer) - Method in class adams.flow.transformer.predictioncheck.PassThrough: Performs the actual checks on the prediction.
doCheckPrediction(EvaluationContainer) - Method in class adams.flow.transformer.predictioncheck.Range: Performs the actual checks on the prediction.
doCompareObjects(Spectrum, Spectrum) - Method in class adams.data.compare.SpectrumCorrelation: Performs the actual comparison of the two objects.
doCompareObjects(Spectrum, Spectrum) - Method in class adams.data.compare.SpectrumCosineSimilarity: Performs the actual comparison of the two objects.
doConvert() - Method in class adams.data.conversion.ArrayToSpectrum: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.JsonToSpectrum: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.MultiSpectrumToSpectra: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.PostProcessingContainerToWekaInstanceContainer: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.ReportToSampleData: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.SampleDataArrayToMap: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.SpectraToMultiSpectrum: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.SpectrumToArray: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.SpectrumToBufferedImage: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.SpectrumToJson: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.SpectrumToSpreadSheet: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.SpectrumToWave: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.SpreadSheetColumnsToSampleData: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.SpreadSheetRowsToSampleData: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.SpreadSheetTo2DTensor: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.SpreadSheetTo3DTensor: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.SpreadSheetToSpectrum: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.SpreadSheetToThreeWayData: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.TensorToSpreadSheet: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.TensorToThreeWayData: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.ThreeWayDataToHeatmap: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.ThreeWayDataToSpreadSheet: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.ThreeWayDataToTensor: Performs the actual conversion.
doConvert() - Method in class adams.data.conversion.WekaPredictionContainerToEvaluationContainer: Performs the actual conversion.
doEvaluate(Actor, Token) - Method in class adams.flow.condition.bool.HasSpectrum: Performs the actual evaluation.
doExecute() - Method in class adams.flow.control.InstanceCleaner: Executes the actor.
doExecute() - Method in class adams.flow.control.SpectrumCleaner: Executes the actor.
doExecute() - Method in class adams.flow.source.NewSpectrum: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.Cleaner: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.Evaluator: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.GetSpectrumAmplitude: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.InstanceGenerator: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.InstanceToSpectrum: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.MergeSampleDataFromMap: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.MultiSpectrumAdd: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.MultiSpectrumFilter: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.MultiSpectrumOperation: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.MultiSpectrumOutlierDetector: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.MultiSpectrumRemove: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.MultiSpectrumReportFilter: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.PostProcessor: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.PredictionCheck: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.SetEvaluationMetaData: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.SetSpectrumAmplitude: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.SpectralAngleMapper: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.SpectrumDiff: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.SpectrumFeatureGenerator: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.SpectrumFileReader: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.SpectrumFileWriter: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.SpectrumInfo: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.SpectrumMinMax: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.SpreadSheetRowGenerator: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.ThreeWayDataFeatureGenerator: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.ThreeWayDataLoadingMatrix: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.ThreeWayDataMerge: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Executes the flow item.
doExecute() - Method in class adams.flow.transformer.ThreeWayDataTrain: Executes the flow item.
doExport(ChildFrame, Properties) - Method in class adams.gui.menu.ExportValidationSets: Peforms the export.
doExport(Object, File) - Method in class adams.gui.visualization.debug.objectexport.SpectrumExporter: Performs the actual export.
doExport(Object, File) - Method in class adams.gui.visualization.debug.objectexport.ThreeWayDataExporter: Performs the actual export.
doExtract(File, Spectrum) - Method in class adams.data.io.input.sampleidextraction.AbstractSampleIDExtraction: Performs the actual extraction.
doExtract(File, Spectrum) - Method in class adams.data.io.input.sampleidextraction.Filename: Performs the actual extraction.
doExtract(File, Spectrum) - Method in class adams.data.io.input.sampleidextraction.RegExp: Performs the actual extraction.
doFindColumns(Instances) - Method in class adams.data.columnfinder.AmplitudeFinder: Returns the columns of interest in the dataset.
doGenerate(Spectrum) - Method in class adams.data.spectrumimage.AbstractSpectrumImageGenerator: Converts the spectrum into an image.
doGenerate(Spectrum) - Method in class adams.data.spectrumimage.AmplitudeRatio: Converts the spectrum into an image.
doGenerate(Spectrum) - Method in class adams.data.spectrumimage.Intensity: Converts the spectrum into an image.
doGenerate(Spectrum) - Method in class adams.data.spectrumimage.Spectrogram: Converts the spectrum into an image.
doImageChanged(ImagePanel.PaintPanel) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.Null: Notifies the overlay that the image has changed.
doImageChanged(ImagePanel.PaintPanel) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Notifies the overlay that the image has changed.
doInitializeFilters() - Method in class adams.gui.chooser.SampleDataFileChooser: Performs the actual initialization of the filters.
doInitializeFilters() - Method in class adams.gui.chooser.SpectrumFileChooser: Performs the actual initialization of the filters.
doInitializeFilters() - Method in class adams.gui.chooser.ThreeWayDataFileChooser: Performs the actual initialization of the filters.
doMerge(ThreeWayData[]) - Method in class adams.flow.transformer.threewaydatamerge.AbstractThreeWayDataMerge: Merges the data containers into a single one.
doMerge(ThreeWayData[]) - Method in class adams.flow.transformer.threewaydatamerge.CollapseX: Merges the data containers into a single one.
doMerge(ThreeWayData[]) - Method in class adams.flow.transformer.threewaydatamerge.Join: Merges the data containers into a single one.
dontUpdateIDTipText() - Method in class adams.data.multifilter.AbstractMultiSpectrumFilter: Returns the tip text for this property.
doPaintOverlay(ImagePanel.PaintPanel, Graphics) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlay: Computes the actual coordinates before doing the actual painting.
doPaintOverlay(ImagePanel.PaintPanel, Graphics) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlayWithDimensions: Computes the actual coordinates before doing the actual painting.
doPaintOverlay(ImagePanel.PaintPanel, Graphics) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.Null: Paints the overlay over the image.
doPaintOverlay(ImagePanel.PaintPanel, Graphics, int, int) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlay: Performs the actual painting.
doPaintOverlay(ImagePanel.PaintPanel, Graphics, int, int) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlayWithDimensions: Performs the actual painting.
doPaintOverlay(ImagePanel.PaintPanel, Graphics, int, int) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Performs the actual painting.
doPerformPaint(Graphics, PaintEvent.PaintMoment) - Method in class adams.gui.visualization.spectrum.SelectedWaveNumberPaintlet: The paint routine of the paintlet.
doPerformPaint(Graphics, PaintEvent.PaintMoment) - Method in class adams.gui.visualization.spectrum.SimpleSpectrumPaintlet: The paint routine of the paintlet.
doPerformPaint(Graphics, PaintEvent.PaintMoment) - Method in class adams.gui.visualization.spectrum.SpectrumPaintlet: The paint routine of the paintlet.
doPostProcess(Spectrum) - Method in class adams.flow.transformer.datacontainer.LoadSampleData: Performs the actual post-processing.
doPostProcess(ThreeWayDataModelContainer) - Method in class adams.flow.transformer.threewaydatatrain.AbstractThreeWayDataTrainPostProcessor: Post-processes the container.
doPostProcess(ThreeWayDataModelContainer) - Method in class adams.flow.transformer.threewaydatatrain.ParafacLossHistory: Post-processes the container.
doPostProcess(ThreeWayDataModelContainer) - Method in class adams.flow.transformer.threewaydatatrain.PassThrough: Post-processes the container.
doPreProcess(SampleData) - Method in class adams.flow.transformer.report.UpdateDatabaseID: Performs the actual pre-processing.
doPreProcess(Spectrum) - Method in class adams.flow.transformer.datacontainer.UpdateDatabaseID: Performs the actual pre-processing.
doProcess(String) - Method in class adams.gui.scripting.SelectWaveNumber: Processes the options.
doProcess(String) - Method in class adams.gui.scripting.WriteSpectrum: Processes the options.
doProcessSelectedRows(SpreadSheetTablePopupMenuItemHelper.TableState) - Method in class adams.gui.core.spreadsheettable.ExportSpectra: Processes the specified row.
doProcessSelectedRows(InstancesTablePopupMenuItemHelper.TableState) - Method in class adams.gui.visualization.instances.instancestable.ExportSpectra: Processes the specified row.
doQuery() - Method in class adams.flow.webservice.Get: Performs the actual webservice query.
doQuery() - Method in class adams.flow.webservice.multispectrum.MultiUpload: Performs the actual webservice query.
doQuery() - Method in class adams.flow.webservice.Put: Performs the actual webservice query.
doQuery() - Method in class adams.flow.webservice.spectrum.Upload: Performs the actual webservice query.
doQuery() - Method in class adams.flow.webservice.Transform: Performs the actual webservice query.
doReceive() - Method in class adams.flow.standalone.rats.WSMultiSpectrumReception: Performs the actual reception of data.
doReceive() - Method in class adams.flow.standalone.rats.WSSpectrumReception: Performs the actual reception of data.
doRefresh() - Method in class adams.gui.selection.SelectSpectrumPanel: Performs the actual refresh.
doRemoveOutliers(MultiSpectrum, MessageCollection) - Method in class adams.data.multispectrumoperation.outlierremoval.AbstractOutlierRemoval: Performs the actual outlier removal.
doRemoveOutliers(MultiSpectrum, MessageCollection) - Method in class adams.data.multispectrumoperation.outlierremoval.CorrelationBasedThreshold: Performs the actual outlier removal.
doRemoveOutliers(MultiSpectrum, MessageCollection) - Method in class adams.data.multispectrumoperation.outlierremoval.CosineSimilarityBasedThreshold: Performs the actual outlier removal.
doRemoveOutliers(MultiSpectrum, MessageCollection) - Method in class adams.data.multispectrumoperation.outlierremoval.MeanSpectrumCosineSimilarityBasedThreshold: Performs the actual outlier removal.
doRemoveOutliers(MultiSpectrum, MessageCollection) - Method in class adams.data.multispectrumoperation.outlierremoval.PassThrough: Performs the actual outlier removal.
doRender(Object, JPanel, Integer) - Method in class adams.gui.visualization.debug.objectrenderer.SpectrumRenderer: Performs the actual rendering.
doRender(Object, JPanel, Integer) - Method in class adams.gui.visualization.debug.objectrenderer.ThreeWayDataHeatmapRenderer: Performs the actual rendering.
doRenderCached(Object, JPanel, Integer) - Method in class adams.gui.visualization.debug.objectrenderer.SpectrumRenderer: Performs the actual rendering.
doRenderCached(Object, JPanel, Integer) - Method in class adams.gui.visualization.debug.objectrenderer.ThreeWayDataHeatmapRenderer: Performs the actual rendering.
doStart() - Method in class adams.flow.webservice.multispectrum.RatsMultiSpectrumServiceWS: Performs the actual start of the service.
doStart() - Method in class adams.flow.webservice.SpectralGetServiceWS: Performs the actual start of the service.
doStart() - Method in class adams.flow.webservice.SpectralPutServiceWS: Performs the actual start of the service.
doStart() - Method in class adams.flow.webservice.SpectralTransformServiceWS: Performs the actual start of the service.
doStart() - Method in class adams.flow.webservice.spectrum.RatsSpectrumServiceWS: Performs the actual start of the service.
doStop() - Method in class adams.flow.webservice.multispectrum.RatsMultiSpectrumServiceWS: Performs the actual stop of the service.
doStop() - Method in class adams.flow.webservice.SpectralGetServiceWS: Performs the actual stop of the service.
doStop() - Method in class adams.flow.webservice.SpectralPutServiceWS: Performs the actual stop of the service.
doStop() - Method in class adams.flow.webservice.SpectralTransformServiceWS: Performs the actual stop of the service.
doStop() - Method in class adams.flow.webservice.spectrum.RatsSpectrumServiceWS: Performs the actual stop of the service.
doStore(String, SampleData) - Method in class adams.db.generic.SampleDataT: Stores the report.
doTransmit() - Method in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: Performs the actual transmission.
doTransmit() - Method in class adams.flow.standalone.rats.LoadSpectrumFileOutput: Performs the actual transmission.
doTransmit() - Method in class adams.flow.standalone.rats.SaveMultiSpectrumFileOutput: Performs the actual transmission.
doTransmit() - Method in class adams.flow.standalone.rats.SaveSpectrumFileOutput: Performs the actual transmission.
DownSample - Class in adams.data.spectrumfilter: A filter that returns only every n-th wave number.
DownSample - Class in adams.data.threewayfilter: A filter that returns only every n-th 1st level and 2nd level point.
DownSample() - Constructor for class adams.data.spectrumfilter.DownSample
DownSample() - Constructor for class adams.data.threewayfilter.DownSample
DPF - Static variable in class adams.data.io.input.opus.OpusBlockHelper: the DPF character sequence.
DPTSpectrumHandler - Class in adams.gui.tools.previewbrowser: Displays the following spectrum types: dpt

Valid options are:
DPTSpectrumHandler() - Constructor for class adams.gui.tools.previewbrowser.DPTSpectrumHandler
DPTSpectrumReader - Class in adams.data.io.input: Reads spectra in DPT format.
DPTSpectrumReader() - Constructor for class adams.data.io.input.DPTSpectrumReader
DPTSpectrumReader.ParsedFile - Class in adams.data.io.input: Class for parsing a DPT file.
DPTSpectrumWriter - Class in adams.data.io.output: Writer that stores spectrums in the simple CSV format.
DPTSpectrumWriter() - Constructor for class adams.data.io.output.DPTSpectrumWriter
drawData(Graphics, Spectrum, Color) - Method in class adams.gui.visualization.spectrum.SimpleSpectrumPaintlet: Draws the data with the given color.
drawData(Graphics, Spectrum, Color, SpectrumPaintlet.MarkerShape) - Method in class adams.gui.visualization.spectrum.SpectrumPaintlet: Draws the data with the given color.
duplicateWindow(boolean) - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Opens a new window with the same content/setup.

E

END - Static variable in class adams.data.io.input.opus.OpusBlockHelper: the END character sequence.
endDateTipText() - Method in class adams.db.AbstractSpectrumConditions: Returns the tip text for this property.
endDateTipText() - Method in class adams.db.OrphanedSampleDataConditions: Returns the tip text for this property.
endPointsTipText() - Method in class adams.data.io.output.NIRSpectrumWriter: Returns the tip text for this property.
endTipText() - Method in class weka.filters.unsupervised.attribute.SavitzkyGolayRange: Returns the tip text for this property.
EnsembleEvaluator - Class in adams.data.evaluator.instance: Builds an ensemble of classifiers on the training data to determine the MAE per classifier, to be used as normalization factor.
At evaluation time, each classifier makes a prediction on the instance and the classification is divided by the normalization factor for this classifier.
EnsembleEvaluator() - Constructor for class adams.data.evaluator.instance.EnsembleEvaluator
ensureConvertor() - Method in class adams.data.spectrumimage.Spectrogram: Makes sure the convertor is available and configured for use.
ENTRY_PROJECT - Static variable in class adams.data.io.input.UnscramblerSpectrumReader
EOCTipText() - Method in class adams.data.io.output.NIRSpectrumWriter: Returns the tip text for this property.
equals(Object) - Method in class adams.data.cleaner.instance.AbstractCleaner: Returns whether the two objects are the same.
equals(Object) - Method in class adams.data.cleaner.spectrum.AbstractCleaner: Returns whether the two objects are the same.
equals(Object) - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.InterPercentileRange: Returns whether two objects are the same.
equals(Object) - Method in class adams.data.evaluator.instance.AbstractEvaluator: Returns whether the two objects are the same.
equals(Object) - Method in class adams.data.multifilter.AbstractMultiSpectrumFilter: Returns whether the two objects are the same.
equals(Object) - Method in class adams.data.multireportfilter.AbstractMultiSpectrumReportFilter: Returns whether the two objects are the same.
equals(Object) - Method in class adams.data.postprocessor.instances.AbstractPostProcessor: Returns whether the two objects are the same.
equals(Object) - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Returns whether the two objects are the same.
equals(Object) - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Returns whether the two objects are the same.
equals(Object) - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Returns whether the two objects are the same.
equals(Object) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.multipageaction.AbstractMultiPageMenuItem: Returns whether the two objects are same.
equalsHeader(Object) - Method in class adams.data.threeway.ThreeWayData: Indicates whether some other chromatogram's header is "equal to" this ones.
EquiDistance - Class in adams.data.spectrumfilter: A filter for interpolating the amplitudes of a spectrum.
EquiDistance() - Constructor for class adams.data.spectrumfilter.EquiDistance
evalMaxTipText() - Method in class adams.data.evaluator.instance.FakeEvaluator: Returns the tip text for this property.
evalMinTipText() - Method in class adams.data.evaluator.instance.FakeEvaluator: Returns the tip text for this property.
evaluate(Instance) - Method in class adams.data.evaluator.instance.AbstractEvaluator: Performs the check.
evaluate(Instance) - Method in interface adams.data.evaluator.instance.Evaluator: Performs the check.
EvaluateJob(AbstractEvaluator, Instances) - Constructor for class adams.flow.transformer.Evaluator.EvaluateJob: Initializes the job.
EvaluationContainer - Class in adams.flow.container: Container for evaluations.
EvaluationContainer() - Constructor for class adams.flow.container.EvaluationContainer: Default constructor.
EvaluationContainer(Instance) - Constructor for class adams.flow.container.EvaluationContainer: Initializes the container with the WEKA instance.
EvaluationContainer(Instance, Map<String, Object>) - Constructor for class adams.flow.container.EvaluationContainer: Initializes the container with the WEKA instance.
EvaluationContainer(Instances) - Constructor for class adams.flow.container.EvaluationContainer: Initializes the container with the WEKA instances.
evaluationTipText() - Method in class adams.flow.transformer.predictioncheck.Range: Returns the tip text for this property.
evaluationToSpreadSheet(Evaluation) - Method in class adams.data.cleaner.instance.RemoveOutliers: Turns the predictions of the evaluation object into a spreadsheet.
Evaluator - Class in adams.flow.transformer: If input is Instances, build this Evaluator.
Evaluator - Interface in adams.data.evaluator.instance: Interface for evaluators.
Evaluator() - Constructor for class adams.flow.transformer.Evaluator
Evaluator.EvaluateJob - Class in adams.flow.transformer
EvaluatorModelLoader - Class in adams.flow.core: Model loader for AbstractEvaluator objects.
EvaluatorModelLoader() - Constructor for class adams.flow.core.EvaluatorModelLoader
evaluatorResetVariableTipText() - Method in class adams.flow.transformer.Evaluator: Returns the tip text for this property.
evaluatorTipText() - Method in class adams.flow.transformer.Evaluator: Returns the tip text for this property.
evalWaitTipText() - Method in class adams.data.evaluator.instance.FakeEvaluator: Returns the tip text for this property.
example(boolean) - Static method in class adams.data.spectrum.SpectrumJsonUtils: Returns an example spectrum in JSON.
excludeDummiesTipText() - Method in class adams.db.AbstractSpectrumConditions: Returns the tip text for this property.
excludeTipText() - Method in class weka.filters.unsupervised.attribute.SegmentedDownSample: Returns the tip text for this property.
excludeTipText() - Method in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: Returns the tip text for this property.
execute() - Method in class adams.flow.control.InstanceCleaner: Executes the flow item.
execute() - Method in class adams.flow.control.SpectrumCleaner: Executes the flow item.
exists(int) - Method in class adams.db.generic.SpectrumT: Checks whether the container exists in the database.
exists(int) - Method in class adams.db.mirrored.SpectrumT: Checks whether the container exists in the database.
exists(int) - Method in class adams.db.SpectrumF: Checks whether the container exists in the database.
exists(int) - Method in interface adams.db.SpectrumIntf: Checks whether the container exists in the database.
exists(DataProvider, Spectrum) - Method in class adams.flow.transformer.SpectrumDbWriter: Returns whether the container already exists in the database.
exists(String) - Method in class adams.db.generic.SampleDataT: Checks whether the report exists in the database.
exists(String) - Method in class adams.db.generic.SpectrumT: Checks whether the container exists in the database.
exists(String) - Method in class adams.db.mirrored.SampleDataT: Checks whether the report exists in the database.
exists(String) - Method in class adams.db.mirrored.SpectrumT: Checks whether the container exists in the database.
exists(String) - Method in class adams.db.SampleDataF: Checks whether the report exists in the database.
exists(String) - Method in interface adams.db.SampleDataIntf: Checks whether the report exists in the database.
exists(String) - Method in class adams.db.SpectrumF: Checks whether the container exists in the database.
exists(String) - Method in interface adams.db.SpectrumIntf: Checks whether the container exists in the database.
exists(String, String) - Method in class adams.db.generic.SpectrumT: Checks whether the container exists in the database.
exists(String, String) - Method in class adams.db.mirrored.SpectrumT: Checks whether the container exists in the database.
exists(String, String) - Method in class adams.db.SpectrumF: Checks whether the container exists in the database.
exists(String, String) - Method in interface adams.db.SpectrumIntf: Checks whether the container exists in the database.
ExportSpectra - Class in adams.gui.core.spreadsheettable: Exports the selected rows as spectra.
ExportSpectra - Class in adams.gui.visualization.instances.instancestable: Exports the selected rows as spectra.
ExportSpectra() - Constructor for class adams.gui.core.spreadsheettable.ExportSpectra
ExportSpectra() - Constructor for class adams.gui.visualization.instances.instancestable.ExportSpectra
ExportValidationSets - Class in adams.gui.menu: Displays the dialog for exporting validation sets.
ExportValidationSets() - Constructor for class adams.gui.menu.ExportValidationSets: Initializes the menu item.
ExportValidationSets(AbstractApplicationFrame) - Constructor for class adams.gui.menu.ExportValidationSets: Initializes the menu item.
ExportVisible - Class in adams.gui.visualization.spectrum.plotpopup: Allows the user to save the visible spectra as ARFF.
ExportVisible() - Constructor for class adams.gui.visualization.spectrum.plotpopup.ExportVisible
exportVisibleSpectra() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Exports the visible spectra to an ARFF file.
expressionTipText() - Method in class adams.data.spectrumfilter.AmplitudeExpression: Returns the tip text for this property.
expressionTipText() - Method in class adams.data.spectrumfilter.WaveNumberExpression: Returns the tip text for this property.
extract(File, Spectrum) - Method in class adams.data.io.input.sampleidextraction.AbstractSampleIDExtraction: Performs the extraction.
extract(File, Spectrum) - Method in interface adams.data.io.input.sampleidextraction.SampleIDExtraction: Performs the extraction.
extractID(SampleData) - Method in class adams.flow.transformer.SampleDataDbWriter: Extracts the ID from the report.
extractID(SampleData) - Method in class adams.flow.transformer.SampleDataValueDbWriter: Extracts the ID from the report.
ExtractIdAndTypeSpectrumReader - Class in adams.data.io.input: Uses the specified ID and group extractor to obtain and update sample ID and type of the spectra read by the specified base reader.
ExtractIdAndTypeSpectrumReader() - Constructor for class adams.data.io.input.ExtractIdAndTypeSpectrumReader
ExtractIdAndTypeThreeWayDataReader - Class in adams.data.io.input: Uses the specified ID and group extractor to obtain and update sample ID and type of the 3-way data read by the specified base reader.
ExtractIdAndTypeThreeWayDataReader() - Constructor for class adams.data.io.input.ExtractIdAndTypeThreeWayDataReader
extractSubset(SampleData) - Method in class adams.flow.transformer.SampleDataValueDbWriter: Generates a subset of the report, which only contains the specified fields.
extractTipText() - Method in class adams.data.spectrumfilter.ReportFieldFromStringValueWithLookup: Returns the tip text for this property.

F

factorTipText() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Returns the tip text for this property.
failureTipText() - Method in class adams.data.spectrumfilter.ConditionalReportField: Returns the tip text for this property.
FakeEvaluator - Class in adams.data.evaluator.instance: Fake evaluator, outputs random values based on min/max values.
FakeEvaluator() - Constructor for class adams.data.evaluator.instance.FakeEvaluator
FastICA - Class in adams.data.spectrumanalysis: Performs independent components analysis and allows access to components and sources.
FastICA() - Constructor for class adams.data.spectrumanalysis.FastICA
FastWavelet - Class in adams.data.spectrumfilter: A filter that transforms the data with a wavelet.

For more information see:

(2009).
FastWavelet() - Constructor for class adams.data.spectrumfilter.FastWavelet
FFT - Class in adams.data.spectrumfilter: A filter that transforms the data with Fast Fourier Transform.

For more information see:

Mark Hale (2009).
FFT() - Constructor for class adams.data.spectrumfilter.FFT
FFTSampleSizeTipText() - Method in class adams.data.conversion.SpectrumToBufferedImage: Returns the tip text for this property.
FFTSampleSizeTipText() - Method in class adams.data.spectrumimage.Spectrogram: Returns the tip text for this property.
FIELD_ABSORBANCE - Static variable in class adams.data.io.input.AbstractJCampSpectrumReader: JCamp field: Absorbance.
FIELD_CONTINUOUS - Static variable in class adams.data.io.input.AbstractJCampSpectrumReader: JCamp field: Continuous.
FIELD_DATACLASS - Static variable in class adams.data.io.input.AbstractJCampSpectrumReader: JCamp field: DataClass.
FIELD_DATATYPE - Static variable in class adams.data.io.input.AbstractJCampSpectrumReader: JCamp field: DataType.
FIELD_DATE - Static variable in class adams.data.io.input.AbstractJCampSpectrumReader: JCamp field: Date.
FIELD_HZTOPPM - Static variable in class adams.data.io.input.AbstractJCampSpectrumReader: JCamp field: HZtoPPM.
FIELD_INCREASING - Static variable in class adams.data.io.input.AbstractJCampSpectrumReader: JCamp field: Increasing.
FIELD_JCAMPDX - Static variable in class adams.data.io.input.AbstractJCampSpectrumReader: JCamp field: Jcampdx.
FIELD_OBSERVEDFREQ - Static variable in class adams.data.io.input.AbstractJCampSpectrumReader: JCamp field: ObservedFreq.
FIELD_OPUS_BLOCK_TYPE_DPF - Static variable in class adams.data.io.input.OpusSpectrumReaderExt
FIELD_OPUS_BLOCK_TYPE_HEX - Static variable in class adams.data.io.input.OpusSpectrumReaderExt
FIELD_OPUS_DIFF - Static variable in class adams.data.io.input.OpusSpectrumReaderExt
FIELD_OPUS_FIRST_X - Static variable in class adams.data.io.input.OpusSpectrumReaderExt
FIELD_OPUS_LAST_X - Static variable in class adams.data.io.input.OpusSpectrumReaderExt
FIELD_OPUS_LOG - Static variable in class adams.data.io.input.OpusSpectrumReaderExt
FIELD_OPUS_NUM_POINTS - Static variable in class adams.data.io.input.OpusSpectrumReaderExt
FIELD_OPUS_SCALE - Static variable in class adams.data.io.input.OpusSpectrumReaderExt
FIELD_ORIGIN - Static variable in class adams.data.io.input.AbstractJCampSpectrumReader: JCamp field: Origin.
FIELD_OWNER - Static variable in class adams.data.io.input.AbstractJCampSpectrumReader: JCamp field: Owner.
FIELD_PATHLENGTH - Static variable in class adams.data.io.input.AbstractJCampSpectrumReader: JCamp field: Pathlength.
FIELD_TIME - Static variable in class adams.data.io.input.AbstractJCampSpectrumReader: JCamp field: Time.
FIELD_TITLE - Static variable in class adams.data.io.input.AbstractJCampSpectrumReader: JCamp field: Title.
FIELD_TRANSMITTANCE - Static variable in class adams.data.io.input.AbstractJCampSpectrumReader: JCamp field: Transmittance.
FIELD_XFACTOR - Static variable in class adams.data.io.input.AbstractJCampSpectrumReader: JCamp field: XFactor.
FIELD_XUNITS - Static variable in class adams.data.io.input.AbstractJCampSpectrumReader: JCamp field: XUnits.
FIELD_YFACTOR - Static variable in class adams.data.io.input.AbstractJCampSpectrumReader: JCamp field: YFactor.
FIELD_YUNITS - Static variable in class adams.data.io.input.AbstractJCampSpectrumReader: JCamp field: YUnits.
FieldInstanceGenerator - Class in adams.data.instances: A generator for turning fields of the sample data of a spectrum into weka.core.Instance objects.
FieldInstanceGenerator() - Constructor for class adams.data.instances.FieldInstanceGenerator
FieldInstanceGeneratorWithClass - Class in adams.data.instances: Turns fields of spectra into weka.core.Instance objects, including class attribute.
FieldInstanceGeneratorWithClass() - Constructor for class adams.data.instances.FieldInstanceGeneratorWithClass
fieldsTipText() - Method in class adams.data.instances.AbstractFieldInstanceGenerator: Returns the tip text for this property.
fieldsTipText() - Method in class adams.data.multireportfilter.PullUpFields: Returns the tip text for this property.
fieldsTipText() - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Returns the tip text for this property.
fieldsTipText() - Method in class adams.data.spreadsheetrowgenerator.SampleDataOnlyRowGenerator: Returns the tip text for this property.
fieldsTipText() - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Returns the tip text for this property.
fieldsTipText() - Method in class adams.db.SpectrumConditionsMulti: Returns the tip text for this property.
fieldsTipText() - Method in class adams.flow.transformer.DeleteDbSampleDataValue: Returns the tip text for this property.
fieldsTipText() - Method in class adams.flow.transformer.DeleteSampleDataValue: Returns the tip text for this property.
fieldsTipText() - Method in class adams.flow.transformer.SampleDataValueDbWriter: Returns the tip text for this property.
fieldsToConditions() - Method in class adams.gui.tools.idprovider.DatabaseSearchPanel: Transfers the fields to the conditions object.
fieldTipText() - Method in class adams.data.cleaner.spectrum.MinMax: Returns the tip text for this property.
fieldTipText() - Method in class adams.data.instances.AbstractFieldInstanceGeneratorWithClass: Returns the tip text for this property.
fieldTipText() - Method in class adams.data.instances.AbstractSpectrumInstanceGeneratorWithClass: Returns the tip text for this property.
fieldTipText() - Method in interface adams.data.instances.InstanceGeneratorWithTargetField: Returns the tip text for this property.
fieldTipText() - Method in class adams.data.multifilter.PickByReportValue: Returns the tip text for this property.
fieldTipText() - Method in class adams.data.spectrum.SpectrumComparatorByReportValue: Returns the tip text for this property.
fieldTipText() - Method in class adams.data.spectrumfilter.Covariance: Returns the tip text for this property.
fieldTipText() - Method in class adams.data.spectrumoutlier.MinMax: Returns the tip text for this property.
fieldTipText() - Method in class adams.data.spectrumoutlier.StringMatcher: Returns the tip text for this property.
fieldTipText() - Method in class adams.db.SpectrumConditionsSingle: Returns the tip text for this property.
fieldTipText() - Method in class adams.flow.transformer.DeleteSampleDataValueByExpression: Returns the tip text for this property.
fieldTipText() - Method in class adams.flow.transformer.GetSampleDataValue: Returns the tip text for this property.
fieldTipText() - Method in class adams.flow.transformer.SetSampleDataValue: Returns the tip text for this property.
fieldTipText() - Method in class adams.gui.visualization.spectrum.SpectrumPaintletNumericField: Returns the tip text for this property.
fieldTipText() - Method in class adams.gui.visualization.spectrum.SpectrumPaintletStringField: Returns the tip text for this property.
FILE_EXTENSION - Static variable in class adams.data.spectrum.Spectrum: the file extension.
fileIDTipText() - Method in class adams.data.io.output.NIRSpectrumWriter: Returns the tip text for this property.
Filename - Class in adams.data.io.input.sampleidextraction: Just uses the filename (without path) as sample ID.
Filename() - Constructor for class adams.data.io.input.sampleidextraction.Filename
FILENAME - Static variable in interface adams.db.SpectralDbBackend: the properties file containing the setup.
FILENAME - Static variable in class adams.gui.scripting.SpectralScriptingEngine: the name of the props file.
filenameGeneratorTipText() - Method in class adams.flow.standalone.rats.SaveMultiSpectrumFileOutput: Returns the tip text for this property.
filenameGeneratorTipText() - Method in class adams.flow.standalone.rats.SaveSpectrumFileOutput: Returns the tip text for this property.
FileParser(String, byte[]) - Constructor for class adams.data.io.input.SPCSpectrumReader.FileParser: Initializes the parser.
fillGaps(Spectrum, Spectrum, DataContainerUtils.GapFilling) - Static method in class adams.data.spectrum.SpectrumUtils: Fills the gaps in the "gaps" spectrum with the data from the "reference" spectrum and the type of gap-filling.
filter() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: pops up GOE dialog for filter.
filter() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: pops up GOE dialog for filter.
filter(MultiSpectrum) - Method in class adams.data.multifilter.AbstractMultiSpectrumFilter: Returns the filtered data.
filter(MultiSpectrum) - Method in class adams.data.multireportfilter.AbstractMultiSpectrumReportFilter: Returns the filtered data.
filter(FilterEvent<Spectrum>) - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Filters the data.
filter(FilterEvent<ThreeWayData>) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Filters the data.
filter(Instance) - Method in class weka.clusterers.SpectrumClusterer: Filters the instance if the Remove filter has been set up, otherwise it just returns the instance as it is.
FilteredMultiSpectrumFilter - Class in adams.data.multifilter: The pre-filters select the spectra from the incoming multi-spectrum and re-package them into a new multi-spectrum.
FilteredMultiSpectrumFilter() - Constructor for class adams.data.multifilter.FilteredMultiSpectrumFilter
FilteredSpectrumReader - Class in adams.data.io.input: Uses the specified reader to read the spectral data before applying the supplied filter to it.
FilteredSpectrumReader() - Constructor for class adams.data.io.input.FilteredSpectrumReader
FilteredSpectrumWriter - Class in adams.data.io.output: Applies the specified filter to the data before outputting it using the supplied writer.
FilteredSpectrumWriter() - Constructor for class adams.data.io.output.FilteredSpectrumWriter
filterTipText() - Method in class adams.data.cleaner.instance.IQRCleaner: Returns the tip text for this property.
filterTipText() - Method in class adams.data.evaluator.instance.DistanceToCenter: Returns the tip text for this property.
filterTipText() - Method in class adams.data.evaluator.instance.DistanceToClosest: Returns the tip text for this property.
filterTipText() - Method in class adams.data.io.input.FilteredSpectrumReader: Returns the tip text for this property.
filterTipText() - Method in class adams.data.io.output.FilteredSpectrumWriter: Returns the tip text for this property.
filterTipText() - Method in class adams.data.postprocessor.instances.WekaFilter: Returns the tip text for this property.
filterTipText() - Method in class adams.data.sampledata.SampleDataReportFilter: Returns the tip text for this property.
filterTipText() - Method in class adams.data.spectrumfilter.Covariance: Returns the tip text for this property.
filterTipText() - Method in class adams.data.spectrumfilter.SubtractSpectrum: Returns the tip text for this property.
filterTipText() - Method in class adams.flow.rest.TransformSpectrum: Returns the tip text for this property.
filterTipText() - Method in class adams.flow.transformer.MultiSpectrumFilter: Returns the tip text for this property.
filterTipText() - Method in class adams.flow.transformer.MultiSpectrumOutlierDetector: Returns the tip text for this property.
filterTipText() - Method in class adams.flow.transformer.MultiSpectrumReportFilter: Returns the tip text for this property.
filterTipText() - Method in class weka.filters.unsupervised.attribute.SpectrumFilter: Returns the tip text for this property.
find(double) - Method in class adams.data.threeway.L1Point: Returns the L2Point with the exact x, null if not found.
find(double, double) - Method in class adams.data.threeway.ThreeWayData: Returns the level 1 point with the exact X, null if not found.
find(float) - Method in class adams.data.spectrum.Spectrum: Returns the SpectrumPoint with the exact wave number, null if not found.
find(String, byte[], int) - Method in class adams.data.io.input.OpusSpectrumReader: Find a given string in byte array, from a starting pos.
findCallableActor() - Method in class adams.flow.transformer.MultiSpectrumAdd: Tries to find the callable actor referenced by its callable name.
findClosest(double) - Method in class adams.data.threeway.L1Point: Returns the L2Point with the z closest to the one provided.
findClosest(double, double) - Method in class adams.data.threeway.ThreeWayData: Returns the level 1 point with a X closest to the one provided.
findClosest(float) - Method in class adams.data.spectrum.Spectrum: Returns the SpectrumPoint with a wave number closest to the one provided.
findClosestSpectrumPoint(SpectrumContainerManager, float) - Static method in class adams.gui.visualization.spectrum.WaveNumberHitDetector: Returns the closest spectrum point to the specified wave number across all visible spectra.
findClosestWaveNumber(List<SpectrumPoint>, float) - Static method in class adams.data.spectrum.SpectrumUtils: Returns the index in points closest to the given wave number.
findClosestXY(List<L1Point>, double, double) - Static method in class adams.data.threeway.ThreeWayDataUtils: Returns the index in points closest to the given timestamp.
findEnclosingWaveNumbers(List<SpectrumPoint>, float) - Static method in class adams.data.spectrum.SpectrumUtils: Returns the indices of points in m_Points that enclose the given wave number.
findID(byte[]) - Method in class adams.data.io.input.opus.OpusBlockHelper.Block: Returns the offset of the ID.
findID(byte[], byte[], int) - Static method in class adams.data.io.input.opus.OpusBlockHelper: Locates the first occurrence of the specified ID in the buffer after the starting position.
findMassCharge(List<L2Point>, double) - Static method in class adams.data.threeway.L1PointUtils: Returns the index in points of the given timestamp.
findSpectra(byte[], List<OpusBlockHelper.Block>) - Method in class adams.data.io.input.OpusSpectrumReaderExt: Locates the spectra and adds them to AbstractDataContainerReader.m_ReadData.
findWaveNumber(List<SpectrumPoint>, float) - Static method in class adams.data.spectrum.SpectrumUtils: Returns the index in points of the given wave number.
findWaveNumber(List<SpectrumPoint>, SpectrumPoint) - Static method in class adams.data.spectrum.SpectrumUtils: Returns the index in points of the given spectrum point, -1 if not found.
findX(List<L2Point>, L2Point) - Static method in class adams.data.threeway.L1PointUtils: Returns the index in points of the given level 2 point, -1 if not found.
findXY(List<L1Point>, double, double) - Static method in class adams.data.threeway.ThreeWayDataUtils: Returns the index in points of the given timestamp.
findXY(List<L1Point>, double, double, boolean) - Static method in class adams.data.threeway.ThreeWayDataUtils: Locates the X for the given X.
findXY(List<L1Point>, L1Point) - Static method in class adams.data.threeway.ThreeWayDataUtils: Returns the index in points of the given LevelOnePoint point, -1 if not found.
finishInit() - Method in class adams.data.spectrum.AbstractSpectrumComparator: Finishes the initialization in the constructor.
finishInit() - Method in class adams.gui.tools.DeleteSampleDataPanel: Finishes up the initialization.
finishInit() - Method in class adams.gui.tools.idprovider.DatabaseSearchPanel: Finishes up the initialization.
finishInit() - Method in class adams.gui.tools.idprovider.ManualListPanel: finishes the initialization.
finishInit() - Method in class adams.gui.tools.idprovider.SpreadSheetIDPanel: finishes the initialization.
finishInit() - Method in class adams.gui.tools.ListSampleDataPanel: Finishes up the initialization.
finishInit() - Method in class adams.gui.tools.UpdateSampleDataPanel: Finishes up the initialization.
finishInit() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Finishes up the initialization.
FIRST_WAVE_NUMBER - Static variable in class adams.data.statistics.SpectrumStatistic
firstTipText() - Method in class adams.data.spectrumfilter.AbstractStandardiseFilter: Returns the tip text for this property.
firstWaveTipText() - Method in class adams.flow.transformer.InstanceToSpectrum: Returns the tip text for this property.
firstXPointTipText() - Method in class adams.data.io.output.ASCSpectrumWriter: Returns the tip text for this property.
FitsLibsReader - Class in adams.data.io.input
FitsLibsReader() - Constructor for class adams.data.io.input.FitsLibsReader
fixKey(String) - Method in class adams.data.io.input.ASCSpectrumReader: Turns the key into a proper SampleData constant.
Flatliner - Class in adams.data.spectrumoutlier: Checks for spectra that consist only of the same value (aka flat-liners).
Flatliner() - Constructor for class adams.data.spectrumoutlier.Flatliner
Flatten - Class in adams.data.threewayfeatures: Simply flattens the 3-way data structure (x -> y -> z).
Flatten() - Constructor for class adams.data.threewayfeatures.Flatten
flipTipText() - Method in class adams.data.spectrumoutlier.Swapped: Returns the tip text for this property.
flushExecution() - Method in class adams.flow.control.InstanceCleaner: Stops the processing of tokens without stopping the flow.
flushExecution() - Method in class adams.flow.control.SpectrumCleaner: Stops the processing of tokens without stopping the flow.
foldsTipText() - Method in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: Returns the tip text for this property.
foldsTipText() - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Returns the tip text for this property.
foldsTipText() - Method in class adams.data.evaluator.instance.CrossValidatedPrediction: Returns the tip text for this property.
foldsTipText() - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Returns the tip text for this property.
fontTipText() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Returns the tip text for this property.
forCommandLine(String) - Static method in class adams.data.cleaner.instance.AbstractCleaner: Instantiates the filter from the given commandline (i.e., classname and optional options).
forCommandLine(String) - Static method in class adams.data.cleaner.spectrum.AbstractCleaner: Instantiates the filter from the given commandline (i.e., classname and optional options).
forCommandLine(String) - Static method in class adams.data.evaluator.instance.AbstractEvaluator: Instantiates the filter from the given commandline (i.e., classname and optional options).
forCommandLine(String) - Static method in class adams.data.multifilter.AbstractMultiSpectrumFilter: Instantiates the filter from the given commandline (i.e., classname and optional options).
forCommandLine(String) - Static method in class adams.data.multireportfilter.AbstractMultiSpectrumReportFilter: Instantiates the filter from the given commandline (i.e., classname and optional options).
forCommandLine(String) - Static method in class adams.data.postprocessor.instances.AbstractPostProcessor: Instantiates the processor from the given commandline (i.e., classname and optional options).
format - Variable in class nz.ac.waikato.adams.webservice.rats.multispectrum.Spectrum
format - Variable in class nz.ac.waikato.adams.webservice.rats.spectrum.Spectrum
format - Variable in class nz.ac.waikato.adams.webservice.rats.spectrum.UploadRequest
format - Variable in class nz.ac.waikato.adams.webservice.rats.spectrum.UploadResponse
format - Variable in class nz.ac.waikato.adams.webservice.spectral.get.GetRequest
format - Variable in class nz.ac.waikato.adams.webservice.spectral.get.GetResponse
format - Variable in class nz.ac.waikato.adams.webservice.spectral.get.Spectrum
format - Variable in class nz.ac.waikato.adams.webservice.spectral.put.PutRequest
format - Variable in class nz.ac.waikato.adams.webservice.spectral.put.PutResponse
format - Variable in class nz.ac.waikato.adams.webservice.spectral.put.Spectrum
format - Variable in class nz.ac.waikato.adams.webservice.spectral.transform.Spectrum
format - Variable in class nz.ac.waikato.adams.webservice.spectral.transform.TransformRequest
format - Variable in class nz.ac.waikato.adams.webservice.spectral.transform.TransformResponse
FORMAT - Static variable in class adams.data.sampledata.SampleData: field name for the format.
FORMAT - Static variable in class adams.data.threewayreport.ThreeWayReport: field name for the format.
formatsTipText() - Method in class adams.data.multifilter.AbstractFormatsBasedMultiSpectrumFilter: Returns the tip text for this property.
formatsTipText() - Method in class adams.data.multifilter.Add: Returns the tip text for this property.
formatsTipText() - Method in class adams.data.multifilter.Atan2: Returns the tip text for this property.
formatsTipText() - Method in class adams.data.multifilter.Average: Returns the tip text for this property.
formatsTipText() - Method in class adams.data.multifilter.Divide: Returns the tip text for this property.
formatsTipText() - Method in class adams.data.multifilter.Fusion: Returns the tip text for this property.
formatsTipText() - Method in class adams.data.multifilter.Mean: Returns the tip text for this property.
formatsTipText() - Method in class adams.data.multifilter.Median: Returns the tip text for this property.
formatsTipText() - Method in class adams.data.multifilter.Multiply: Returns the tip text for this property.
formatsTipText() - Method in class adams.data.multifilter.Subtract: Returns the tip text for this property.
formatTipText() - Method in class adams.data.conversion.ArrayToSpectrum: Returns the tip text for this property.
formatTipText() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Returns the tip text for this property.
formatTipText() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns the tip text for this property.
formatTipText() - Method in class adams.data.conversion.SpreadSheetToSpectrum: Returns the tip text for this property.
formatTipText() - Method in class adams.data.io.input.AbstractSampleDataReader: Returns the tip text for this property.
formatTipText() - Method in class adams.data.io.input.AbstractSpectrumReader: Returns the tip text for this property.
formatTipText() - Method in class adams.data.io.input.AbstractThreeWayDataReader: Returns the tip text for this property.
formatTipText() - Method in class adams.data.multispectrumoperation.Remove: Returns the tip text for this property.
formatTipText() - Method in class adams.db.AbstractSpectrumConditions: Returns the tip text for this property.
formatTipText() - Method in class adams.db.SpectrumIDConditions: Returns the tip text for this property.
formatTipText() - Method in class adams.flow.condition.bool.HasSpectrum: Returns the tip text for this property.
formatTipText() - Method in class adams.flow.transformer.datacontainer.LoadSampleData: Returns the tip text for this property.
formatTipText() - Method in class adams.flow.transformer.DeleteSpectrum: Returns the tip text for this property.
formatTipText() - Method in class adams.flow.transformer.MultiSpectrumRemove: Returns the tip text for this property.
formatTipText() - Method in class adams.flow.transformer.report.UpdateDatabaseID: Returns the tip text for this property.
formatTipText() - Method in class adams.flow.transformer.SpectrumDbReader: Returns the tip text for this property.
formatTipText() - Method in class adams.flow.webservice.Get: Description of this option.
forName(String, String[]) - Static method in class adams.data.cleaner.instance.AbstractCleaner: Instantiates the filter with the given options.
forName(String, String[]) - Static method in class adams.data.cleaner.spectrum.AbstractCleaner: Instantiates the filter with the given options.
forName(String, String[]) - Static method in class adams.data.evaluator.instance.AbstractEvaluator: Instantiates the filter with the given options.
forName(String, String[]) - Static method in class adams.data.multifilter.AbstractMultiSpectrumFilter: Instantiates the filter with the given options.
forName(String, String[]) - Static method in class adams.data.multireportfilter.AbstractMultiSpectrumReportFilter: Instantiates the filter with the given options.
forName(String, String[]) - Static method in class adams.data.postprocessor.instances.AbstractPostProcessor: Instantiates the processor with the given options.
FossFields(int) - Constructor for class adams.data.io.input.foss.FossHelper.FossFields: Constructor.
FossHelper - Class in adams.data.io.input.foss: Helper for handling Foss cal files.
FossHelper(byte[]) - Constructor for class adams.data.io.input.foss.FossHelper: Constructor.
FossHelper.FossFields - Class in adams.data.io.input.foss: Stores non-spectral data for a row.
FossOutputHelper - Class in adams.data.io.output.foss: Classes and Methods for creating a byte array of a FOSS .nir or .cal file.
FossOutputHelper() - Constructor for class adams.data.io.output.foss.FossOutputHelper
FossOutputHelper.ConstituentValues - Class in adams.data.io.output.foss: Constituent (or reference) values.
FossOutputHelper.DataBlock - Class in adams.data.io.output.foss: Data Block.
FossOutputHelper.Generalheader - Class in adams.data.io.output.foss: General Header.
FossOutputHelper.InstrumentHeader - Class in adams.data.io.output.foss: Instrument Header class.
FossOutputHelper.InstrumentHeader.InstrumentType - Enum in adams.data.io.output.foss: Type of FOSS instrument.
FossOutputHelper.SampleHeader - Class in adams.data.io.output.foss: Sample Header.
FossOutputHelper.SampleInfo - Class in adams.data.io.output.foss: Sample Info.
FossStdise - Class in adams.data.io.input.foss: Load, and perform standardisation/unstandardisation from foss standardisation file NOTE: Only does slope and intercept standardisation NOTE 2: Established by looking at .std files with hex editor.
FossStdise(byte[]) - Constructor for class adams.data.io.input.foss.FossStdise: Constructor.
fromJson(JsonObject) - Static method in class adams.data.spectrum.SpectrumJsonUtils: Creates a spectrum from the JSON object (spectral + report).
fromValue(String) - Static method in enum nz.ac.waikato.adams.webservice.rats.multispectrum.DataType
fromValue(String) - Static method in enum nz.ac.waikato.adams.webservice.rats.spectrum.DataType
fromValue(String) - Static method in enum nz.ac.waikato.adams.webservice.spectral.get.DataType
fromValue(String) - Static method in enum nz.ac.waikato.adams.webservice.spectral.put.DataType
fromValue(String) - Static method in enum nz.ac.waikato.adams.webservice.spectral.transform.DataType
Fusion - Class in adams.data.multifilter: Fuses the sub-spectra specified by the format option, by placing them side-by-side using the format option as the order.
Fusion() - Constructor for class adams.data.multifilter.Fusion
FXV - Static variable in class adams.data.io.input.opus.OpusBlockHelper: the FXV character sequence.

G

genASCString(Spectrum) - Method in class adams.data.io.output.ASCSpectrumWriter: Generate the ASC String to output.
genByteArray(Spectrum) - Method in class adams.data.io.output.NIRSpectrumWriter: Generate the byte array that makes up the .nir file.
genByteArray(List<Spectrum>) - Method in class adams.data.io.output.NIRSpectrumWriter: Generate the byte array that makes up the .nir file.
Generalheader() - Constructor for class adams.data.io.output.foss.FossOutputHelper.Generalheader
generate(Spectrum) - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Process the given spectrum.
generate(Spectrum) - Method in class adams.data.spectrumimage.AbstractSpectrumImageGenerator: Converts the spectrum into an image.
generate(Spectrum) - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Returns the generated data, generates it if necessary.
generate(ThreeWayData) - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Process the given data.
generateComponent() - Method in class adams.flow.sink.SpectrumImageWriter: Generates the component to display in the frame.
generateFilename() - Method in class adams.flow.sink.SpectrumImageWriter: Generates the filename for the output.
generateHeader(Spectrum) - Method in class adams.data.instances.AbstractSpectrumInstanceGenerator: Generates the header of the output data.
generateHeader(Spectrum) - Method in class adams.data.instances.AbstractSpectrumInstanceGeneratorWithClass: Generates the header of the output data.
generateHeader(Spectrum) - Method in class adams.data.instances.FieldInstanceGenerator: Generates the header of the output data.
generateHeader(Spectrum) - Method in class adams.data.instances.FieldInstanceGeneratorWithClass: Generates the header of the output data.
generateHeader(Spectrum) - Method in class adams.data.instances.SimpleInstanceGenerator: Generates the header of the output data.
generateHeader(Spectrum) - Method in class adams.data.instances.SimpleSpectralInstanceGenerator: Generates the header of the output data.
generateHeader(Spectrum) - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Generates the header of the output data.
generateHeader(Spectrum) - Method in class adams.data.spreadsheetrowgenerator.SampleDataOnlyRowGenerator: Generates the header of the output data.
generateHeader(Spectrum) - Method in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: Generates the header of the output data.
generateLine(Spectrum, double[]) - Method in class adams.data.spectrumbaseline.LinearRegressionBased: Generates fake data for the plotting the line.
generateOutput(Spectrum) - Method in class adams.data.instances.FieldInstanceGenerator: Generates the actual data.
generateOutput(Spectrum) - Method in class adams.data.instances.FieldInstanceGeneratorWithClass: Generates the actual data.
generateOutput(Spectrum) - Method in class adams.data.instances.SimpleInstanceGenerator: Generates the actual data.
generateOutput(Spectrum) - Method in class adams.data.instances.SimpleSpectralInstanceGenerator: Generates the actual data.
generateOutput(Spectrum) - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Generates the actual data.
generateOutput(Spectrum) - Method in class adams.data.spreadsheetrowgenerator.SampleDataOnlyRowGenerator: Generates the actual data.
generateOutput(Spectrum) - Method in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: Generates the actual data.
generateRows(Spectrum) - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Performs the actual feature genration.
generateRows(Spectrum) - Method in class adams.data.spectrum.Amplitudes: Performs the actual feature genration.
generateRows(ThreeWayData) - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Performs the actual feature generation.
generateRows(ThreeWayData) - Method in class adams.data.threewayfeatures.Flatten: Performs the actual feature generation.
generateRows(ThreeWayData) - Method in class adams.data.threewayfeatures.Histogram: Performs the actual feature generation.
generateRows(ThreeWayData) - Method in class adams.data.threewayfeatures.Max: Performs the actual feature generation.
generateRows(ThreeWayData) - Method in class adams.data.threewayfeatures.Mean: Performs the actual feature generation.
generateRows(ThreeWayData) - Method in class adams.data.threewayfeatures.Median: Performs the actual feature generation.
generateRows(ThreeWayData) - Method in class adams.data.threewayfeatures.Min: Performs the actual feature generation.
generateRows(ThreeWayData) - Method in class adams.data.threewayfeatures.MultiThreeWayDataFeatureGenerator: Performs the actual feature generation.
generateRows(ThreeWayData) - Method in class adams.data.threewayfeatures.StdDev: Performs the actual feature generation.
generates() - Method in class adams.data.compare.SpectrumCorrelation: Returns the type of output that it generates.
generates() - Method in class adams.data.compare.SpectrumCosineSimilarity: Returns the type of output that it generates.
generates() - Method in class adams.data.conversion.ArrayToSpectrum: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.JsonToSpectrum: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.MultiSpectrumToSpectra: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.PostProcessingContainerToWekaInstanceContainer: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.ReportToSampleData: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.SampleDataArrayToMap: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.SpectraToMultiSpectrum: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.SpectrumToArray: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.SpectrumToBufferedImage: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.SpectrumToJson: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.SpectrumToSpreadSheet: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.SpectrumToWave: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.SpreadSheetColumnsToSampleData: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.SpreadSheetRowsToSampleData: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.SpreadSheetTo2DTensor: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.SpreadSheetTo3DTensor: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.SpreadSheetToSpectrum: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.SpreadSheetToThreeWayData: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.TensorToSpreadSheet: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.TensorToThreeWayData: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.ThreeWayDataToHeatmap: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.ThreeWayDataToSpreadSheet: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.ThreeWayDataToTensor: Returns the class that is generated as output.
generates() - Method in class adams.data.conversion.WekaPredictionContainerToEvaluationContainer: Returns the class that is generated as output.
generates() - Method in class adams.data.multispectrumoperation.Remove: Returns the class of objects that it generates.
generates() - Method in class adams.flow.control.InstanceCleaner: Returns the class of objects that it generates.
generates() - Method in class adams.flow.control.SpectrumCleaner: Returns the class of objects that it generates.
generates() - Method in class adams.flow.source.NewSpectrum: Returns the class of objects that it generates.
generates() - Method in class adams.flow.standalone.rats.WSMultiSpectrumReception: Returns the type of data this scheme generates.
generates() - Method in class adams.flow.standalone.rats.WSSpectrumReception: Returns the type of data this scheme generates.
generates() - Method in class adams.flow.transformer.AbstractInPlaceSpectrumTransformer: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.BulkSpectrumDbWriter: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.Cleaner: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.DeleteSampleDataValue: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.DeleteSampleDataValueByExpression: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.DeleteSpectrum: Returns the class that the consumer accepts.
generates() - Method in class adams.flow.transformer.Evaluator: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.GetSpectrumAmplitude: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.InstanceGenerator: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.InstanceToSpectrum: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.MergeSampleDataFromMap: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.MultiSpectrumAdd: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.MultiSpectrumFilter: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.MultiSpectrumOperation: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.MultiSpectrumOutlierDetector: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.MultiSpectrumRemove: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.MultiSpectrumReportFilter: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.PostProcessor: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.PredictionCheck: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.SampleDataDbReader: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.SampleDataValueDbWriter: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.SetEvaluationMetaData: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.SetSampleDataValue: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.SpectralAngleMapper: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.SpectrumDbReader: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.SpectrumDbWriter: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.SpectrumDiff: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.SpectrumFeatureGenerator: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.SpectrumInfo: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.SpectrumMinMax: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.SpreadSheetRowGenerator: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.ThreeWayDataFeatureGenerator: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.ThreeWayDataLoadingMatrix: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.ThreeWayDataMerge: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Returns the class of objects that it generates.
generates() - Method in class adams.flow.transformer.ThreeWayDataTrain: Returns the class of objects that it generates.
generates() - Method in class adams.flow.webservice.Get: Returns the classes that this client generates.
generates() - Method in class adams.flow.webservice.Transform: Returns the classes that this client generates.
generateSampleIDsTipText() - Method in interface adams.flow.source.SampleIdSource: Returns the tip text for this property.
generateSampleIDsTipText() - Method in class adams.flow.source.SpectrumIdSupplier: Returns the tip text for this property.
generateSpectra(List<String>, List<String>, Map<String, Range>, Map<String, Range>, List<TFloatList>) - Method in class adams.data.io.input.UnscramblerSpectrumReader: Generates the spectra from the parsed data.
generatorTipText() - Method in class adams.data.conversion.SpectrumToBufferedImage: Returns the tip text for this property.
generatorTipText() - Method in class adams.data.io.output.SpectrumImageWriter: Returns the tip text for this property.
generatorTipText() - Method in class adams.data.spectrumanalysis.AbstractWekaSpectrumAnalysis: Returns the tip text for this property.
generatorTipText() - Method in class adams.data.spectrumfilter.LRCoeff: Returns the tip text for this property.
generatorTipText() - Method in class adams.data.spectrumfilter.PCA: Tip text for this property.
generatorTipText() - Method in class adams.data.spectrumfilter.PLS: Tip text for this property.
generatorTipText() - Method in class adams.data.spectrumfilter.WekaFilterToReport: Returns the tip text for this property.
generatorTipText() - Method in class adams.data.spectrumimage.Spectrogram: Returns the tip text for this property.
generatorTipText() - Method in class adams.data.threewayfeatures.Histogram: Returns the tip text for this property.
generatorTipText() - Method in class adams.flow.transformer.InstanceGenerator: Returns the tip text for this property.
generatorTipText() - Method in class adams.flow.transformer.SpreadSheetRowGenerator: Returns the tip text for this property.
generatorTipText() - Method in class adams.gui.visualization.spectrum.SpectrumPaintletNumericField: Returns the tip text for this property.
get(double, double, double) - Method in class adams.data.threeway.ThreeWayData: Returns the L2 point associated with the given x, y and z.
get(int) - Method in class adams.flow.control.InstanceCleaner: Returns the actor at the given position.
get(int) - Method in class adams.flow.control.SpectrumCleaner: Returns the actor at the given position.
get(String) - Method in class adams.data.io.input.opus.OpusBlockHelper.CommandlineData: Returns the value associated with the key.
get(String, String) - Method in class adams.flow.rest.GetSpectrum: Retrieves a spectrum and returns it as JSON.
get(GetRequest) - Method in class adams.flow.webservice.SimpleSpectralGetService: Uploads a spectrum.
get(GetRequest) - Method in interface nz.ac.waikato.adams.webservice.spectral.get.SpectralGetService
Get - Class in adams.flow.webservice: Gets a spectrum.
Get() - Constructor for class adams.flow.webservice.Get
getABCount(byte[]) - Method in class adams.data.io.input.OpusSpectrumReader: Get number of spectral values
getABDataOffset(byte[]) - Method in class adams.data.io.input.OpusSpectrumReader: Get position of nir data.
getABOffset(byte[]) - Method in class adams.data.io.input.OpusSpectrumReader: Find position of AB Block offset
getAbsdiff() - Method in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: Returns the absolute difference.
getAbsolute() - Method in class adams.data.spectrumfilter.Covariance: Get absolute?
getAbsolute() - Method in class adams.data.spectrumfilter.LRCoeff: Get absolute?
getAbsolute() - Method in class adams.flow.transformer.SpectrumDiff: Returns whether to compute absolute difference or with sign.
getAbstentionClassification(Instance) - Method in class weka.classifiers.meta.SpectrumClassifier: The prediction that made the classifier abstain.
getAbstentionDistribution(Instance) - Method in class weka.classifiers.meta.SpectrumClassifier: The class distribution that made the classifier abstain.
getAcceptedConditions() - Method in class adams.flow.source.SpectrumIdSupplier: Returns the accepted classes for condition objects.
getAccessoryName() - Method in class adams.data.io.output.ASCSpectrumWriter: Get accessory name.
getAction() - Method in class adams.flow.webservice.Transform: Returns the action (callable actor on the server side) to execute.
getAction() - Method in class adams.gui.scripting.SelectWaveNumber: Returns the action string used in the command processor.
getAction() - Method in class adams.gui.scripting.WriteSpectrum: Returns the action string used in the command processor.
getAction() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.TransformRequest: Gets the value of the action property.
getActorHandlerInfo() - Method in class adams.flow.control.InstanceCleaner: Returns some information about the actor handler, e.g., whether it can contain standalones and the actor execution.
getActorHandlerInfo() - Method in class adams.flow.control.SpectrumCleaner: Returns some information about the actor handler, e.g., whether it can contain standalones and the actor execution.
getActualFormatExtensions() - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Returns the underlying format extensions.
getActualFormatExtensions() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Returns the underlying format extensions.
getAddCommandLines() - Method in class adams.data.io.input.OpusSpectrumReaderExt: Returns whether to add the other command-lines to the report.
getAddDatabaseID() - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Returns whether to add the database ID.
getAddDatabaseID() - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Returns whether the database ID is added.
getAddID() - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Returns whether to add the ID.
getAdditionalData() - Method in class adams.data.spectrumfilter.MultiplicativeScatterCorrection: Returns the additional data.
getAdditionalFields() - Method in class adams.data.instances.AbstractSpectrumInstanceGenerator: Returns the additional fields to add.
getAdditionalFieldsPosition() - Method in class adams.data.instances.AbstractSpectrumInstanceGenerator: Returns the position used in the "Add" filter for adding the additional fields to the dataset.
getAdditionalFieldsPosition() - Method in class adams.data.instances.AbstractSpectrumInstanceGeneratorWithClass: Returns the position used in the "Add" filter for adding the additional fields to the dataset.
getAdditionalFieldsPrefix() - Method in class adams.data.instances.AbstractSpectrumInstanceGenerator: Returns the prefix to use for the additional fields.
getAddLog() - Method in class adams.data.io.input.OpusSpectrumReaderExt: Returns whether to add the entire log to the report.
getAddRawMetaData() - Method in class adams.data.io.input.JCampDX2SpectrumReader: Returns whether to add the raw meta-data to the report.
getAddRawMetaData() - Method in class adams.data.io.input.JCampDXSpectrumReader: Returns whether to add the raw meta-data to the report.
getAddSampleID() - Method in class adams.data.instances.AbstractSpectrumBasedInstanceGenerator: Returns whether the sample ID is added.
getAddSampleID() - Method in interface adams.data.instances.InstanceGeneratorWithSampleID: Returns whether the sample ID is added.
getAddSampleID() - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Returns whether the sample ID is added.
getAddTraceToReport() - Method in class adams.data.io.input.OpusSpectrumReader: Returns whether to add the trace to the report.
getAddWaveNumber() - Method in class adams.data.instances.SimpleInstanceGenerator: Returns whether the wave number gets added to the output as well.
getAddWaveNumber() - Method in class adams.data.instances.SimpleSpectralInstanceGenerator: Returns whether the wave number gets added to the output as well.
getAddWaveNumber() - Method in class adams.data.spectrum.Amplitudes: Returns whether to add the wave numbers as well (preceding the amplitude).
getAdjustToVisibleData() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Returns whether the display is adjusted to only the visible spectrums or all of them.
getAlgorithm() - Method in class adams.data.spectrumfilter.PLS: Returns PLS algorithm in use.
getAlgorithm() - Method in class adams.flow.transformer.SpectrumFeatureGenerator: Returns the algorithm in use.
getAlgorithm() - Method in class adams.flow.transformer.ThreeWayDataFeatureGenerator: Returns the algorithm in use.
getAlgorithm() - Method in class adams.flow.transformer.ThreeWayDataMerge: Returns the algorithm in use.
getAlgorithm() - Method in class adams.flow.transformer.ThreeWayDataTrain: Returns the algorithm in use.
getAllData() - Method in class adams.data.threeway.ThreeWayData: Returns all unique data values.
getAllPanels() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Returns the all panels.
getAllSpectra() - Method in class adams.data.io.input.OpusSpectrumReaderExt: Returns whether to load all spectra.
getAllVisible() - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: Returns (a copy of) all currently stored containers.
getAllX() - Method in class adams.data.threeway.ThreeWayData: Returns all unique Xs.
getAllY() - Method in class adams.data.threeway.ThreeWayData: Returns all unique Ys.
getAllZ() - Method in class adams.data.threeway.ThreeWayData: Returns all unique Zs.
getAlwaysShowMarkers() - Method in class adams.gui.visualization.spectrum.SpectrumPaintlet: Returns whether marker shapes are always drawn.
getAmplitude() - Method in class adams.data.spectrum.SpectrumPoint: Returns the amplitude.
getAmplitude() - Method in class adams.flow.transformer.SetSpectrumAmplitude: Returns the amplitude to set.
getAmplitude() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.Wave: Gets the value of the amplitude property.
getAmplitude() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.Wave: Gets the value of the amplitude property.
getAmplitude() - Method in class nz.ac.waikato.adams.webservice.spectral.get.Wave: Gets the value of the amplitude property.
getAmplitude() - Method in class nz.ac.waikato.adams.webservice.spectral.put.Wave: Gets the value of the amplitude property.
getAmplitude() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.Wave: Gets the value of the amplitude property.
getAmplitudeName(float) - Static method in class adams.data.instances.ArffUtils: Returns the name of an attribute for an amplitude.
getAmplitudeName(int) - Static method in class adams.data.instances.ArffUtils: Returns the name of an attribute for an amplitude.
getAmplitudeName(String, float) - Static method in class adams.data.instances.ArffUtils: Returns the name of an attribute for an amplitude.
getAmplitudeName(String, int) - Static method in class adams.data.instances.ArffUtils: Returns the name of an attribute for an amplitude.
getAmplitudePrefix() - Method in class adams.data.instances.AbstractSpectrumInstanceGenerator: Returns the prefix for the wave number attributes.
getAmplitudePrefix() - Method in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: Returns the column prefix for the amplitudes.
getAmplitudeRanges() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.DataCollector: Returns the inter-percentile ranges for the amplitudes.
getAmplitudeRows() - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Returns the range of rows containing the amplitudes.
getAmplitudeType() - Method in class adams.data.io.input.SoilCaresScannerSpectrumReader: Returns the type of amplitude to read.
getApply() - Method in class adams.data.spectrumfilter.LRCoeff: Get apply coeff to spectrum?
getApprovedConditions() - Method in class adams.gui.selection.SelectSpectrumPanel: Returns the approved conditions that can be used.
getAtomicMove() - Method in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: Returns whether to attempt atomic move operation.
getAtomicMove() - Method in class adams.flow.standalone.rats.LoadSpectrumFileOutput: Returns whether to attempt atomic move operation.
getAttributeName() - Method in class adams.data.cleaner.instance.MinMax: Returns the name of the attribute to work on.
getAttributeRange() - Method in class adams.data.cleaner.instance.IQRCleaner: Returns the attribute range to work on.
getAttributeRange() - Method in class adams.data.spectrumanalysis.FastICA: Returns the attribute range parameter.
getAutoCommit() - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Returns whether to use auto-commit for bulk transactions.
getAutoCommit() - Method in class adams.flow.transformer.BulkSpectrumDbWriter: Returns whether to use auto-commit for bulk transactions.
getBackendFor(AbstractDatabaseConnection) - Method in class adams.db.mirrored.SpectralDbBackend: Returns the corresponding backend for the connection URL provided.
getBackends() - Method in class adams.db.mirrored.SpectralDbBackend: Returns the backends in use.
getBase() - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Get the base classifier to be used.
getBaseFilter() - Method in class adams.data.multifilter.FilteredMultiSpectrumFilter: Returns the base filter.
getBatchFilter() - Method in class adams.data.spectrumfilter.KennardStone: Get the batch filter to apply before selection
getBatchSize() - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Returns the batch size in use.
getBatchSize() - Method in class adams.flow.transformer.BulkSpectrumDbWriter: Returns the batch size in use.
getBelowCountThreshold() - Method in class adams.data.multispectrumoperation.outlierremoval.CorrelationBasedThreshold: Returns the number of spectra below threshold that trigger rejection of the spectrum.
getBelowCountThreshold() - Method in class adams.data.multispectrumoperation.outlierremoval.CosineSimilarityBasedThreshold: Returns the number of spectra below threshold that trigger rejection of the spectrum.
getBlockOffset(byte[], byte, byte, byte, byte) - Method in class adams.data.io.input.OpusSpectrumReader: Starting from blocks_offset, find sequence of bytes Return position of sequence, or -1 if not found
getBlockOffsetReverse(byte[], int, byte, byte, byte, byte) - Method in class adams.data.io.input.OpusSpectrumReader: Starting from blocks_offset, find sequence of bytes Return position of sequence, or -1 if not found
getBlockSize() - Method in class adams.data.io.input.foss.FossHelper: Get block size of a row in bytes.
getBufferSection() - Method in class adams.data.io.input.opus.OpusBlockHelper.Block: Returns the sub-section of the buffer (copy operation!).
getBufferSize() - Method in class adams.data.io.input.ZippedSpectrumReader: Returns the buffer size for the stream.
getBuildWait() - Method in class adams.data.evaluator.instance.FakeEvaluator: Returns the time in msec to wait when calling buildClassifier.
getByte(byte[], int) - Method in class adams.data.io.input.opus.OpusBlockHelper.Block: Returns the long with the given ID.
getByte(int) - Method in class adams.data.io.input.opus.OpusBlockHelper.Block: Returns the byte at the specified offset.
getBytes() - Method in class adams.data.io.output.foss.FossOutputHelper.ConstituentValues: Get byte array for the constituent values.
getBytes() - Method in class adams.data.io.output.foss.FossOutputHelper.DataBlock: Get byte array for sample block.
getBytes() - Method in class adams.data.io.output.foss.FossOutputHelper.Generalheader: Get byte array of General Header.
getBytes() - Method in class adams.data.io.output.foss.FossOutputHelper.InstrumentHeader: Get byte array of Instrument Header.
getBytes() - Method in class adams.data.io.output.foss.FossOutputHelper.SampleHeader: Get byte array for sample header.
getBytes() - Method in class adams.data.io.output.foss.FossOutputHelper.SampleInfo: Get byte array for sample info.
getBytesRead() - Method in class adams.data.io.input.SPCSpectrumReader.AbstractParser: Returns the number of bytes that were read.
getCache() - Method in class adams.flow.transformer.SpectralAngleMapper: Gets the name of the LRU cache to use.
getCallableActor() - Method in class adams.flow.transformer.MultiSpectrumAdd: Returns the currently set callable actor.
getCallableName() - Method in class adams.flow.transformer.MultiSpectrumAdd: Returns the name of the callable actor in use.
getCapabilities() - Method in class weka.classifiers.meta.SpectrumClassifier: Returns default capabilities of the classifier.
getCapabilities() - Method in class weka.clusterers.SpectrumClusterer: Returns default capabilities of the clusterer.
getCapabilities() - Method in class weka.filters.unsupervised.attribute.BestBySLR: Returns the Capabilities of this filter.
getCapabilities() - Method in class weka.filters.unsupervised.attribute.SpectrumFilter: Returns the Capabilities of this filter.
getCategory() - Method in class adams.gui.menu.DeleteSampleData: Returns the category of the menu item in which it should appear, i.e., the name of the menu.
getCategory() - Method in class adams.gui.menu.DeleteSpectra: Returns the category of the menu item in which it should appear, i.e., the name of the menu.
getCategory() - Method in class adams.gui.menu.ExportValidationSets: Returns the category of the menu item in which it should appear, i.e., the name of the menu.
getCategory() - Method in class adams.gui.menu.ListSampleData: Returns the category of the menu item in which it should appear, i.e., the name of the menu.
getCategory() - Method in class adams.gui.menu.SpectrumExplorer: Returns the category of the menu item in which it should appear, i.e., the name of the menu.
getCategory() - Method in class adams.gui.menu.ThreeWayDataHeatmapViewer: Returns the category of the menu item in which it should appear, i.e., the name of the menu.
getCategory() - Method in class adams.gui.menu.UpdateSampleData: Returns the category of the menu item in which it should appear, i.e., the name of the menu.
getCheck() - Method in class adams.flow.transformer.PredictionCheck: Returns the check in use.
getCheckWaveNumberAlignment() - Method in class adams.flow.transformer.SpectralAngleMapper: Gets whether wave-number alignment should be checked.
getChunkSize() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.DataCollector: Returns the size of the chunks being used.
getChunkSize() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Returns the chunk size to use for loading data from the database.
getClassCrossReferences() - Method in class adams.data.conversion.MultiSpectrumToSpectra: Returns the cross-referenced classes.
getClassCrossReferences() - Method in class adams.data.conversion.SpectraToMultiSpectrum: Returns the cross-referenced classes.
getClassCrossReferences() - Method in class adams.data.spectrumfilter.SAX: Returns the cross-referenced classes.
getClassCrossReferences() - Method in class adams.flow.transformer.MergeSampleDataFromMap: Returns the cross-referenced classes.
getClassCrossReferences() - Method in class adams.flow.transformer.MultiSpectrumFilter: Returns the cross-referenced classes.
getClassifier() - Method in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: Returns the classifier.
getClassifier() - Method in class adams.data.cleaner.instance.RemoveOutliers: Returns the classifier.
getClassifier() - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Returns the classifier in use.
getClassifier() - Method in class adams.data.evaluator.instance.CrossValidatedPrediction: Returns the classifier in use.
getClassifier() - Method in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: Returns the interval estimator in use.
getClassifier() - Method in interface adams.data.evaluator.instance.WekaClassifierBasedEvaluator: Returns the classifier in use.
getClassifierFirst() - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Returns the classifier to be used in conjunction with Savitzky-Golay filter with first derivative.
getClassifierNone() - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Returns the classifier to be used in conjunction with Savitzky-Golay filter with no derivative.
getClassifiers() - Method in class adams.data.evaluator.instance.EnsembleEvaluator: Returns the classifiers in use.
getClassifiers() - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Get the classifiers to be used.
getClassifiers() - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Returns the classifiers to use internally.
getClassifierSecond() - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Returns the classifier to be used in conjunction with Savitzky-Golay filter with second derivative.
getClassLabels() - Method in class adams.data.instances.AbstractFieldInstanceGeneratorWithClass: Returns the labels for a nominal class attribute.
getClassLabels() - Method in class adams.data.instances.AbstractSpectrumInstanceGeneratorWithClass: Returns the labels for a nominal class attribute.
getClassLabels() - Method in interface adams.data.instances.InstanceGeneratorWithClassLabels: Returns the labels for a nominal class attribute.
getCleanAfterBuild() - Method in class adams.flow.transformer.Evaluator: Returns whether to discard the internal evaluator again after building it.
getCleaned() - Method in class adams.flow.transformer.Cleaner.CleanJob: Returns the cleaned data.
getCleaner() - Method in class adams.flow.control.InstanceCleaner: Returns the cleaner.
getCleaner() - Method in class adams.flow.control.SpectrumCleaner: Returns the cleaner.
getCleaner() - Method in class adams.flow.transformer.Cleaner: Returns the cleaner in use.
getCleanerDetailsOutput() - Method in class adams.flow.transformer.Cleaner: Returns the file for the cleaner details.
getCleaners() - Static method in class adams.data.cleaner.instance.AbstractCleaner: Returns a list with classnames of filters.
getCleaners() - Static method in class adams.data.cleaner.spectrum.AbstractCleaner: Returns a list with classnames of filters.
getCleanInstancesError() - Method in class adams.data.cleaner.instance.AbstractCleaner: Returns the error message that was recorded during cleaning the Instances object (if any).
getClient() - Method in class adams.data.io.output.NIRSpectrumWriter: Get client.
getClone() - Method in class adams.data.threeway.L1Point: Returns a clone of itself.
getClosestPoints(double, List<SpectrumPoint>, int) - Method in class adams.data.spectrumfilter.StandardiseByInterpolation
getCode() - Method in enum adams.data.io.output.foss.FossOutputHelper.InstrumentHeader.InstrumentType: Get file code for instrument type.
getCoefficientOffset() - Method in class adams.data.io.input.foss.FossStdise: Get start of coefficents.
getCoefficients() - Method in class adams.data.io.input.foss.FossStdise: Get coefficients as array.
getColor() - Method in class adams.gui.visualization.spectrum.SelectedWaveNumberPaintlet: Returns the currently set color to paint the point with.
getColor() - Method in class adams.gui.visualization.spectrum.SpectrumContainer: Returns the current color in use.
getColor(int) - Method in class adams.gui.visualization.spectrum.ReportColorSpectrumPaintlet: Returns the color for the data with the given index.
getColor(int) - Method in class adams.gui.visualization.spectrum.SimpleSpectrumPaintlet: Returns the color for the data with the given index.
getColor(int) - Method in class adams.gui.visualization.spectrum.SpectrumPaintlet: Returns the color for the data with the given index.
getColor(int) - Method in class adams.gui.visualization.spectrum.SpectrumPaintletNumericField: Returns the color for the data with the given index.
getColor(int) - Method in class adams.gui.visualization.spectrum.SpectrumPaintletStringField: Returns the color for the data with the given index.
getColor(SpectrumContainer) - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: Returns the color for the container.
getColorField() - Method in class adams.gui.visualization.spectrum.ReportColorSpectrumPaintlet: Returns the report field that contains the color.
getColorGenerator() - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Returns the generator for the color gradient.
getColorGenerator() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Returns the generator for the color gradient.
getColorLookup() - Method in class adams.data.conversion.SpectrumToBufferedImage: Generates the color lookup.
getColorProvider() - Method in class adams.flow.sink.SpectrumDisplay: Returns the color provider in use.
getColorProvider() - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: Returns the color provider to use.
getColorProvider() - Method in class adams.gui.visualization.spectrum.SpectrumPaintletStringField: Returns the color provider in use.
getColSampleDataNames() - Method in class adams.data.conversion.SpreadSheetColumnsToSampleData: Returns the column that contains the sample data names.
getColSampleDataNames() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Returns the column that contains the sample data names.
getColsSampleDataValues() - Method in class adams.data.conversion.SpreadSheetColumnsToSampleData: Returns the columns to get the sample data values from.
getColumnAmplitude() - Method in class adams.data.conversion.SpreadSheetToSpectrum: Returns the column with the amplitude information.
getColumnClass(int) - Method in class adams.gui.selection.SelectSpectrumPanel.TableModel: Returns the class type of the column.
getColumnClass(int) - Method in class adams.gui.visualization.spectrum.SpectrumTableModel: Returns the most specific superclass for all the cell values in the column.
getColumnCount() - Method in class adams.gui.selection.SelectSpectrumPanel.TableModel: Returns the number of columns in the table, i.e., 3.
getColumnCount() - Method in class adams.gui.visualization.spectrum.SpectrumTableModel: Returns the number of columns in the model.
getColumnData() - Method in class adams.data.conversion.SpreadSheetTo3DTensor: Returns the data column.
getColumnData() - Method in class adams.data.conversion.SpreadSheetToThreeWayData: Returns the data column.
getColumnID() - Method in class adams.data.conversion.SpreadSheetRowsToSampleData: Returns the (optional) column that contains the sample ID.
getColumnID() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns the (optional) column that contains the sample ID.
getColumnMapping() - Method in class adams.db.generic.SampleDataT: Column mapping for table.
getColumnMapping() - Method in class adams.db.generic.SpectrumT: Return columns for this table.
getColumnMeasurementName() - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Returns the name of the column with the reference value name.
getColumnMeasurementValue() - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Returns the name of the column with the reference value.
getColumnName(int) - Method in class adams.gui.selection.SelectSpectrumPanel.TableModel: Returns the name of the column.
getColumnName(int) - Method in class adams.gui.visualization.spectrum.SpectrumTableModel: Returns the name of the column.
getColumns() - Method in class adams.data.conversion.SpreadSheetTo2DTensor: Returns the columns of the matrix.
getColumnSampleID() - Method in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: Returns the column with the sample ID.
getColumnSampleID() - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Returns the name of the column with the sample ID.
getColumnSampleType() - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Returns the name of the column with the sample type.
getColumnsAmplitude() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Returns the columns with the amplitude information.
getColumnsAmplitude() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns the columns with amplitude information.
getColumnsBoolean() - Method in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: Returns the columns with boolean reference values.
getColumnsNumeric() - Method in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: Returns the columns with numeric reference values.
getColumnsSampleData() - Method in class adams.data.conversion.SpreadSheetRowsToSampleData: Returns the columns with sampledata.
getColumnsSampleData() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns the columns with sampledata.
getColumnsSampleData() - Method in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: Returns the columns with the reference values.
getColumnWaveNumber() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Returns the column with the wavenumber information.
getColumnWaveNumber() - Method in class adams.data.conversion.SpreadSheetToSpectrum: Returns the column with the wavenumber information.
getColumnX() - Method in class adams.data.conversion.SpreadSheetTo3DTensor: Returns the X column.
getColumnX() - Method in class adams.data.conversion.SpreadSheetToThreeWayData: Returns the X column.
getColumnY() - Method in class adams.data.conversion.SpreadSheetTo3DTensor: Returns the Y column.
getColumnY() - Method in class adams.data.conversion.SpreadSheetToThreeWayData: Returns the Y column.
getColumnZ() - Method in class adams.data.conversion.SpreadSheetTo3DTensor: Returns the Z column.
getColumnZ() - Method in class adams.data.conversion.SpreadSheetToThreeWayData: Returns the Z column.
getCombine() - Method in class adams.gui.visualization.spectrum.SpectrumExportDialog: Returns whether files should get combined if possible.
getComparator() - Method in class adams.data.spectrum.MultiSpectrum: Returns the comparator in use (custom one if defined, otherwise the default one).
getComparator() - Method in class adams.data.spectrum.Spectrum: Returns the comparator in use.
getComparator() - Static method in class adams.data.spectrum.SpectrumUtils: Returns the comparator used for finding wave numbers.
getComparator() - Method in class adams.data.threeway.L1Point: Returns the comparator in use.
getComparator() - Method in class adams.data.threeway.ThreeWayData: Returns the comparator in use.
getComparator() - Static method in class adams.data.threeway.ThreeWayDataUtils: Returns the comparator used for finding timestamps.
getComponent() - Method in class adams.data.conversion.WekaPredictionContainerToEvaluationContainer: Returns the component to use for the evaluation.
getComponent() - Method in class adams.flow.transformer.Evaluator: Returns the component identifier.
getComponents() - Method in class adams.data.spectrumanalysis.FastICA: Returns the components.
getCondition() - Method in class adams.data.spectrumfilter.ConditionalReportField: Returns the condition to evaluate.
getConditionBoolean() - Method in class adams.data.multifilter.PickByReportValue: Returns whether the boolean field must be true or false.
getConditionNumericMax() - Method in class adams.data.multifilter.PickByReportValue: Returns the upper bound that numeric fields must match.
getConditionNumericMin() - Method in class adams.data.multifilter.PickByReportValue: Returns the lower bound that numeric fields must match.
getConditions() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Returns the conditions container to use for retrieving the spectra.
getConditions() - Method in class adams.data.spectrumfilter.Covariance: Returns the conditions container to use for retrieving the spectra.
getConditions() - Method in class adams.data.spectrumfilter.LRCoeff: Returns the conditions container to use for retrieving the spectra.
getConditions() - Method in class adams.flow.source.OrphanedSampleDataIdSupplier: Returns whether to output the items as array or as single strings.
getConditionString() - Method in class adams.data.multifilter.PickByReportValue: Returns the regular expression to apply to string fields.
getConfidenceLevel() - Method in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: Returns the confidence level in use.
getConsecutiveRegion(List<SpectrumPoint>, SpectrumPoint, SpectrumPoint) - Static method in class adams.data.spectrum.SpectrumUtils: Returns a region for the given range, starting just after the wave number of "lastEnd" and ending (including) at "end".
getConstituents() - Method in class adams.data.io.output.CALSpectrumWriter: Returns the constituents.
getConstituentValues(Spectrum) - Method in class adams.data.io.output.CALSpectrumWriter: Create ConstituentValues for a spectrum.
getConstituentValues(Spectrum) - Method in class adams.data.io.output.NIRSpectrumWriter: Create ConstituentValues for a spectrum.
getContainerManager() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Returns the current container manager.
getContainerPaintlet() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Returns the paintlet used for painting the containers.
getContainerPanel() - Method in class adams.gui.visualization.spectrum.SpectrumZoomOverviewPaintlet: Returns the panel to obtain plot and containers from.
getConversion() - Method in class adams.data.spectrumfilter.ReportFieldFromStringValue: Returns the conversion to apply to the extracted string value.
getConversion() - Method in class adams.flow.transformer.SetEvaluationMetaData: Returns the type of conversion to perform on the value before storing it in the evaluation container.
getConverter() - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Returns the feature converter in use.
getConverter() - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Returns the feature converter in use.
getCorrection() - Method in class adams.data.spectrumfilter.Detrend: Returns the correction scheme in use.
getCorrection() - Method in class adams.data.spectrumfilter.MultiplicativeScatterCorrection: Returns the correction scheme in use.
getCount() - Method in class adams.data.io.input.foss.FossHelper: Number of non-deleted rows.
getCrossHairTracker() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Returns the cross-hair tracker.
getCurrentFile() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Returns the current file.
getCurrentPanel() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerMultiPagePane: Returns the currently selected panel.
getCurrentPanel() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Returns the currently selected heatmap panel.
getCustomComparator() - Method in class adams.data.conversion.SpectraToMultiSpectrum: Returns the custom comparator.
getCustomComparator() - Method in class adams.data.spectrum.MultiSpectrum: Returns the custom comparaor in use.
getCustomComparator() - Method in class adams.flow.transformer.SpectrumFileReader: Returns the custom comparator.
getData() - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Get training data.
getData() - Method in class adams.data.statistics.SpectrumStatistic: Returns the currently stored spectrum.
getData() - Method in class adams.data.threeway.L2Point: Returns the value.
getData() - Method in class adams.gui.visualization.spectrum.SpectrumContainer: Returns the stored spectrum.
getData() - Method in class adams.gui.visualization.spectrum.SpectrumContainerTableColumnNameGenerator: Returns the name of the column with the actual data in it.
getData() - Method in class adams.gui.visualization.spectrum.SpectrumTableModel: Returns the underlying spectrum.
getData() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: The current data on display.
getDatabaseConnection() - Method in class adams.data.cleaner.instance.AbstractDatabaseConnectionCleaner: Returns the currently used database connection object, can be null.
getDatabaseConnection() - Method in class adams.data.cleaner.spectrum.AbstractDatabaseConnectionCleaner: Returns the currently used database connection object, can be null.
getDatabaseConnection() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Returns the currently used database connection object, can be null.
getDatabaseConnection() - Method in class adams.data.io.input.AbstractSampleDataReader: Returns the currently used database connection object, can be null.
getDatabaseConnection() - Method in class adams.flow.source.InstrumentSupplier: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.flow.source.OrphanedSampleDataIdSupplier: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.flow.source.SpectrumIdSupplier: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.flow.source.SQLSpectrumIdSupplier: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.flow.transformer.BulkSpectrumDbWriter: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.flow.transformer.DeleteDbSampleDataValue: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.flow.transformer.DeleteSpectrum: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.flow.transformer.MultiSpectrumFilter: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.flow.transformer.MultiSpectrumOutlierDetector: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.flow.transformer.MultiSpectrumReportFilter: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.flow.transformer.report.UpdateDatabaseID: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.flow.transformer.SampleDataDbReader: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.flow.transformer.SampleDataDbWriter: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.flow.transformer.SampleDataFileReader: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.flow.transformer.SampleDataValueDbWriter: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.flow.transformer.SpectrumDbReader: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.flow.transformer.SpectrumDbWriter: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.flow.transformer.SpectrumFilter: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.flow.transformer.ThreeWayDataFilter: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.flow.webservice.multispectrum.SimpleRatsMultiSpectrumService: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.flow.webservice.SimpleSpectralGetService: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.flow.webservice.SimpleSpectralPutService: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.flow.webservice.SimpleSpectralTransformService: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.flow.webservice.spectrum.SimpleRatsSpectrumService: Determines the database connection in the flow.
getDatabaseConnection() - Method in class adams.gui.selection.SelectSpectrumDialog: Returns the currently used database connection object, can be null.
getDatabaseConnection() - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: Returns the currently used database connection object, can be null.
getDatabaseConnection() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Returns the currently used database connection object, can be null.
getDatabaseID() - Method in class adams.data.spectrum.Spectrum: Returns the database ID of the sequence.
getDatabaseID() - Method in class adams.data.threeway.ThreeWayData: Get database id.
getDatabaseID() - Method in class adams.gui.visualization.spectrum.SpectrumContainer: Returns the database ID.
getDatabaseID(String) - Method in class adams.db.generic.SpectrumT: Returns the database ID for given spectrum ID.
getDatabaseID(String) - Method in class adams.db.mirrored.SpectrumT: Returns the database ID for given spectrum ID.
getDatabaseID(String) - Method in class adams.db.SpectrumF: Returns the database ID for given spectrum ID.
getDatabaseID(String) - Method in interface adams.db.SpectrumIntf: Returns the database ID for given spectrum ID.
getDatabaseID(String, String) - Method in class adams.db.generic.SpectrumT: Returns the database ID for given sample ID and type.
getDatabaseID(String, String) - Method in class adams.db.mirrored.SpectrumT: Returns the database ID for given sample ID and type.
getDatabaseID(String, String) - Method in class adams.db.SpectrumF: Returns the database ID for given sample ID and type.
getDatabaseID(String, String) - Method in interface adams.db.SpectrumIntf: Returns the database ID for given sample ID and type.
getDataBlock(Spectrum) - Method in class adams.data.io.output.NIRSpectrumWriter: Create a DataBlock from a spectrum.
getDataContainerClass() - Method in class adams.flow.transformer.SpectrumAppend: Returns the data container class that the transformer handles.
getDataContainerClass() - Method in class adams.flow.transformer.SpectrumFileWriter: Returns the data container class in use.
getDataContainerClass() - Method in class adams.flow.transformer.SpectrumFilter: Returns the data container class in use.
getDataContainerClass() - Method in class adams.flow.transformer.ThreeWayDataFileWriter: Returns the data container class in use.
getDataContainerClass() - Method in class adams.flow.transformer.ThreeWayDataFilter: Returns the data container class in use.
getDataContainerPanel() - Method in class adams.gui.scripting.SpectralCommandProcessor: Returns the DataContainer panel.
getDataFromOffset(int) - Method in class adams.data.io.input.foss.FossStdise: Get array of values starting from given offset.
getDataPaintlet() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Returns the paintlet used for painting the data.
getDataPanel() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractThreeWayDataOverlay: Returns the data panel this overlay is for.
getDataPoints() - Method in class adams.data.io.output.ASCSpectrumWriter: Get number of data points. -1 means use as many as in spectrum.
getDataProvider() - Method in class adams.flow.transformer.DeleteSpectrum: Returns the data provider to use for storing the container in the database.
getDataProvider() - Method in class adams.flow.transformer.SpectrumDbReader: Returns the data provider to use for storing the container in the database.
getDataProvider(Spectrum) - Method in class adams.flow.transformer.SpectrumDbWriter: Returns the data provider to use for storing the container in the database.
getDataSet() - Method in class weka.core.converters.CALSpectrumLoader: Return the full data set.
getDatasetFormat() - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Returns the class of the dataset that the converter generates.
getDatasetFormat() - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Returns the class of the dataset that the converter generates.
getDataTypes() - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Returns the data types to import
getDataWidth() - Method in class adams.gui.visualization.spectrum.SpectrumContainerTableColumnNameGenerator: Returns the width of the data column.
getDateFormat() - Method in class adams.data.io.input.MPSSpectrumReader: Returns the date format for parsing the MPSSpectrumReader.KEY_TIME_MEASURED field.
getDBIDs(AbstractConditions) - Method in class adams.db.generic.SampleDataT: Return a list of database IDs of data containers that match the defined conditions.
getDBIDs(AbstractConditions) - Method in class adams.db.mirrored.SampleDataT: Return a list of database IDs of data containers that match the defined conditions.
getDBIDs(AbstractConditions) - Method in class adams.db.SampleDataF: Return a list of database IDs of data containers that match the defined conditions.
getDBIDs(AbstractConditions) - Method in interface adams.db.SampleDataIntf: Return a list of database IDs of data containers that match the defined conditions.
getDefault() - Method in class adams.data.spectrumsmoothing.LOWESSBased: Returns the default LOWESS filter.
getDefault() - Method in class adams.data.spectrumsmoothing.SavitzkyGolayBased: Returns the default Savitzky-Golay filter.
getDefaultClassifier() - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Returns the default classifier.
getDefaultClassifier() - Method in class adams.data.evaluator.instance.CrossValidatedPrediction: Returns the default classifier.
getDefaultClassifier(int) - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Returns the default classifier for the specified derivative.
getDefaultColor() - Method in class adams.gui.visualization.spectrum.ReportColorSpectrumPaintlet: Returns the default color to use when no color information in the report.
getDefaultColor() - Method in class adams.gui.visualization.spectrum.SpectrumPaintletNumericField: Returns the default color to use when then report field is missing or invalid.
getDefaultColor() - Method in class adams.gui.visualization.spectrum.SpectrumPaintletStringField: Returns the default color to use when then report field is missing or invalid.
getDefaultConditions() - Method in class adams.flow.source.OrphanedSampleDataIdSupplier: Returns the conditions container to use for retrieving the spectra.
getDefaultConditions() - Method in class adams.flow.source.SpectrumIdSupplier: Returns the conditions container to use for retrieving the spectra.
getDefaultConditions() - Method in class adams.gui.selection.SelectSpectrumPanel: Returns the default conditions to use.
getDefaultDatabaseConnection() - Method in class adams.data.instances.AbstractSpectrumBasedInstanceGenerator: Returns the default database connection.
getDefaultDatabaseConnection() - Method in class adams.data.spectrumfilter.AbstractDatabaseFilter: Returns the default database connection.
getDefaultDatabaseConnection() - Method in class adams.data.spectrumfilter.Covariance: Returns the default database connection.
getDefaultDatabaseConnection() - Method in class adams.data.spectrumfilter.LRCoeff: Returns the default database connection.
getDefaultDatabaseConnection() - Method in class adams.data.spectrumfilter.SubtractSpectrum: Returns the default database connection.
getDefaultDatabaseConnection() - Method in class adams.flow.source.InstrumentSupplier: Returns the default database connection.
getDefaultDatabaseConnection() - Method in class adams.flow.source.OrphanedSampleDataIdSupplier: Returns the default database connection.
getDefaultDatabaseConnection() - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Returns the default database connection.
getDefaultDatabaseConnection() - Method in class adams.flow.transformer.BulkSpectrumDbWriter: Returns the default database connection.
getDefaultDatabaseConnection() - Method in class adams.flow.transformer.DeleteDbSampleDataValue: Returns the default database connection.
getDefaultDatabaseConnection() - Method in class adams.flow.transformer.DeleteSpectrum: Returns the default database connection.
getDefaultDatabaseConnection() - Method in class adams.flow.transformer.report.UpdateDatabaseID: Returns the default database connection.
getDefaultDatabaseConnection() - Method in class adams.flow.transformer.SampleDataDbReader: Returns the default database connection.
getDefaultDatabaseConnection() - Method in class adams.flow.transformer.SampleDataDbWriter: Returns the default database connection.
getDefaultDatabaseConnection() - Method in class adams.flow.transformer.SampleDataFileReader: Returns the default database connection.
getDefaultDatabaseConnection() - Method in class adams.flow.transformer.SampleDataValueDbWriter: Returns the default database connection.
getDefaultDatabaseConnection() - Method in class adams.flow.transformer.SpectrumDbReader: Returns the default database connection.
getDefaultDatabaseConnection() - Method in class adams.flow.transformer.SpectrumDbWriter: Returns the default database connection.
getDefaultDatabaseConnection() - Method in class adams.gui.selection.SelectSpectrumPanel: Returns the default database connection.
getDefaultDatabaseConnection() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Returns the default database connection.
getDefaultField() - Method in class adams.flow.transformer.DeleteSampleDataValueByExpression: Returns the default field for the option.
getDefaultField() - Method in class adams.flow.transformer.GetSampleDataValue: Returns the default field for the option.
getDefaultField() - Method in class adams.flow.transformer.SetSampleDataValue: Returns the default field for the option.
getDefaultFields() - Method in class adams.flow.transformer.DeleteDbSampleDataValue: Returns the default fields for the option.
getDefaultFields() - Method in class adams.flow.transformer.DeleteSampleDataValue: Returns the default fields for the option.
getDefaultFields() - Method in class adams.flow.transformer.SampleDataValueDbWriter: Returns the default fields for the option.
getDefaultFilenameGenerator() - Method in class adams.flow.standalone.rats.SaveMultiSpectrumFileOutput: Returns the default filename generator to use.
getDefaultFilenameGenerator() - Method in class adams.flow.standalone.rats.SaveSpectrumFileOutput: Returns the default filename generator to use.
getDefaultFilter() - Method in class adams.data.io.input.FilteredSpectrumReader: Returns the default instrument of the spectra.
getDefaultFilter() - Method in class adams.data.io.output.FilteredSpectrumWriter: Returns the default instrument of the spectra.
getDefaultFilter() - Method in class adams.data.postprocessor.instances.WekaFilter: Returns the default filter to use.
getDefaultFormat() - Method in class adams.data.io.input.AbstractSpectrumReader: Returns the default format of the spectra.
getDefaultFormat() - Method in class adams.data.io.input.AbstractThreeWayDataReader: Returns the default format of the spectra.
getDefaultFormat() - Method in class adams.flow.condition.bool.HasSpectrum: Returns the default format of the spectra.
getDefaultFormat() - Method in class adams.flow.transformer.report.UpdateDatabaseID: Returns the default format of the spectra.
getDefaultHeight() - Method in class adams.flow.sink.SpectrumDisplay: Returns the default height for the dialog.
getDefaultHeight() - Method in class adams.flow.sink.SpectrumImageWriter: Returns the default height for the dialog.
getDefaultHeight() - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Returns the default height for the dialog.
getDefaultHeight() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlayWithDimensions: Returns the default height for the overlay.
getDefaultHeight() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Returns the default height for the overlay.
getDefaultInstrument() - Method in class adams.data.io.input.AbstractSpectrumReader: Returns the default instrument of the spectra.
getDefaultInstrument() - Method in class adams.data.io.input.AbstractThreeWayDataReader: Returns the default instrument of the spectra.
getDefaultKeepFormat() - Method in class adams.data.io.input.AbstractSpectrumReader: Returns the default for keeping the format.
getDefaultKeepFormat() - Method in class adams.data.io.input.AbstractThreeWayDataReader: Returns the default for keeping the format.
getDefaultList() - Method in class adams.core.discovery.genetic.SegmentedSavitzkyGolayDerivativeOrder: Returns the default list.
getDefaultMaxAmplitude() - Method in class adams.data.spectrumimage.AbstractSpectrumImageGeneratorWithRange: Returns the default maximum amplitude.
getDefaultMaximum() - Method in class adams.core.discovery.genetic.SegmentedDownSampleNthPoints: Returns the default maximum.
getDefaultMaximum() - Method in class adams.core.discovery.genetic.SegmentedSavitzkyGolayDerivativeOrder: Returns the default maximum.
getDefaultMaximum() - Method in class adams.core.discovery.genetic.SegmentedSavitzkyGolayNumPoints: Returns the default maximum.
getDefaultMenuItem() - Method in class adams.gui.core.spreadsheettable.ExportSpectra: Returns the default name for the menu item.
getDefaultMenuItem() - Method in class adams.gui.visualization.instances.instancestable.ExportSpectra: Returns the default name for the menu item.
getDefaultMinAmplitude() - Method in class adams.data.spectrumimage.AbstractSpectrumImageGeneratorWithRange: Returns the default minimum amplitude.
getDefaultMinAmplitude() - Method in class adams.data.spectrumimage.AmplitudeRatio: Returns the default minimum amplitude.
getDefaultMinimum() - Method in class adams.core.discovery.genetic.SegmentedDownSampleNthPoints: Returns the default minimum.
getDefaultMinimum() - Method in class adams.core.discovery.genetic.SegmentedSavitzkyGolayDerivativeOrder: Returns the default minimum.
getDefaultMinimum() - Method in class adams.core.discovery.genetic.SegmentedSavitzkyGolayNumPoints: Returns the default minimum.
getDefaultMissingEvaluation() - Method in class adams.data.evaluator.instance.AbstractEvaluator: Returns the default value in case of missing evaluations.
getDefaultMissingEvaluation() - Method in class adams.data.evaluator.instance.AbstractNearestNeighborBasedEvaluator: Returns the default value in case of missing evaluations.
getDefaultMissingEvaluation() - Method in class adams.data.evaluator.instance.EnsembleEvaluator: Returns the default value in case of missing evaluations.
getDefaultMissingEvaluation() - Method in class adams.data.evaluator.instance.FakeEvaluator: Returns the default value in case of missing evaluations.
getDefaultMissingEvaluation() - Method in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: Returns the default value in case of missing evaluations.
getDefaultMissingEvaluation() - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Returns the default value in case of missing evaluations.
getDefaultMissingEvaluation() - Method in class adams.data.evaluator.instance.NullEvaluator: Returns the default value in case of missing evaluations.
getDefaultMissingEvaluation() - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Returns the default value in case of missing evaluations.
getDefaultNewFormat() - Method in class adams.data.multifilter.AbstractFormatsBasedMultiSpectrumFilter: Returns the default format for the generated spectrum.
getDefaultNewFormat() - Method in class adams.data.multifilter.Add: Returns the default format for the generated spectrum.
getDefaultNewFormat() - Method in class adams.data.multifilter.Atan2: Returns the default format for the generated spectrum.
getDefaultNewFormat() - Method in class adams.data.multifilter.Average: Returns the default format for the generated spectrum.
getDefaultNewFormat() - Method in class adams.data.multifilter.Divide: Returns the default format for the generated spectrum.
getDefaultNewFormat() - Method in class adams.data.multifilter.Fusion: Returns the default format for the generated spectrum.
getDefaultNewFormat() - Method in class adams.data.multifilter.Mean: Returns the default format for the generated spectrum.
getDefaultNewFormat() - Method in class adams.data.multifilter.Median: Returns the default format for the generated spectrum.
getDefaultNewFormat() - Method in class adams.data.multifilter.Multiply: Returns the default format for the generated spectrum.
getDefaultNewFormat() - Method in class adams.data.multifilter.Subtract: Returns the default format for the generated spectrum.
getDefaultOutputType() - Method in class adams.opt.genetic.RonWeasley: Returns the default output type to use.
getDefaultPopupActions() - Method in class adams.gui.visualization.spectrum.SampleDataFactory.Table: Returns the default actions for the popup menu.
getDefaultReader() - Method in class adams.data.io.input.FilteredSpectrumReader: Returns the default instrument of the spectra.
getDefaultReader() - Method in class adams.data.io.input.ThreeWayHeatmapReader: Returns the default reader to use.
getDefaultReader() - Method in class adams.flow.control.SpectrumFileChecker: Returns the default reader for loading the data.
getDefaultReader() - Method in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: Returns the default reader to use.
getDefaultReader() - Method in class adams.flow.standalone.rats.LoadSpectrumFileOutput: Returns the default reader to use.
getDefaultReader() - Method in class adams.flow.transformer.SampleDataFileReader: Returns the default reader.
getDefaultReader() - Method in class adams.flow.transformer.SpectrumFileReader: Returns the default reader to use.
getDefaultReader() - Method in class adams.flow.transformer.ThreeWayDataFileReader: Returns the default reader to use.
getDefaultReader() - Method in class adams.gui.chooser.SampleDataFileChooser: Returns the default reader.
getDefaultReader() - Method in class adams.gui.chooser.SpectrumFileChooser: Returns the default reader.
getDefaultReader() - Method in class adams.gui.chooser.ThreeWayDataFileChooser: Returns the default reader.
getDefaultRefRegExp() - Method in class weka.core.converters.CALSpectrumLoader: Returns the default regexp for the references.
getDefaultSearch() - Method in class adams.data.evaluator.instance.AbstractNearestNeighborBasedEvaluator: Returns the default search algorithm to use.
getDefaultSearch() - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Returns the default search algorithm to use.
getDefaultSearch() - Method in class adams.data.evaluator.instance.CrossValidatedPrediction: Returns the default search algorithm to use.
getDefaultSearch() - Method in class adams.data.evaluator.instance.DistanceToCenter: Returns the default search algorithm to use.
getDefaultSearch() - Method in class adams.data.evaluator.instance.DistanceToClosest: Returns the default search algorithm to use.
getDefaultSize() - Method in class adams.core.discovery.genetic.SegmentedDownSampleNthPoints
getDefaultSize() - Method in class adams.core.discovery.genetic.SegmentedSavitzkyGolayNumPoints
getDefaultTitle() - Method in class adams.flow.sink.SpectrumImageWriter: Returns the default title for the dialog.
getDefaultTitle() - Method in class adams.gui.visualization.spectrum.SpectrumDatasetExportDialog: Returns the default title for the dialog.
getDefaultTitle() - Method in class adams.gui.visualization.spectrum.SpectrumExportDialog: Returns the default title for the dialog.
getDefaultURL() - Method in class adams.flow.webservice.multispectrum.RatsMultiSpectrumServiceWS: Returns the default URL for the service.
getDefaultURL() - Method in class adams.flow.webservice.SpectralGetServiceWS: Returns the default URL for the service.
getDefaultURL() - Method in class adams.flow.webservice.SpectralPutServiceWS: Returns the default URL for the service.
getDefaultURL() - Method in class adams.flow.webservice.SpectralTransformServiceWS: Returns the default URL for the service.
getDefaultURL() - Method in class adams.flow.webservice.spectrum.RatsSpectrumServiceWS: Returns the default URL for the service.
getDefaultUseAbsoluteSource() - Method in class adams.data.io.input.AbstractSpectrumReader: Returns the default for using absolute source filename.
getDefaultUseAbsoluteSource() - Method in class adams.data.io.input.AbstractThreeWayDataReader: Returns the default for using absolute source filename.
getDefaultWebService() - Method in class adams.flow.standalone.rats.WSMultiSpectrumReception: Returns the default webservice provider to use.
getDefaultWebService() - Method in class adams.flow.standalone.rats.WSSpectrumReception: Returns the default webservice provider to use.
getDefaultWidth() - Method in class adams.flow.sink.SpectrumDisplay: Returns the default width for the dialog.
getDefaultWidth() - Method in class adams.flow.sink.SpectrumImageWriter: Returns the default width for the dialog.
getDefaultWidth() - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Returns the default width for the dialog.
getDefaultWidth() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlayWithDimensions: Returns the default width for the overlay.
getDefaultWidth() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Returns the default width for the overlay.
getDefaultWriter() - Method in class adams.data.io.output.FilteredSpectrumWriter: Returns the default instrument of the spectra.
getDefaultWriter() - Method in class adams.flow.standalone.rats.SaveMultiSpectrumFileOutput: Returns the default writer to use.
getDefaultWriter() - Method in class adams.flow.standalone.rats.SaveSpectrumFileOutput: Returns the default writer to use.
getDefaultWriter() - Method in class adams.flow.transformer.SampleDataFileWriter: Returns the default writer.
getDefaultWriter() - Method in class adams.flow.transformer.SpectrumFileWriter: Returns the default writer to use.
getDefaultWriter() - Method in class adams.flow.transformer.ThreeWayDataFileWriter: Returns the default writer to use.
getDefaultWriter() - Method in class adams.gui.chooser.SampleDataFileChooser: Returns the default writer.
getDefaultWriter() - Method in class adams.gui.chooser.SpectrumFileChooser: Returns the default writer.
getDefaultWriter() - Method in class adams.gui.chooser.ThreeWayDataFileChooser: Returns the default writer.
getDefaultX() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlay: Returns the default X position for the overlay.
getDefaultY() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlay: Returns the default Y position for the overlay.
getDefinition() - Method in class adams.data.io.input.opus.OpusBlockHelper.Block: Returns the definition that the block is based on.
getDefinitionKey() - Method in class adams.gui.scripting.SpectralScriptingEngine: Returns the properties key to use for retrieving the properties.
getDeltaOffset() - Method in class adams.data.io.input.foss.FossStdise: Get start of intercept data.
getDenormalize() - Method in class adams.data.io.input.SimpleEEMReader: Returns whether to denormalize the amplitudes using the 'Normalized by ' value.
getDerivativeOrder() - Method in class weka.filters.unsupervised.attribute.SavitzkyGolayRange: Returns the order of the derivative.
getDerivativeOrder() - Method in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: Returns the order of the derivative.
getDescending() - Method in class adams.data.io.output.ASCSpectrumWriter: Returns whether to output spectrum points by descending x-axis.
getDescending() - Method in class adams.data.io.output.DPTSpectrumWriter: Returns whether to output spectrum points by descending x-axis.
getDescription() - Method in class adams.gui.scripting.SelectWaveNumber: Returns the full description of the action.
getDescription() - Method in class adams.gui.scripting.WriteSpectrum: Returns the full description of the action.
getDetails() - Method in interface adams.data.cleaner.CleanerDetails: Returns details for the cleaner.
getDetails() - Method in class adams.data.cleaner.instance.IQRCleaner: Returns details on the IQR filter.
getDetails() - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Returns details for the cleaner.
getDetails() - Method in interface adams.data.postprocessor.PostProcessorDetails: Returns details for the cleaner.
getDetector() - Method in class adams.data.cleaner.instance.RemoveOutliers: Returns the detector.
getDetector() - Method in class adams.flow.transformer.MultiSpectrumOutlierDetector: Returns the outlier detector in use.
getDialog(Dialog, Dialog.ModalityType) - Static method in class adams.gui.visualization.spectrum.HistogramFactory: Returns a new dialog for displaying histograms.
getDialog(Dialog, Dialog.ModalityType) - Static method in class adams.gui.visualization.spectrum.SampleDataFactory: Returns a new dialog for displaying quantitation reports.
getDialog(Frame, boolean) - Static method in class adams.gui.visualization.spectrum.HistogramFactory: Returns a new dialog for displaying displaying histograms.
getDialog(Frame, boolean) - Static method in class adams.gui.visualization.spectrum.SampleDataFactory: Returns a new dialog for displaying quantitation reports.
getDisplay(ReportContainer) - Method in class adams.gui.visualization.spectrum.SampleDataContainerDisplayIDGenerator: Returns the display ID for the spectrum.
getDisplay(SpectrumContainer) - Method in class adams.gui.visualization.spectrum.SpectrumContainerDisplayIDGenerator: Returns the display ID for the spectrum.
getDisplayID() - Method in class adams.gui.visualization.spectrum.SpectrumContainer: Returns an ID to be used in the GUI (the DB ID with added single quotes to make it unique among the spectrums in the container manager).
getDisplayID() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataContainer: Returns the displayed container's ID.
getDontUpdateID() - Method in class adams.data.multifilter.AbstractMultiSpectrumFilter: Returns whether ID update is suppressed.
getDouble(byte[], int) - Method in class adams.data.io.input.opus.OpusBlockHelper.Block: Returns the double with the given ID.
getDouble(byte[], int) - Static method in class adams.data.io.input.opus.OpusBlockHelper: Returns the double with the given ID.
getDouble(int) - Method in class adams.data.io.input.opus.OpusBlockHelper.Block: Returns the double at the specified offset.
getEnd() - Method in class adams.data.io.input.opus.OpusBlockHelper.Block: Returns the end of the block.
getEnd() - Method in class weka.filters.unsupervised.attribute.SavitzkyGolayRange: Returns the last amplitude
getEndDate() - Method in class adams.db.AbstractSpectrumConditions: Returns the end date.
getEndDate() - Method in class adams.db.OrphanedSampleDataConditions: Returns the end date.
getEndPoints() - Method in class adams.data.io.output.NIRSpectrumWriter: Get end points.
getEOC() - Method in class adams.data.io.output.NIRSpectrumWriter: Get number of EOC's per rev (whatever that is!!)
getEvalMax() - Method in class adams.data.evaluator.instance.FakeEvaluator: Returns the maximum value to output.
getEvalMin() - Method in class adams.data.evaluator.instance.FakeEvaluator: Returns the minimum value to output.
getEvaluation() - Method in class adams.flow.transformer.predictioncheck.Range: Returns the evaluation to check.
getEvaluator() - Method in class adams.flow.transformer.Evaluator: Returns the evaluator in use.
getEvaluatorResetVariable() - Method in class adams.flow.transformer.Evaluator: Returns the variable to monitor for changes in order to reset the evaluator.
getEvaluators() - Static method in class adams.data.evaluator.instance.AbstractEvaluator: Returns a list with classnames of filters.
getEvaluators() - Static method in class adams.data.postprocessor.instances.AbstractPostProcessor: Returns a list with classnames of processors.
getEvalWait() - Method in class adams.data.evaluator.instance.FakeEvaluator: Returns the time in msec to wait when calling classifyInstance.
getExclude() - Method in class weka.filters.unsupervised.attribute.SegmentedDownSample: Returns the regular expression that identifies attributes to be excluded from the splits.
getExclude() - Method in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: Returns the regular expression that identifies attributes to be excluded from the splits.
getExcludeDummies() - Method in class adams.db.AbstractSpectrumConditions: Returns whether spectra with reports flagged as dummies are excluded or not.
getExpression() - Method in class adams.data.spectrumfilter.AmplitudeExpression: Returns the mathematical expression to evaluate.
getExpression() - Method in class adams.data.spectrumfilter.WaveNumberExpression: Returns the mathematical expression to evaluate.
getExtensions() - Method in class adams.gui.tools.previewbrowser.ASCIIXYSpectrumHandler: Returns the list of extensions (without dot) that this handler can take care of.
getExtensions() - Method in class adams.gui.tools.previewbrowser.ASCSpectrumHandler: Returns the list of extensions (without dot) that this handler can take care of.
getExtensions() - Method in class adams.gui.tools.previewbrowser.CALSpectrumHandler: Returns the list of extensions (without dot) that this handler can take care of.
getExtensions() - Method in class adams.gui.tools.previewbrowser.CMLSpectrumHandler: Returns the list of extensions (without dot) that this handler can take care of.
getExtensions() - Method in class adams.gui.tools.previewbrowser.DPTSpectrumHandler: Returns the list of extensions (without dot) that this handler can take care of.
getExtensions() - Method in class adams.gui.tools.previewbrowser.JCampDX2SpectrumHandler: Returns the list of extensions (without dot) that this handler can take care of.
getExtensions() - Method in class adams.gui.tools.previewbrowser.JCampDXSpectrumHandler: Returns the list of extensions (without dot) that this handler can take care of.
getExtensions() - Method in class adams.gui.tools.previewbrowser.JsonSpectrumHandler: Returns the list of extensions (without dot) that this handler can take care of.
getExtensions() - Method in class adams.gui.tools.previewbrowser.MPSSpectrumHandler: Returns the list of extensions (without dot) that this handler can take care of.
getExtensions() - Method in class adams.gui.tools.previewbrowser.NIRSpectrumHandler: Returns the list of extensions (without dot) that this handler can take care of.
getExtensions() - Method in class adams.gui.tools.previewbrowser.OpusSpectrumExtHandler: Returns the list of extensions (without dot) that this handler can take care of.
getExtensions() - Method in class adams.gui.tools.previewbrowser.OpusSpectrumHandler: Returns the list of extensions (without dot) that this handler can take care of.
getExtensions() - Method in class adams.gui.tools.previewbrowser.RelabSpectrumHandler: Returns the list of extensions (without dot) that this handler can take care of.
getExtensions() - Method in class adams.gui.tools.previewbrowser.SimpleCSVSampleDataHandler: Returns the list of extensions (without dot) that this handler can take care of.
getExtensions() - Method in class adams.gui.tools.previewbrowser.SimpleSampleDataHandler: Returns the list of extensions (without dot) that this handler can take care of.
getExtensions() - Method in class adams.gui.tools.previewbrowser.SimpleSpectrumHandler: Returns the list of extensions (without dot) that this handler can take care of.
getExtensions() - Method in class adams.gui.tools.previewbrowser.SPASpectrumHandler: Returns the list of extensions (without dot) that this handler can take care of.
getExtensions() - Method in class adams.gui.tools.previewbrowser.SPCSpectrumHandler: Returns the list of extensions (without dot) that this handler can take care of.
getExtensions() - Method in class adams.gui.tools.previewbrowser.SpecLibSpectrumHandler: Returns the list of extensions (without dot) that this handler can take care of.
getExtensions() - Method in class adams.gui.tools.previewbrowser.ThreeWayEEMHandler: Returns the list of extensions (without dot) that this handler can take care of.
getExtensions() - Method in class adams.gui.tools.previewbrowser.ThreeWayXYZHandler: Returns the list of extensions (without dot) that this handler can take care of.
getExtract() - Method in class adams.data.spectrumfilter.ReportFieldFromStringValueWithLookup: Returns the regexp for extracting the substring to use in the lookup.
getFactor() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Returns the factor to multiply the inter-percentile range with.
getFailure() - Method in class adams.data.spectrumfilter.ConditionalReportField: Returns the failure value, ie the value to use when the condition evaluates to true.
getFFTSampleSize() - Method in class adams.data.conversion.SpectrumToBufferedImage: Returns the FFT samepl size (power of 2).
getFFTSampleSize() - Method in class adams.data.spectrumimage.Spectrogram: Returns the FFT sample size (power of 2).
getField() - Method in class adams.data.cleaner.spectrum.MinMax: Returns the field in use.
getField() - Method in class adams.data.instances.AbstractFieldInstanceGeneratorWithClass: Returns the field that acts as class attribute.
getField() - Method in class adams.data.instances.AbstractSpectrumInstanceGeneratorWithClass: Returns the field that acts as class attribute.
getField() - Method in interface adams.data.instances.InstanceGeneratorWithTargetField: Returns the field that acts as class attribute.
getField() - Method in class adams.data.multifilter.PickByReportValue: Returns the field to inspect.
getField() - Method in class adams.data.spectrum.SpectrumComparatorByReportValue: Returns the field to inspect.
getField() - Method in class adams.data.spectrumfilter.Covariance: get Field.
getField() - Method in class adams.data.spectrumoutlier.MinMax: Returns the field.
getField() - Method in class adams.data.spectrumoutlier.StringMatcher: Returns the current reference (i.e., class).
getField() - Method in class adams.db.SpectrumConditionsSingle: Returns the required field.
getField() - Method in class adams.flow.transformer.DeleteSampleDataValueByExpression: Returns the fields to delete from the report.
getField() - Method in class adams.flow.transformer.GetSampleDataValue: Returns the field to retrieve from the report.
getField() - Method in class adams.flow.transformer.SetSampleDataValue: Returns the field to retrieve from the report.
getField() - Method in class adams.gui.tools.UpdateSampleDataPanel: Returns the current values as field.
getField() - Method in class adams.gui.visualization.spectrum.SpectrumPaintletNumericField: Returns the numeric field to determine the color with.
getField() - Method in class adams.gui.visualization.spectrum.SpectrumPaintletStringField: Returns the string field to determine the color with.
getFieldRanges() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.DataCollector: Returns the ranges for the fields.
getFields() - Method in class adams.data.instances.AbstractFieldInstanceGenerator: Returns the targets to add.
getFields() - Method in class adams.data.multireportfilter.PullUpFields: Returns the fields to pull up.
getFields() - Method in class adams.data.sampledata.SampleDataReportFilter: Returns the fields to keep.
getFields() - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Returns the targets to add.
getFields() - Method in class adams.data.spreadsheetrowgenerator.SampleDataOnlyRowGenerator: Returns the fields to add.
getFields() - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Returns the targets to add.
getFields() - Method in class adams.db.mirrored.SampleDataT: Returns all available fields.
getFields() - Method in class adams.db.SampleDataF: Returns all available fields.
getFields() - Method in class adams.db.SpectrumConditionsMulti: Returns the required fields.
getFields() - Method in class adams.flow.transformer.DeleteDbSampleDataValue: Returns the fields to delete from the report.
getFields() - Method in class adams.flow.transformer.DeleteSampleDataValue: Returns the fields to delete from the report.
getFields() - Method in class adams.flow.transformer.SampleDataValueDbWriter: Returns the fields to store in the database.
getFields(int) - Method in class adams.data.io.input.foss.FossHelper: Get the non-spectral data for a given row.
getFields(DataType) - Method in class adams.db.generic.SampleDataT: Returns all available fields.
getFields(DataType) - Method in class adams.db.mirrored.SampleDataT: Returns all available fields.
getFields(DataType) - Method in class adams.db.SampleDataF: Returns all available fields.
getFields(DataType) - Method in interface adams.db.SampleDataIntf: Returns all available fields.
getFile() - Method in class adams.env.SpectralDbBackendDefinition: Returns the properties file name (no path) this definition is for.
getFile() - Method in class adams.env.SpectralScriptingEngineDefinition: Returns the properties file name (no path) this definition is for.
getFileAsBytes(File) - Static method in class adams.data.io.input.foss.FossStdise: Get array of bytes from file.
getFileDescription() - Method in class weka.core.converters.CALSpectrumLoader: Get a one line description of the type of file
getFileExtension() - Method in class weka.core.converters.CALSpectrumLoader: Get the file extension used for this type of file
getFileExtensions() - Method in class weka.core.converters.CALSpectrumLoader: Gets all the file extensions used for this type of file
getFileHeader() - Method in class adams.data.spectrum.Spectrum: Returns the file header.
getFileID() - Method in class adams.data.io.output.NIRSpectrumWriter: Get file id.
getFilenameGenerator() - Method in class adams.flow.standalone.rats.SaveMultiSpectrumFileOutput: Returns the filename generator in use.
getFilenameGenerator() - Method in class adams.flow.standalone.rats.SaveSpectrumFileOutput: Returns the filename generator in use.
getFilter() - Method in class adams.data.cleaner.instance.IQRCleaner: Returns the IQR filter.
getFilter() - Method in class adams.data.evaluator.instance.DistanceToCenter: Returns the filter to use.
getFilter() - Method in class adams.data.evaluator.instance.DistanceToClosest: Returns the filter to use.
getFilter() - Method in class adams.data.io.input.FilteredSpectrumReader: Returns the filter to apply to the data that was read.
getFilter() - Method in class adams.data.io.output.FilteredSpectrumWriter: Returns the filter to apply to the data that was read.
getFilter() - Method in class adams.data.postprocessor.instances.WekaFilter: Returns the filter in use.
getFilter() - Method in class adams.data.spectrumbaseline.LOWESSBased: Returns a new instance of a LOWESS filter.
getFilter() - Method in class adams.data.spectrumbaseline.SavitzkyGolayBased: Returns a new instance of a SavitzkyGolay filter.
getFilter() - Method in class adams.data.spectrumfilter.Covariance: Get filter.
getFilter() - Method in class adams.data.spectrumfilter.SubtractSpectrum: Returns the filter being used.
getFilter() - Method in class adams.flow.rest.TransformSpectrum: Returns the filter in use.
getFilter() - Method in class adams.flow.transformer.MultiSpectrumFilter: Returns the filter in use.
getFilter() - Method in class adams.flow.transformer.MultiSpectrumOutlierDetector: Returns the filter in use.
getFilter() - Method in class adams.flow.transformer.MultiSpectrumReportFilter: Returns the filter in use.
getFilter() - Method in class weka.filters.unsupervised.attribute.SpectrumFilter: Returns the base filter.
getFilters() - Static method in class adams.data.multifilter.AbstractMultiSpectrumFilter: Returns a list with classnames of filters.
getFilters() - Static method in class adams.data.multireportfilter.AbstractMultiSpectrumReportFilter: Returns a list with classnames of filters.
getFirst() - Method in class adams.data.spectrumfilter.AbstractStandardiseFilter: Returns the start data point
getFirstWave() - Method in class adams.flow.transformer.InstanceToSpectrum: Returns the starting point for the wave numbers.
getFirstX() - Method in class adams.data.io.input.SPCSpectrumReader.FileParser: Returns the X of the first value.
getFirstXPoint() - Method in class adams.data.io.output.ASCSpectrumWriter: Get first X wavenumber.
getFlip() - Method in class adams.data.spectrumoutlier.Swapped: Returns whether to swap left and right half for the comparison.
getFlowContext() - Method in class adams.data.cleaner.instance.AbstractCleaner: Returns the flow context.
getFlowContext() - Method in class adams.data.cleaner.spectrum.AbstractCleaner: Returns the flow context.
getFlowContext() - Method in class adams.data.postprocessor.instances.AbstractPostProcessor: Returns the flow context.
getFlowContext() - Method in class adams.data.spectrumfilter.WekaFilterToReport: Returns the flow context.
getFolds() - Method in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: Returns the folds.
getFolds() - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Returns the number of folds.
getFolds() - Method in class adams.data.evaluator.instance.CrossValidatedPrediction: Returns the number of folds.
getFolds() - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Returns the number of folds in use.
getFont() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Returns the font for the text.
getFormat() - Method in class adams.data.conversion.ArrayToSpectrum: Returns the format.
getFormat() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Returns the format to use for the spectrum.
getFormat() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns the format to use for the spectrum.
getFormat() - Method in class adams.data.conversion.SpreadSheetToSpectrum: Returns the format to use for the spectrum.
getFormat() - Method in class adams.data.io.input.AbstractSampleDataReader: The format of spectrum to use.
getFormat() - Method in class adams.data.io.input.AbstractSpectrumReader: Returns the format string of the data.
getFormat() - Method in class adams.data.io.input.AbstractThreeWayDataReader: Returns the format string of the data.
getFormat() - Method in class adams.data.multispectrumoperation.Remove: Returns the regular expression that the format of a spectrum must match in order to get removed.
getFormat() - Method in class adams.data.spectrum.Spectrum: Returns the data format.
getFormat() - Method in class adams.db.AbstractSpectrumConditions: Returns the regular expression for the format.
getFormat() - Method in class adams.db.SpectrumIDConditions: Returns the regular expression for the format.
getFormat() - Method in class adams.flow.condition.bool.HasSpectrum: Returns the format string of the data.
getFormat() - Method in class adams.flow.transformer.datacontainer.LoadSampleData: Returns the format of the spectrum to obtain the reference data from.
getFormat() - Method in class adams.flow.transformer.DeleteSpectrum: Returns the format of spectrum to retrieve from the database.
getFormat() - Method in class adams.flow.transformer.MultiSpectrumRemove: Returns the regular expression that the format of a spectrum must match in order to get removed.
getFormat() - Method in class adams.flow.transformer.report.UpdateDatabaseID: Returns the format string of the data.
getFormat() - Method in class adams.flow.transformer.SpectrumDbReader: Returns the format of spectrum to retrieve from the database.
getFormat() - Method in class adams.flow.webservice.Get: Returns the format of the spectrum to retrieve.
getFormat() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.Spectrum: Gets the value of the format property.
getFormat() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.Spectrum: Gets the value of the format property.
getFormat() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.UploadRequest: Gets the value of the format property.
getFormat() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.UploadResponse: Gets the value of the format property.
getFormat() - Method in class nz.ac.waikato.adams.webservice.spectral.get.GetRequest: Gets the value of the format property.
getFormat() - Method in class nz.ac.waikato.adams.webservice.spectral.get.GetResponse: Gets the value of the format property.
getFormat() - Method in class nz.ac.waikato.adams.webservice.spectral.get.Spectrum: Gets the value of the format property.
getFormat() - Method in class nz.ac.waikato.adams.webservice.spectral.put.PutRequest: Gets the value of the format property.
getFormat() - Method in class nz.ac.waikato.adams.webservice.spectral.put.PutResponse: Gets the value of the format property.
getFormat() - Method in class nz.ac.waikato.adams.webservice.spectral.put.Spectrum: Gets the value of the format property.
getFormat() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.Spectrum: Gets the value of the format property.
getFormat() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.TransformRequest: Gets the value of the format property.
getFormat() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.TransformResponse: Gets the value of the format property.
getFormatDescription() - Method in class adams.data.io.input.AniMLSpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.ASCIIXYSpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.ASCSpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.CALSpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.CMLSpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.DPTSpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.ExtractIdAndTypeSpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.ExtractIdAndTypeThreeWayDataReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.FilteredSpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.FitsLibsReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.JCampDX2SpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.JCampDXSpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.JsonSpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.MPSSpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.NIRSpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.OpusSpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.OpusSpectrumReaderExt: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.RelabSpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.ScioLabExportSpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.SimpleEEMReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.SimpleSpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.SimpleXYZReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.SoilCaresScannerSpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.SPASpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.SPCSpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.SpecLibSampleDataReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.SpecLibSpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.ThreeWayHeatmapReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.TrinamixSpectrumJsonReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.TrinamixSpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.UnscramblerSpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.input.ZippedSpectrumReader: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.output.ASCIIXYSpectrumWriter: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.output.ASCSpectrumWriter: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.output.CALSpectrumWriter: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.output.DPTSpectrumWriter: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.output.FilteredSpectrumWriter: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.output.JCampDX2SpectrumWriter: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.output.JsonSpectrumWriter: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.output.NIRSpectrumWriter: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.output.SimpleEEMWriter: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.output.SimpleSpectrumWriter: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.output.SimpleXYZWriter: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.output.SpectrumImageWriter: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.output.SpreadSheetSpectrumWriter: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.data.io.output.TrinamixSpectrumWriter: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.gui.visualization.debug.objectexport.SpectrumExporter: Returns a string describing the format (used in the file chooser).
getFormatDescription() - Method in class adams.gui.visualization.debug.objectexport.ThreeWayDataExporter: Returns a string describing the format (used in the file chooser).
getFormatExtensions() - Method in class adams.data.io.input.AniMLSpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.ASCIIXYSpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.ASCSpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.CALSpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.CMLSpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.DPTSpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.ExtractIdAndTypeSpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.ExtractIdAndTypeThreeWayDataReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.FilteredSpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.FitsLibsReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.JCampDX2SpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.JCampDXSpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.JsonSpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.MPSSpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.NIRSpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.OpusSpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.OpusSpectrumReaderExt: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.RelabSpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.ScioLabExportSpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.SimpleEEMReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.SimpleSpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.SimpleXYZReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.SoilCaresScannerSpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.SPASpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.SPCSpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.SpecLibSampleDataReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.SpecLibSpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.ThreeWayHeatmapReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.TrinamixSpectrumJsonReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.TrinamixSpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.UnscramblerSpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.input.ZippedSpectrumReader: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.output.ASCIIXYSpectrumWriter: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.output.ASCSpectrumWriter: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.output.CALSpectrumWriter: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.output.DPTSpectrumWriter: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.output.FilteredSpectrumWriter: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.output.JCampDX2SpectrumWriter: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.output.JsonSpectrumWriter: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.output.NIRSpectrumWriter: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.output.SimpleEEMWriter: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.output.SimpleSpectrumWriter: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.output.SimpleXYZWriter: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.output.SpectrumImageWriter: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.output.SpreadSheetSpectrumWriter: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.data.io.output.TrinamixSpectrumWriter: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.gui.visualization.debug.objectexport.SpectrumExporter: Returns the extension(s) of the format.
getFormatExtensions() - Method in class adams.gui.visualization.debug.objectexport.ThreeWayDataExporter: Returns the extension(s) of the format.
getFormats() - Method in class adams.data.multifilter.AbstractFormatsBasedMultiSpectrumFilter: Returns the formats of the specta to use.
getGeneralHeader(List<Spectrum>) - Method in class adams.data.io.output.CALSpectrumWriter: Create GeneralHeader from list of Spectra.
getGeneralHeader(List<Spectrum>) - Method in class adams.data.io.output.NIRSpectrumWriter: Create GeneralHeader from list of Spectra.
getGenerateSampleIDs() - Method in interface adams.flow.source.SampleIdSource: Returns whether to read from the active or store table.
getGenerateSampleIDs() - Method in class adams.flow.source.SpectrumIdSupplier: Returns whether to read from the active or store table.
getGenerator() - Method in class adams.data.conversion.SpectrumToBufferedImage: Returns the color generator.
getGenerator() - Method in class adams.data.io.output.SpectrumImageWriter: Returns the generator to use.
getGenerator() - Method in class adams.data.spectrumanalysis.AbstractWekaSpectrumAnalysis: Returns the instance generator.
getGenerator() - Method in class adams.data.spectrumfilter.LRCoeff: Returns the generator in use.
getGenerator() - Method in class adams.data.spectrumfilter.PCA: Returns the instance generator in use.
getGenerator() - Method in class adams.data.spectrumfilter.PLS: Returns the instance generator in use.
getGenerator() - Method in class adams.data.spectrumfilter.WekaFilterToReport: Returns the generator in use.
getGenerator() - Method in class adams.data.spectrumimage.Spectrogram: Returns the color generator.
getGenerator() - Method in class adams.data.threewayfeatures.Histogram: Returns the histogram generator.
getGenerator() - Method in class adams.flow.transformer.InstanceGenerator: Returns the generator in use.
getGenerator() - Method in class adams.flow.transformer.SpreadSheetRowGenerator: Returns the generator in use.
getGenerator() - Method in class adams.gui.visualization.spectrum.SpectrumDatasetExportDialog: Returns the generator to use.
getGenerator() - Method in class adams.gui.visualization.spectrum.SpectrumPaintletNumericField: Returns the color gradient generator to use.
getGetProductCodeFromAttribute() - Method in class adams.flow.transformer.InstanceToSpectrum: Get product code from instance attribute?
getGOEDialog() - Method in class adams.gui.visualization.spectrum.MultiSpectrumPanel: Returns the GOE dialog.
getGradientColors() - Method in class adams.data.conversion.SpectrumToBufferedImage: Generates the gradient colors.
getGrammar() - Method in class adams.data.spectrumfilter.AmplitudeExpression: Returns a string representation of the grammar.
getGrammar() - Method in class adams.data.spectrumfilter.WaveNumberExpression: Returns a string representation of the grammar.
getGroup() - Method in class adams.data.io.input.sampleidextraction.RegExp: Returns the regular expression group that contains the sample ID from the file name (w/o path).
getGroup() - Method in class adams.data.spectrumfilter.ReportFieldFromStringValue: Returns group expression for generating the value to be stored.
getGroup() - Method in class adams.gui.visualization.spectrum.containerlistpopup.Information: The group this customizer belongs to.
getGroup() - Method in class adams.gui.visualization.spectrum.containerlistpopup.SampleData: The group this customizer belongs to.
getGroup() - Method in class adams.gui.visualization.spectrum.containerlistpopup.SpectralData: The group this customizer belongs to.
getGroup() - Method in class adams.gui.visualization.spectrum.plotpopup.Adjust: The group this customizer belongs to.
getGroup() - Method in class adams.gui.visualization.spectrum.plotpopup.CrossHair: The group this customizer belongs to.
getGroup() - Method in class adams.gui.visualization.spectrum.plotpopup.ExportVisible: The group this customizer belongs to.
getGroup() - Method in class adams.gui.visualization.spectrum.plotpopup.GotoWaveNumber: The group this customizer belongs to.
getGroup() - Method in class adams.gui.visualization.spectrum.plotpopup.Histogram: The group this customizer belongs to.
getGroup() - Method in class adams.gui.visualization.spectrum.plotpopup.Hits: The group this customizer belongs to.
getGroup() - Method in class adams.gui.visualization.spectrum.plotpopup.SaveVisible: The group this customizer belongs to.
getGroup() - Method in class adams.gui.visualization.spectrum.plotpopup.Statistics: The group this customizer belongs to.
getGroup() - Method in class adams.gui.visualization.spectrum.plotpopup.Viewport: The group this customizer belongs to.
getGroup() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.multipageaction.AbstractMultiPageMenuItem: The name of the group this item belongs to.
getGroup() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.multipageaction.OpenContainingFolder: The name of the group this item belongs to.
getGroup() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.multipageaction.Statistics: The name of the group this item belongs to.
getGroup() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.multipageaction.ViewAsSpreadSheet: The name of the group this item belongs to.
getGroupExtraction() - Method in class adams.data.io.input.ExtractIdAndTypeSpectrumReader: Returns the scheme for extracting the sample type.
getGroupExtraction() - Method in class adams.data.io.input.ExtractIdAndTypeThreeWayDataReader: Returns the scheme for extracting the sample type.
getHeader() - Method in class adams.data.spectrum.Spectrum: Returns a spectrum with just the header information, but no spectrum points.
getHeader(List<SpectrumPoint>) - Static method in class adams.data.spectrum.SpectrumUtils: Creates a header based on the given spectrum points.
getHeader(List<L1Point>) - Static method in class adams.data.threeway.ThreeWayDataUtils: Creates a header based on the given LevelOnePoint points.
getHeaderContainsWaveNumber() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Returns whether to extract the wave number from the header columns.
getHeight() - Method in class adams.data.spectrumimage.Intensity: Returns the height of the image.
getHeight() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlay: Returns the height.
getHeight() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlayWithDimensions: Returns the currently set height of the overlay.
getHistogram(L1Point, int) - Static method in class adams.data.threeway.L1PointUtils: Generates data for a histogram display.
getHitDetector() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Returns the hit detector.
getICA() - Method in class adams.data.spectrumanalysis.FastICA: Returns the ICA analysis.
getIcon() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.multipageaction.AbstractMultiPageMenuItem: Returns the icon to use.
getIconName() - Method in class adams.gui.menu.DeleteSampleData: Returns the file name of the icon.
getIconName() - Method in class adams.gui.menu.DeleteSpectra: Returns the file name of the icon.
getIconName() - Method in class adams.gui.menu.ExportValidationSets: Returns the file name of the icon.
getIconName() - Method in class adams.gui.menu.ListSampleData: Returns the file name of the icon.
getIconName() - Method in class adams.gui.menu.SpectrumExplorer: Returns the file name of the icon.
getIconName() - Method in class adams.gui.menu.ThreeWayDataHeatmapViewer: Returns the file name of the icon.
getIconName() - Method in class adams.gui.menu.UpdateSampleData: Returns the file name of the icon.
getIconName() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.multipageaction.AbstractMultiPageMenuItem: The name of the icon to use.
getIconName() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.multipageaction.OpenContainingFolder: The name of the icon to use.
getIconName() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.multipageaction.Statistics: The name of the icon to use.
getIconName() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.multipageaction.ViewAsSpreadSheet: The name of the icon to use.
getId() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.MultiSpectrum: Gets the value of the id property.
getId() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.Spectrum: Gets the value of the id property.
getId() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.UploadRequest: Gets the value of the id property.
getId() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.UploadResponse: Gets the value of the id property.
getId() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.Spectrum: Gets the value of the id property.
getId() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.UploadRequest: Gets the value of the id property.
getId() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.UploadResponse: Gets the value of the id property.
getId() - Method in class nz.ac.waikato.adams.webservice.spectral.get.GetRequest: Gets the value of the id property.
getId() - Method in class nz.ac.waikato.adams.webservice.spectral.get.GetResponse: Gets the value of the id property.
getId() - Method in class nz.ac.waikato.adams.webservice.spectral.get.Spectrum: Gets the value of the id property.
getId() - Method in class nz.ac.waikato.adams.webservice.spectral.put.PutRequest: Gets the value of the id property.
getId() - Method in class nz.ac.waikato.adams.webservice.spectral.put.PutResponse: Gets the value of the id property.
getId() - Method in class nz.ac.waikato.adams.webservice.spectral.put.Spectrum: Gets the value of the id property.
getId() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.Spectrum: Gets the value of the id property.
getId() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.TransformRequest: Gets the value of the id property.
getId() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.TransformResponse: Gets the value of the id property.
getID() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.InterPercentileRange: Returns the ID.
getID() - Method in class adams.data.conversion.ArrayToSpectrum: Returns the sample ID.
getID() - Method in class adams.data.conversion.SpreadSheetToSpectrum: Returns the ID to use for the spectrum.
getID() - Method in class adams.data.conversion.WekaPredictionContainerToEvaluationContainer: Returns the ID to use for the evaluation (to be used instead of component).
getID() - Method in class adams.data.io.input.ASCSpectrumReader.ParsedFile: Returns the ID.
getID() - Method in class adams.data.sampledata.SampleData: Returns the ID.
getID() - Method in class adams.data.threewayreport.ThreeWayReport: Returns the ID.
getID() - Method in class adams.flow.condition.bool.HasSpectrum: Returns the ID to look, if not obtained from the passing through ID handler.
getID() - Method in class adams.flow.source.NewSpectrum: Returns the ID to use for the spectrum.
getID() - Method in class adams.flow.webservice.Get: Returns the ID of the spectrum to retrieve.
getID() - Method in class adams.gui.visualization.spectrum.SpectrumContainer: Returns the ID used for display.
getID() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataContainer: Returns the container's ID.
getID(FossHelper.FossFields) - Method in class adams.data.io.input.CALSpectrumReader: Get SampleID.
getIDExtraction() - Method in class adams.data.io.input.ExtractIdAndTypeSpectrumReader: Returns the sample ID extractor to use.
getIDExtraction() - Method in class adams.data.io.input.ExtractIdAndTypeThreeWayDataReader: Returns the sample ID extractor to use.
getIdfield() - Method in class adams.data.io.input.CALSpectrumReader: Get id field.
getIDs() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.DataCollector: Returns the IDs used for data collection.
getIDs() - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: Returns a hashset with all the IDs of the currently stored containers.
getIDs(AbstractConditions) - Method in class adams.db.generic.SampleDataT: Return a list (Vector) of IDs of spectra that match the defined conditions.
getIDs(AbstractConditions) - Method in class adams.db.mirrored.SampleDataT: Return a list (Vector) of IDs of spectra that match the defined conditions.
getIDs(AbstractConditions) - Method in class adams.db.SampleDataF: Return a list of IDs of spectra that match the defined conditions.
getIDs(AbstractConditions) - Method in interface adams.db.SampleDataIntf: Return a list (Vector) of IDs of spectra that match the defined conditions.
getIDs(String[], AbstractConditions) - Method in class adams.db.generic.SampleDataT: Return a list (Vector) of IDs of spectra that match the defined conditions.
getIDs(String[], AbstractConditions) - Method in class adams.db.mirrored.SampleDataT: Return a list (Vector) of IDs of spectra that match the defined conditions.
getIDs(String[], AbstractConditions) - Method in class adams.db.SampleDataF: Return a list of IDs of spectra that match the defined conditions.
getIDs(String[], AbstractConditions) - Method in interface adams.db.SampleDataIntf: Return a list (Vector) of IDs of spectra that match the defined conditions.
getIDs(String[], AbstractConditions, boolean) - Method in class adams.db.generic.SampleDataT: Return a list (Vector) of IDs of spectra that match the defined conditions.
getIDs(StringBuilder) - Method in class adams.flow.source.SpectrumIdSupplier: Returns the IDs from the database.
getIgnoreWaveNumbers() - Method in class adams.data.io.input.SimpleEEMReader: Returns whether to ignore the wave numbers and use row/col indices instead.
getImagePanel() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Returns the underlying image panel
getImageType() - Method in class adams.data.spectrumimage.AbstractSpectrumImageGenerator: Returns the type of image to generate.
getImplementation() - Method in class adams.flow.webservice.multispectrum.RatsMultiSpectrumServiceWS: Returns the webservice implementation to use.
getImplementation() - Method in class adams.flow.webservice.SpectralGetServiceWS: Returns the webservice implementation to use.
getImplementation() - Method in class adams.flow.webservice.SpectralPutServiceWS: Returns the webservice implementation to use.
getImplementation() - Method in class adams.flow.webservice.SpectralTransformServiceWS: Returns the webservice implementation to use.
getImplementation() - Method in class adams.flow.webservice.spectrum.RatsSpectrumServiceWS: Returns the webservice implementation to use.
getIncrements() - Method in class adams.data.io.output.NIRSpectrumWriter: Get increments.
getIndex() - Method in class adams.data.multifilter.PickByIndex: Returns the index of the spectrum to select.
getIndex() - Method in class adams.flow.transformer.GetSpectrumAmplitude: Returns the index of the amplitude to retrieve.
getIndex() - Method in class adams.flow.transformer.SetSpectrumAmplitude: Returns the index of the amplitude to set.
getIndices() - Method in class adams.db.generic.SampleDataT: Get table indices.
getIndices() - Method in class adams.db.generic.SpectrumT: Return indices for this table.
getInput() - Method in class adams.flow.transformer.SpectralAngleMapper: Gets the input spectrum from the input token.
getInstances(Spectrum) - Method in class adams.data.spectrumbaseline.LinearRegressionBased: Returns the dataset for linear regression.
getInstrument() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Returns the instrument to use for the spectrum.
getInstrument() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns the instrument to use for the spectrum.
getInstrument() - Method in class adams.data.conversion.SpreadSheetToSpectrum: Returns the instrument to use for the spectrum.
getInstrument() - Method in class adams.data.io.input.AbstractSpectrumReader: Returns the instrument's name.
getInstrument() - Method in class adams.data.io.input.AbstractThreeWayDataReader: Returns the instrument's name.
getInstrument() - Method in class adams.db.AbstractSpectrumConditions: Returns the regular expression for the instrument name.
getInstrumentHeader() - Method in class adams.data.io.output.CALSpectrumWriter: Create InstrumentHeader using parameters.
getInstrumentHeader() - Method in class adams.data.io.output.NIRSpectrumWriter: Create InstrumentHeader using parameters.
getInstrumentName() - Method in class adams.data.io.output.ASCSpectrumWriter: Get instrument name.
getInstrumentName() - Method in class adams.data.io.output.NIRSpectrumWriter: Get instrument name.
getInstrumentName() - Method in class adams.data.io.output.TrinamixSpectrumWriter: Get instrument name.
getInstruments() - Method in class adams.db.generic.SampleDataT: Returns all the various instruments.
getInstruments() - Method in class adams.db.mirrored.SampleDataT: Returns all the various instruments.
getInstruments() - Method in class adams.db.SampleDataF: Returns all the various instruments.
getInstruments() - Method in interface adams.db.SampleDataIntf: Returns all the various instruments.
getInt(byte[], int) - Method in class adams.data.io.input.OpusSpectrumReader: Get int from 4bytes, LSByte first
getInt(int, int, int[]) - Method in class adams.opt.genetic.RonWeasley
getIntercepts() - Method in class adams.data.io.input.foss.FossStdise: Get intercepts as array.
getInterval() - Method in class adams.flow.transformer.SpectrumMinMax: Returns the interval (ie number of spectra processed) when to output the min/max spectra.
getInvert() - Method in class adams.data.spectrumfilter.KennardStone: Get whether to return the remaining spectra are returned rather than the chosen ones.
getInvert() - Method in class adams.data.spectrumfilter.Remove: Returns whether to invert the matching sense.
getInvert() - Method in class adams.data.spectrumfilter.SubRange: Returns whether to invert the matching sense.
getInvert() - Method in class adams.data.spectrumoutlier.StringMatcher: Returns whether to invert the matching sense.
getInvertMatching() - Method in class adams.data.io.input.ZippedSpectrumReader: Returns whether to invert the matching sense of the regular expression.
getIqr() - Method in class adams.data.cleaner.instance.IQRCleaner: Returns the iqr multiplier.
getIQRMultiplier() - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Returns the IQR multipliers per classifier.
getItemAt(int) - Method in class adams.gui.selection.SelectSpectrumPanel.TableModel: Returns the ID at the specified position.
getItemClass() - Method in class adams.flow.source.OrphanedSampleDataIdSupplier: Returns the based class of the items.
getItemClass() - Method in class adams.flow.source.SpectrumIdSupplier: Returns the based class of the items.
getItemClass() - Method in class adams.flow.transformer.SampleDataFileReader: Returns the base class of the items.
getItemClass() - Method in class adams.flow.transformer.SpectrumFileReader: Returns the base class of the items.
getItemClass() - Method in class adams.flow.transformer.ThreeWayDataFileReader: Returns the base class of the items.
getItemClass() - Method in class adams.gui.selection.SelectSpectrumPanel: Returns the class of the items displayed, same as "T".
getIterations() - Method in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: Returns the iterations.
getKeepAttributeNames() - Method in class weka.filters.unsupervised.attribute.SpectrumFilter: Returns whether to keep the attribute names generated by the base filter.
getKeepFormat() - Method in class adams.data.io.input.AbstractSpectrumReader: Returns whether to keep the format obtained from the file.
getKeepFormat() - Method in class adams.data.io.input.AbstractThreeWayDataReader: Returns whether to keep the format obtained from the file.
getKey() - Method in class adams.data.io.input.OpusSpectrumReaderExt: Returns the command-line key from which to retrieve the sample ID.
getKey() - Method in class adams.env.SpectralDbBackendDefinition: Returns the key this definition is for.
getKey() - Method in class adams.env.SpectralScriptingEngineDefinition: Returns the key this definition is for.
getKey() - Method in class adams.flow.transformer.SetEvaluationMetaData: Returns the key to use for storing the value.
getKey() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.Property: Gets the value of the key property.
getKey() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.Property: Gets the value of the key property.
getKey() - Method in class nz.ac.waikato.adams.webservice.spectral.get.Property: Gets the value of the key property.
getKey() - Method in class nz.ac.waikato.adams.webservice.spectral.put.Property: Gets the value of the key property.
getKey() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.Property: Gets the value of the key property.
getLast() - Method in class adams.data.spectrumfilter.AbstractStandardiseFilter: Returns the last data point
getLastError() - Method in class adams.data.io.input.ASCSpectrumReader.ParsedFile: Returns the last error that occurred.
getLastError() - Method in class adams.data.io.input.DPTSpectrumReader.ParsedFile: Returns the last error that occurred.
getLastWave() - Method in class adams.flow.transformer.InstanceToSpectrum: Returns the end point for the wave numbers.
getLastX() - Method in class adams.data.io.input.SPCSpectrumReader.FileParser: Returns the X of the last value.
getLastXPoint() - Method in class adams.data.io.output.ASCSpectrumWriter: Get last X wavenumber.
getLatest() - Method in class adams.db.AbstractSpectrumConditions: Returns whether only the latest ones are returned (= reverse order).
getLatest() - Method in class adams.db.OrphanedSampleDataConditions: Returns whether only the latest ones are returned (= reverse order).
getLenient() - Method in class adams.data.conversion.SpreadSheetColumnsToSampleData: Returns whether whether to skip over errors.
getLenient() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Returns whether whether to skip over errors.
getLenient() - Method in class adams.data.conversion.SpreadSheetRowsToSampleData: Returns whether whether to skip over errors.
getLenient() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns whether whether to skip over errors.
getLenient() - Method in class adams.flow.transformer.InstanceGenerator: Returns whether lenient, ie whether errors only get logged rather than returned (and possibly causing the flow to stop).
getLenient() - Method in class adams.flow.transformer.MergeSampleDataFromMap: Returns whether to use lenient mode (missing IDs in map won't cause error).
getLenient() - Method in class adams.flow.transformer.SpreadSheetRowGenerator: Returns whether lenient, ie whether errors only get logged rather than returned (and possibly causing the flow to stop).
getLoadings() - Method in class adams.data.spectrumanalysis.PCA: Returns the loadings.
getLoadings() - Method in class adams.data.spectrumanalysis.PLS: Returns the loadings.
getLoadSampleData() - Method in class adams.data.instances.AbstractSpectrumBasedInstanceGenerator: Returns whether to load the sample data via the sample ID if only dummy report available.
getLocale() - Method in class adams.data.io.input.ASCSpectrumReader: Returns the locale in use.
getLocale() - Method in class adams.data.io.input.DPTSpectrumReader: Returns the locale in use.
getLocale() - Method in class adams.data.io.output.ASCSpectrumWriter: Returns the locale in use.
getLocale() - Method in class adams.data.io.output.DPTSpectrumWriter: Returns the locale in use.
getLogBase() - Method in class adams.data.spectrumfilter.LogTransform: Returns the base of the log ("e" or a positive number greater than 1).
getLogger() - Method in class adams.gui.tools.idprovider.AbstractIDProviderPanel: Returns the logger in use.
getLong(byte[], int) - Method in class adams.data.io.input.opus.OpusBlockHelper.Block: Returns the long with the given ID.
getLong(byte[], int) - Static method in class adams.data.io.input.opus.OpusBlockHelper: Returns the long at the specified offset.
getLong(int) - Method in class adams.data.io.input.opus.OpusBlockHelper.Block: Returns the long at the specified offset.
getLookup() - Method in class adams.data.spectrumfilter.ReportFieldFromStringValueWithLookup: Returns the key-value pairs that make up the lookup table.
getLowerMaxAmplitude() - Method in class adams.data.spectrumimage.AbstractSpectrumImageGeneratorWithRange: Returns the lower bound for the maximum amplitude.
getLowerMaxAmplitude() - Method in class adams.data.spectrumimage.AmplitudeRatio: Returns the lower bound for the maximum amplitude.
getLowerMinAmplitude() - Method in class adams.data.spectrumimage.AbstractSpectrumImageGeneratorWithRange: Returns the lower bound for the minimum amplitude.
getLowerMinAmplitude() - Method in class adams.data.spectrumimage.AmplitudeRatio: Returns the lower bound for the minimum amplitude.
getLowerPercentile() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.DataCollector: Returns the lower percentile.
getLowerPercentile() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Returns the lower percentile.
getLowerPercentile() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.InterPercentileRange: Returns the lower percentile.
getMarkerExtent() - Method in class adams.gui.visualization.spectrum.SpectrumPaintlet: Returns the current marker extent (which is the width and height of the shape).
getMarkerShape(int) - Method in class adams.gui.visualization.spectrum.SpectrumPaintlet: Determines the shape to paint around the data points, based on the index of the data.
getMaster() - Method in class adams.data.io.output.NIRSpectrumWriter: Get serial no of master.
getMatrix() - Method in class adams.flow.transformer.ThreeWayDataLoadingMatrix: Returns the name of the loading matrix to retrieve.
getMax() - Method in class adams.data.io.input.CALSpectrumReader: Returns the nth point setting.
getMax() - Method in class adams.data.io.input.OpusSpectrumReader: Returns the nth point setting.
getMax() - Method in class adams.data.spectrumfilter.amplitudetransform.Triangle: Returns the maximum for the triangle.
getMax() - Method in class adams.data.spectrumoutlier.MinMax: Returns the currently set max.
getMax() - Method in class adams.data.threewayoutlier.ValueRange: Returns the currently set max.
getMaxAmplitude() - Method in class adams.data.io.input.SpecLibSpectrumReader: Returns the largest allowed amplitude.
getMaxAmplitude() - Method in class adams.data.spectrum.Spectrum: Get point with greatest amplitude.
getMaxAmplitude() - Method in class adams.data.spectrumfilter.Scale: Returns the maximum amplitude to scale to.
getMaxAmplitude() - Method in class adams.data.spectrumimage.AbstractSpectrumImageGeneratorWithRange: Returns the maximum amplitude to assume.
getMaxAttributeNames() - Method in class adams.data.spectrumfilter.PCA: Returns the maximum number of attribute names.
getMaxAttributes() - Method in class adams.data.spectrumfilter.PCA: Returns the maximum attributes.
getMaximum() - Method in class adams.data.cleaner.instance.MinMax: Returns the maximum value the field is allowed to have (incl).
getMaximum() - Method in class adams.data.cleaner.spectrum.MinMax: Returns the maximum value the field is allowed to have (incl).
getMaximum() - Method in class adams.data.compare.SpectrumCosineSimilarity: Returns the maximum for the cosine similarity.
getMaximumValue() - Method in class adams.db.SpectrumConditionsSingle: Returns the maximum values for the fields.
getMaximumValues() - Method in class adams.db.SpectrumConditionsMulti: Returns the maximum values for the fields.
getMaxNonRemovalIterations() - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Returns the maximum number of non-removal iterations per classifier.
getMaxPLS() - Method in class adams.opt.genetic.RonWeasley: Get max PLS components
getMaxSG() - Method in class adams.opt.genetic.RonWeasley: Get max sg smoothing windows
getMaxWaveNumber() - Method in class adams.data.io.input.SpecLibSpectrumReader: Returns the largest allowed wavenumber.
getMaxWaveNumber() - Method in class adams.data.spectrum.Spectrum: Get point with greatest wave number.
getMaxWaveNumber() - Method in class adams.data.spectrumfilter.SubRange: Returns the maximum wave number to include in the output.
getMaxWaveNumber() - Method in class adams.data.spectrumoutlier.Oscillation: Returns the maximum wave number to include in the output.
getMaxWaves() - Method in class adams.data.spectrumoutlier.MaxWaves: Returns the currently set maximum number of wave numbers.
getMaxX() - Method in class adams.data.conversion.ThreeWayDataToHeatmap: Returns the maximum X layer to use.
getMaxX() - Method in class adams.data.threeway.L1Point: Get point with greatest X.
getMaxX() - Method in class adams.data.threeway.ThreeWayData: Get point with greatest timestamp.
getMaxY() - Method in class adams.data.threeway.L1Point: Get point with greatest X.
getMaxY() - Method in class adams.data.threeway.ThreeWayData: Get point with greatest abundance.
getMeanDeltaX(Spectrum) - Method in class adams.data.spectrumfilter.SAX: Computes the mean difference between data points on the X axis.
getMenuBar() - Method in class adams.gui.tools.DeleteSpectrumPanel: Creates a menu bar (singleton per panel object).
getMenuBar() - Method in class adams.gui.visualization.spectrum.MultiSpectrumPanel: Initializes the menubar.
getMenuBar() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Creates a menu bar (singleton per panel object).
getMenuBar() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Creates a menu bar (singleton per panel object).
getMenuItem(ThreeWayDataHeatmapViewerMultiPagePane) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.multipageaction.AbstractMultiPageMenuItem: Creates the menu item.
getMenuItem(ThreeWayDataHeatmapViewerMultiPagePane) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.multipageaction.OpenContainingFolder: Creates the menu item.
getMenuItem(ThreeWayDataHeatmapViewerMultiPagePane) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.multipageaction.Statistics: Creates the menu item.
getMenuItem(ThreeWayDataHeatmapViewerMultiPagePane) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.multipageaction.ViewAsSpreadSheet: Creates the menu item.
getMerge() - Method in class adams.flow.transformer.MergeSampleDataFromMap: Returns the merge type.
getMergeReports() - Method in class adams.flow.transformer.ThreeWayDataMerge: Returns whether to merge the reports into a single one and use in the outgoing data.
getMessage() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.UploadResponse: Gets the value of the message property.
getMessage() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.UploadResponse: Gets the value of the message property.
getMessage() - Method in class nz.ac.waikato.adams.webservice.spectral.get.GetResponse: Gets the value of the message property.
getMessage() - Method in class nz.ac.waikato.adams.webservice.spectral.put.PutResponse: Gets the value of the message property.
getMessage() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.TransformResponse: Gets the value of the message property.
getMetaData(byte[]) - Method in class adams.data.io.input.OpusSpectrumReader: Returns the meta-data from the buffer.
getMetaDataFields() - Method in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: Returns the meta-data fields to add.
getMetaDataPrefix() - Method in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: Returns the column prefix for the meta-data values.
getMetaDataValues() - Method in class adams.data.conversion.SpectrumToJson: Returns the meta-data values to output.
getMetaDataValues() - Method in class adams.data.io.output.JsonSpectrumWriter: Returns the meta-data values to output.
getMin() - Method in class adams.data.spectrumfilter.amplitudetransform.Triangle: Returns the minimum for the triangle.
getMin() - Method in class adams.data.spectrumoutlier.MinMax: Returns the currently set minimum.
getMin() - Method in class adams.data.threewayoutlier.ValueRange: Returns the currently set minimum.
getMinAmplitude() - Method in class adams.data.io.input.SpecLibSpectrumReader: Returns the smallest allowed amplitude.
getMinAmplitude() - Method in class adams.data.spectrum.Spectrum: Get point with smallest amplitude.
getMinAmplitude() - Method in class adams.data.spectrumfilter.Scale: Returns the minimum amplitude to scale to.
getMinAmplitude() - Method in class adams.data.spectrumimage.AbstractSpectrumImageGeneratorWithRange: Returns the minimum amplitude to assume.
getMinimum() - Method in class adams.data.cleaner.instance.MinMax: Returns the minimum value the field can have (incl.).
getMinimum() - Method in class adams.data.cleaner.spectrum.MinMax: Returns the minimum value the field can have (incl.).
getMinimum() - Method in class adams.data.compare.SpectrumCorrelation: Returns the minimum for the correlation coefficient.
getMinimum() - Method in class adams.flow.transformer.predictioncheck.MinProbability: Returns the minimum probability (included) that the highest probability in the class distribution must achieve.
getMinimumValue() - Method in class adams.db.SpectrumConditionsSingle: Returns the minimum value for the field.
getMinimumValues() - Method in class adams.db.SpectrumConditionsMulti: Returns the minimum values for the fields.
getMinPLS() - Method in class adams.opt.genetic.RonWeasley: Get minimum pls components
getMinSG() - Method in class adams.opt.genetic.RonWeasley: Get minimum sg
getMinWaveNumber() - Method in class adams.data.io.input.SpecLibSpectrumReader: Returns the smallest allowed wavenumber.
getMinWaveNumber() - Method in class adams.data.spectrum.Spectrum: Get point with smallest wave number.
getMinWaveNumber() - Method in class adams.data.spectrumfilter.SubRange: Returns the minimum wave number to include in the output.
getMinWaveNumber() - Method in class adams.data.spectrumoutlier.Oscillation: Returns the minimum wave number to include in the detection.
getMinWaves() - Method in class adams.data.spectrumoutlier.MinWaves: Returns the currently set minimum number of wave numbers.
getMinX() - Method in class adams.data.conversion.ThreeWayDataToHeatmap: Returns the minimum X layer to use.
getMinX() - Method in class adams.data.threeway.L1Point: Get point with smallest X.
getMinX() - Method in class adams.data.threeway.ThreeWayData: Get point with smallest Timestamp.
getMinY() - Method in class adams.data.threeway.L1Point: Get point with smallest Y.
getMinY() - Method in class adams.data.threeway.ThreeWayData: Get point with smallest abundance.
getMirrorFor(AbstractDatabaseConnection) - Method in class adams.db.mirrored.SpectralDbBackend: Returns the corresponding mirror for the connection URL provided.
getMirrors() - Method in class adams.db.mirrored.SpectralDbBackend: Returns the mirror connections in use.
getMirrorsForUrls() - Method in class adams.db.mirrored.SpectralDbBackend: Returns the URLs that the mirrors are for.
getMissingEvaluation() - Method in class adams.data.evaluator.instance.AbstractEvaluator: Returns the replacement string for missing evaluations.
getMissingEvaluation() - Method in interface adams.data.evaluator.instance.Evaluator: Returns the replacement string for missing evaluations.
getMissingRegions(Spectrum, Spectrum) - Static method in class adams.data.spectrum.SpectrumUtils: Returns all the regions that are in "a", but not in "b".
getMissingValueColor() - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Returns the color for missing values.
getMissingValueColor() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Returns the color to use for missing values.
getMode() - Method in class adams.data.io.input.JCampDX2SpectrumReader: Returns the reader mode.
getModel(SampleData) - Static method in class adams.gui.visualization.spectrum.SampleDataFactory: Returns a new model for the given report.
getModelActor() - Method in class adams.data.spectrumfilter.WekaFilterToReport: Returns the filter source actor.
getModelActor() - Method in class adams.flow.transformer.Cleaner: Returns the filter source actor.
getModelActor() - Method in class adams.flow.transformer.Evaluator: Returns the filter source actor.
getModelActor() - Method in class adams.flow.transformer.PostProcessor: Returns the filter source actor.
getModelActor() - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Returns the filter source actor.
getModelFile() - Method in class adams.data.spectrumfilter.WekaFilterToReport: Returns the file to load the model from.
getModelFile() - Method in class adams.flow.transformer.Cleaner: Returns the file to load the model from.
getModelFile() - Method in class adams.flow.transformer.Evaluator: Returns the file to load the model from.
getModelFile() - Method in class adams.flow.transformer.PostProcessor: Returns the file to load the model from.
getModelFile() - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Returns the file to load the model from.
getModelFromContainer(AbstractContainer, MessageCollection) - Method in class adams.flow.core.CleanerModelLoader: Retrieves the model from the container.
getModelFromContainer(AbstractContainer, MessageCollection) - Method in class adams.flow.core.EvaluatorModelLoader: Retrieves the model from the container.
getModelFromContainer(AbstractContainer, MessageCollection) - Method in class adams.flow.core.PostProcessorModelLoader: Retrieves the model from the container.
getModelFromContainer(AbstractContainer, MessageCollection) - Method in class adams.flow.core.ThreeWayDataModelFilterLoader: Retrieves the model from the container.
getModelLoadingType() - Method in class adams.data.spectrumfilter.WekaFilterToReport: Returns the loading type.
getModelLoadingType() - Method in class adams.flow.transformer.Cleaner: Returns the loading type.
getModelLoadingType() - Method in class adams.flow.transformer.Evaluator: Returns the loading type.
getModelLoadingType() - Method in class adams.flow.transformer.PostProcessor: Returns the loading type.
getModelLoadingType() - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Returns the loading type.
getModelResetVariable() - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Returns the variable to monitor for changes in order to reset the model.
getModelStorage() - Method in class adams.data.spectrumfilter.WekaFilterToReport: Returns the filter storage item.
getModelStorage() - Method in class adams.flow.transformer.Cleaner: Returns the filter storage item.
getModelStorage() - Method in class adams.flow.transformer.Evaluator: Returns the filter storage item.
getModelStorage() - Method in class adams.flow.transformer.PostProcessor: Returns the filter storage item.
getModelStorage() - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Returns the filter storage item.
getModified() - Method in class adams.flow.transformer.SpectralAngleMapper: Gets whether to use the modified algorithm.
getName() - Method in class adams.data.io.input.opus.OpusBlockHelper.Block: Returns the name of the block.
getName() - Method in class adams.gui.visualization.spectrum.containerlistpopup.Information: The name.
getName() - Method in class adams.gui.visualization.spectrum.containerlistpopup.SampleData: The name.
getName() - Method in class adams.gui.visualization.spectrum.containerlistpopup.SpectralData: The name.
getName() - Method in class adams.gui.visualization.spectrum.plotpopup.Adjust: The name.
getName() - Method in class adams.gui.visualization.spectrum.plotpopup.CrossHair: The name.
getName() - Method in class adams.gui.visualization.spectrum.plotpopup.ExportVisible: The name.
getName() - Method in class adams.gui.visualization.spectrum.plotpopup.GotoWaveNumber: The name.
getName() - Method in class adams.gui.visualization.spectrum.plotpopup.Histogram: The name.
getName() - Method in class adams.gui.visualization.spectrum.plotpopup.Hits: The name.
getName() - Method in class adams.gui.visualization.spectrum.plotpopup.SaveVisible: The name.
getName() - Method in class adams.gui.visualization.spectrum.plotpopup.Statistics: The name.
getName() - Method in class adams.gui.visualization.spectrum.plotpopup.Viewport: The name.
getName() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.multipageaction.AbstractMultiPageMenuItem: The name for the menu item.
getName() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.multipageaction.OpenContainingFolder: The name for the menu item.
getName() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.multipageaction.Statistics: The name for the menu item.
getName() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.multipageaction.ViewAsSpreadSheet: The name for the menu item.
getNewConnection() - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Returns whether to use a new connection for this update.
getNewConnection() - Method in class adams.flow.transformer.BulkSpectrumDbWriter: Returns whether to use a new connection for this update.
getNewFormat() - Method in class adams.data.multifilter.AbstractFormatsBasedMultiSpectrumFilter: Returns the new format for the generated spectrum.
getNewFormatSeparator() - Method in class adams.data.multifilter.Fusion: Returns the separator to use when automatically generating a new format string.
getNextInstance(Instances) - Method in class weka.core.converters.CALSpectrumLoader: CALSpectrumLoader is unable to process a data set incrementally.
getNirArray(byte[]) - Method in class adams.data.io.input.OpusSpectrumReader: Get array of nir data from byte array of bruker file image
getNIRArray() - Method in class adams.data.io.input.ASCSpectrumReader.ParsedFile: Returns the NIR array.
getNoAdditionalFieldsPrefix() - Method in class adams.data.instances.AbstractSpectrumInstanceGenerator: Returns whether to drop the prefix for the additional fields.
getNoCopy() - Method in class adams.flow.transformer.AbstractInPlaceSpectrumTransformer: Returns whether to skip creating a copy of the spectrum before processing it.
getNoCopy() - Method in class adams.flow.transformer.Evaluator: Returns whether to skip creating a copy of the container before updating it.
getNoCopy() - Method in class adams.flow.transformer.PredictionCheck: Returns whether to skip creating a copy of the data before processing t.
getNoCopy() - Method in class adams.flow.transformer.SetEvaluationMetaData: Returns whether to skip creating a copy of the container before updating it.
getNonMirroredBackend() - Method in class adams.db.mirrored.SpectralDbBackend: Returns the backend to use for non-mirrored connections.
getNormalize() - Method in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: Returns whether to normalize the confidence intervals using the class range.
getNormalize() - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Returns whether to normalize the predictions to the class attribute range.
getNormalizeByLiveTime() - Method in class adams.data.io.input.MPSSpectrumReader: Returns whether to normalize the amplitudes with the MPSSpectrumReader.KEY_LIVE_TIME field.
getNotes() - Method in class adams.data.instances.AbstractSpectrumBasedInstanceGenerator: Returns the current notes to add as attributes.
getNotes() - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Returns the current notes to add as attributes.
getNotes() - Method in class adams.data.spectrum.MultiSpectrum: Returns the currently stored notes.
getNotes() - Method in class adams.data.spectrum.Spectrum: Returns the currently stored notes.
getNotes() - Method in class adams.data.threeway.ThreeWayData: Returns the currently stored notes.
getNotes() - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Returns the current notes to add as attributes.
getNthPoint() - Method in class adams.data.threewayfeatures.Flatten: Returns the nth point setting.
getNthPoints() - Method in class weka.filters.unsupervised.attribute.SegmentedDownSample: Returns the blank-separated list number of points to use for the savitzky-golay window (>= 1).
getNumAdditional() - Method in class adams.data.spectrumfilter.PadPower2: Returns the number of additional wave numbers to add (beyond the power of 2).
getNumAttributes() - Method in class weka.filters.unsupervised.attribute.BestBySLR: Get the number of attributes (< 1 percentage, >= 1 absolute number).
getNumber() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.Wave: Gets the value of the number property.
getNumber() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.Wave: Gets the value of the number property.
getNumber() - Method in class nz.ac.waikato.adams.webservice.spectral.get.Wave: Gets the value of the number property.
getNumber() - Method in class nz.ac.waikato.adams.webservice.spectral.put.Wave: Gets the value of the number property.
getNumber() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.Wave: Gets the value of the number property.
getNumberInSubset() - Method in class adams.data.spectrumfilter.KennardStone: get the number of spectra to select in subset
getNumDatapoints() - Method in class adams.data.io.input.ASCSpectrumReader.ParsedFile: Returns the number of data points.
getNumDatapoints() - Method in class adams.data.io.input.foss.FossHelper: Number of spectral data points.
getNumDatapoints() - Method in class adams.data.io.input.foss.FossStdise: Get number of nir wavelengths.
getNumFiles() - Method in class adams.data.io.input.SPCSpectrumReader.FileParser: Returns the number of sub-files.
getNumFolds() - Method in class adams.data.cleaner.instance.RemoveOutliers: Returns the number of folds to use in CV.
getNumFolds() - Method in class adams.data.evaluator.instance.EnsembleEvaluator: Returns the number of folds.
getNumFolds() - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Returns the number of cross-validation folds per classifier.
getNumIterations() - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Returns the number of iterations per classifier.
getNumNeighbors() - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Returns the number of neighbors to use in the neighborhood.
getNumNeighbors() - Method in class adams.data.evaluator.instance.CrossValidatedPrediction: Returns the number of neighbors to use in the neighborhood.
getNumNeighbors() - Method in class adams.data.evaluator.instance.DistanceToCenter: Returns the number of neighbors to use in the neighborhood.
getNumPoints() - Method in class adams.data.io.input.SPCSpectrumReader.FileParser: Returns the number of points to read.
getNumPoints() - Method in class adams.data.spectrumfilter.AndrewsCurves: Returns the number of points to generate.
getNumPoints() - Method in class adams.data.spectrumfilter.CenterBurst: Returns the number of points to use.
getNumPoints() - Method in class weka.filters.unsupervised.attribute.SavitzkyGolayRange: Returns the number of points for the window (window = numPoints*2 + 1).
getNumPoints() - Method in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: Returns the blank-separated list number of points to use for the savitzky-golay window (>= 1).
getNumSegments() - Method in class adams.data.io.input.foss.FossHelper: get number of segments
getNumSegments() - Method in class adams.opt.genetic.RonWeasley
getNumThreads() - Method in class adams.data.cleaner.instance.RemoveOutliers: Returns the number of threads to use for cross-validation.
getNumThreads() - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Returns the number of threads to use for cross-validation.
getOffline() - Method in class adams.data.io.input.AbstractSampleDataReader: Returns whether to work in offline mode, i.e., not query the database.
getOffsetX() - Method in class adams.data.threewayfilter.Shift: Returns the offset for X.
getOffsetX() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Returns the currently set X offset for the text.
getOffsetY() - Method in class adams.data.threewayfilter.Shift: Returns the offset for Y.
getOffsetY() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Returns the currently set Y offset of the text.
getOffsetZ() - Method in class adams.data.threewayfilter.Shift: Returns the offset for Z.
getOnlyDummies() - Method in class adams.db.AbstractSpectrumConditions: Returns whether only spectra with reports flagged as dummies are included or not.
getOnlyWarning() - Method in class adams.flow.transformer.MultiSpectrumOutlierDetector: Returns whether the detections are added as error or warning.
getOperation() - Method in class adams.data.io.input.opus.OpusBlockHelper.CommandlineData: Returns the commandline operation.
getOperation() - Method in class adams.data.io.input.OpusSpectrumReaderExt: Returns the command-line operation from which to retrieve the sample ID.
getOperation() - Method in class adams.flow.transformer.MultiSpectrumOperation: Returns the multi-spectrum operation to apply.
getOperator() - Method in class adams.data.io.output.NIRSpectrumWriter: Get operator.
getOptionManager() - Method in class adams.data.spectrum.AbstractSpectrumComparator: Returns the option manager.
getOptions() - Method in class weka.core.converters.CALSpectrumLoader: Gets the current option settings for the OptionHandler.
getOptions() - Method in class weka.filters.unsupervised.attribute.BestBySLR: Gets the current settings of the filter.
getOptions() - Method in class weka.filters.unsupervised.attribute.RangeBasedSavitzkyGolay: Gets the current settings of the filter.
getOptions() - Method in class weka.filters.unsupervised.attribute.SegmentedDownSample: Gets the current settings of the filter.
getOptions() - Method in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: Gets the current settings of the filter.
getOptions() - Method in class weka.filters.unsupervised.attribute.SpectrumFilter: Gets the current settings of the filter.
getOptionsDescription() - Method in class adams.gui.scripting.SelectWaveNumber: Returns a one-line listing of the options of the action.
getOptionsDescription() - Method in class adams.gui.scripting.WriteSpectrum: Returns a one-line listing of the options of the action.
getOriginalPoint(DataPoint, Spectrum) - Method in class adams.data.spectrumbaseline.SavitzkyGolayBased: Retrieves the data point from the original signal that corresponds to the provided new one.
getOrphanedIDs(OrphanedSampleDataConditions) - Method in class adams.db.generic.SampleDataT: Returns a list of sample IDs of sample data without associated spectra.
getOrphanedIDs(OrphanedSampleDataConditions) - Method in class adams.db.mirrored.SampleDataT: Returns a list of sample IDs of of sample data without associated spectra.
getOrphanedIDs(OrphanedSampleDataConditions) - Method in class adams.db.SampleDataF: Returns a list of sample IDs of of sample data without associated spectra.
getOrphanedIDs(OrphanedSampleDataConditions) - Method in interface adams.db.SampleDataIntf: Returns a list of sample IDs of of sample data without associated spectra.
getOutlierRemoval() - Method in class adams.data.multispectrumoperation.OutlierRemoval: Returns the outlier removal scheme to apply.
getOutputContainer() - Method in class adams.flow.transformer.InstanceGenerator: Returns whether to output a container with the instance alongside the * report or just the instance.
getOutputContainer() - Method in class adams.flow.transformer.PostProcessor: Returns whether to output a container.
getOutputContainerClass() - Method in class adams.flow.transformer.SpectrumFilter: Returns the container class in use for the output.
getOutputContainerClass() - Method in class adams.flow.transformer.ThreeWayDataFilter: Returns the container class in use for the output.
getOutputHeader() - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Returns the current header.
getOutputMultiSpectrum() - Method in class adams.flow.transformer.SpectrumFileReader: Returns whether to output a MultiSpectrum instead.
getOutputReport() - Method in class adams.data.conversion.MultiSpectrumToSpectra: Returns whether to output the global report of the multi-spectrum as separate (= first) report-only spectrum (ie no spectral data).
getOutputReport() - Method in class adams.flow.transformer.SpectrumFileWriter: Returns whether to output the global report of the multi-spectrum as separate (= first) report-only spectrum (ie no spectral data).
getOutputSampleData() - Method in class adams.data.io.output.JCampDX2SpectrumWriter: Returns whether to output eh sample data as well.
getOutputSampleData() - Method in class adams.data.io.output.SimpleSpectrumWriter: Returns whether to output eh sample data as well.
getOutputSampleData() - Method in class adams.data.io.output.SimpleXYZWriter: Returns whether to output eh sample data as well.
getOverlapFactor() - Method in class adams.data.conversion.SpectrumToBufferedImage: Returns the overlap factor (1/factor).
getOverlapFactor() - Method in class adams.data.spectrumimage.Spectrogram: Returns the overlap factor (1/factor).
getOverlays() - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Returns the overlays to use.
getOverrideSerializedFile() - Method in class adams.data.cleaner.instance.AbstractSerializableCleaner: Returns whether to override an existing serialized setup.
getOverrideSerializedFile() - Method in class adams.data.cleaner.spectrum.AbstractSerializableCleaner: Returns whether to override an existing serialized setup.
getOverrideSerializedFile() - Method in class adams.data.evaluator.instance.AbstractSerializableEvaluator: Returns whether to override an existing serialized setup.
getOverrideSerializedFile() - Method in class adams.data.postprocessor.instances.AbstractSerializablePostProcessor: Returns whether to override an existing serialized setup.
getOverrideSerializedFile() - Method in class adams.data.spectrumfilter.AbstractSerializableFilter: Returns whether to override an existing serialized setup.
getOverwriteExisting() - Method in interface adams.flow.transformer.SpectrumDatabaseWriter: Returns whether to remove existing containers.
getOwner() - Method in interface adams.flow.webservice.multispectrum.OwnedByRatsMultiSpectrumServiceWS: Returns the current owner.
getOwner() - Method in class adams.flow.webservice.multispectrum.SimpleRatsMultiSpectrumService: Returns the current owner of this webservice.
getOwner() - Method in interface adams.flow.webservice.OwnedBySpectralGetServiceWS: Returns the current owner.
getOwner() - Method in interface adams.flow.webservice.OwnedBySpectralPutServiceWS: Returns the current owner.
getOwner() - Method in interface adams.flow.webservice.OwnedBySpectralTransformServiceWS: Returns the current owner.
getOwner() - Method in class adams.flow.webservice.SimpleSpectralGetService: Returns the current owner of this webservice.
getOwner() - Method in class adams.flow.webservice.SimpleSpectralPutService: Returns the current owner of this webservice.
getOwner() - Method in class adams.flow.webservice.SimpleSpectralTransformService: Returns the current owner of this webservice.
getOwner() - Method in interface adams.flow.webservice.spectrum.OwnedByRatsSpectrumServiceWS: Returns the current owner.
getOwner() - Method in class adams.flow.webservice.spectrum.SimpleRatsSpectrumService: Returns the current owner of this webservice.
getOwner() - Method in class adams.gui.tools.idprovider.AbstractIDProviderPanel: Returns the owning panel.
getOwner() - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: Returns the owning panel.
getOwner() - Method in class adams.gui.visualization.spectrum.SpectrumPointHitDetector: Returns the owner.
getOwner() - Method in class adams.gui.visualization.spectrum.WaveNumberHitDetector: Returns the owner.
getOwner() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Returns the owner.
getPaddingType() - Method in class adams.data.spectrumfilter.PadPower2: Returns the type of padding.
getPadLeft() - Method in class adams.data.spectrumfilter.PadPower2: Returns whether to pad on the left rather than on the right.
getPaintAll() - Method in class adams.gui.visualization.spectrum.SpectrumPaintlet: Returns whether marker shapes are disabled.
getPaintlet() - Method in class adams.flow.sink.SpectrumDisplay: Returns the paintlet in use.
getPaintMoment() - Method in class adams.gui.visualization.spectrum.SelectedWaveNumberPaintlet: Returns when this paintlet is to be executed.
getPaintMoment() - Method in class adams.gui.visualization.spectrum.SimpleSpectrumPaintlet: Returns when this paintlet is to be executed.
getPaintMoment() - Method in class adams.gui.visualization.spectrum.SpectrumPaintlet: Returns when this paintlet is to be executed.
getPanel() - Static method in class adams.gui.visualization.spectrum.HistogramFactory: Returns an instance of a new panel for displaying histograms.
getPanel(SampleData) - Static method in class adams.gui.visualization.spectrum.SampleDataFactory: Returns a new panel for the given report.
getPanel(List<ReportContainer>) - Static method in class adams.gui.visualization.spectrum.SampleDataFactory: Returns a new table for the given reports.
getPanelAt(int) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Returns the specified heatmap panel.
getPanelCount() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Returns the number of panels open.
getPanelForReports(List) - Static method in class adams.gui.visualization.spectrum.SampleDataFactory: Returns a new table for the given reports.
getPanelName() - Method in class adams.gui.tools.idprovider.AbstractIDProviderPanel: Returns the name of the panel.
getPanelName() - Method in class adams.gui.tools.idprovider.DatabaseSearchPanel: Returns the name of the panel.
getPanelName() - Method in class adams.gui.tools.idprovider.ManualListPanel: Returns the name of the panel.
getPanelName() - Method in class adams.gui.tools.idprovider.SpreadSheetIDPanel: Returns the name of the panel.
getPanelProperties() - Method in class adams.gui.tools.idprovider.AbstractIDProviderPanel: Returns the parameters as options.
getPanelProperties() - Method in class adams.gui.tools.idprovider.DatabaseSearchPanel: Returns the parameters as options.
getPanelProperties() - Method in class adams.gui.tools.idprovider.ManualListPanel: Returns the parameters as options.
getPanelProperties() - Method in class adams.gui.tools.idprovider.SpreadSheetIDPanel: Returns the parameters as options.
getParallelAndMerge() - Method in class adams.data.spectrumfilter.MultiFilter: Returns whether the filters are executed in parallel or series.
getParallelAndMerge() - Method in class adams.data.threewayfilter.MultiFilter: Returns whether the filters are executed in parallel or series.
getParent() - Method in class adams.data.io.input.SPCSpectrumReader.AbstractParser: Returns the parent parser if any.
getParent() - Method in class adams.data.spectrum.MultiSpectrum: Returns the container this point belongs to.
getParent() - Method in class adams.data.spectrum.Spectrum: Returns the container this point belongs to.
getParent() - Method in class adams.data.threeway.L1Point: Returns the parent this point belongs to.
getPCA() - Method in class adams.data.spectrumanalysis.PCA: Returns the PCA analysis.
getPlotUpdater() - Method in class adams.flow.sink.SpectrumDisplay: Returns the plot updater in use.
getPLS() - Method in class adams.data.spectrumanalysis.PLS: Returns the PLS analysis.
getPLSBits() - Method in class adams.opt.genetic.RonWeasley
getPLSComponentFromWeights(int[]) - Method in class adams.opt.genetic.RonWeasley
getPoint() - Method in class adams.gui.visualization.spectrum.SelectedWaveNumberPaintlet: Returns the currently set point to highlight.
getPoints() - Method in class adams.data.io.input.DPTSpectrumReader.ParsedFile
getPolynomial() - Method in class adams.data.spectrumfilter.StandardiseByInterpolation: Returns the polynomial for interpolation
getPolynomialOrder() - Method in class weka.filters.unsupervised.attribute.SavitzkyGolayRange: Returns the polynominal order.
getPolynomialOrder() - Method in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: Returns the polynominal order.
getPostProcessor() - Method in class adams.flow.transformer.PostProcessor: Returns the post-processor in use.
getPostProcessor() - Method in class adams.flow.transformer.ThreeWayDataTrain: Returns the post-processor to use on the model.
getPostProcessorDetailsOutput() - Method in class adams.flow.transformer.PostProcessor: Returns the file for the post-processor details.
getPreferJobRunner() - Method in class adams.flow.transformer.Cleaner: Returns whether to offload processing to a JobRunner instance if available.
getPreferJobRunner() - Method in class adams.flow.transformer.Evaluator: Returns whether to offload processing to a JobRunner instance if available.
getPreFilter() - Method in class adams.data.cleaner.instance.AbstractCleaner: Returns the filter to use for pre-filtering the data.
getPreFilter() - Method in class adams.data.cleaner.spectrum.AbstractCleaner: Returns the filter to use for pre-filtering the data.
getPreFilter() - Method in class adams.data.multispectrumoperation.outlierremoval.CorrelationBasedThreshold: Returns the pre-filter to use.
getPreFilter() - Method in class adams.data.multispectrumoperation.outlierremoval.CosineSimilarityBasedThreshold: Returns the pre-filter to use.
getPreFilter() - Method in class adams.data.multispectrumoperation.outlierremoval.MeanSpectrumCosineSimilarityBasedThreshold: Returns the pre-filter to use.
getPreFilter() - Method in class adams.data.spectrumfilter.KennardStone: Get the filter to apply before selection
getPreFilter() - Method in class adams.data.spectrumfilter.multiplicativescattercorrection.AbstractMultiplicativeScatterCorrection: Returns the prefilter to use.
getPreFilter() - Method in class adams.data.spectrumfilter.MultiplicativeScatterCorrection: Returns the prefilter to use.
getPreFilters() - Method in class adams.data.multifilter.FilteredMultiSpectrumFilter: Returns the pre-filters.
getPrefix() - Method in class adams.data.instances.FieldInstanceGenerator: Returns the prefix for the attribute names.
getPrefix() - Method in class adams.data.spectrumfilter.WekaFilterToReport: Returns the prefix for the report fields.
getPrefix() - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Returns the (optional) prefix for the feature names.
getPrefixNew() - Method in class weka.filters.unsupervised.attribute.SpectrumFilter: Returns the (new) attribute prefix to use.
getPrefixOld() - Method in class weka.filters.unsupervised.attribute.SpectrumFilter: Returns the (old) attribute prefix to look for.
getPrettyPrinting() - Method in class adams.data.conversion.SpectrumToJson: Returns whether pretty-printing is used or not.
getPrettyPrinting() - Method in class adams.data.io.output.JsonSpectrumWriter: Returns whether pretty-printing is used or not.
getPreview(File[]) - Method in class adams.gui.tools.previewbrowser.AbstractSpectrumHandler: Returns the preview for the specified files.
getProductCode() - Method in class adams.data.io.output.ASCSpectrumWriter: Get Product Code.
getProductCode() - Method in class adams.data.io.output.NIRSpectrumWriter: Get Product Code.
getProductCode() - Method in class adams.flow.transformer.InstanceToSpectrum: Get Product Code.
getProductCodeFromAttributeTipText() - Method in class adams.flow.transformer.InstanceToSpectrum: Returns the tip text for this property.
getProductCodeFromField() - Method in class adams.data.io.output.ASCSpectrumWriter: Get product code from instance attribute?
getProductCodeFromField() - Method in class adams.data.io.output.NIRSpectrumWriter: Get product code from instance attribute?
getProp() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.Properties: Gets the value of the prop property.
getProp() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.Properties: Gets the value of the prop property.
getProp() - Method in class nz.ac.waikato.adams.webservice.spectral.get.Properties: Gets the value of the prop property.
getProp() - Method in class nz.ac.waikato.adams.webservice.spectral.put.Properties: Gets the value of the prop property.
getProp() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.Properties: Gets the value of the prop property.
getProperties() - Method in class adams.data.io.input.ASCSpectrumReader.ParsedFile: get hashtable property data.
getProperties() - Static method in class adams.db.AbstractSpectralDbBackend: Returns the underlying properties.
getProperties() - Method in class adams.gui.scripting.SpectralScriptingEngine: Provides access to the properties object.
getProperties() - Method in class adams.gui.tools.DeleteSampleDataPanel: Returns the session properties.
getProperties() - Method in interface adams.gui.tools.idprovider.IDConsumer: Returns the session properties.
getProperties() - Method in class adams.gui.tools.ListSampleDataPanel: Returns the session properties.
getProperties() - Method in class adams.gui.tools.UpdateSampleDataPanel: Returns the session properties.
getProperties() - Static method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Returns the properties for this panel.
getProperties() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Returns the properties for this panel.
getProps() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.MultiSpectrum: Gets the value of the props property.
getProps() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.Spectrum: Gets the value of the props property.
getProps() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.Spectrum: Gets the value of the props property.
getProps() - Method in class nz.ac.waikato.adams.webservice.spectral.get.Spectrum: Gets the value of the props property.
getProps() - Method in class nz.ac.waikato.adams.webservice.spectral.put.Spectrum: Gets the value of the props property.
getProps() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.Spectrum: Gets the value of the props property.
getProvider() - Method in class adams.flow.source.InstrumentSupplier: Returns the instrument provider to use for retrieving the instruments.
getQueueFailed() - Method in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: Returns the name for the queue in the internal storage for failed files.
getQueueFailed() - Method in class adams.flow.standalone.rats.LoadSpectrumFileOutput: Returns the name for the queue in the internal storage for failed files.
getQueueSpectra() - Method in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: Returns the name for the queue in the internal storage for failed files.
getQueueSpectra() - Method in class adams.flow.standalone.rats.LoadSpectrumFileOutput: Returns the name for the queue in the internal storage for failed files.
getQueueSuccessful() - Method in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: Returns the name for the queue in the internal storage for successful files.
getQueueSuccessful() - Method in class adams.flow.standalone.rats.LoadSpectrumFileOutput: Returns the name for the queue in the internal storage for successful files.
getQuickInfo() - Method in class adams.data.conversion.SpectrumToArray: Returns a quick info about the object, which can be displayed in the GUI.
getQuickInfo() - Method in class adams.data.conversion.SpectrumToJson: Returns a quick info about the object, which can be displayed in the GUI.
getQuickInfo() - Method in class adams.data.conversion.SpreadSheetColumnsToSampleData: Returns a quick info about the object, which can be displayed in the GUI.
getQuickInfo() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Returns a quick info about the object, which can be displayed in the GUI.
getQuickInfo() - Method in class adams.data.conversion.SpreadSheetRowsToSampleData: Returns a quick info about the object, which can be displayed in the GUI.
getQuickInfo() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns a quick info about the object, which can be displayed in the GUI.
getQuickInfo() - Method in class adams.data.conversion.WekaPredictionContainerToEvaluationContainer: Returns a quick info about the object, which can be displayed in the GUI.
getQuickInfo() - Method in class adams.data.multispectrumoperation.AbstractMultiSpectrumOperation: Returns a quick info about the object, which can be displayed in the GUI.
getQuickInfo() - Method in class adams.data.multispectrumoperation.outlierremoval.AbstractOutlierRemoval: Returns a quick info about the object, which can be displayed in the GUI.
getQuickInfo() - Method in class adams.data.multispectrumoperation.outlierremoval.CorrelationBasedThreshold: Returns a quick info about the object, which can be displayed in the GUI.
getQuickInfo() - Method in class adams.data.multispectrumoperation.outlierremoval.CosineSimilarityBasedThreshold: Returns a quick info about the object, which can be displayed in the GUI.
getQuickInfo() - Method in class adams.data.multispectrumoperation.OutlierRemoval: Returns a quick info about the object, which can be displayed in the GUI.
getQuickInfo() - Method in class adams.data.multispectrumoperation.outlierremoval.MeanSpectrumCosineSimilarityBasedThreshold: Returns a quick info about the object, which can be displayed in the GUI.
getQuickInfo() - Method in class adams.data.multispectrumoperation.Remove: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.data.spectrumoutlier.Oscillation: Returns a quick info about the object, which can be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.condition.bool.HasSpectrum: Returns the quick info string to be displayed in the flow editor.
getQuickInfo() - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.source.NewSpectrum: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.source.SpectrumIdSupplier: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.standalone.rats.LoadSpectrumFileOutput: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.standalone.rats.SaveMultiSpectrumFileOutput: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.standalone.rats.SaveSpectrumFileOutput: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.BulkSpectrumDbWriter: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.Cleaner: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.DeleteSpectrum: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.Evaluator: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.GetSpectrumAmplitude: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.InstanceGenerator: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.MergeSampleDataFromMap: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.MultiSpectrumAdd: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.MultiSpectrumFilter: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.MultiSpectrumOperation: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.MultiSpectrumOutlierDetector: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.MultiSpectrumRemove: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.MultiSpectrumReportFilter: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.PostProcessor: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.predictioncheck.AbstractPredictionCheck: Returns a quick info about the object, which can be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.PredictionCheck: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.predictioncheck.MinProbability: Returns a quick info about the object, which can be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.predictioncheck.Range: Returns a quick info about the object, which can be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.SetEvaluationMetaData: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.SetSpectrumAmplitude: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.SpectralAngleMapper: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.SpectrumDbReader: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.SpectrumDbWriter: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.SpectrumDiff: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.SpectrumFeatureGenerator: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.SpectrumInfo: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.SpectrumMinMax: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.SpreadSheetRowGenerator: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.ThreeWayDataFeatureGenerator: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.ThreeWayDataLoadingMatrix: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.ThreeWayDataMerge: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Returns a quick info about the actor, which will be displayed in the GUI.
getQuickInfo() - Method in class adams.flow.transformer.ThreeWayDataTrain: Returns a quick info about the actor, which will be displayed in the GUI.
getRandom() - Method in class adams.data.evaluator.instance.FakeEvaluator: Returns the random number generator to use.
getRange() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.InterPercentileRange: Returns the range between the upper and lower percentile.
getRange() - Method in class adams.data.spectrumfilter.Remove: Returns the range of amplitudes to remove.
getRange() - Method in class adams.flow.transformer.predictioncheck.Range: Returns the allowed range of the numeric value.
getRanges() - Method in class adams.data.spectrumfilter.detrend.RangeBased: Returns the wave number ranges.
getRanges() - Method in class adams.data.spectrumfilter.multiplicativescattercorrection.RangeBased: Returns the wave number ranges.
getRanges() - Method in class weka.filters.unsupervised.attribute.RangeBasedSavitzkyGolay: Returns the ranges to use.
getRangeX() - Method in class adams.data.threewayfilter.Crop: Returns the range for X.
getRangeY() - Method in class adams.data.threewayfilter.Crop: Returns the range for Y.
getRangeZ() - Method in class adams.data.threewayfilter.Crop: Returns the range for Z.
getRatInput() - Method in class adams.flow.webservice.multispectrum.RatsMultiSpectrumServiceWS: Returns the Rat input associated with this webservice.
getRatInput() - Method in class adams.flow.webservice.spectrum.RatsSpectrumServiceWS: Returns the Rat input associated with this webservice.
getRatsMultiSpectrumServicePort() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.RatsMultiSpectrumServiceService
getRatsMultiSpectrumServicePort(WebServiceFeature...) - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.RatsMultiSpectrumServiceService
getRatsSpectrumServicePort() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.RatsSpectrumServiceService
getRatsSpectrumServicePort(WebServiceFeature...) - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.RatsSpectrumServiceService
getReader() - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Returns the spreadsheet reader in use.
getReader() - Method in class adams.data.io.input.ExtractIdAndTypeSpectrumReader: Returns the base reader to use.
getReader() - Method in class adams.data.io.input.ExtractIdAndTypeThreeWayDataReader: Returns the base reader to use.
getReader() - Method in class adams.data.io.input.FilteredSpectrumReader: Returns the underlying reader.
getReader() - Method in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: Returns the spreadsheet reader in use.
getReader() - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Returns the spreadsheet reader in use.
getReader() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Returns the spreadsheet reader in use.
getReader() - Method in class adams.data.io.input.ThreeWayHeatmapReader: Returns the reader to use.
getReader() - Method in class adams.data.io.input.ZippedSpectrumReader: Returns the reader to use.
getReader() - Method in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: Returns the reader in use.
getReader() - Method in class adams.flow.standalone.rats.LoadSpectrumFileOutput: Returns the reader in use.
getReader(File) - Method in class adams.gui.tools.previewbrowser.AbstractSpectrumHandler: Returns the reader to use.
getReader(File) - Method in class adams.gui.tools.previewbrowser.ASCIIXYSpectrumHandler: Returns the reader to use.
getReader(File) - Method in class adams.gui.tools.previewbrowser.ASCSpectrumHandler: Returns the reader to use.
getReader(File) - Method in class adams.gui.tools.previewbrowser.CALSpectrumHandler: Returns the reader to use.
getReader(File) - Method in class adams.gui.tools.previewbrowser.CMLSpectrumHandler: Returns the reader to use.
getReader(File) - Method in class adams.gui.tools.previewbrowser.DPTSpectrumHandler: Returns the reader to use.
getReader(File) - Method in class adams.gui.tools.previewbrowser.JCampDX2SpectrumHandler: Returns the reader to use.
getReader(File) - Method in class adams.gui.tools.previewbrowser.JCampDXSpectrumHandler: Returns the reader to use.
getReader(File) - Method in class adams.gui.tools.previewbrowser.JsonSpectrumHandler: Returns the reader to use.
getReader(File) - Method in class adams.gui.tools.previewbrowser.MPSSpectrumHandler: Returns the reader to use.
getReader(File) - Method in class adams.gui.tools.previewbrowser.NIRSpectrumHandler: Returns the reader to use.
getReader(File) - Method in class adams.gui.tools.previewbrowser.OpusSpectrumExtHandler: Returns the reader to use.
getReader(File) - Method in class adams.gui.tools.previewbrowser.OpusSpectrumHandler: Returns the reader to use.
getReader(File) - Method in class adams.gui.tools.previewbrowser.RelabSpectrumHandler: Returns the reader to use.
getReader(File) - Method in class adams.gui.tools.previewbrowser.SimpleCSVSampleDataHandler: Returns the reader to use.
getReader(File) - Method in class adams.gui.tools.previewbrowser.SimpleSampleDataHandler: Returns the reader to use.
getReader(File) - Method in class adams.gui.tools.previewbrowser.SimpleSpectrumHandler: Returns the reader to use.
getReader(File) - Method in class adams.gui.tools.previewbrowser.SPASpectrumHandler: Returns the reader to use.
getReader(File) - Method in class adams.gui.tools.previewbrowser.SPCSpectrumHandler: Returns the reader to use.
getReader(File) - Method in class adams.gui.tools.previewbrowser.SpecLibSpectrumHandler: Returns the reader to use.
getReaderClass() - Method in class adams.gui.chooser.SpectrumFileChooser: Returns the reader superclass for the GOE.
getReaderClass() - Method in class adams.gui.chooser.ThreeWayDataFileChooser: Returns the reader superclass for the GOE.
getReaders() - Static method in class adams.data.io.input.AbstractSpectrumReader: Returns a list with classnames of readers.
getReaders() - Static method in class adams.data.io.input.AbstractThreeWayDataReader: Returns a list with classnames of readers.
getRefCount() - Method in class adams.data.io.input.foss.FossHelper: number of reference values.
getReferenceNames() - Method in class adams.data.io.input.foss.FossHelper: Get names of references.
getReferences() - Method in class adams.flow.transformer.SpectralAngleMapper: Gets the name of the storage location for reference spectra.
getReferences(StorageName, String) - Method in class adams.flow.transformer.SpectralAngleMapper: Retrieves the reference spectra from storage.
getReferenceValuePrefix() - Method in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: Returns the column prefix for the reference values.
getReferenceValues() - Method in class adams.data.conversion.SpectrumToJson: Returns the reference values to output.
getReferenceValues() - Method in class adams.data.io.output.JsonSpectrumWriter: Returns the reference values to output.
getReferenceValues() - Method in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: Returns the reference value fields to add.
getRefForRow(int) - Method in class adams.data.io.input.foss.FossHelper: Get reference values for a row.
getRefOffsetForRow(int) - Method in class adams.data.io.input.foss.FossHelper: Get start of reference for given row.
getRefRegExp() - Method in class weka.core.converters.CALSpectrumLoader: Returns the regexp to use for matching the reference names to include in the dataset.
getRegExp() - Method in class adams.data.io.input.sampleidextraction.RegExp: Returns the regular expression in use to extract the sample ID from the file name (w/o path).
getRegExp() - Method in class adams.data.io.input.ZippedSpectrumReader: Returns the regular expression that the filenames must match.
getRegExp() - Method in class adams.data.spectrumfilter.ReportFieldFromStringValue: Returns the regular expression to apply for identifying the group(s) to extract from the string.
getRegExp() - Method in class adams.data.spectrumfilter.WekaFilterToReport: Returns the regular expression that the Instance attribute names must match in order to get transferred into the report.
getRegExp() - Method in class adams.data.spectrumoutlier.StringMatcher: Returns the regular expression to match the strings against.
getRegExp() - Method in class adams.gui.visualization.spectrum.SpectrumPaintletStringField: Returns regular expression to apply to the string field; the string obtained from the first group is associated with a color.
getRegion(List<SpectrumPoint>, SpectrumPoint, SpectrumPoint) - Static method in class adams.data.spectrum.SpectrumUtils: Returns a region for the given range, including both, start and end point.
getRejectedTokensActor() - Method in class adams.flow.control.InstanceCleaner: Returns the actor the rejected tokens are sent to.
getRejectedTokensActor() - Method in class adams.flow.control.SpectrumCleaner: Returns the actor the rejected tokens are sent to.
getRejectionMessagesActor() - Method in class adams.flow.control.InstanceCleaner: Returns the actor to send the rejection messages to.
getRejectionMessagesActor() - Method in class adams.flow.control.SpectrumCleaner: Returns the actor to send the rejection messages to.
getReldiff() - Method in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: Returns the relative difference.
getRemoveAsString() - Method in class adams.opt.genetic.RonWeasley.RonWeasleyJob: Generates a range string of attributes to keep (= one has to use the inverse matching sense with the Remove filter).
getRemoveFilter(Instances) - Static method in class adams.data.instances.ArffUtils: Initializes the Remove filter for removing all IDs (and string attributes) from the dataset.
getRemoveUnused() - Method in class weka.filters.unsupervised.attribute.RangeBasedSavitzkyGolay: Gets whether unused attributes (ones that are not covered by any of the ranges) are removed from the output.
getRemoveUnused() - Method in class weka.filters.unsupervised.attribute.SegmentedDownSample: Gets whether unused attributes (ones that are not covered by any of the ranges) are removed from the output.
getRemoveUnused() - Method in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: Gets whether unused attributes (ones that are not covered by any of the ranges) are removed from the output.
getRemoveWithMissing() - Method in class adams.data.cleaner.instance.IQRCleaner: Returns whether to remove instances with missing values.
getReport() - Method in class adams.data.spectrum.MultiSpectrum: get sample data.
getReport() - Method in class adams.data.spectrum.Spectrum: get sample data.
getReport() - Method in class adams.data.threeway.ThreeWayData: Get the report (reference values).
getReportField() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Returns the report field to output.
getReportProvider() - Method in class adams.flow.transformer.DeleteDbSampleDataValue: Returns the report provider to use for removing the
getReportProvider() - Method in class adams.flow.transformer.SampleDataDbReader: Returns the report provider to use.
getReportProvider() - Method in class adams.flow.transformer.SampleDataDbWriter: Returns the report provider to use for writing the reports to the database.
getReportProvider() - Method in class adams.flow.transformer.SampleDataValueDbWriter: Returns the report provider to use for removing the
getReportProvider() - Method in class adams.gui.visualization.spectrum.SampleDataFactory.Table: Returns the provider for accessing the reports in the database.
GetRequest - Class in nz.ac.waikato.adams.webservice.spectral.get: Java class for getRequest complex type.
GetRequest() - Constructor for class nz.ac.waikato.adams.webservice.spectral.get.GetRequest
getRequiredField() - Method in class adams.db.SpectrumConditionsSingle: Returns the required field.
getRequiredFields() - Method in class adams.db.SpectrumConditionsMulti: Returns the required fields.
getRequiredFlowClass() - Method in class adams.gui.scripting.SpectralCommandProcessor: Returns the class that is required in the flow.
getRequirements() - Method in class adams.gui.scripting.AbstractSpectrumPanelScriptlet: Returns the class(es) of an object that must be present for this action to be executed.
GetResponse - Class in nz.ac.waikato.adams.webservice.spectral.get: Java class for getResponse complex type.
GetResponse() - Constructor for class nz.ac.waikato.adams.webservice.spectral.get.GetResponse
getRevision() - Method in class weka.classifiers.meta.SpectrumClassifier: Returns the revision string.
getRevision() - Method in class weka.clusterers.SpectrumClusterer: Returns the revision string.
getRevision() - Method in class weka.core.converters.CALSpectrumLoader: Returns the revision string.
getRevision() - Method in class weka.filters.unsupervised.attribute.BestBySLR: Returns the revision string.
getRevision() - Method in class weka.filters.unsupervised.attribute.SpectrumFilter: Returns the revision string.
getRowCount() - Method in class adams.gui.selection.SelectSpectrumPanel.TableModel: Returns the actual number of entries in the table.
getRowCount() - Method in class adams.gui.visualization.spectrum.SpectrumTableModel: Returns the number of rows in the model.
getRowFinder() - Method in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: Returns the row finder to use for locating the rows to import.
getRowFinder() - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Returns the row finder to use for locating the rows to import.
getRowFinder() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Returns the row finder to use for filtering the rows.
getRowFormat() - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Returns the class of the row that the converter generates.
getRowFormat() - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Returns the class of the row that the converter generates.
getRowID() - Method in class adams.data.conversion.SpreadSheetColumnsToSampleData: Returns the (optional) row that contains the sample ID.
getRowID() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Returns the (optional) row that contains the sample ID.
getRowNum() - Method in class adams.data.io.input.foss.FossHelper.FossFields: Get actual (non-deleted)m row number.
getRowSampleDataNames() - Method in class adams.data.conversion.SpreadSheetRowsToSampleData: Returns the row that contains the sample data names.
getRowSampleDataNames() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns the row that contains the sample data names.
getRowsAmplitude() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Returns the rows with amplitude information.
getRowsAmplitude() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns the rows with the amplitude information.
getRowsSampleData() - Method in class adams.data.conversion.SpreadSheetColumnsToSampleData: Returns the rows with sampledata.
getRowsSampleData() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Returns the rows with sampledata.
getRowsSampleDataValues() - Method in class adams.data.conversion.SpreadSheetRowsToSampleData: Returns the rows with the sample data values.
getRowWaveNumber() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns the row with the wavenumber information.
getSampleData() - Method in class adams.data.io.input.AbstractSampleDataReader: Returns the table object to use for accessing the reports.
getSampleData(AbstractDatabaseConnection) - Method in class adams.db.autodetect.SpectralDbBackend: Returns the handler for the sample data table.
getSampleData(AbstractDatabaseConnection) - Method in class adams.db.h2.SpectralDbBackend: Returns the handler for the sample data table.
getSampleData(AbstractDatabaseConnection) - Method in class adams.db.mirrored.SpectralDbBackend: Returns the handler for the sample data table.
getSampleData(AbstractDatabaseConnection) - Method in class adams.db.mssql.SpectralDbBackend: Returns the handler for the sample data table.
getSampleData(AbstractDatabaseConnection) - Method in class adams.db.mysql.SpectralDbBackend: Returns the handler for the sample data table.
getSampleData(AbstractDatabaseConnection) - Method in class adams.db.postgresql.SpectralDbBackend: Returns the handler for the sample data table.
getSampleData(AbstractDatabaseConnection) - Method in interface adams.db.SpectralDbBackend: Returns the handler for the sample data table.
getSampleData(AbstractDatabaseConnection) - Method in class adams.db.sqlite.SpectralDbBackend: Returns the handler for the sample data table.
getSampleDataColumns() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Returns the columns containing the sample data.
getSampleDataF() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Returns the SampleDataT singleton to use.
getSampleDataFormat() - Method in class adams.data.spectrumfilter.ChangeFormat: Returns the format for the sample data.
getSampleDataHandler() - Method in class adams.db.h2.SpectrumT: Returns the corresponding SampleData handler.
getSampleDataHandler() - Method in class adams.db.mirrored.SpectrumT: Returns the corresponding SampleData handler.
getSampleDataHandler() - Method in class adams.db.mssql.SpectrumT: Returns the corresponding SampleData handler.
getSampleDataHandler() - Method in class adams.db.mysql.SpectrumT: Returns the corresponding SampleData handler.
getSampleDataHandler() - Method in class adams.db.postgresql.SpectrumT: Returns the corresponding SampleData handler.
getSampleDataHandler() - Method in class adams.db.SpectrumF: Returns the corresponding SampleData handler.
getSampleDataHandler() - Method in interface adams.db.SpectrumIntf: Returns the corresponding SampleData handler.
getSampleDataHandler() - Method in class adams.db.sqlite.SpectrumT: Returns the corresponding SampleData handler.
getSampleDataLabelsColumn() - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Returns the column containing the labels for the sample data values.
getSampleDataNamesInHeader() - Method in class adams.data.conversion.SpreadSheetRowsToSampleData: Returns whether the sample data names are in the header.
getSampleDataNamesInHeader() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns whether the sample data names are in the header.
getSampleDataRows() - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Returns the range of rows containing the sample data.
getSampleDataTable() - Method in class adams.data.spectrumfilter.AbstractDatabaseFilter: Returns the correct table object based on the filter's setup.
getSampleDataTable() - Method in class adams.gui.selection.SelectSpectrumPanel: Returns the correct table object, depending whether active or store table is used.
GetSampleDataValue - Class in adams.flow.transformer: Retrieves a value from sample data.
GetSampleDataValue() - Constructor for class adams.flow.transformer.GetSampleDataValue: Default constructor.
GetSampleDataValue(Field) - Constructor for class adams.flow.transformer.GetSampleDataValue: Constructor with field.
GetSampleDataValue(Field, Conversion) - Constructor for class adams.flow.transformer.GetSampleDataValue: Constructor with field and conversion.
getSampleHeader(Spectrum, int) - Method in class adams.data.io.output.NIRSpectrumWriter: Create a SampleHeader from a Spectrum and position in list/file.
getSampleID() - Method in class adams.data.io.input.OpusSpectrumReader: Get id field.
getSampleID() - Method in class adams.data.multispectrumoperation.Remove: Returns the regular expression that the sample ID of a spectrum must match in order to get removed.
getSampleID() - Method in class adams.flow.transformer.InstanceToSpectrum: Get sample id regex.
getSampleID() - Method in class adams.flow.transformer.MultiSpectrumRemove: Returns the regular expression that the sample ID of a spectrum must match in order to get removed.
getSampleID1() - Method in class adams.data.io.output.NIRSpectrumWriter: Get sample id1.
getSampleID2() - Method in class adams.data.io.output.NIRSpectrumWriter: Get sample id2.
getSampleID3() - Method in class adams.data.io.output.NIRSpectrumWriter: Get sample id3.
getSampleIdAt(int) - Method in class adams.gui.tools.idprovider.TableModel: Returns the sample ID at the specified location.
getSampleIDColumn() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Returns the column containing the sample ID.
getSampleIDExtraction() - Method in class adams.data.io.input.ASCIIXYSpectrumReader: Returns the scheme for extracting the sample ID from the filename.
getSampleIDExtraction() - Method in interface adams.data.io.input.SpectrumReaderWithSampleIDExtraction: Returns the scheme for extracting the sample ID from the filename.
getSampleIDLocation() - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Returns the where the sample ID is located.
getSampleIDName() - Static method in class adams.data.instances.ArffUtils: Returns the name of the attribute containing the sample ID of the spectrum.
getSampleIDRegExp() - Method in class adams.db.AbstractSpectrumConditions: Returns the regular expression for the spectrum name.
getSampleIDRegExp() - Method in interface adams.db.SampleIDRegExpSupporter: Returns the regular expression to use on the sample ID.
getSampleIDRegExp() - Method in class adams.db.SpectrumIDConditions: Returns the regular expression for the spectrum name.
getSampleIDRow() - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Returns the row that contains the sample ID.
getSampleInfo(Spectrum, int) - Method in class adams.data.io.output.NIRSpectrumWriter: Create a SampleInfo for the file footer based on a Spectrum and it's position in list/file.
getSampleType() - Method in class adams.data.multispectrumoperation.Remove: Returns the regular expression that the sample Type of a spectrum must match in order to get removed.
getSampleType() - Method in class adams.flow.transformer.MultiSpectrumRemove: Returns the regular expression that the sample Type of a spectrum must match in order to get removed.
getSampleType(FossHelper.FossFields) - Method in class adams.data.io.input.CALSpectrumReader: Get Sampletype.
getSampleTypeRegExp() - Method in class adams.db.AbstractSpectrumConditions: Returns the regular expression for the sample type.
getSampleTypeRegExp() - Method in interface adams.db.SampleTypeRegExpSupporter: Returns the regular expression to use on the sample type.
getSampleTypeRegExp() - Method in class adams.db.SpectrumIDConditions: Returns the regular expression for the sample type.
getScale() - Method in class adams.data.spectrumfilter.Covariance: Get scale?
getScale() - Method in class adams.data.spectrumfilter.LRCoeff: Get scale?
getScores() - Method in class adams.data.spectrumanalysis.PCA: Returns the scores.
getScores() - Method in class adams.data.spectrumanalysis.PLS: Returns the scores.
getScriptingEngine() - Method in class adams.gui.visualization.spectrum.SpectrumContainerTable: Returns the current scripting engine, can be null.
getScriptingEngine() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Returns the current scripting engine, can be null.
getScriptingEngine() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Returns the current scripting engine, can be null.
getSearch() - Method in class adams.data.evaluator.instance.AbstractNearestNeighborBasedEvaluator: Returns the nearest neighbor search algorithm.
getSeed() - Method in class adams.data.cleaner.instance.RemoveOutliers: Returns the seed value.
getSeed() - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Returns the seed value for cross-validation.
getSeed() - Method in class adams.data.evaluator.instance.CrossValidatedPrediction: Returns the seed value for cross-validation.
getSeed() - Method in class adams.data.evaluator.instance.EnsembleEvaluator: Returns the seed value.
getSeed() - Method in class adams.data.evaluator.instance.FakeEvaluator: Returns the seed value for the random values.
getSeed() - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Returns the seed value.
getSeed() - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Returns the seed value.
getSegmentEnd() - Method in class adams.data.io.input.foss.FossHelper
getSegmentInc() - Method in class adams.data.io.input.foss.FossHelper
getSegmentLengths() - Method in class adams.data.io.input.foss.FossHelper
getSegments() - Method in class adams.opt.genetic.RonWeasley: Get number of s-g segments
getSegmentsOffset() - Method in class adams.data.io.input.foss.FossStdise: Get start of segments data.
getSegmentStart() - Method in class adams.data.io.input.foss.FossHelper
getSegmentsType() - Method in class adams.data.io.input.foss.FossHelper: Get segment type (00=TILFIL, 01=EQLSPC, 02=FILFIL, 03=SINSPA
getSegmentWidths() - Method in class adams.data.io.output.NIRSpectrumWriter: Get segments.
getSegs() - Method in class adams.data.io.input.foss.FossStdise: Get segments as array.
getSelectedIndices() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Returns the indices of the selected spectra.
getSelectedPanel() - Method in class adams.gui.visualization.spectrum.MultiSpectrumPanel: Returns the currently selected spectrum panel.
getSelectedSampleIDs() - Method in class adams.gui.tools.idprovider.TableModel: Returns the selected items (sample IDs).
getSelectedSpectra() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Returns the selected spectra.
getSelectedWaveNumberPaintlet() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Returns the paintlet for painting the selected wave number.
getSendToClasses() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Returns the classes that the supporter generates.
getSendToClasses() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Returns the classes that the supporter generates.
getSendToItem(Class[]) - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Returns the object to send.
getSendToItem(Class[]) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Returns the object to send.
getSeparator() - Method in class adams.data.io.input.ASCIIXYSpectrumReader: Returns the separator in use.
getSeparator() - Method in class adams.data.io.input.SimpleXYZReader: Returns the string used as separator for the columns, '\t' for tab.
getSeparator() - Method in class adams.data.io.output.ASCIIXYSpectrumWriter: Returns the separator to use between X and Y columns.
getSeparator() - Method in class adams.data.io.output.SimpleXYZWriter: Returns the string used as separator for the columns, '\t' for tab.
getSequencePanel() - Method in class adams.gui.visualization.spectrum.AbstractSpectrumPaintlet: Returns the sequence panel currently in use.
getSerializationFile() - Method in class adams.data.cleaner.instance.AbstractSerializableCleaner: Returns the current file to serialize to.
getSerializationFile() - Method in class adams.data.cleaner.spectrum.AbstractSerializableCleaner: Returns the current file to serialize to.
getSerializationFile() - Method in class adams.data.evaluator.instance.AbstractSerializableEvaluator: Returns the current file to serialize to.
getSerializationFile() - Method in class adams.data.postprocessor.instances.AbstractSerializablePostProcessor: Returns the current file to serialize to.
getSerializationFile() - Method in class adams.data.spectrumfilter.AbstractSerializableFilter: Returns the current file to serialize to.
getSerialNo() - Method in class adams.data.io.output.NIRSpectrumWriter: Get serial no.
getSetupDialog(Dialog, Dialog.ModalityType) - Static method in class adams.gui.visualization.spectrum.HistogramFactory: Returns an instance of a setup dialog for displaying histograms.
getSetupDialog(Frame, boolean) - Static method in class adams.gui.visualization.spectrum.HistogramFactory: Returns an instance of a setup dialog for displaying histograms.
getSGBits() - Method in class adams.opt.genetic.RonWeasley
getSGFromWeights(int, int[]) - Method in class adams.opt.genetic.RonWeasley
getShowReportTable() - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Returns whether the report table is visible.
getShowSidePanel() - Method in class adams.flow.sink.SpectrumDisplay: Returns whether to show the side panel or not.
getSingleton() - Static method in class adams.db.AbstractSpectralDbBackend: Returns the singleton.
getSingleton(AbstractDatabaseConnection) - Static method in class adams.db.generic.SampleDataT: Returns the singleton of the table (active).
getSingleton(AbstractDatabaseConnection) - Static method in class adams.db.generic.SpectrumT: Returns the singleton of the table (active).
getSingleton(AbstractDatabaseConnection) - Static method in class adams.db.h2.SampleDataT: Returns the singleton of the table (active).
getSingleton(AbstractDatabaseConnection) - Static method in class adams.db.h2.SpectrumT: Returns the singleton of the table (active).
getSingleton(AbstractDatabaseConnection) - Static method in class adams.db.mssql.SampleDataT: Returns the singleton of the table (active).
getSingleton(AbstractDatabaseConnection) - Static method in class adams.db.mssql.SpectrumT: Returns the singleton of the table (active).
getSingleton(AbstractDatabaseConnection) - Static method in class adams.db.mysql.SampleDataT: Returns the singleton of the table (active).
getSingleton(AbstractDatabaseConnection) - Static method in class adams.db.mysql.SpectrumT: Returns the singleton of the table (active).
getSingleton(AbstractDatabaseConnection) - Static method in class adams.db.postgresql.SampleDataT: Returns the singleton of the table (active).
getSingleton(AbstractDatabaseConnection) - Static method in class adams.db.postgresql.SpectrumT: Returns the singleton of the table (active).
getSingleton(AbstractDatabaseConnection) - Static method in class adams.db.SampleDataF: Returns the singleton of the facade.
getSingleton(AbstractDatabaseConnection) - Static method in class adams.db.SpectrumF: Returns the singleton of the facade.
getSingleton(AbstractDatabaseConnection) - Static method in class adams.db.sqlite.SampleDataT: Returns the singleton of the table (active).
getSingleton(AbstractDatabaseConnection) - Static method in class adams.db.sqlite.SpectrumT: Returns the singleton of the table (active).
getSingleton(AbstractDatabaseConnection) - Static method in class adams.gui.scripting.SpectralScriptingEngine: Returns the singleton instance of the scripting engine.
getSingleton(AbstractDatabaseConnection, SampleDataIntf) - Static method in class adams.db.mirrored.SampleDataT: Returns the singleton of the table.
getSingleton(AbstractDatabaseConnection, SpectrumIntf) - Static method in class adams.db.mirrored.SpectrumT: Returns the singleton of the table.
getSkipFields() - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Returns whether to skip fields.
getSkipFieldsRegExp() - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Returns the regular expression for identifying fields to skip (if enabled).
getSortedAttributeArray(Instances) - Method in class weka.filters.unsupervised.attribute.BestBySLR: Return array of attributes in sorted order
getSortOnInsertTimestamp() - Method in class adams.db.AbstractSpectrumConditions: Returns whether to sort on SampleData.INSERT_TIMESTAMP instead of auto ID.
getSortOnSampleID() - Method in class adams.db.AbstractSpectrumConditions: Returns whether to sort on SampleData.SAMPLE_ID instead of auto ID.
getSource() - Method in class adams.data.spectrumfilter.ReportFieldFromStringValue: Returns the source field in the report to get the string to apply the regular expression to.
getSource() - Method in class adams.data.spectrumfilter.ReportFieldFromStringValueWithLookup: Returns the source field to use.
getSources() - Method in class adams.data.spectrumanalysis.FastICA: Returns the sources.
getSpectra() - Method in class adams.data.io.input.SPCSpectrumReader.FileParser: Returns the parsed spectra.
getSpectra() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.MultiSpectrum: Gets the value of the spectra property.
getSpectraBlockSize() - Method in class adams.data.io.input.foss.FossHelper: Get size of the spectral data block.
getSpectraForRow(int) - Method in class adams.data.io.input.foss.FossHelper: Get spectrum of row.
getSpectralDataAttributes() - Method in class adams.flow.transformer.InstanceToSpectrum: Get which attributes to use for spectral data.
getSpectralGetServicePort() - Method in class nz.ac.waikato.adams.webservice.spectral.get.SpectralGetServiceService
getSpectralGetServicePort(WebServiceFeature...) - Method in class nz.ac.waikato.adams.webservice.spectral.get.SpectralGetServiceService
getSpectralPutServicePort() - Method in class nz.ac.waikato.adams.webservice.spectral.put.SpectralPutServiceService
getSpectralPutServicePort(WebServiceFeature...) - Method in class nz.ac.waikato.adams.webservice.spectral.put.SpectralPutServiceService
getSpectralTransformServicePort() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.SpectralTransformServiceService
getSpectralTransformServicePort(WebServiceFeature...) - Method in class nz.ac.waikato.adams.webservice.spectral.transform.SpectralTransformServiceService
getSpectraOffsetForRow(int) - Method in class adams.data.io.input.foss.FossHelper: Get start of spectrum for given row.
getSpectrum() - Method in class adams.data.io.input.AbstractSampleDataReader: Returns the table object to use for accessing the spectra.
getSpectrum() - Method in class adams.data.io.input.SPCSpectrumReader.SubFileParser: Returns the parsed spectrum.
getSpectrum() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.UploadRequest: Gets the value of the spectrum property.
getSpectrum() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.UploadRequest: Gets the value of the spectrum property.
getSpectrum() - Method in class nz.ac.waikato.adams.webservice.spectral.get.GetResponse: Gets the value of the spectrum property.
getSpectrum() - Method in class nz.ac.waikato.adams.webservice.spectral.put.PutRequest: Gets the value of the spectrum property.
getSpectrum() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.TransformRequest: Gets the value of the spectrum property.
getSpectrum() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.TransformResponse: Gets the value of the spectrum property.
getSpectrum(AbstractDatabaseConnection) - Method in class adams.db.autodetect.SpectralDbBackend: Returns the handler for the spectrum table.
getSpectrum(AbstractDatabaseConnection) - Method in class adams.db.h2.SpectralDbBackend: Returns the handler for the spectrum table.
getSpectrum(AbstractDatabaseConnection) - Method in class adams.db.mirrored.SpectralDbBackend: Returns the handler for the spectrum table.
getSpectrum(AbstractDatabaseConnection) - Method in class adams.db.mssql.SpectralDbBackend: Returns the handler for the spectrum table.
getSpectrum(AbstractDatabaseConnection) - Method in class adams.db.mysql.SpectralDbBackend: Returns the handler for the spectrum table.
getSpectrum(AbstractDatabaseConnection) - Method in class adams.db.postgresql.SpectralDbBackend: Returns the handler for the spectrum table.
getSpectrum(AbstractDatabaseConnection) - Method in interface adams.db.SpectralDbBackend: Returns the handler for the spectrum table.
getSpectrum(AbstractDatabaseConnection) - Method in class adams.db.sqlite.SpectralDbBackend: Returns the handler for the spectrum table.
GetSpectrum - Class in adams.flow.rest: REST plugin for retrieving spectra.
GetSpectrum() - Constructor for class adams.flow.rest.GetSpectrum
GetSpectrumAmplitude - Class in adams.flow.transformer: Retrieves the spectrum's amplitude either via its index or wave number.
GetSpectrumAmplitude() - Constructor for class adams.flow.transformer.GetSpectrumAmplitude
GetSpectrumAmplitude.RetrievalType - Enum in adams.flow.transformer: Defines how to retrieve the amplitude.
getSpectrumBlockType() - Method in class adams.data.io.input.OpusSpectrumReaderExt: Returns the block type of the spectrum to extract.
getSpectrumColumns() - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Returns the coumns containing spectral data.
getSpectrumF() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.DataCollector: Returns the SpectrumT singleton to use.
getSpectrumF() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Returns the SpectrumT singleton to use.
getSpectrumFormat() - Method in class adams.data.spectrumfilter.ChangeFormat: Returns the format for the spectrum.
getSpectrumHandler() - Method in class adams.db.h2.SampleDataT: Returns the corresponding Spectrum handler.
getSpectrumHandler() - Method in class adams.db.mirrored.SampleDataT: Returns the corresponding Spectrum handler.
getSpectrumHandler() - Method in class adams.db.mssql.SampleDataT: Returns the corresponding Spectrum handler.
getSpectrumHandler() - Method in class adams.db.mysql.SampleDataT: Returns the corresponding Spectrum handler.
getSpectrumHandler() - Method in class adams.db.postgresql.SampleDataT: Returns the corresponding Spectrum handler.
getSpectrumHandler() - Method in class adams.db.SampleDataF: Returns the corresponding Spectrum handler.
getSpectrumHandler() - Method in interface adams.db.SampleDataIntf: Returns the corresponding Spectrum handler.
getSpectrumHandler() - Method in class adams.db.sqlite.SampleDataT: Returns the corresponding Spectrum handler.
GetSpectrumHelper - Class in adams.flow.core: Helper class for converting spectra.
GetSpectrumHelper() - Constructor for class adams.flow.core.GetSpectrumHelper
getSpectrumPanel() - Method in class adams.gui.scripting.AbstractSpectrumPanelScriptlet: Returns the spectrum panel, if available.
getSpectrumPanel() - Method in class adams.gui.scripting.SpectralCommandProcessor: Returns the spectrum panel, if available.
getSpectrumPanel() - Method in class adams.gui.visualization.spectrum.SimpleSpectrumPaintlet: Returns the currently set total ion count panel, can be null.
getSpectrumPanel() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Returns the panel for painting the spectrums.
getSpectrumPanel() - Method in class adams.gui.visualization.spectrum.SpectrumPaintlet: Returns the currently set total ion count panel, can be null.
getSpectrumTable() - Method in class adams.data.spectrumfilter.AbstractDatabaseFilter: Returns the correct table object based on the filter's setup.
getSpectrumTable() - Method in class adams.gui.selection.SelectSpectrumPanel: Returns the correct table object, depending whether active or store table is used.
getSpectrumType() - Method in class adams.data.io.input.SoilCaresScannerSpectrumReader: Returns the type of spectrum to read.
getStandardize() - Method in class adams.data.multifilter.Average: Returns the filter to use for standardizing the spectra.
getStart() - Method in class adams.data.io.input.CALSpectrumReader: Returns the start point setting.
getStart() - Method in class adams.data.io.input.opus.OpusBlockHelper.Block: Returns the start of the block.
getStart() - Method in class adams.data.io.input.OpusSpectrumReader: Returns the start point setting.
getStart() - Method in class adams.data.spectrumfilter.Rebase: Returns the new starting point for the wave numbers.
getStart() - Method in class weka.filters.unsupervised.attribute.SavitzkyGolayRange: Returns the first amplitude
getStartDate() - Method in class adams.db.AbstractSpectrumConditions: Returns the start date.
getStartDate() - Method in class adams.db.OrphanedSampleDataConditions: Returns the start date.
getStartPoints() - Method in class adams.data.io.output.NIRSpectrumWriter: Get start points.
getStatistic() - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Returns the statistic used as evaluation output.
getStatistic() - Method in class adams.data.evaluator.instance.CrossValidatedPrediction: Returns the statistic used as evaluation output.
getStatistic() - Method in class adams.flow.transformer.threewaydatamerge.CollapseX: Returns the type of statistic to calculate.
getStatisticDescription() - Method in class adams.data.statistics.L1PointStatistic: Returns a description for this statistic, i.e., chromatgram ID and timestamp.
getStatisticDescription() - Method in class adams.data.statistics.SpectrumStatistic: Returns a description for this statistic, i.e., spectrum ID.
getStatisticDescription() - Method in class adams.data.statistics.ThreeWayDataStatistic: Returns a description for this statistic, i.e., ID.
getStep() - Method in class adams.data.spectrumfilter.AbstractStandardiseFilter: Returns the step
getStorageName() - Method in class adams.flow.transformer.MergeSampleDataFromMap: Returns the name of the stored map with the sample data objects.
getStorageName() - Method in class adams.flow.transformer.MultiSpectrumAdd: Returns the name of the stored value.
getStoreWaveNo() - Method in class adams.flow.transformer.BulkSpectrumDbWriter: Returns whether to store the wave numbers as well.
getStoreWaveNo() - Method in class adams.flow.transformer.SpectrumDbWriter: Returns whether to store the wave numbers as well.
getStructure() - Method in class weka.core.converters.CALSpectrumLoader: Determines and returns (if possible) the structure (internally the header) of the data set as an empty set of instances.
getSubGenerators() - Method in class adams.data.threewayfeatures.MultiThreeWayDataFeatureGenerator: Returns the generators to use.
getSuccess() - Method in class adams.data.spectrumfilter.ConditionalReportField: Returns the success value, ie the value to use when the condition evaluates to true.
getTable(SampleData) - Static method in class adams.gui.visualization.spectrum.SampleDataFactory: Returns a new table for the given report.
getTarget() - Method in class adams.data.spectrumfilter.ConditionalReportField: Returns the target field in the report to store the result in.
getTarget() - Method in class adams.data.spectrumfilter.ReportFieldFromStringValue: Returns the target field in the report to store the result in.
getTarget() - Method in class adams.data.spectrumfilter.ReportFieldFromStringValueWithLookup: Returns the target field to use for the result.
getTechnicalInformation() - Method in class adams.data.spectrumfilter.AndrewsCurves: Returns an instance of a TechnicalInformation object, containing detailed information about the technical background of this class, e.g., paper reference or book this class is based on.
getTechnicalInformation() - Method in class adams.flow.transformer.SpectralAngleMapper: Returns an instance of a TechnicalInformation object, containing detailed information about the technical background of this class, e.g., paper reference or book this class is based on.
getTechnicalInformation() - Method in class weka.filters.unsupervised.attribute.RangeBasedSavitzkyGolay: Returns an instance of a TechnicalInformation object, containing detailed information about the technical background of this class, e.g., paper reference or book this class is based on.
getTechnicalInformation() - Method in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: Returns an instance of a TechnicalInformation object, containing detailed information about the technical background of this class, e.g., paper reference or book this class is based on.
getText() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Returns the fixed text to output.
getText(byte[], int) - Method in class adams.data.io.input.opus.OpusBlockHelper.Block: Returns the text with the given ID.
getText(byte[], int) - Static method in class adams.data.io.input.opus.OpusBlockHelper: Returns the 0-terminated text at the specified offset.
getText(int) - Method in class adams.data.io.input.opus.OpusBlockHelper.Block: Returns the text at the specified offset.
getTextBlockOffset(byte[]) - Method in class adams.data.io.input.OpusSpectrumReader: Get position of Text Data.
getTextBlockSize(byte[]) - Method in class adams.data.io.input.OpusSpectrumReader: Size of Text Block (in 4-byte words).
getTextColor() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Returns the color for the text.
getTextOffset(byte[]) - Method in class adams.data.io.input.OpusSpectrumReader: Find position of Text Block offset
getThreshold() - Method in class adams.data.multispectrumoperation.outlierremoval.CorrelationBasedThreshold: Returns the threshold to use.
getThreshold() - Method in class adams.data.multispectrumoperation.outlierremoval.CosineSimilarityBasedThreshold: Returns the threshold to use.
getThreshold() - Method in class adams.data.multispectrumoperation.outlierremoval.MeanSpectrumCosineSimilarityBasedThreshold: Returns the threshold to use.
getThreshold() - Method in class adams.data.spectrumoutlier.Oscillation: Returns the threshold for the correlation coefficient.
getTimestamp() - Method in class adams.data.io.output.NIRSpectrumWriter: Get the timestamp to use in the file.
getTitle() - Method in class adams.gui.menu.DeleteSampleData: Returns the title of the window (and text of menuitem).
getTitle() - Method in class adams.gui.menu.DeleteSpectra: Returns the title of the window (and text of menuitem).
getTitle() - Method in class adams.gui.menu.ExportValidationSets: Returns the title of the window (and text of menuitem).
getTitle() - Method in class adams.gui.menu.ListSampleData: Returns the title of the window (and text of menuitem).
getTitle() - Method in class adams.gui.menu.SpectrumExplorer: Returns the title of the window (and text of menuitem).
getTitle() - Method in class adams.gui.menu.ThreeWayDataHeatmapViewer: Returns the title of the window (and text of menuitem).
getTitle() - Method in class adams.gui.menu.UpdateSampleData: Returns the title of the window (and text of menuitem).
getTitle() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Returns the database ID or filename as title.
getTolerateHeaderChanges() - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Returns whether to tolerate header changes and merely re-generating the header instead of throwing an exception.
getTotal() - Method in class adams.data.io.input.foss.FossHelper: Total number of rows, including deleted rows.
getTransferPrefix() - Method in class adams.data.conversion.MultiSpectrumToSpectra: Returns the (optional) prefix for report fields that get transferred.
getTransferPrefix() - Method in class adams.flow.transformer.MultiSpectrumFilter: Returns the (optional) prefix for report fields that get transferred.
getTransferRegExp() - Method in class adams.data.conversion.MultiSpectrumToSpectra: Returns the regular expression that the field names must match in order to get transferred.
getTransferRegExp() - Method in class adams.flow.transformer.MultiSpectrumFilter: Returns the regular expression that the field names must match in order to get transferred.
getTransferReport() - Method in class adams.data.conversion.MultiSpectrumToSpectra: Returns whether to transfer the report values from the multi-spectrum into the sub-spectra.
getTransferReport() - Method in class adams.flow.transformer.MultiSpectrumFilter: Returns whether to transfer the report values from the multi-spectrum into the sub-spectra.
getTransformer() - Method in class adams.data.spectrumfilter.AmplitudeTransform: Returns the transformer to use.
getType() - Method in class adams.data.conversion.SpectrumToArray: Returns the type of data to output.
getType() - Method in class adams.data.io.input.ASCSpectrumReader.ParsedFile: Returns the type.
getType() - Method in class adams.data.io.input.opus.OpusBlockHelper.Block: Returns the type of the block.
getType() - Method in class adams.data.io.input.opus.OpusBlockHelper.CommandlineData: Returns the operation type.
getType() - Method in class adams.data.io.input.ScioLabExportSpectrumReader: Returns the type of spectrum to read.
getType() - Method in class adams.data.spectrum.Spectrum: Returns the sample type.
getType() - Method in class adams.flow.transformer.GetSpectrumAmplitude: Returns how to retrieve the amplitude.
getType() - Method in class adams.flow.transformer.SetSpectrumAmplitude: Returns how to retrieve the amplitude.
getType() - Method in class adams.flow.transformer.SpectrumInfo: Returns the type of information to generate.
getType() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.Property: Gets the value of the type property.
getType() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.Property: Gets the value of the type property.
getType() - Method in class nz.ac.waikato.adams.webservice.spectral.get.Property: Gets the value of the type property.
getType() - Method in class nz.ac.waikato.adams.webservice.spectral.put.Property: Gets the value of the type property.
getType() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.Property: Gets the value of the type property.
getTypefield() - Method in class adams.data.io.input.CALSpectrumReader: Get type field.
getUndoObject() - Method in class adams.gui.scripting.SpectralCommandProcessor: Returns the object that is to be used for the undo point.
getUniqueName(HashSet<String>, String) - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: Creates a unique ID from of the given one, if necessary, testing against the specified IDs.
getUnsigned() - Method in class adams.data.io.input.FitsLibsReader: Returns whether the numbers are to be interpreted as unsigned.
getUpdateContainerColor() - Method in class adams.gui.visualization.spectrum.ReportColorSpectrumPaintlet: Returns whether to update the container's color with the color determined by this paintlet.
getUpdateInterval() - Method in class adams.flow.sink.spectrumdisplay.SimplePlotUpdater: Returns the number of tokens after which the display is being updated.
getUpdateWaveNumbers() - Method in class adams.data.spectrumfilter.Rebase: Returns whether to update the wave numbers using the specified step size.
getUpperMaxAmplitude() - Method in class adams.data.spectrumimage.AbstractSpectrumImageGeneratorWithRange: Returns the upper bound for the maximum amplitude.
getUpperMinAmplitude() - Method in class adams.data.spectrumimage.AbstractSpectrumImageGeneratorWithRange: Returns the upper bound for the minimum amplitude.
getUpperPercentile() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.DataCollector: Returns the upper percentile.
getUpperPercentile() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Returns the upper percentile.
getUpperPercentile() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.InterPercentileRange: Returns the upper percentile.
getUseAbsoluteError() - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Returns whether to use an absolute error (ie no direction).
getUseAbsoluteSource() - Method in class adams.data.io.input.AbstractSpectrumReader: Returns whether to use absolute source filename rather than just name.
getUseAbsoluteSource() - Method in class adams.data.io.input.AbstractThreeWayDataReader: Returns whether to use absolute source filename rather than just name.
getUseCompression() - Method in class adams.data.io.output.SimpleSpectrumWriter: Returns whether compression is in use.
getUseCompression() - Method in class adams.data.io.output.SimpleXYZWriter: Returns whether compression is in use.
getUseCustomComparator() - Method in class adams.data.conversion.SpectraToMultiSpectrum: Returns whether to use a custom comparator.
getUseCustomComparator() - Method in class adams.flow.transformer.SpectrumFileReader: Returns whether to use a custom comparator.
getUseEvaluatorResetVariable() - Method in class adams.flow.transformer.Evaluator: Returns whether to use a variable to monitor for changes in order to reset the evaluator.
getUseFilenameAsID() - Method in class adams.data.io.input.AbstractJCampSpectrumReader: Returns whether to use the filename as ID.
getUseFilenameAsID() - Method in class adams.data.io.input.JCampDX2SpectrumReader: Returns whether to use the filename as ID.
getUseFilenameAsSampleID() - Method in class adams.data.io.input.RelabSpectrumReader: Returns whether to use the filename (without path, uppercase) in the sample id as well.
getUseModelResetVariable() - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Returns whether to use a variable to monitor for changes in order to reset the model.
getUseReferenceAndMetaData() - Method in class adams.data.conversion.SpectrumToJson: Returns whether only the specified reference and meta-data report values are output (in separate sections).
getUseReferenceAndMetaData() - Method in class adams.data.io.output.JsonSpectrumWriter: Returns whether only the specified reference and meta-data report values are output (in separate sections).
getUserMode() - Method in class adams.gui.menu.DeleteSampleData: Returns the user mode, which determines visibility as well.
getUserMode() - Method in class adams.gui.menu.DeleteSpectra: Returns the user mode, which determines visibility as well.
getUserMode() - Method in class adams.gui.menu.ExportValidationSets: Returns the user mode, which determines visibility as well.
getUserMode() - Method in class adams.gui.menu.ListSampleData: Returns the user mode, which determines visibility as well.
getUserMode() - Method in class adams.gui.menu.SpectrumExplorer: Returns the user mode, which determines visibility as well.
getUserMode() - Method in class adams.gui.menu.ThreeWayDataHeatmapViewer: Returns the user mode, which determines visibility as well.
getUserMode() - Method in class adams.gui.menu.UpdateSampleData: Returns the user mode, which determines visibility as well.
getUseStoreTable() - Method in class adams.data.spectrumfilter.AbstractDatabaseFilter: Returns whether to read from the active or store table.
getValidate() - Method in class adams.data.io.input.JCampDX2SpectrumReader: Returns whether to use a validating parser.
getValue() - Method in class adams.flow.transformer.SetEvaluationMetaData: Returns the value to store.
getValue() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.Property: Gets the value of the value property.
getValue() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.Property: Gets the value of the value property.
getValue() - Method in class nz.ac.waikato.adams.webservice.spectral.get.Property: Gets the value of the value property.
getValue() - Method in class nz.ac.waikato.adams.webservice.spectral.put.Property: Gets the value of the value property.
getValue() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.Property: Gets the value of the value property.
getValue(PropertyPath.PropertyContainer) - Method in class adams.core.discovery.genetic.SegmentedDownSampleNthPoints: Returns the integer value from the property container.
getValue(PropertyPath.PropertyContainer) - Method in class adams.core.discovery.genetic.SegmentedSavitzkyGolayDerivativeOrder: Returns the integer value from the property container.
getValue(PropertyPath.PropertyContainer) - Method in class adams.core.discovery.genetic.SegmentedSavitzkyGolayNumPoints: Returns the integer value from the property container.
getValue(DataPoint) - Method in class adams.data.spectrumfilter.FastWavelet: Returns the X-value of the DataPoint.
getValue(DataPoint) - Method in class adams.data.spectrumfilter.FFT: Returns the Y-value of the DataPoint.
getValue(DataPoint) - Method in class adams.data.spectrumfilter.SavitzkyGolay: Returns the X-value of the DataPoint.
getValue(DataPoint) - Method in class adams.data.spectrumfilter.SimpleSavitzkyGolay: Returns the Y-value of the point.
getValue(DataPoint) - Method in class adams.data.spectrumsmoothing.SlidingWindow: Returns the X-value of the data point.
getValueAt(int, int) - Method in class adams.gui.selection.SelectSpectrumPanel.TableModel: Returns the ID at the given position.
getValueAt(int, int) - Method in class adams.gui.visualization.spectrum.SpectrumTableModel: Returns the value for the cell at columnIndex and rowIndex.
getValueFor(String, byte[]) - Method in class adams.data.io.input.OpusSpectrumReader: Get value for key, from Text Block.
getValues(String[], SpectrumIDConditions) - Method in class adams.db.generic.SpectrumT: returns all the specified fields in the database, separated by TABs.
getValues(String[], SpectrumIDConditions) - Method in class adams.db.mirrored.SpectrumT: returns all the specified fields in the database, separated by TABs.
getValues(String[], SpectrumIDConditions) - Method in class adams.db.SpectrumF: returns all the specified fields in the database, separated by TABs.
getValues(String[], SpectrumIDConditions) - Method in interface adams.db.SpectrumIntf: returns all the specified fields in the database, separated by TABs.
getValues(String[], String, SpectrumIDConditions) - Method in class adams.db.generic.SpectrumT: returns all the specified fields in the database, separated by TABs.
getValues(String[], String, SpectrumIDConditions) - Method in class adams.db.mirrored.SpectrumT: returns all the specified fields in the database, separated by TABs.
getValues(String[], String, SpectrumIDConditions) - Method in class adams.db.SpectrumF: returns all the specified fields in the database, separated by TABs.
getValues(String[], String, SpectrumIDConditions) - Method in interface adams.db.SpectrumIntf: returns all the specified fields in the database, separated by TABs.
getValues(String[], String, String, SpectrumIDConditions) - Method in class adams.db.generic.SpectrumT: returns all the specified fields in the database, separated by TABs.
getValues(String[], String, String, SpectrumIDConditions) - Method in class adams.db.mirrored.SpectrumT: returns all the specified fields in the database, separated by TABs.
getValues(String[], String, String, SpectrumIDConditions) - Method in class adams.db.SpectrumF: returns all the specified fields in the database, separated by TABs.
getValues(String[], String, String, SpectrumIDConditions) - Method in interface adams.db.SpectrumIntf: returns all the specified fields in the database, separated by TABs.
getVariableName() - Method in class adams.flow.transformer.SpectrumFeatureGenerator: Returns the name of the variable to monitor.
getVariableName() - Method in class adams.flow.transformer.ThreeWayDataFeatureGenerator: Returns the name of the variable to monitor.
getVariance() - Method in class adams.data.spectrumfilter.PCA: Returns the variance.
getVersion() - Method in class adams.data.conversion.WekaPredictionContainerToEvaluationContainer: Returns the version to use for the evaluation.
getVersion() - Method in class adams.flow.transformer.Evaluator: Returns the version.
getVisible(int) - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: Returns the nth visible container.
getVisibleIndices() - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: Returns the indices of all visible containers.
getWaitPoll() - Method in class adams.flow.standalone.rats.WSMultiSpectrumReception: Returns the number of milli-seconds to wait before polling again whether data has arrived.
getWaitPoll() - Method in class adams.flow.standalone.rats.WSSpectrumReception: Returns the number of milli-seconds to wait before polling again whether data has arrived.
getWave() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.Waves: Gets the value of the wave property.
getWave() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.Waves: Gets the value of the wave property.
getWave() - Method in class nz.ac.waikato.adams.webservice.spectral.get.Waves: Gets the value of the wave property.
getWave() - Method in class nz.ac.waikato.adams.webservice.spectral.put.Waves: Gets the value of the wave property.
getWave() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.Waves: Gets the value of the wave property.
getWaveColumns() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Returns the columns containing the wave amplitudes.
getWaveNoInc() - Method in class adams.data.conversion.ArrayToSpectrum: Returns the increment to use between wave numbers.
getWaveNoStart() - Method in class adams.data.conversion.ArrayToSpectrum: Returns the first wave number to use.
getWaveNumber() - Method in class adams.data.spectrum.SpectrumPoint: Returns the wave number.
getWaveNumber() - Method in class adams.flow.transformer.GetSpectrumAmplitude: Returns the wave number of the amplitude to retrieve.
getWaveNumber() - Method in class adams.flow.transformer.SetSpectrumAmplitude: Returns the wave number of the amplitude to set.
getWaveNumberArray() - Method in class adams.data.io.input.ASCSpectrumReader.ParsedFile: Returns the Wave number array.
getWaveNumberAsSuffix() - Method in class adams.data.instances.SimpleInstanceGenerator: Returns whether the wave number is used as suffix instead of the index.
getWaveNumberAsSuffix() - Method in class adams.data.instances.SimpleSpectralInstanceGenerator: Returns whether the wave number is used as suffix instead of the index.
getWaveNumberColumn() - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Returns the column containing the wave numbers.
getWaveNumberName(float) - Static method in class adams.data.instances.ArffUtils: Returns the name of an attribute for a wave number.
getWaveNumberName(int) - Static method in class adams.data.instances.ArffUtils: Returns the name of an attribute for a wave number.
getWaveNumberName(String, float) - Static method in class adams.data.instances.ArffUtils: Returns the name of an attribute for a wave number.
getWaveNumberName(String, int) - Static method in class adams.data.instances.ArffUtils: Returns the name of an attribute for a wave number.
getWaveNumberPrefix() - Method in class adams.data.instances.AbstractSpectrumInstanceGenerator: Returns the prefix for the wave number attributes.
getWaveNumberRegExp() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Returns the regular expression to identify the wave number (1st group is used).
getWaveNumberRegExp() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns the regular expression to identify the wave number (1st group is used).
getWaveNumberRegExp() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Returns the regular expression to identify the wave number (1st group is used).
getWavenumbers() - Method in class adams.data.io.input.foss.FossHelper
getWaveNumbers(byte[]) - Method in class adams.data.io.input.OpusSpectrumReader
getWaveNumbersInHeader() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns whether the wave numbers are in the header.
getWaveNumbersInHeader() - Method in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: Returns whether to use the wave numbers in the header.
getWaveNumberStarts() - Method in class adams.data.multifilter.Fusion: Returns the starting wave number for each sub-spectrum.
getWaveNumberStepSize() - Method in class adams.data.spectrumfilter.PadPower2: Returns the step size for the additional wave numbers.
getWaveNumberStepSizes() - Method in class adams.data.multifilter.Fusion: Returns the wave number step sizes for each sub-spectrum.
getWaves() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.Spectrum: Gets the value of the waves property.
getWaves() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.Spectrum: Gets the value of the waves property.
getWaves() - Method in class nz.ac.waikato.adams.webservice.spectral.get.Spectrum: Gets the value of the waves property.
getWaves() - Method in class nz.ac.waikato.adams.webservice.spectral.put.Spectrum: Gets the value of the waves property.
getWaves() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.Spectrum: Gets the value of the waves property.
getWaveStep() - Method in class adams.data.spectrumfilter.Rebase: Returns the difference between two wave numbers when updating them.
getWaveStep() - Method in class adams.flow.transformer.InstanceToSpectrum: Returns the step size for the wave numbers, if lastWave is not defined.
getWebService() - Method in class adams.flow.standalone.rats.WSMultiSpectrumReception: Returns the webservice provider in use.
getWebService() - Method in class adams.flow.standalone.rats.WSSpectrumReception: Returns the webservice provider in use.
getWidth() - Method in class adams.data.spectrumimage.Intensity: Returns the width of the image.
getWidth() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlay: Returns the width.
getWidth() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlayWithDimensions: Returns the currently set width of the overlay.
getWindowSize() - Method in class adams.data.sampledata.SignalToNoiseRatio: Returns the window size for determining the 'smoothed' abundances.
getWindowSize() - Method in class adams.data.spectrumoutlier.Oscillation: Returns the polynominal order.
getWindowSizeFirst() - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Returns the Savitzky-Golay window size for filter with first derivative.
getWindowSizeNone() - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Returns the Savitzky-Golay window size for filter with no derivative.
getWindowSizeSecond() - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Returns the Savitzky-Golay window size for filter with second derivative.
getWrap() - Method in class adams.data.postprocessor.instances.WekaFilter: Returns whether to wrap the filter in a SpectrumFilter.
getWriter() - Method in class adams.data.io.output.FilteredSpectrumWriter: Returns the underlying writer.
getWriter() - Method in class adams.data.io.output.SpreadSheetSpectrumWriter: Returns the spreadsheet to use.
getWriter() - Method in class adams.flow.standalone.rats.SaveMultiSpectrumFileOutput: Returns the writer in use.
getWriter() - Method in class adams.flow.standalone.rats.SaveSpectrumFileOutput: Returns the writer in use.
getWriterClass() - Method in class adams.gui.chooser.SpectrumFileChooser: Returns the writer superclass for the GOE.
getWriterClass() - Method in class adams.gui.chooser.ThreeWayDataFileChooser: Returns the writer superclass for the GOE.
getWriters() - Static method in class adams.data.io.output.AbstractSpectrumWriter: Returns a list with classnames of writers.
getWsdlLocation() - Method in class adams.flow.webservice.Get: Returns the WSDL location.
getWsdlLocation() - Method in class adams.flow.webservice.multispectrum.MultiUpload: Returns the WSDL location.
getWsdlLocation() - Method in class adams.flow.webservice.Put: Returns the WSDL location.
getWsdlLocation() - Method in class adams.flow.webservice.spectrum.Upload: Returns the WSDL location.
getWsdlLocation() - Method in class adams.flow.webservice.Transform: Returns the WSDL location.
getX() - Method in class adams.data.io.input.SimpleEEMReader: Returns the value to use for the X axis.
getX() - Method in class adams.data.threeway.L1Point: Return the X.
getX() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlay: Returns the currently set X position of the overlay.
getX(DataPoint) - Method in class adams.data.spectrumfilter.Autocorrelation: Returns the X value of the DataPoint.
getX(DataPoint) - Method in class adams.data.spectrumfilter.SAX: Obtains the X value from the given data point.
getXSubset(double) - Method in class adams.data.threeway.ThreeWayData: Returns a data structure which contains only the given x values.
getY() - Method in class adams.data.threeway.L1Point: Returns the Y.
getY() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlay: Returns the currently set Y position of the overlay.
getY(DataPoint) - Method in class adams.data.spectrumfilter.Autocorrelation: Returns the Y value of the DataPoint.
getY(DataPoint) - Method in class adams.data.spectrumfilter.Histogram: Obtains the Y value from the given data point.
getY(DataPoint) - Method in class adams.data.spectrumfilter.SAX: Obtains the Y value from the given data point.
getZ() - Method in class adams.data.threeway.L2Point: Returns the Z.
getZeroTerminatedString(int) - Method in class adams.data.io.input.foss.FossHelper: Build string until reaching zero termination.
getZoom() - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Returns the zoom level in percent.
getZoom() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Returns the zoom factor (0-16).
getZoomOverview() - Method in class adams.flow.sink.SpectrumDisplay: Returns whether the zoom overview gets displayed.
getZoomOverviewPanel() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Returns the zoom overview panel.
globalInfo() - Method in class adams.core.discovery.genetic.SegmentedDownSampleNthPoints: Returns a string describing the object.
globalInfo() - Method in class adams.core.discovery.genetic.SegmentedSavitzkyGolayDerivativeOrder: Returns a string describing the object.
globalInfo() - Method in class adams.core.discovery.genetic.SegmentedSavitzkyGolayNumPoints: Returns a string describing the object.
globalInfo() - Method in class adams.data.cleaner.instance.IQRCleaner: Returns a string describing the object.
globalInfo() - Method in class adams.data.cleaner.instance.MinMax: Returns a string describing the object.
globalInfo() - Method in class adams.data.cleaner.instance.PassThrough: Returns a string describing the object.
globalInfo() - Method in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: Returns a string describing the object.
globalInfo() - Method in class adams.data.cleaner.instance.RemoveOutliers: Returns a string describing the object.
globalInfo() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Returns a string describing the object.
globalInfo() - Method in class adams.data.cleaner.spectrum.MinMax: Returns a string describing the object.
globalInfo() - Method in class adams.data.cleaner.spectrum.PassThrough: Returns a string describing the object.
globalInfo() - Method in class adams.data.columnfinder.AmplitudeFinder: Returns a string describing the object.
globalInfo() - Method in class adams.data.compare.SpectrumCorrelation: Returns a string describing the object.
globalInfo() - Method in class adams.data.compare.SpectrumCosineSimilarity: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.ArrayToSpectrum: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.JsonToSpectrum: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.MultiSpectrumToSpectra: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.PostProcessingContainerToWekaInstanceContainer: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.ReportToSampleData: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.SampleDataArrayToMap: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.SpectraToMultiSpectrum: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.SpectrumToArray: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.SpectrumToBufferedImage: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.SpectrumToJson: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.SpectrumToSpreadSheet: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.SpectrumToWave: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.SpreadSheetColumnsToSampleData: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.SpreadSheetRowsToSampleData: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.SpreadSheetTo2DTensor: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.SpreadSheetTo3DTensor: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.SpreadSheetToSpectrum: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.SpreadSheetToThreeWayData: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.TensorToSpreadSheet: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.TensorToThreeWayData: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.ThreeWayDataToHeatmap: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.ThreeWayDataToSpreadSheet: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.ThreeWayDataToTensor: Returns a string describing the object.
globalInfo() - Method in class adams.data.conversion.WekaPredictionContainerToEvaluationContainer: Returns a string describing the object.
globalInfo() - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Returns a string describing the object.
globalInfo() - Method in class adams.data.evaluator.instance.CrossValidatedPrediction: Returns a string describing the object.
globalInfo() - Method in class adams.data.evaluator.instance.DistanceToCenter: Returns a string describing the object.
globalInfo() - Method in class adams.data.evaluator.instance.DistanceToClosest: Returns a string describing the object.
globalInfo() - Method in class adams.data.evaluator.instance.EnsembleEvaluator: Returns a string describing the object.
globalInfo() - Method in class adams.data.evaluator.instance.FakeEvaluator: Returns a string describing the object.
globalInfo() - Method in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: Returns a string describing the object.
globalInfo() - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Global info.
globalInfo() - Method in class adams.data.evaluator.instance.NullEvaluator: Returns a string describing the object.
globalInfo() - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Returns a string describing the object.
globalInfo() - Method in class adams.data.instances.FieldInstanceGenerator: Returns a string describing the object.
globalInfo() - Method in class adams.data.instances.FieldInstanceGeneratorWithClass: Returns a string describing the object.
globalInfo() - Method in class adams.data.instances.SimpleInstanceGenerator: Returns a string describing the object.
globalInfo() - Method in class adams.data.instances.SimpleSpectralInstanceGenerator: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.AniMLSpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.ASCIIXYSpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.ASCSpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.CALSpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.CMLSpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.DPTSpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.ExtractIdAndTypeSpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.ExtractIdAndTypeThreeWayDataReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.FilteredSpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.FitsLibsReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.JCampDX2SpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.JCampDXSpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.JsonSpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.MPSSpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.NIRSpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.OpusSpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.OpusSpectrumReaderExt: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.RelabSpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.sampleidextraction.Filename: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.sampleidextraction.RegExp: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.ScioLabExportSpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.SimpleEEMReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.SimpleSpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.SimpleXYZReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.SoilCaresScannerSpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.SPASpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.SPCSpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.SpecLibSampleDataReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.SpecLibSpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.ThreeWayHeatmapReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.TrinamixSpectrumJsonReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.TrinamixSpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.UnscramblerSpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.input.ZippedSpectrumReader: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.output.ASCIIXYSpectrumWriter: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.output.ASCSpectrumWriter: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.output.DPTSpectrumWriter: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.output.FilteredSpectrumWriter: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.output.JCampDX2SpectrumWriter: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.output.JsonSpectrumWriter: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.output.NIRSpectrumWriter: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.output.SimpleEEMWriter: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.output.SimpleSpectrumWriter: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.output.SimpleXYZWriter: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.output.SpectrumImageWriter: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.output.SpreadSheetSpectrumWriter: Returns a string describing the object.
globalInfo() - Method in class adams.data.io.output.TrinamixSpectrumWriter: Returns a string describing the object.
globalInfo() - Method in class adams.data.multifilter.Add: Returns a string describing the object.
globalInfo() - Method in class adams.data.multifilter.Atan2: Returns a string describing the object.
globalInfo() - Method in class adams.data.multifilter.Average: Returns a string describing the object.
globalInfo() - Method in class adams.data.multifilter.Divide: Returns a string describing the object.
globalInfo() - Method in class adams.data.multifilter.FilteredMultiSpectrumFilter: Returns a string describing the object.
globalInfo() - Method in class adams.data.multifilter.Fusion: Returns a string describing the object.
globalInfo() - Method in class adams.data.multifilter.Mean: Returns a string describing the object.
globalInfo() - Method in class adams.data.multifilter.Median: Returns a string describing the object.
globalInfo() - Method in class adams.data.multifilter.Multiply: Returns a string describing the object.
globalInfo() - Method in class adams.data.multifilter.PickByIndex: Returns a string describing the object.
globalInfo() - Method in class adams.data.multifilter.PickByReportValue: Returns a string describing the object.
globalInfo() - Method in class adams.data.multifilter.Subtract: Returns a string describing the object.
globalInfo() - Method in class adams.data.multireportfilter.DistributeSampleData: Returns a string describing the object.
globalInfo() - Method in class adams.data.multireportfilter.PassThrough: Returns a string describing the object.
globalInfo() - Method in class adams.data.multireportfilter.PullUpFields: Returns a string describing the object.
globalInfo() - Method in class adams.data.multispectrumoperation.outlierremoval.CorrelationBasedThreshold: Returns a string describing the object.
globalInfo() - Method in class adams.data.multispectrumoperation.outlierremoval.CosineSimilarityBasedThreshold: Returns a string describing the object.
globalInfo() - Method in class adams.data.multispectrumoperation.OutlierRemoval: Returns a string describing the object.
globalInfo() - Method in class adams.data.multispectrumoperation.outlierremoval.MeanSpectrumCosineSimilarityBasedThreshold: Returns a string describing the object.
globalInfo() - Method in class adams.data.multispectrumoperation.outlierremoval.PassThrough: Returns a string describing the object.
globalInfo() - Method in class adams.data.multispectrumoperation.PassThrough: Returns a string describing the object.
globalInfo() - Method in class adams.data.multispectrumoperation.Remove: Returns a string describing the object.
globalInfo() - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Returns a string describing the object.
globalInfo() - Method in class adams.data.postprocessor.instances.WekaFilter: Returns a string describing the object.
globalInfo() - Method in class adams.data.sampledata.SampleDataReportFilter: Returns a string describing the object.
globalInfo() - Method in class adams.data.sampledata.SignalToNoiseRatio
globalInfo() - Method in class adams.data.spectrum.AbstractSpectrumComparator: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrum.Amplitudes: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrum.SpectrumComparator
globalInfo() - Method in class adams.data.spectrum.SpectrumComparatorByReportValue: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumanalysis.FastICA: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumanalysis.PCA: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumanalysis.PLS: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.AmplitudeExpression: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.amplitudetransform.ApplyMultiplicativeScatterCorrection: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.AmplitudeTransform: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.amplitudetransform.PassThrough: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.amplitudetransform.Triangle: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.AndrewsCurves: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.Autocorrelation: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.CenterBurst: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.ChangeFormat: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.ConditionalReportField: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.Covariance: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.Derivative: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.Detrend: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.detrend.Mean: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.detrend.RangeBased: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.DownSample: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.EquiDistance: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.Histogram: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.KennardStone
globalInfo() - Method in class adams.data.spectrumfilter.LogTransform: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.LRCoeff: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.MultiFilter: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.MultiplicativeScatterCorrection: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.multiplicativescattercorrection.RangeBased: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.PadPower2: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.PCA: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.PLS: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.Rebase: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.Remove: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.ReportFieldFromStringValue: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.ReportFieldFromStringValueWithLookup: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.Reverse: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.RowNorm: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.RowZeroMin: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.SAX: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.Scale: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.StandardiseByInterpolation: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.SubRange: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.SubtractSpectrum: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.WaveNumberExpression: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.WekaFilterToReport: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumfilter.ZeroCenterBurst: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumimage.AmplitudeRatio: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumimage.Intensity: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumimage.Spectrogram: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumoutlier.AmplitudeRange: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumoutlier.Flatliner: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumoutlier.MaxWaves: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumoutlier.MinMax: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumoutlier.MinWaves: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumoutlier.Oscillation: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumoutlier.StringMatcher: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumoutlier.Swapped: Returns a string describing the object.
globalInfo() - Method in class adams.data.spectrumsmoothing.SlidingWindow: Returns a string describing the object.
globalInfo() - Method in class adams.data.spreadsheetrowgenerator.SampleDataOnlyRowGenerator: Returns a string describing the object.
globalInfo() - Method in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: Returns a string describing the object.
globalInfo() - Method in class adams.data.statistics.L1PointStatistic: Returns a string describing the object.
globalInfo() - Method in class adams.data.statistics.SpectrumStatistic: Returns a string describing the object.
globalInfo() - Method in class adams.data.statistics.ThreeWayDataStatistic: Returns a string describing the object.
globalInfo() - Method in class adams.data.threewayfeatures.Flatten: Returns a string describing the object.
globalInfo() - Method in class adams.data.threewayfeatures.Histogram: Returns a string describing the object.
globalInfo() - Method in class adams.data.threewayfeatures.Max: Returns a string describing the object.
globalInfo() - Method in class adams.data.threewayfeatures.Mean: Returns a string describing the object.
globalInfo() - Method in class adams.data.threewayfeatures.Median: Returns a string describing the object.
globalInfo() - Method in class adams.data.threewayfeatures.Min: Returns a string describing the object.
globalInfo() - Method in class adams.data.threewayfeatures.MultiThreeWayDataFeatureGenerator: Returns a string describing the object.
globalInfo() - Method in class adams.data.threewayfeatures.StdDev: Returns a string describing the object.
globalInfo() - Method in class adams.data.threewayfilter.Crop: Returns a string describing the object.
globalInfo() - Method in class adams.data.threewayfilter.DownSample: Returns a string describing the object.
globalInfo() - Method in class adams.data.threewayfilter.MultiFilter: Returns a string describing the object.
globalInfo() - Method in class adams.data.threewayfilter.Shift: Returns a string describing the object.
globalInfo() - Method in class adams.data.threewayoutlier.ValueRange: Returns a string describing the object.
globalInfo() - Method in class adams.db.autodetect.SpectralDbBackend
globalInfo() - Method in class adams.db.h2.SpectralDbBackend
globalInfo() - Method in class adams.db.mirrored.SpectralDbBackend: Returns a string describing the object.
globalInfo() - Method in class adams.db.mssql.SpectralDbBackend
globalInfo() - Method in class adams.db.mysql.SpectralDbBackend
globalInfo() - Method in class adams.db.OrphanedSampleDataConditions: Returns a string describing the object.
globalInfo() - Method in class adams.db.postgresql.SpectralDbBackend
globalInfo() - Method in class adams.db.SpectrumConditionsMulti: Returns a string describing the object.
globalInfo() - Method in class adams.db.SpectrumConditionsSingle: Returns a string describing the object.
globalInfo() - Method in class adams.db.SpectrumIDConditions: Returns a string describing the object.
globalInfo() - Method in class adams.db.sqlite.SpectralDbBackend
globalInfo() - Method in class adams.flow.condition.bool.HasSpectrum: Returns a string describing the object.
globalInfo() - Method in class adams.flow.control.InstanceCleaner: Returns a string describing the object.
globalInfo() - Method in class adams.flow.control.SpectrumCleaner: Returns a string describing the object.
globalInfo() - Method in class adams.flow.control.SpectrumFileChecker: Returns a string describing the object.
globalInfo() - Method in class adams.flow.core.CleanerModelLoader: Returns a string describing the object.
globalInfo() - Method in class adams.flow.core.EvaluatorModelLoader: Returns a string describing the object.
globalInfo() - Method in class adams.flow.core.PostProcessorModelLoader: Returns a string describing the object.
globalInfo() - Method in class adams.flow.core.ThreeWayDataModelFilterLoader: Returns a string describing the object.
globalInfo() - Method in class adams.flow.rest.DeleteSpectrum: Returns a string describing the object.
globalInfo() - Method in class adams.flow.rest.GetSpectrum: Returns a string describing the object.
globalInfo() - Method in class adams.flow.rest.PutSampleData: Returns a string describing the object.
globalInfo() - Method in class adams.flow.rest.PutSpectrum: Returns a string describing the object.
globalInfo() - Method in class adams.flow.rest.TransformSpectrum: Returns a string describing the object.
globalInfo() - Method in class adams.flow.sink.SampleDataDisplay: Returns a string describing the object.
globalInfo() - Method in class adams.flow.sink.SpectrumDisplay: Returns a string describing the object.
globalInfo() - Method in class adams.flow.sink.spectrumdisplay.SimplePlotUpdater: Returns a string describing the object.
globalInfo() - Method in class adams.flow.sink.SpectrumImageWriter: Returns a string describing the object.
globalInfo() - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Returns a string describing the object.
globalInfo() - Method in class adams.flow.source.InstrumentSupplier: Returns a string describing the object.
globalInfo() - Method in class adams.flow.source.NewSpectrum: Returns a string describing the object.
globalInfo() - Method in class adams.flow.source.OrphanedSampleDataIdSupplier: Returns a string describing the object.
globalInfo() - Method in class adams.flow.source.SpectrumIdSupplier: Returns a string describing the object.
globalInfo() - Method in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: Returns a string describing the object.
globalInfo() - Method in class adams.flow.standalone.rats.LoadSpectrumFileOutput: Returns a string describing the object.
globalInfo() - Method in class adams.flow.standalone.rats.SaveMultiSpectrumFileOutput: Returns a string describing the object.
globalInfo() - Method in class adams.flow.standalone.rats.SaveSpectrumFileOutput: Returns a string describing the object.
globalInfo() - Method in class adams.flow.standalone.rats.WSMultiSpectrumReception: Returns a string describing the object.
globalInfo() - Method in class adams.flow.standalone.rats.WSSpectrumReception: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.BulkSpectrumDbWriter: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.Cleaner: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.datacontainer.LoadSampleData: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.datacontainer.UpdateDatabaseID: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.DeleteDbSampleDataValue: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.DeleteSampleDataValue: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.DeleteSampleDataValueByExpression: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.DeleteSpectrum: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.Evaluator: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.GetSampleDataValue: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.GetSpectrumAmplitude: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.InstanceGenerator: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.InstanceToSpectrum: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.MergeSampleDataFromMap: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.MultiSpectrumAdd: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.MultiSpectrumFilter: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.MultiSpectrumOperation: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.MultiSpectrumOutlierDetector: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.MultiSpectrumRemove: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.MultiSpectrumReportFilter: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.PostProcessor: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.PredictionCheck: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.predictioncheck.MinProbability: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.predictioncheck.PassThrough: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.predictioncheck.Range: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.report.UpdateDatabaseID: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.SampleDataDbReader: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.SampleDataDbWriter: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.SampleDataFileReader: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.SampleDataFileWriter: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.SampleDataValueDbWriter: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.SetEvaluationMetaData: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.SetSampleDataValue: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.SetSpectrumAmplitude: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.SpectralAngleMapper: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.SpectrumAppend: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.SpectrumDbReader: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.SpectrumDbWriter: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.SpectrumDiff: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.SpectrumFeatureGenerator: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.SpectrumFileReader: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.SpectrumFileWriter: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.SpectrumInfo: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.SpectrumMinMax: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.SpreadSheetRowGenerator: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.ThreeWayDataFeatureGenerator: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.ThreeWayDataFileReader: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.ThreeWayDataFileWriter: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.ThreeWayDataLoadingMatrix: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.threewaydatamerge.CollapseX: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.ThreeWayDataMerge: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.threewaydatamerge.Join: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.ThreeWayDataTrain: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.threewaydatatrain.ParafacLossHistory: Returns a string describing the object.
globalInfo() - Method in class adams.flow.transformer.threewaydatatrain.PassThrough: Returns a string describing the object.
globalInfo() - Method in class adams.flow.webservice.Get: Returns a string describing the object.
globalInfo() - Method in class adams.flow.webservice.multispectrum.MultiUpload: Returns a string describing the object.
globalInfo() - Method in class adams.flow.webservice.multispectrum.RatsMultiSpectrumServiceWS: Returns a string describing the object.
globalInfo() - Method in class adams.flow.webservice.multispectrum.SimpleRatsMultiSpectrumService: Returns a string for the GUI that describes this object.
globalInfo() - Method in class adams.flow.webservice.Put: Returns a string describing the object.
globalInfo() - Method in class adams.flow.webservice.SimpleSpectralGetService: Returns a string for the GUI that describes this object.
globalInfo() - Method in class adams.flow.webservice.SimpleSpectralPutService: Returns a string for the GUI that describes this object.
globalInfo() - Method in class adams.flow.webservice.SimpleSpectralTransformService: Returns a string for the GUI that describes this object.
globalInfo() - Method in class adams.flow.webservice.SpectralGetServiceWS: Returns a string describing the object.
globalInfo() - Method in class adams.flow.webservice.SpectralPutServiceWS: Returns a string describing the object.
globalInfo() - Method in class adams.flow.webservice.SpectralTransformServiceWS: Returns a string describing the object.
globalInfo() - Method in class adams.flow.webservice.spectrum.RatsSpectrumServiceWS: Returns a string describing the object.
globalInfo() - Method in class adams.flow.webservice.spectrum.SimpleRatsSpectrumService: Returns a string for the GUI that describes this object.
globalInfo() - Method in class adams.flow.webservice.spectrum.Upload: Returns a string describing the object.
globalInfo() - Method in class adams.flow.webservice.Transform: Returns a string describing the object.
globalInfo() - Method in class adams.gui.core.spreadsheettable.ExportSpectra: Returns a string describing the object.
globalInfo() - Method in class adams.gui.tools.previewbrowser.AbstractSpectrumHandler: Returns a string describing the object.
globalInfo() - Method in class adams.gui.tools.previewbrowser.CleanerDetailsViewer: Returns a string describing the object.
globalInfo() - Method in class adams.gui.tools.previewbrowser.ThreeWayEEMHandler: Returns a string describing the object.
globalInfo() - Method in class adams.gui.tools.previewbrowser.ThreeWayXYZHandler: Returns a string describing the object.
globalInfo() - Method in class adams.gui.visualization.instances.instancestable.ExportSpectra: Returns a string describing the object.
globalInfo() - Method in class adams.gui.visualization.spectrum.ReportColorSpectrumPaintlet: Returns a string describing the object.
globalInfo() - Method in class adams.gui.visualization.spectrum.SelectedWaveNumberPaintlet: Returns a string describing the object.
globalInfo() - Method in class adams.gui.visualization.spectrum.SimpleSpectrumPaintlet: Returns a string describing the object.
globalInfo() - Method in class adams.gui.visualization.spectrum.SpectrumPaintlet: Returns a string describing the object.
globalInfo() - Method in class adams.gui.visualization.spectrum.SpectrumPaintletNumericField: Returns a string describing the object.
globalInfo() - Method in class adams.gui.visualization.spectrum.SpectrumPaintletStringField: Returns a string describing the object.
globalInfo() - Method in class adams.gui.visualization.spectrum.SpectrumPointHitDetector: Returns a string describing the object.
globalInfo() - Method in class adams.gui.visualization.spectrum.WaveNumberHitDetector: Returns a string describing the object.
globalInfo() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.Null: Returns a string describing the object.
globalInfo() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Returns a string describing the object.
globalInfo() - Method in class adams.opt.genetic.RonWeasley: Returns a string describing the object.
globalInfo() - Method in class weka.classifiers.meta.SpectrumClassifier: Returns a string describing this classifier.
globalInfo() - Method in class weka.clusterers.SpectrumClusterer: Returns a string describing this clusterer.
globalInfo() - Method in class weka.core.converters.CALSpectrumLoader: Returns a string describing the object.
globalInfo() - Method in class weka.filters.unsupervised.attribute.BestBySLR: Returns a string describing this filter.
globalInfo() - Method in class weka.filters.unsupervised.attribute.RangeBasedSavitzkyGolay: Returns a string describing this filter.
globalInfo() - Method in class weka.filters.unsupervised.attribute.SavitzkyGolayRange: Returns a string describing the object.
globalInfo() - Method in class weka.filters.unsupervised.attribute.SegmentedDownSample: Returns a string describing this filter.
globalInfo() - Method in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: Returns a string describing this filter.
globalInfo() - Method in class weka.filters.unsupervised.attribute.SpectrumFilter: Returns a string describing this classifier.
GotoWaveNumber - Class in adams.gui.visualization.spectrum.plotpopup: Displays the selected wave number.
GotoWaveNumber() - Constructor for class adams.gui.visualization.spectrum.plotpopup.GotoWaveNumber
GRAY - adams.data.spectrumimage.ImageType
groupExtractionTipText() - Method in class adams.data.io.input.ExtractIdAndTypeSpectrumReader: Returns the tip text for this property.
groupExtractionTipText() - Method in class adams.data.io.input.ExtractIdAndTypeThreeWayDataReader: Returns the tip text for this property.
groupTipText() - Method in class adams.data.io.input.sampleidextraction.RegExp: Returns the tip text for this property.
groupTipText() - Method in class adams.data.spectrumfilter.ReportFieldFromStringValue: Returns the tip text for this property.

H

handles(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>) - Method in class adams.gui.visualization.spectrum.containerlistpopup.Information: Checks whether this action can handle the panel.
handles(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>) - Method in class adams.gui.visualization.spectrum.containerlistpopup.SampleData: Checks whether this action can handle the panel.
handles(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>) - Method in class adams.gui.visualization.spectrum.containerlistpopup.SpectralData: Checks whether this action can handle the panel.
handles(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>) - Method in class adams.gui.visualization.spectrum.plotpopup.Adjust: Checks whether this action can handle the panel.
handles(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>) - Method in class adams.gui.visualization.spectrum.plotpopup.CrossHair: Checks whether this action can handle the panel.
handles(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>) - Method in class adams.gui.visualization.spectrum.plotpopup.ExportVisible: Checks whether this action can handle the panel.
handles(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>) - Method in class adams.gui.visualization.spectrum.plotpopup.GotoWaveNumber: Checks whether this action can handle the panel.
handles(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>) - Method in class adams.gui.visualization.spectrum.plotpopup.Histogram: Checks whether this action can handle the panel.
handles(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>) - Method in class adams.gui.visualization.spectrum.plotpopup.Hits: Checks whether this action can handle the panel.
handles(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>) - Method in class adams.gui.visualization.spectrum.plotpopup.SaveVisible: Checks whether this action can handle the panel.
handles(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>) - Method in class adams.gui.visualization.spectrum.plotpopup.Statistics: Checks whether this action can handle the panel.
handles(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>) - Method in class adams.gui.visualization.spectrum.plotpopup.Viewport: Checks whether this action can handle the panel.
handles(Class) - Method in class adams.gui.visualization.debug.objectexport.SpectrumExporter: Checks whether the exporter can handle the specified class.
handles(Class) - Method in class adams.gui.visualization.debug.objectexport.ThreeWayDataExporter: Checks whether the exporter can handle the specified class.
handles(Class) - Method in class adams.gui.visualization.debug.objectrenderer.SpectrumRenderer: Checks whether the renderer can handle the specified class.
handles(Class) - Method in class adams.gui.visualization.debug.objectrenderer.ThreeWayDataHeatmapRenderer: Checks whether the renderer can handle the specified class.
handles(Object) - Method in class adams.core.discovery.genetic.SegmentedDownSampleNthPoints: Checks whether this object is handled by this discovery handler.
handles(Object) - Method in class adams.core.discovery.genetic.SegmentedSavitzkyGolayDerivativeOrder: Checks whether this object is handled by this discovery handler.
handles(Object) - Method in class adams.core.discovery.genetic.SegmentedSavitzkyGolayNumPoints: Checks whether this object is handled by this discovery handler.
handles(Object) - Method in class adams.gui.tools.previewbrowser.CleanerDetailsViewer: Returns whether viewer handles this object.
has(String) - Method in class adams.data.io.input.opus.OpusBlockHelper.CommandlineData: Checks whether the key is present.
hasCallableActor() - Method in class adams.flow.transformer.MultiSpectrumAdd: Checks whether a reference to the callable actor is currently available.
hasCleanInstancesError() - Method in class adams.data.cleaner.instance.AbstractCleaner: Checks whether there was an error during cleaning the Instances object.
hasCurrentPanel() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerMultiPagePane: Returns whether a panel is currently selected.
hashCode() - Method in class adams.data.spectrum.Spectrum: Returns the hash code for this DataContainer.
hashCode() - Method in class adams.data.threeway.ThreeWayData: Returns the hashcode.
hashCode() - Method in class adams.gui.visualization.spectrum.SpectrumContainer: Returns the hashcode of the ID string.
hasID(byte[]) - Method in class adams.data.io.input.opus.OpusBlockHelper.Block: Returns whether the ID is present in the block.
hasInput() - Method in class adams.flow.control.InstanceCleaner: Returns whether an input token is currently present.
hasInput() - Method in class adams.flow.control.SpectrumCleaner: Returns whether an input token is currently present.
hasNext() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader.ChunkedSheetIterator: Returns true if the iteration has more elements.
hasNext() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader.MultiSheetIterator: Returns true if the iteration has more elements.
hasNext() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader.SingleSheetIterator: Returns true if the iteration has more elements.
hasParent() - Method in class adams.data.spectrum.MultiSpectrum: Returns whether the point belongs to a container.
hasParent() - Method in class adams.data.spectrum.Spectrum: Returns whether the point belongs to a container.
hasParent() - Method in class adams.data.threeway.L1Point: Returns whether the point has a parent.
hasPendingOutput() - Method in class adams.flow.control.InstanceCleaner: Checks whether there is pending output to be collected after executing the flow item.
hasPendingOutput() - Method in class adams.flow.control.SpectrumCleaner: Checks whether there is pending output to be collected after executing the flow item.
hasPendingOutput() - Method in class adams.flow.standalone.rats.WSMultiSpectrumReception: Checks whether any output can be collected.
hasPendingOutput() - Method in class adams.flow.standalone.rats.WSSpectrumReception: Checks whether any output can be collected.
hasPendingOutput() - Method in class adams.flow.transformer.SpectrumFeatureGenerator: Checks whether there is pending output to be collected after executing the flow item.
hasPendingOutput() - Method in class adams.flow.transformer.SpectrumInfo: Checks whether there is pending output to be collected after executing the flow item.
hasPendingOutput() - Method in class adams.flow.transformer.ThreeWayDataFeatureGenerator: Checks whether there is pending output to be collected after executing the flow item.
hasReport() - Method in class adams.data.spectrum.MultiSpectrum: Returns whether sample data is present.
hasReport() - Method in class adams.data.spectrum.Spectrum: Returns whether sample data is present.
hasReport() - Method in class adams.data.threeway.ThreeWayData: True if Quantitation Report exists for this chromatogram.
hasSendToItem(Class[]) - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Checks whether something to send is available.
hasSendToItem(Class[]) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Checks whether something to send is available.
hasSidePanel() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Returns whether the panel has a side panel.
HasSpectrum - Class in adams.flow.condition.bool: Checks whether a spectrum with either the specified ID or the ID from the passing through ID handler is already present in the database.
A specified ID takes precedence of any ID of the token passing through.
HasSpectrum() - Constructor for class adams.flow.condition.bool.HasSpectrum
head_end - Static variable in class adams.data.io.input.foss.FossHelper: data header end.
HEADER - adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader.SampleIDLocation
HEADER_LENGTH - Static variable in class adams.data.io.input.opus.OpusBlockHelper: maximum length of header (made up value!).
headerContainsWaveNumberTipText() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Returns the tip text for this property.
heightTipText() - Method in class adams.data.spectrumimage.Intensity: Returns the tip text for this property.
heightTipText() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlayWithDimensions: Returns the tip text for this property.
heightTipText() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Returns the tip text for this property.
hide(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>, List<SpectrumContainer>) - Method in class adams.gui.visualization.spectrum.plotpopup.Viewport: Allows the user to hide the spectra.
hideOthers(DataContainerPanelWithContainerList<Spectrum, SpectrumContainerManager, SpectrumContainer>, List<SpectrumContainer>) - Method in class adams.gui.visualization.spectrum.plotpopup.Viewport: Allows the user to hide all other spectra.
Histogram - Class in adams.data.spectrumfilter: Generates a histogram from the spectrum.
Histogram - Class in adams.data.threewayfeatures: Generates a histogram from the data values.
Histogram - Class in adams.gui.visualization.spectrum.plotpopup: Generates histograms from the visible containers.
Histogram() - Constructor for class adams.data.spectrumfilter.Histogram
Histogram() - Constructor for class adams.data.threewayfeatures.Histogram
Histogram() - Constructor for class adams.gui.visualization.spectrum.plotpopup.Histogram
HistogramFactory - Class in adams.gui.visualization.spectrum: A factory for histogram related objects.
HistogramFactory() - Constructor for class adams.gui.visualization.spectrum.HistogramFactory
HistogramFactory.Dialog - Class in adams.gui.visualization.spectrum: Dialog for displaying histograms generated from spectrums.
HistogramFactory.Panel - Class in adams.gui.visualization.spectrum: A panel for displaying a histogram based on the GC data of a spectrum.
HistogramFactory.SetupDialog - Class in adams.gui.visualization.spectrum: A dialog that queries the user about parameters for displaying histograms.
Hits - Class in adams.gui.visualization.spectrum.plotpopup: Allows operations on the "hits", ie the spectra currently under the mouse cursor.
Hits() - Constructor for class adams.gui.visualization.spectrum.plotpopup.Hits

I

ica() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Performs ICA on the visible spectra.
ICATipText() - Method in class adams.data.spectrumanalysis.FastICA: Returns the tip text for this property.
id - Variable in class adams.data.io.input.foss.FossHelper.FossFields: ID field.
id - Variable in class nz.ac.waikato.adams.webservice.rats.multispectrum.MultiSpectrum
id - Variable in class nz.ac.waikato.adams.webservice.rats.multispectrum.Spectrum
id - Variable in class nz.ac.waikato.adams.webservice.rats.multispectrum.UploadRequest
id - Variable in class nz.ac.waikato.adams.webservice.rats.multispectrum.UploadResponse
id - Variable in class nz.ac.waikato.adams.webservice.rats.spectrum.Spectrum
id - Variable in class nz.ac.waikato.adams.webservice.rats.spectrum.UploadRequest
id - Variable in class nz.ac.waikato.adams.webservice.rats.spectrum.UploadResponse
id - Variable in class nz.ac.waikato.adams.webservice.spectral.get.GetRequest
id - Variable in class nz.ac.waikato.adams.webservice.spectral.get.GetResponse
id - Variable in class nz.ac.waikato.adams.webservice.spectral.get.Spectrum
id - Variable in class nz.ac.waikato.adams.webservice.spectral.put.PutRequest
id - Variable in class nz.ac.waikato.adams.webservice.spectral.put.PutResponse
id - Variable in class nz.ac.waikato.adams.webservice.spectral.put.Spectrum
id - Variable in class nz.ac.waikato.adams.webservice.spectral.transform.Spectrum
id - Variable in class nz.ac.waikato.adams.webservice.spectral.transform.TransformRequest
id - Variable in class nz.ac.waikato.adams.webservice.spectral.transform.TransformResponse
ID - adams.flow.transformer.SpectrumInfo.InfoType: the spectrum ID.
id1 - Variable in class adams.data.io.input.foss.FossHelper.FossFields: other ID fields.
id2 - Variable in class adams.data.io.input.foss.FossHelper.FossFields: other ID fields.
id3 - Variable in class adams.data.io.input.foss.FossHelper.FossFields: other ID fields.
IDConsumer - Interface in adams.gui.tools.idprovider: Interface for components that consume IDs generated by the IDProviders.
identifySampleData(SpreadSheet, int[]) - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Returns the sample data fields.
identifyWaveNumbers(SpreadSheet, int[]) - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Indentifies the wave numbers.
IDExtractionTipText() - Method in class adams.data.io.input.ExtractIdAndTypeSpectrumReader: Returns the tip text for this property.
IDExtractionTipText() - Method in class adams.data.io.input.ExtractIdAndTypeThreeWayDataReader: Returns the tip text for this property.
idfieldTipText() - Method in class adams.data.io.input.CALSpectrumReader: Returns the tip text for this property.
IDTipText() - Method in class adams.data.conversion.ArrayToSpectrum: Returns the tip text for this property.
IDTipText() - Method in class adams.data.conversion.SpreadSheetToSpectrum: Returns the tip text for this property.
IDTipText() - Method in class adams.data.conversion.WekaPredictionContainerToEvaluationContainer: Returns the tip text for this property.
IDTipText() - Method in class adams.flow.condition.bool.HasSpectrum: Returns the tip text for this property.
IDTipText() - Method in class adams.flow.source.NewSpectrum: Returns the tip text for this property.
IDTipText() - Method in class adams.flow.webservice.Get: Description of this option.
iee754Dump(double[]) - Method in class adams.data.io.input.foss.FossStdise: Testing: Dump array is iee754 encoded ints.
ignoreWaveNumbersTipText() - Method in class adams.data.io.input.SimpleEEMReader: Returns the tip text for this property.
ImageType - Enum in adams.data.spectrumimage: Enumeration of type of image to generate.
imageTypeTipText() - Method in class adams.data.spectrumimage.AbstractSpectrumImageGenerator: Returns the tip text for this property.
implementationTipText() - Method in class adams.flow.webservice.multispectrum.RatsMultiSpectrumServiceWS: Description of this option.
implementationTipText() - Method in class adams.flow.webservice.SpectralGetServiceWS: Description of this option.
implementationTipText() - Method in class adams.flow.webservice.SpectralPutServiceWS: Description of this option.
implementationTipText() - Method in class adams.flow.webservice.SpectralTransformServiceWS: Description of this option.
implementationTipText() - Method in class adams.flow.webservice.spectrum.RatsSpectrumServiceWS: Description of this option.
implementsMoreEfficientBatchPrediction() - Method in class weka.classifiers.meta.SpectrumClassifier: Return true if this classifier can generate batch predictions in an efficient manner.
incrementsTipText() - Method in class adams.data.io.output.NIRSpectrumWriter: Returns the tip text for this property.
INDEX - adams.flow.transformer.GetSpectrumAmplitude.RetrievalType
INDEX - adams.flow.transformer.SetSpectrumAmplitude.UpdateType
indexOf(Integer) - Method in class adams.gui.selection.SelectSpectrumPanel.TableModel: Returns the index of the given (visible) ID, -1 if not found.
indexOf(String) - Method in class adams.flow.control.InstanceCleaner: Returns the index of the actor.
indexOf(String) - Method in class adams.flow.control.SpectrumCleaner: Returns the index of the actor.
indexOf(String) - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: Determines the index of the spectrum with the specified ID.
indexOf(String) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataContainerManager: Returns the index of the first ID or display ID that matches the specified one.
indexTipText() - Method in class adams.data.multifilter.PickByIndex: Returns the tip text for this property.
indexTipText() - Method in class adams.flow.transformer.GetSpectrumAmplitude: Returns the tip text for this property.
indexTipText() - Method in class adams.flow.transformer.SetSpectrumAmplitude: Returns the tip text for this property.
Information - Class in adams.gui.visualization.spectrum.containerlistpopup: Displays information about the spectra.
Information() - Constructor for class adams.gui.visualization.spectrum.containerlistpopup.Information
INFRATEC - adams.data.io.output.foss.FossOutputHelper.InstrumentHeader.InstrumentType
init() - Method in class adams.db.generic.SpectrumT: Initialise table & sub-tables.
init() - Method in class adams.db.mirrored.SampleDataT: Initialise table & sub-tables.
init() - Method in class adams.db.mirrored.SpectrumT: Initialise table & sub-tables.
init() - Method in class adams.db.SampleDataF: Initialise table & sub-tables.
init() - Method in interface adams.db.SampleDataIntf: Initialise table & sub-tables.
init() - Method in class adams.db.SpectrumF: Initialise table & sub-tables.
init() - Method in interface adams.db.SpectrumIntf: Initialise table & sub-tables.
initFields() - Method in class adams.data.sampledata.SampleData: Set field types.
initFields() - Method in class adams.data.threewayreport.ThreeWayReport: Set field types.
initFilterHelp() - Method in class adams.flow.container.SpectrumFilterContainer: Initializes help strings specific to the filter.
initFilterHelp() - Method in class adams.flow.container.ThreeWayDataFilterContainer: Initializes help strings specific to the filter.
initFilterHelp() - Method in class adams.flow.container.ThreeWayDataModelContainer: Initializes help strings specific to the filter.
initGUI() - Method in class adams.flow.sink.SpectrumDisplay.DisplayPanel
initGUI() - Method in class adams.gui.selection.SelectSpectrumPanel: initializes the GUI elements.
initGUI() - Method in class adams.gui.tools.DeleteSampleDataPanel: Initializes the members.
initGUI() - Method in class adams.gui.tools.DeleteSpectrumPanel: Initializes the widgets.
initGUI() - Method in class adams.gui.tools.idprovider.DatabaseSearchPanel: Initializes the members.
initGUI() - Method in class adams.gui.tools.idprovider.ManualListPanel: For initializing the GUI.
initGUI() - Method in class adams.gui.tools.idprovider.SpreadSheetIDPanel: For initializing the GUI.
initGUI() - Method in class adams.gui.tools.ListSampleDataPanel: Initializes the members.
initGUI() - Method in class adams.gui.tools.UpdateSampleDataPanel: Initializes the members.
initGUI() - Method in class adams.gui.visualization.spectrum.MultiSpectrumPanel: Initializes the widgets.
initGUI() - Method in class adams.gui.visualization.spectrum.SpectrumContainerList: Initializes the widgets.
initGUI() - Method in class adams.gui.visualization.spectrum.SpectrumDatasetExportDialog: Initializes the widgets.
initGUI() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Initializes the widgets.
initGUI() - Method in class adams.gui.visualization.spectrum.SpectrumExportDialog: Initializes the widgets.
initGUI() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Initializes the GUI.
initGUI() - Method in class adams.gui.visualization.spectrum.SpectrumPanelWithSampleData: Initializes the members.
initGUI() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Initializes the widgets.
initGUI() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerMultiPagePane: Initializes the widgets.
initGUI() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Initializes the widgets.
initHelp() - Method in class adams.flow.container.CleaningContainer: Initializes the help strings.
initHelp() - Method in class adams.flow.container.EvaluationContainer: Initializes the help strings.
initHelp() - Method in class adams.flow.container.PostProcessingContainer: Initializes the help strings.
initialize() - Method in class adams.data.cleaner.instance.AbstractDatabaseConnectionCleaner: Initializes the members.
initialize() - Method in class adams.data.cleaner.instance.AbstractSerializableCleaner: Initializes the members.
initialize() - Method in class adams.data.cleaner.instance.IQRCleaner: Initializes the members.
initialize() - Method in class adams.data.cleaner.spectrum.AbstractDatabaseConnectionCleaner: Initializes the members.
initialize() - Method in class adams.data.cleaner.spectrum.AbstractSerializableCleaner: Initializes the members.
initialize() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Initializes the members.
initialize() - Method in class adams.data.evaluator.instance.AbstractSerializableEvaluator: Initializes the members.
initialize() - Method in class adams.data.io.input.AbstractSampleDataReader: Initializes the members.
initialize() - Method in class adams.data.io.input.ZippedSpectrumReader: Initializes the reader.
initialize() - Method in class adams.data.io.output.AbstractThreeWayDataWriter: Initializes the members.
initialize() - Method in class adams.data.io.output.ASCIIXYSpectrumWriter: Initializes the members.
initialize() - Method in class adams.data.io.output.ASCSpectrumWriter: Initializes the members.
initialize() - Method in class adams.data.io.output.DPTSpectrumWriter: Initializes the members.
initialize() - Method in class adams.data.io.output.JCampDX2SpectrumWriter: Initializes the members.
initialize() - Method in class adams.data.io.output.JsonSpectrumWriter: Initializes the members.
initialize() - Method in class adams.data.io.output.NIRSpectrumWriter: Initializes the members.
initialize() - Method in class adams.data.io.output.SimpleSpectrumWriter: Initializes the members.
initialize() - Method in class adams.data.io.output.SpectrumImageWriter: Initializes the members.
initialize() - Method in class adams.data.io.output.SpreadSheetSpectrumWriter: Initializes the scheme.
initialize() - Method in class adams.data.io.output.TrinamixSpectrumWriter: Initializes the members.
initialize() - Method in class adams.data.postprocessor.instances.AbstractSerializablePostProcessor: Initializes the members.
initialize() - Method in class adams.data.spectrum.AbstractSpectrumComparator: Initializes the members.
initialize() - Method in class adams.data.spectrumfilter.AbstractSerializableFilter: Initializes the members.
initialize() - Method in class adams.data.spectrumfilter.Remove: Initializes the members.
initialize() - Method in class adams.data.spectrumfilter.WekaFilterToReport: Initializes the members.
initialize() - Method in class adams.data.spectrumoutlier.AmplitudeRange: Initializes the members.
initialize() - Method in class adams.flow.control.InstanceCleaner: Initializes the members.
initialize() - Method in class adams.flow.control.SpectrumCleaner: Initializes the members.
initialize() - Method in class adams.flow.standalone.rats.WSMultiSpectrumReception: Initializes the members.
initialize() - Method in class adams.flow.standalone.rats.WSSpectrumReception: Initializes the members.
initialize() - Method in class adams.flow.transformer.Cleaner: Initializes the members.
initialize() - Method in class adams.flow.transformer.Evaluator: Initializes the members.
initialize() - Method in class adams.flow.transformer.MultiSpectrumAdd: Initializes the members.
initialize() - Method in class adams.flow.transformer.PostProcessor: Initializes the members.
initialize() - Method in class adams.flow.transformer.SpectrumFeatureGenerator: Initializes the members.
initialize() - Method in class adams.flow.transformer.SpectrumInfo: Initializes the members.
initialize() - Method in class adams.flow.transformer.ThreeWayDataFeatureGenerator: Initializes the members.
initialize() - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Initializes the members.
initialize() - Method in class adams.gui.tools.DeleteSampleDataPanel: Initializes the members.
initialize() - Method in class adams.gui.tools.idprovider.DatabaseSearchPanel: Initializes the members.
initialize() - Method in class adams.gui.tools.idprovider.ManualListPanel: For initializing members.
initialize() - Method in class adams.gui.tools.idprovider.SpreadSheetIDPanel: For initializing members.
initialize() - Method in class adams.gui.tools.ListSampleDataPanel: Initializes the members.
initialize() - Method in class adams.gui.tools.UpdateSampleDataPanel: Initializes the members.
initialize() - Method in class adams.gui.visualization.spectrum.MultiSpectrumPanel: Initializes the members.
initialize() - Method in class adams.gui.visualization.spectrum.SelectedWaveNumberPaintlet: Initializes the members.
initialize() - Method in class adams.gui.visualization.spectrum.SpectrumContainer: Initializes members.
initialize() - Method in class adams.gui.visualization.spectrum.SpectrumContainerModel: Initializes members.
initialize() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Initializes the members.
initialize() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: For initializing members.
initialize() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Initializes the members.
initialize() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerMultiPagePane: For initializing members.
initialize() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Initializes the members.
initialize(Spectrum) - Method in class adams.data.spectrumfilter.amplitudetransform.AbstractAmplitudeTransformer: Hook method for initializing the transformer.
initialize(Spectrum) - Method in class adams.data.spectrumfilter.amplitudetransform.ApplyMultiplicativeScatterCorrection: Hook method for initializing the transformer.
initSampleData(Map<String, String>, SampleData) - Method in class adams.data.io.input.AbstractJCampSpectrumReader: Initializes the sample data.
initSearch(Instances) - Method in class adams.data.evaluator.instance.AbstractNearestNeighborBasedEvaluator: Initializes the search algorithm.
initSerializationSetup() - Method in class adams.data.cleaner.instance.IQRCleaner: Regenerates all the objects that are necessary for serialization.
initSerializationSetup() - Method in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: Regenerates all the objects that are necessary for serialization.
initSerializationSetup() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Regenerates all the objects that are necessary for serialization.
initSerializationSetup() - Method in class adams.data.evaluator.instance.AbstractNearestNeighborBasedEvaluator: Regenerates all the objects that are necessary for serialization.
initSerializationSetup() - Method in class adams.data.evaluator.instance.DistanceToCenter: Regenerates all the objects that are necessary for serialization.
initSerializationSetup() - Method in class adams.data.evaluator.instance.DistanceToClosest: Regenerates all the objects that are necessary for serialization.
initSerializationSetup() - Method in class adams.data.evaluator.instance.EnsembleEvaluator: Regenerates all the objects that are necessary for serialization.
initSerializationSetup() - Method in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: Regenerates all the objects that are necessary for serialization.
initSerializationSetup() - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Regenerates all the objects that are necessary for serialization.
initSerializationSetup() - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Regenerates all the objects that are necessary for serialization.
initSerializationSetup() - Method in class adams.data.postprocessor.instances.WekaFilter: Regenerates all the objects that are necessary for serialization.
initTable(AbstractDatabaseConnection) - Static method in class adams.db.generic.SampleDataT: Initializes the table.
initTable(AbstractDatabaseConnection) - Static method in class adams.db.generic.SpectrumT: Initializes the table.
initTable(AbstractDatabaseConnection) - Static method in class adams.db.h2.SampleDataT: Initializes the table.
initTable(AbstractDatabaseConnection) - Static method in class adams.db.h2.SpectrumT: Initializes the table.
initTable(AbstractDatabaseConnection) - Static method in class adams.db.mssql.SampleDataT: Initializes the table.
initTable(AbstractDatabaseConnection) - Static method in class adams.db.mssql.SpectrumT: Initializes the table.
initTable(AbstractDatabaseConnection) - Static method in class adams.db.mysql.SampleDataT: Initializes the table.
initTable(AbstractDatabaseConnection) - Static method in class adams.db.mysql.SpectrumT: Initializes the table.
initTable(AbstractDatabaseConnection) - Static method in class adams.db.postgresql.SampleDataT: Initializes the table.
initTable(AbstractDatabaseConnection) - Static method in class adams.db.postgresql.SpectrumT: Initializes the table.
initTable(AbstractDatabaseConnection) - Static method in class adams.db.sqlite.SampleDataT: Initializes the table.
initTable(AbstractDatabaseConnection) - Static method in class adams.db.sqlite.SpectrumT: Initializes the table.
input(Token) - Method in class adams.flow.control.InstanceCleaner: The method that accepts the input token and then processes it.
input(Token) - Method in class adams.flow.control.SpectrumCleaner: The method that accepts the input token and then processes it.
INS - Static variable in class adams.data.io.input.opus.OpusBlockHelper: the INS character sequence.
INSERT - adams.flow.transformer.SetSpectrumAmplitude.UpdateType
INSERT_TIMESTAMP - Static variable in class adams.data.sampledata.SampleData: field name for time of insertion into database.
INSERT_TIMESTAMP - Static variable in class adams.data.threewayreport.ThreeWayReport: field name for time of insertion into database.
InstanceCleaner - Class in adams.flow.control: 'Cleanses' the tokens being passed through.
InstanceCleaner() - Constructor for class adams.flow.control.InstanceCleaner
InstanceGenerator - Class in adams.flow.transformer: Generates weka.core.Instance objects from spectra or reports/sample data.
InstanceGenerator() - Constructor for class adams.flow.transformer.InstanceGenerator
InstanceGeneratorWithClassLabels - Interface in adams.data.instances: Instance generator with a support for class labels.
InstanceGeneratorWithSampleID - Interface in adams.data.instances: Instance generator with sample ID.
InstanceGeneratorWithTargetField - Interface in adams.data.instances: Instance generator with a target field, i.e., class.
InstanceToSpectrum - Class in adams.flow.transformer: Converts a weka.core.Instance to a Spectrum.
By default, the wave numbers start at 0 and use an increment of 1.
If 'first' and 'last' wave number are supplied, the step size is calculated based on the number of amplitudes present in the Instance.
If only 'first' wave number is supplied, then the supplied wave step size is used.
'first' and 'last' get ignored if a value of less than 0 is supplied.
InstanceToSpectrum() - Constructor for class adams.flow.transformer.InstanceToSpectrum
INSTRUMENT - Static variable in class adams.data.sampledata.SampleData: field name for the instrument.
INSTRUMENT - Static variable in class adams.data.threewayreport.ThreeWayReport: field name for the instrument.
InstrumentHeader() - Constructor for class adams.data.io.output.foss.FossOutputHelper.InstrumentHeader
instrumentNameTipText() - Method in class adams.data.io.output.ASCSpectrumWriter: Returns the tip text for this property.
instrumentNameTipText() - Method in class adams.data.io.output.NIRSpectrumWriter: Returns the tip text for this property.
instrumentNameTipText() - Method in class adams.data.io.output.TrinamixSpectrumWriter: Returns the tip text for this property.
InstrumentSupplier - Class in adams.flow.source: Returns instrument names from the database.
InstrumentSupplier() - Constructor for class adams.flow.source.InstrumentSupplier
instrumentTipText() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Returns the tip text for this property.
instrumentTipText() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns the tip text for this property.
instrumentTipText() - Method in class adams.data.conversion.SpreadSheetToSpectrum: Returns the tip text for this property.
instrumentTipText() - Method in class adams.data.io.input.AbstractSpectrumReader: Returns the tip text for this property.
instrumentTipText() - Method in class adams.data.io.input.AbstractThreeWayDataReader: Returns the tip text for this property.
instrumentTipText() - Method in class adams.db.AbstractSpectrumConditions: Returns the tip text for this property.
Intensity - Class in adams.data.spectrumimage: Generates a simple intensity image.
Intensity() - Constructor for class adams.data.spectrumimage.Intensity
INTERFEROGRAM - adams.data.io.input.SoilCaresScannerSpectrumReader.AmplitudeType
INTERFEROGRAM - Static variable in class adams.data.io.input.SoilCaresScannerSpectrumReader: the column name for the interferogram.
interp(double, List<SpectrumPoint>, int) - Method in class adams.data.spectrumfilter.AbstractStandardiseFilter
InterPercentileRange(Comparable, double, double) - Constructor for class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.InterPercentileRange: Initializes the container.
InterPercentileRangeCleaner - Class in adams.data.cleaner.spectrum
InterPercentileRangeCleaner() - Constructor for class adams.data.cleaner.spectrum.InterPercentileRangeCleaner
InterPercentileRangeCleaner.DataCollector - Class in adams.data.cleaner.spectrum: A helper class for collecting the data from the database and computing the inter-percentile ranges (IPRs).
InterPercentileRangeCleaner.InterPercentileRange - Class in adams.data.cleaner.spectrum: Container class for storing the lower and upper percentile, as well as the wave number.
interpolate(double, L1Point, L1Point) - Static method in class adams.data.threeway.L1PointUtils: Interpolates the two level 1 points and the corresponding level 2 data.
interpolate(float, SpectrumPoint, SpectrumPoint) - Method in class adams.data.spectrumfilter.EquiDistance: Returns a SpectrumPoint with interpolated amplitude.
interpretePosition(SpreadSheet, String) - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Interpretes the position string based on the given dataset.
intersect(Spectrum, Spectrum) - Static method in class adams.data.spectrum.SpectrumUtils: Returns a spectrum that contains all the points that are in "a" and in "b".
IntervalEstimatorEvaluator - Class in adams.data.evaluator.instance: Stores the interval provided by the interval estimator classifier
IntervalEstimatorEvaluator() - Constructor for class adams.data.evaluator.instance.IntervalEstimatorEvaluator
intervalTipText() - Method in class adams.flow.transformer.SpectrumMinMax: Returns the tip text for this property.
invalidateMinMax() - Method in class adams.data.spectrum.Spectrum: Invalidates the min/max amplitude/wavenumber points.
invalidateMinMax() - Method in class adams.data.threeway.L1Point: Invalidates the min/max abundance/timestamp points.
invalidateMinMax() - Method in class adams.data.threeway.ThreeWayData: Invalidates the min/max abundance/timestamp points.
invertMatchingTipText() - Method in class adams.data.io.input.ZippedSpectrumReader: Returns the tip text for this property.
invertTipText() - Method in class adams.data.spectrumfilter.KennardStone: Description for this property.
invertTipText() - Method in class adams.data.spectrumfilter.Remove: Returns the tip text for this property.
invertTipText() - Method in class adams.data.spectrumfilter.SubRange: Returns the tip text for this property.
invertTipText() - Method in class adams.data.spectrumoutlier.StringMatcher: Returns the tip text for this property.
IQRCleaner - Class in adams.data.cleaner.instance: Removes instances outside the given IQR multiplier.
IQRCleaner() - Constructor for class adams.data.cleaner.instance.IQRCleaner
IQRMultiplierTipText() - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Returns the tip text for this property.
iqrTipText() - Method in class adams.data.cleaner.instance.IQRCleaner: Returns the tip text for this property.
isAntiAliasingEnabled() - Method in class adams.gui.visualization.spectrum.SimpleSpectrumPaintlet: Returns whether anti-aliasing is used.
isAntiAliasingEnabled() - Method in class adams.gui.visualization.spectrum.SpectrumPaintlet: Returns whether anti-aliasing is used.
isAntiAliasingEnabled() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Returns whether anti-aliasing is used.
isHit(MouseEvent) - Method in class adams.gui.visualization.spectrum.SpectrumPointHitDetector: Checks for a hit.
isHit(MouseEvent) - Method in class adams.gui.visualization.spectrum.WaveNumberHitDetector: Checks for a hit.
isLoggingEnabled() - Method in class adams.gui.tools.idprovider.AbstractIDProviderPanel: Returns whether logging is enabled.
isMarkersDisabled() - Method in class adams.gui.visualization.spectrum.SpectrumPaintlet: Returns whether marker shapes are disabled.
isMatch(SpectrumContainer, String, boolean) - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: Returns whether the container matches the current search.
isMatch(ThreeWayDataContainer, String, boolean) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataContainerManager: Returns whether the container matches the current search.
isReloadable() - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: Returns whether the spectrums can be reloaded from the database or not.
isReportVisible() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Returns whether the report table is visible.
isSearchMatch(SearchParameters, int) - Method in class adams.gui.selection.SelectSpectrumPanel.TableModel: Tests whether the search matches the specified row.
isSearchPanelVisible() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Returns whether the search panel is visible.
isSetupLoadedOrGenerated() - Method in class adams.data.cleaner.instance.AbstractSerializableCleaner: Returns whether the setup was loaded/generated.
isSetupLoadedOrGenerated() - Method in class adams.data.cleaner.spectrum.AbstractSerializableCleaner: Returns whether the setup was loaded/generated.
isSetupLoadedOrGenerated() - Method in class adams.data.evaluator.instance.AbstractSerializableEvaluator: Returns whether the setup was loaded/generated.
isSetupLoadedOrGenerated() - Method in class adams.data.postprocessor.instances.AbstractSerializablePostProcessor: Returns whether the setup was loaded/generated.
isSetupLoadedOrGenerated() - Method in class adams.data.spectrumfilter.AbstractSerializableFilter: Returns whether the setup was loaded/generated.
isSingleton() - Method in class adams.gui.menu.DeleteSampleData: Whether the panel can only be displayed once.
isSingleton() - Method in class adams.gui.menu.DeleteSpectra: Whether the panel can only be displayed once.
isSingleton() - Method in class adams.gui.menu.ExportValidationSets: Whether the panel can only be displayed once.
isSingleton() - Method in class adams.gui.menu.ListSampleData: Whether the panel can only be displayed once.
isSingleton() - Method in class adams.gui.menu.SpectrumExplorer: Whether the panel can only be displayed once.
isSingleton() - Method in class adams.gui.menu.ThreeWayDataHeatmapViewer: Whether the panel can only be displayed once.
isSingleton() - Method in class adams.gui.menu.UpdateSampleData: Whether the panel can only be displayed once.
isStopped() - Method in class adams.data.cleaner.instance.RemoveOutliers: Whether the execution has been stopped.
isStopped() - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Whether the execution has been stopped.
isStopped() - Method in class adams.data.evaluator.instance.EnsembleEvaluator: Whether the execution has been stopped.
isStopped() - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Whether the execution has been stopped.
isStopped() - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Whether the execution has been stopped.
isSuccess() - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.UploadResponse: Gets the value of the success property.
isSuccess() - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.UploadResponse: Gets the value of the success property.
isSuccess() - Method in class nz.ac.waikato.adams.webservice.spectral.get.GetResponse: Gets the value of the success property.
isSuccess() - Method in class nz.ac.waikato.adams.webservice.spectral.put.PutResponse: Gets the value of the success property.
isSuccess() - Method in class nz.ac.waikato.adams.webservice.spectral.transform.TransformResponse: Gets the value of the success property.
isTrained() - Method in class adams.data.spectrumfilter.MultiplicativeScatterCorrection: Returns whether the filter has been trained already and is ready to use.
isTrained() - Method in class adams.data.spectrumoutlier.AmplitudeRange: Returns whether the detector has been trained already and is ready to use.
isUsingAmplitude() - Method in class adams.data.spectrum.SpectrumPointComparator: Returns whether the amplitude or the wave number is used for ordering.
isUsingData() - Method in class adams.data.threeway.L2PointComparator: Returns whether the data is used for ordering as well.
isUsingStorage() - Method in class adams.flow.transformer.MergeSampleDataFromMap: Returns whether storage items are being used.
isUsingStorage() - Method in class adams.flow.transformer.MultiSpectrumAdd: Returns whether storage items are being used.
isUsingStorage() - Method in class adams.flow.transformer.SpectralAngleMapper: Returns whether storage items are being used.
isUsingY() - Method in class adams.data.threeway.L1PointComparator: Returns whether the Y used for ordering as well.
isValid() - Method in class adams.flow.container.CleaningContainer: Checks whether the setup of the container is valid.
isValid() - Method in class adams.flow.container.EvaluationContainer: Checks whether the setup of the container is valid.
isValid() - Method in class adams.flow.container.PostProcessingContainer: Checks whether the setup of the container is valid.
isValid() - Method in class adams.flow.container.ThreeWayDataModelContainer: Checks whether the setup of the container is valid.
isVisible() - Method in class adams.gui.visualization.spectrum.SpectrumContainer: Returns whether the spectrum is visible.
isVisible(int) - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: Returns whether the container at the specified position is visible.
isWorking() - Method in class adams.gui.tools.idprovider.AbstractIDProviderPanel: Returns whether IDs are currently being determined.
isWorking() - Method in class adams.gui.tools.idprovider.DatabaseSearchPanel: Returns whether IDs are currently being determined.
isWorking() - Method in class adams.gui.tools.idprovider.ManualListPanel: Returns whether IDs are currently being determined.
isWorking() - Method in class adams.gui.tools.idprovider.SpreadSheetIDPanel: Returns whether IDs are currently being determined.
isZoomOverviewPanelVisible() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Returns whether the zoom overview panel is visible or not.
isZoomOverviewPanelVisible() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Returns whether the zoom overview panel is visible or not.
iterate(Instances, int, Classifier, int, long, double, int, int) - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Cleans the data using the specified classifier and parameters.
iterationsTipText() - Method in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: Returns the tip text for this property.

J

JCampDX2SpectrumHandler - Class in adams.gui.tools.previewbrowser: Displays the following spectrum types: jdx, dx

Valid options are:
JCampDX2SpectrumHandler() - Constructor for class adams.gui.tools.previewbrowser.JCampDX2SpectrumHandler
JCampDX2SpectrumReader - Class in adams.data.io.input: Reads spectra in JCamp-DX format.

For more information see:
http://www.jcamp-dx.org/
JCampDX2SpectrumReader() - Constructor for class adams.data.io.input.JCampDX2SpectrumReader
JCampDX2SpectrumReader.ReaderMode - Enum in adams.data.io.input: The enum for the reader mode.
JCampDX2SpectrumWriter - Class in adams.data.io.output: Writer that stores spectrums in the simple CSV format.
JCampDX2SpectrumWriter() - Constructor for class adams.data.io.output.JCampDX2SpectrumWriter
JCampDXSpectrumHandler - Class in adams.gui.tools.previewbrowser: Displays the following spectrum types: jdx, dx

Valid options are:
JCampDXSpectrumHandler() - Constructor for class adams.gui.tools.previewbrowser.JCampDXSpectrumHandler
JCampDXSpectrumReader - Class in adams.data.io.input: Reads spectra in JCamp-DX format.

For more information see:
http://www.jcamp-dx.org/

Valid options are:
JCampDXSpectrumReader() - Constructor for class adams.data.io.input.JCampDXSpectrumReader
Join - Class in adams.flow.transformer.threewaydatamerge: Simply merges all the data points into a single container.
Join() - Constructor for class adams.flow.transformer.threewaydatamerge.Join
JsonSpectrumHandler - Class in adams.gui.tools.previewbrowser: Displays the following spectrum types: json

Valid options are:
JsonSpectrumHandler() - Constructor for class adams.gui.tools.previewbrowser.JsonSpectrumHandler
JsonSpectrumReader - Class in adams.data.io.input: Reads spectra in JSON format.
Input format (single spectrum):
- complete report stored:
{
"id": "someid",
"format": "NIR",
"waves": [1.0, 2.0],
"amplitudes": [1.1, 2.1],
"report": {
"Sample ID": "someid",
"GLV2": 1.123,
"valid": true
}
}

- specific reference and meta-data values stored:
{
"id": "someid",
"format": "NIR",
"waves": [1.0, 2.0],
"amplitudes": [1.1, 2.1],
"reference": {
"GLV2": 1.123
},
"meta-data": {
"valid": true
}
}

Multiple spectra are wrapped in an array called 'spectra'.
JsonSpectrumReader() - Constructor for class adams.data.io.input.JsonSpectrumReader
JsonSpectrumWriter - Class in adams.data.io.output: Writes spectra in JSON format.
Output format for single spectrum:
- outputting the complete report:
{
"id": "someid",
"format": "NIR",
"waves": [1.0, 2.0],
"amplitudes": [1.1, 2.1],
"report": {
"Sample ID": "someid",
"GLV2": 1.123,
"valid": true
}
}

- outputting specific reference and meta-data values:
{
"id": "someid",
"format": "NIR",
"waves": [1.0, 2.0],
"amplitudes": [1.1, 2.1],
"reference": {
"GLV2": 1.123
},
"meta-data": {
"valid": true
}
}

Multiple spectra get wrapped in an array called 'spectra'.
JsonSpectrumWriter() - Constructor for class adams.data.io.output.JsonSpectrumWriter
JsonToSpectrum - Class in adams.data.conversion: Turns a JSON string into a spectrum.
Input format:
- complete report stored:
{
"id": "someid",
"format": "NIR",
"waves": [1.0, 2.0],
"amplitudes": [1.1, 2.1],
"report": {
"Sample ID": "someid",
"GLV2": 1.123,
"valid": true
}
}

- specific reference and meta-data values stored:
{
"id": "someid",
"format": "NIR",
"waves": [1.0, 2.0],
"amplitudes": [1.1, 2.1],
"reference": {
"GLV2": 1.123
},
"meta-data": {
"valid": true
}
}
JsonToSpectrum() - Constructor for class adams.data.conversion.JsonToSpectrum

K

keepAttributeNamesTipText() - Method in class weka.filters.unsupervised.attribute.SpectrumFilter: Returns the tip text for this property.
keepFormatTipText() - Method in class adams.data.io.input.AbstractSpectrumReader: Returns the tip text for this property.
keepFormatTipText() - Method in class adams.data.io.input.AbstractThreeWayDataReader: Returns the tip text for this property.
KennardStone - Class in adams.data.spectrumfilter: Batch filter that applies the Kennard-stone algorithm to select a subset of spectra Created by Michael on 5/19/2016.
KennardStone() - Constructor for class adams.data.spectrumfilter.KennardStone
key - Variable in class nz.ac.waikato.adams.webservice.rats.multispectrum.Property
key - Variable in class nz.ac.waikato.adams.webservice.rats.spectrum.Property
key - Variable in class nz.ac.waikato.adams.webservice.spectral.get.Property
key - Variable in class nz.ac.waikato.adams.webservice.spectral.put.Property
key - Variable in class nz.ac.waikato.adams.webservice.spectral.transform.Property
KEY - Static variable in class adams.env.SpectralDbBackendDefinition: the key as constant.
KEY - Static variable in class adams.env.SpectralScriptingEngineDefinition: the key as constant.
KEY_AMPLITUDES - Static variable in class adams.data.spectrum.SpectrumJsonUtils
KEY_ATTRIBUTES - Static variable in class adams.gui.visualization.instances.instancestable.ExportSpectra
KEY_BACKEND - Static variable in class adams.db.AbstractSpectralDbBackend
KEY_COLUMNS - Static variable in class adams.gui.core.spreadsheettable.ExportSpectra
KEY_DBID - Static variable in class adams.data.statistics.L1PointStatistic: the key for the database ID.
KEY_DBID - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for the database ID.
KEY_DIRECTORY - Static variable in class adams.gui.core.spreadsheettable.ExportSpectra
KEY_DIRECTORY - Static variable in class adams.gui.visualization.instances.instancestable.ExportSpectra
KEY_EXTRACTWAVENOS - Static variable in class adams.gui.core.spreadsheettable.ExportSpectra
KEY_EXTRACTWAVENOS - Static variable in class adams.gui.visualization.instances.instancestable.ExportSpectra
KEY_FIRST_X - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for first X.
KEY_FIRST_Y - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for first Y.
KEY_FIRST_Z - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for first Z.
KEY_GAIN_FIT - Static variable in class adams.data.io.input.MPSSpectrumReader
KEY_ID - Static variable in class adams.data.spectrum.SpectrumJsonUtils
KEY_LAST_X - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for last X.
KEY_LAST_Y - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for last Y.
KEY_LAST_Z - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for last Z.
KEY_LIVE_TIME - Static variable in class adams.data.io.input.MPSSpectrumReader
KEY_LOSSHISTORY - Static variable in class adams.flow.transformer.threewaydatatrain.ParafacLossHistory: the name in the container for the loss history.
KEY_MAX_DATA - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for max data.
KEY_MAX_DELTA_X - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for max delta X.
KEY_MAX_DELTA_Y - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for max delta Y.
KEY_MAX_DELTA_Z - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for max delta Z.
KEY_MAX_X - Static variable in class adams.data.statistics.L1PointStatistic: the key for max x.
KEY_MAX_Y - Static variable in class adams.data.statistics.L1PointStatistic: the key for max y.
KEY_MEAN_DATA - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for mean data.
KEY_MEAN_DELTA_X - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for mean delta X.
KEY_MEAN_DELTA_Y - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for mean delta Y.
KEY_MEAN_DELTA_Z - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for mean delta Z.
KEY_MEAN_X - Static variable in class adams.data.statistics.L1PointStatistic: the key for mean x.
KEY_MEAN_Y - Static variable in class adams.data.statistics.L1PointStatistic: the key for mean y.
KEY_MEDIAN_DATA - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for median data.
KEY_MEDIAN_DELTA_X - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for median delta X.
KEY_MEDIAN_DELTA_Y - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for median delta Y.
KEY_MEDIAN_DELTA_Z - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for median delta Z.
KEY_MEDIAN_X - Static variable in class adams.data.statistics.L1PointStatistic: the key for median x.
KEY_MEDIAN_Y - Static variable in class adams.data.statistics.L1PointStatistic: the key for median y.
KEY_METADATA - Static variable in class adams.data.spectrum.SpectrumJsonUtils
KEY_MIN_DATA - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for min data.
KEY_MIN_DELTA_X - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for min delta X.
KEY_MIN_DELTA_Y - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for min delta Y.
KEY_MIN_DELTA_Z - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for min delta Z.
KEY_MIN_X - Static variable in class adams.data.statistics.L1PointStatistic: the key for min x.
KEY_MIN_Y - Static variable in class adams.data.statistics.L1PointStatistic: the key for min y.
KEY_NUM_DATA - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for number of unique data values.
KEY_NUM_LEVEL2 - Static variable in class adams.data.statistics.L1PointStatistic: the key for number of MS points.
KEY_NUM_X - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for number of unique x values.
KEY_NUM_Y - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for number of unique y values.
KEY_NUM_Z - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for number of unique z values.
KEY_REFERENCE - Static variable in class adams.data.spectrum.SpectrumJsonUtils
KEY_REPORT - Static variable in class adams.data.spectrum.SpectrumJsonUtils
KEY_SAMPLE_IDENT - Static variable in class adams.data.io.input.MPSSpectrumReader
KEY_SAMPLEID - Static variable in class adams.data.io.input.opus.OpusBlockHelper: the key for the sample ID.
KEY_SAMPLEID - Static variable in class adams.gui.core.spreadsheettable.ExportSpectra
KEY_SAMPLEID - Static variable in class adams.gui.visualization.instances.instancestable.ExportSpectra
KEY_SAMPLEID2 - Static variable in class adams.data.io.input.opus.OpusBlockHelper: the key for the sample ID (2).
KEY_STDEV_DATA - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for stdev data.
KEY_STDEV_DELTA_X - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for stdev delta X.
KEY_STDEV_DELTA_Y - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for stdev delta Y.
KEY_STDEV_DELTA_Z - Static variable in class adams.data.statistics.ThreeWayDataStatistic: the key for stdev delta Z.
KEY_TIME_MEASURED - Static variable in class adams.data.io.input.MPSSpectrumReader
KEY_WAVENOGROUP - Static variable in class adams.gui.core.spreadsheettable.ExportSpectra
KEY_WAVENOGROUP - Static variable in class adams.gui.visualization.instances.instancestable.ExportSpectra
KEY_WAVENOREGEXP - Static variable in class adams.gui.core.spreadsheettable.ExportSpectra
KEY_WAVENOREGEXP - Static variable in class adams.gui.visualization.instances.instancestable.ExportSpectra
KEY_WAVES - Static variable in class adams.data.spectrum.SpectrumJsonUtils
KEY_WRITER - Static variable in class adams.gui.core.spreadsheettable.ExportSpectra
KEY_WRITER - Static variable in class adams.gui.visualization.instances.instancestable.ExportSpectra
KEY_X - Static variable in class adams.data.statistics.L1PointStatistic: the key for the timestamp.
KEY_Y - Static variable in class adams.data.statistics.L1PointStatistic: the key for abundance.
KEY_ZERO_FIT - Static variable in class adams.data.io.input.MPSSpectrumReader
keySet() - Method in class adams.data.io.input.opus.OpusBlockHelper.CommandlineData: Returns the keys of the values.
keyTipText() - Method in class adams.data.io.input.OpusSpectrumReaderExt: Returns the tip text for this property.
keyTipText() - Method in class adams.flow.transformer.SetEvaluationMetaData: Returns the tip text for this property.
KEYWORD_CMDLINE - Static variable in class adams.data.io.input.opus.OpusBlockHelper: the command line keyword.
knirToWebservice(MultiSpectrum) - Static method in class adams.flow.core.RatsMultiSpectrumHelper: Converts a KNIR spectrum into a Webservice one.
knirToWebservice(Spectrum) - Static method in class adams.flow.core.GetSpectrumHelper: Converts a KNIR spectrum into a Webservice one.
knirToWebservice(Spectrum) - Static method in class adams.flow.core.PutSpectrumHelper: Converts a KNIR spectrum into a Webservice one.
knirToWebservice(Spectrum) - Static method in class adams.flow.core.RatsSpectrumHelper: Converts a KNIR spectrum into a Webservice one.
knirToWebservice(Spectrum) - Static method in class adams.flow.core.TransformSpectrumHelper: Converts a KNIR spectrum into a Webservice one.

L

L(double, List<SpectrumPoint>, int) - Method in class adams.data.spectrumfilter.AbstractStandardiseFilter
L1Point - Class in adams.data.threeway: Level 1 data point.
L1Point() - Constructor for class adams.data.threeway.L1Point: Constructor.
L1Point(double, double) - Constructor for class adams.data.threeway.L1Point: Constructor.
L1Point(ThreeWayData, double, double) - Constructor for class adams.data.threeway.L1Point: Constructor.
L1PointComparator - Class in adams.data.threeway: A comparator for level one points.
L1PointComparator() - Constructor for class adams.data.threeway.L1PointComparator: The default constructor uses comparison by X in ascending manner.
L1PointComparator(boolean, boolean) - Constructor for class adams.data.threeway.L1PointComparator: This constructor initializes the comparator either with comparison by X or Y as well.
L1PointStatistic - Class in adams.data.statistics: A Level 1 point specific statistic.
L1PointStatistic() - Constructor for class adams.data.statistics.L1PointStatistic: Initializes the statistic.
L1PointStatistic(L1Point) - Constructor for class adams.data.statistics.L1PointStatistic: Initializes the statistic.
L1PointUtils - Class in adams.data.threeway: A helper class for the Level 2 points of a given Level 1 point.
L1PointUtils() - Constructor for class adams.data.threeway.L1PointUtils
L2Point - Class in adams.data.threeway: Level 2 data point.
L2Point() - Constructor for class adams.data.threeway.L2Point: Constructor.
L2Point(double, double) - Constructor for class adams.data.threeway.L2Point: Constructor.
L2Point(L1Point, double, double) - Constructor for class adams.data.threeway.L2Point: Constructor.
L2PointComparator - Class in adams.data.threeway: A comparator for level 2 points.
L2PointComparator() - Constructor for class adams.data.threeway.L2PointComparator: The default constructor uses comparison by x in ascending manner.
L2PointComparator(boolean, boolean) - Constructor for class adams.data.threeway.L2PointComparator: This constructor initializes the comparator either with comparison by x or by y as well.
LAST_WAVE_NUMBER - Static variable in class adams.data.statistics.SpectrumStatistic
lastError - Variable in class adams.data.io.input.ASCSpectrumReader.ParsedFile: the last error that occurred.
lastTipText() - Method in class adams.data.spectrumfilter.AbstractStandardiseFilter: Returns the tip text for this property.
lastWaveTipText() - Method in class adams.flow.transformer.InstanceToSpectrum: Returns the tip text for this property.
lastXPointTipText() - Method in class adams.data.io.output.ASCSpectrumWriter: Returns the tip text for this property.
latestTipText() - Method in class adams.db.AbstractSpectrumConditions: Returns the tip text for this property.
latestTipText() - Method in class adams.db.OrphanedSampleDataConditions: Returns the tip text for this property.
launch() - Method in class adams.gui.menu.DeleteSampleData: Launches the functionality of the menu item.
launch() - Method in class adams.gui.menu.DeleteSpectra: Launches the functionality of the menu item.
launch() - Method in class adams.gui.menu.ExportValidationSets: Launches the functionality of the menu item.
launch() - Method in class adams.gui.menu.ListSampleData: Launches the functionality of the menu item.
launch() - Method in class adams.gui.menu.SpectrumExplorer: Launches the functionality of the menu item.
launch() - Method in class adams.gui.menu.ThreeWayDataHeatmapViewer: Launches the functionality of the menu item.
launch() - Method in class adams.gui.menu.UpdateSampleData: Launches the functionality of the menu item.
len - Variable in class adams.opt.genetic.RonWeasley
lengthBlocks - Variable in class adams.data.io.input.opus.OpusBlockHelper.BlockDefinition: the length in 4-byte blocks.
lengthBytes - Variable in class adams.data.io.input.opus.OpusBlockHelper.BlockDefinition: the length in bytes.
lenientTipText() - Method in class adams.data.conversion.SpreadSheetColumnsToSampleData: Returns the tip text for this property.
lenientTipText() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Returns the tip text for this property.
lenientTipText() - Method in class adams.data.conversion.SpreadSheetRowsToSampleData: Returns the tip text for this property.
lenientTipText() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns the tip text for this property.
lenientTipText() - Method in class adams.flow.transformer.InstanceGenerator: Returns the tip text for this property.
lenientTipText() - Method in class adams.flow.transformer.MergeSampleDataFromMap: Returns the tip text for this property.
lenientTipText() - Method in class adams.flow.transformer.SpreadSheetRowGenerator: Returns the tip text for this property.
LIMIT_LOWER - Static variable in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: the lower limit.
LIMIT_UPPER - Static variable in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: the upper limit.
LinearRegressionBased - Class in adams.data.spectrumbaseline: A simple linear regression based baseline correction scheme.
Fits a line through the data using linear regression and then removes this line from the data to correct the baseline.
LinearRegressionBased() - Constructor for class adams.data.spectrumbaseline.LinearRegressionBased
listMatrixFiles(ZipFile, ZipArchiveEntry) - Method in class adams.data.io.input.UnscramblerSpectrumReader: Parses the project.xml file and extracts the data matrices.
listOptions() - Method in class weka.core.converters.CALSpectrumLoader: Returns an enumeration describing the available options.
listOptions() - Method in class weka.filters.unsupervised.attribute.BestBySLR: Returns an enumeration describing the available options.
listOptions() - Method in class weka.filters.unsupervised.attribute.RangeBasedSavitzkyGolay: Returns an enumeration describing the available options.
listOptions() - Method in class weka.filters.unsupervised.attribute.SegmentedDownSample: Returns an enumeration describing the available options.
listOptions() - Method in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: Returns an enumeration describing the available options.
listOptions() - Method in class weka.filters.unsupervised.attribute.SpectrumFilter: Returns an enumeration describing the available options.
ListSampleData - Class in adams.gui.menu: Displays the dialog for listing all sample data for IDs.
ListSampleData() - Constructor for class adams.gui.menu.ListSampleData: Initializes the menu item.
ListSampleData(AbstractApplicationFrame) - Constructor for class adams.gui.menu.ListSampleData: Initializes the menu item.
ListSampleDataPanel - Class in adams.gui.tools: Allows the user to list sample data from selected spectra.
ListSampleDataPanel() - Constructor for class adams.gui.tools.ListSampleDataPanel
load() - Method in class adams.gui.tools.idprovider.ManualListPanel: Loads the spreadsheet and determines the IDs.
load() - Method in class adams.gui.tools.idprovider.SpreadSheetIDPanel: Loads the spreadsheet and determines the IDs.
load() - Method in class adams.gui.visualization.spectrum.MultiSpectrumPanel: Displays a dialog for opening a spectrum file.
load() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Loads data structures from disk, popping up a file chooser dialog.
load(int) - Method in class adams.db.generic.SpectrumT: Load a spectrum with given database ID.
load(int) - Method in class adams.db.mirrored.SpectrumT: Load a spectrum with given database ID.
load(int) - Method in class adams.db.SpectrumF: Load a spectrum with given database ID.
load(int) - Method in interface adams.db.SpectrumIntf: Load a spectrum with given database ID.
load(PlaceholderFile, boolean) - Method in class adams.gui.visualization.spectrum.MultiSpectrumPanel: Loads the spectra from the file.
load(AbstractSpectrumReader) - Method in class adams.gui.visualization.spectrum.MultiSpectrumPanel: Loads the spectra using the configured reader.
load(DataProvider, Spectrum) - Method in class adams.flow.transformer.SpectrumDbWriter: Loads the container from the database.
load(File[], AbstractThreeWayDataReader) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Loads data structures from disk, popping up a file chooser dialog.
load(String) - Method in class adams.db.generic.SampleDataT: Get params.
load(String) - Method in class adams.db.generic.SpectrumT: Load a spectrum with given ID.
load(String) - Method in class adams.db.mirrored.SampleDataT: Get params.
load(String) - Method in class adams.db.mirrored.SpectrumT: Load a spectrum with given ID.
load(String) - Method in class adams.db.SampleDataF: Get params.
load(String) - Method in interface adams.db.SampleDataIntf: Get params.
load(String) - Method in class adams.db.SpectrumF: Load a spectrum with given ID.
load(String) - Method in interface adams.db.SpectrumIntf: Load a spectrum with given ID.
load(String, String) - Method in class adams.db.generic.SpectrumT: Load a spectrum with given sample ID and type.
load(String, String) - Method in class adams.db.mirrored.SpectrumT: Load a spectrum with given sample ID and type.
load(String, String) - Method in class adams.db.SpectrumF: Load a spectrum with given sample ID and type.
load(String, String) - Method in interface adams.db.SpectrumIntf: Load a spectrum with given sample ID and type.
loadData() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: pops up the dialog for loading the data from a database.
loadDataFromDisk() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: pops up file chooser dialog for spectrum readers.
loadFromDB(int, String, boolean) - Method in class adams.db.generic.SpectrumT: Load a spectrum from DB with given auto_id.
loadFromDB(int, String, boolean) - Method in class adams.db.mirrored.SpectrumT: Load a spectrum from DB with given auto_id.
loadFromDB(int, String, boolean) - Method in class adams.db.SpectrumF: Load a spectrum from DB with given auto_id.
loadFromDB(int, String, boolean) - Method in interface adams.db.SpectrumIntf: Load a spectrum from DB with given auto_id.
loadFromDB(String, String, boolean) - Method in class adams.db.generic.SpectrumT: Load a spectrum from DB with given sample_id and format.
loadFromDB(String, String, boolean) - Method in class adams.db.mirrored.SpectrumT: Load a spectrum from DB with given sample_id and format.
loadFromDB(String, String, boolean) - Method in class adams.db.SpectrumF: Load a spectrum from DB with given sample_id and format.
loadFromDB(String, String, boolean) - Method in interface adams.db.SpectrumIntf: Load a spectrum from DB with given sample_id and format.
loadMatrix(ZipFile, ZipArchiveEntry) - Method in class adams.data.io.input.UnscramblerSpectrumReader: Loads the specified matrix.
LoadMultiSpectrumFileOutput - Class in adams.flow.standalone.rats: Loads spectrum files with the specified reader and puts them in the specified queue as MultiSpectrum.
Depending on whether a file could be successfully loaded or not, either .success or .failure gets appended to the filename.
LoadMultiSpectrumFileOutput() - Constructor for class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput
loadRaw(int) - Method in class adams.db.generic.SpectrumT: Load a data container with given auto_id, without passing it through the global filter.
loadRaw(int) - Method in class adams.db.mirrored.SpectrumT: Load a data container with given auto_id, without passing it through the global filter.
loadRaw(int) - Method in class adams.db.SpectrumF: Load a data container with given auto_id, without passing it through the global filter.
loadRaw(int) - Method in interface adams.db.SpectrumIntf: Load a data container with given auto_id, without passing it through the global filter.
loadRaw(String, String) - Method in class adams.db.generic.SpectrumT: Load a spectrum with given sample ID and type, without filtering through the global container filter.
loadRaw(String, String) - Method in class adams.db.mirrored.SpectrumT: Load a spectrum with given sample ID and type, without filtering through the global container filter.
loadRaw(String, String) - Method in class adams.db.SpectrumF: Load a spectrum with given sample ID and type, without filtering through the global container filter.
loadRaw(String, String) - Method in interface adams.db.SpectrumIntf: Load a spectrum with given sample ID and type, without filtering through the global container filter.
LoadSampleData - Class in adams.flow.transformer.datacontainer: Obtains the reference data from the spectrum with the same sample ID and the specified format.
LoadSampleData() - Constructor for class adams.flow.transformer.datacontainer.LoadSampleData
loadSampleDataTipText() - Method in class adams.data.instances.AbstractSpectrumBasedInstanceGenerator: Returns the tip text for this property.
LoadSpectrumFileOutput - Class in adams.flow.standalone.rats: Loads spectrum files with the specified reader and puts them in the specified queue.
Depending on whether a file could be successfully loaded or not, either .success or .failure gets appended to the filename.
LoadSpectrumFileOutput() - Constructor for class adams.flow.standalone.rats.LoadSpectrumFileOutput
localeTipText() - Method in class adams.data.io.input.ASCSpectrumReader: Returns the tip text for this property.
localeTipText() - Method in class adams.data.io.input.DPTSpectrumReader: Returns the tip text for this property.
localeTipText() - Method in class adams.data.io.output.ASCSpectrumWriter: Returns the tip text for this property.
localeTipText() - Method in class adams.data.io.output.DPTSpectrumWriter: Returns the tip text for this property.
locateColumn(SpreadSheet, String, boolean) - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Locates the column and returns the key for the column.
logBaseTipText() - Method in class adams.data.spectrumfilter.LogTransform: Returns the tip text for this property.
logDensityForInstance(Instance) - Method in class weka.clusterers.SpectrumClusterer: Computes the density for a given instance.
logDensityPerClusterForInstance(Instance) - Method in class weka.clusterers.SpectrumClusterer: Computes the log of the conditional density (per cluster) for a given instance.
logJointDensitiesForInstance(Instance) - Method in class weka.clusterers.SpectrumClusterer: Returns the logs of the joint densities for a given instance.
LogTransform - Class in adams.data.spectrumfilter: Transforms the amplitudes using log.
LogTransform() - Constructor for class adams.data.spectrumfilter.LogTransform
longFrom2Bytes(byte[], int) - Method in class adams.data.io.input.foss.FossHelper: Get long from 2 bytes LSByte first.
longFrom2Bytes(byte[], int) - Method in class adams.data.io.input.foss.FossStdise: Get long from 2 bytes LSByte first.
lookupTipText() - Method in class adams.data.spectrumfilter.ReportFieldFromStringValueWithLookup: Returns the tip text for this property.
lowerPercentileTipText() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Returns the tip text for this property.
LOWESS - Class in adams.data.spectrumfilter: A filter that applies LOWESS smoothing.

For more information see:

WikiPedia.
LOWESS() - Constructor for class adams.data.spectrumfilter.LOWESS
LOWESSBased - Class in adams.data.spectrumbaseline: A baseline correction scheme that uses LOWESS smoothing to determine the baseline.

For more information see:

WikiPedia.
LOWESSBased - Class in adams.data.spectrumsmoothing: A LOWESS based smoothing algorithm.
For more information on LOWESS see:

WikiPedia.
LOWESSBased() - Constructor for class adams.data.spectrumbaseline.LOWESSBased
LOWESSBased() - Constructor for class adams.data.spectrumsmoothing.LOWESSBased
LRCoeff - Class in adams.data.spectrumfilter: A filter that returns only every n-th wave number.
LRCoeff() - Constructor for class adams.data.spectrumfilter.LRCoeff
LXV - Static variable in class adams.data.io.input.opus.OpusBlockHelper: the LXV character sequence.

M

m_AbsDiff - Variable in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: absolute difference.
m_Absolute - Variable in class adams.data.spectrumfilter.Covariance: display absolute values.
m_Absolute - Variable in class adams.data.spectrumfilter.LRCoeff: display absolute values.
m_Absolute - Variable in class adams.flow.transformer.SpectrumDiff: whether to return the absolute difference.
m_AccessoryName - Variable in class adams.data.io.output.ASCSpectrumWriter: The Accessory Name to put in ASC header.
m_Action - Variable in class adams.flow.webservice.Transform: the actor to call.
m_ActualAlgorithm - Variable in class adams.flow.transformer.SpectrumFeatureGenerator: the actual algorithm to apply to the image.
m_ActualAlgorithm - Variable in class adams.flow.transformer.ThreeWayDataFeatureGenerator: the actual algorithm to apply to the image.
m_ActualClassifier - Variable in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: the actual classifier in use.
m_ActualClassifierFirst - Variable in class adams.data.evaluator.instance.SavitzkyGolayRange: the actual classifier in use for first derivative.
m_ActualClassifierNone - Variable in class adams.data.evaluator.instance.SavitzkyGolayRange: the actual classifier in use for no derivative.
m_ActualClassifiers - Variable in class adams.data.evaluator.instance.EnsembleEvaluator: the actual classifiers in use.
m_ActualClassifierSecond - Variable in class adams.data.evaluator.instance.SavitzkyGolayRange: the actual classifier in use for second derivative.
m_ActualCleaner - Variable in class adams.flow.transformer.Cleaner: the cleaner used for training/evaluating.
m_ActualClusterer - Variable in class weka.clusterers.SpectrumClusterer: The actual clusterer.
m_ActualEvaluator - Variable in class adams.flow.transformer.Evaluator: the evaluator used for training/evaluating.
m_ActualFilter - Variable in class adams.data.cleaner.instance.IQRCleaner: the actual IQR filter.
m_ActualFilter - Variable in class adams.data.evaluator.instance.DistanceToCenter: the actual filter.
m_ActualFilter - Variable in class adams.data.evaluator.instance.DistanceToClosest: the actual filter.
m_ActualFilter - Variable in class adams.data.postprocessor.instances.WekaFilter: the actual WEKA filter to use.
m_ActualLogBase - Variable in class adams.data.spectrumfilter.LogTransform: the actual base.
m_ActualModel - Variable in class adams.flow.transformer.ThreeWayDataModelFilter: the model used for training/evaluating.
m_ActualPostProcessor - Variable in class adams.flow.transformer.PostProcessor: the postprocessor used for doing the actual work.
m_ActualPreFilter - Variable in class adams.data.cleaner.instance.AbstractCleaner: the actual pre-filter to use.
m_ActualPreFilter - Variable in class adams.data.cleaner.spectrum.AbstractCleaner: the actual pre-filter to use.
m_ActualSearch - Variable in class adams.data.evaluator.instance.AbstractNearestNeighborBasedEvaluator: the actual nearest neighbor algorithm in use.
m_AddCommandLines - Variable in class adams.data.io.input.OpusSpectrumReaderExt: whether to add the meta-data of the other commandlines.
m_AddDatabaseID - Variable in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: whether to add the database ID.
m_AddDatabaseID - Variable in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: whether to add the database ID.
m_AddID - Variable in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: whether to add the container ID.
m_AdditionalFields - Variable in class adams.data.instances.AbstractSpectrumInstanceGenerator: additional fields to add to the output data.
m_AddLog - Variable in class adams.data.io.input.OpusSpectrumReaderExt: whether to add the complete log to the report.
m_AddRawMetaData - Variable in class adams.data.io.input.JCampDX2SpectrumReader: whether to add the raw meta-data.
m_AddRawMetaData - Variable in class adams.data.io.input.JCampDXSpectrumReader: whether to add the raw meta-data.
m_AddSampleID - Variable in class adams.data.instances.AbstractSpectrumBasedInstanceGenerator: whether to add the sample ID.
m_AddSampleID - Variable in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: whether to add the sample ID.
m_AddTraceToReport - Variable in class adams.data.io.input.OpusSpectrumReader: whether to add the trace to the report.
m_AddWaveNumber - Variable in class adams.data.instances.SimpleInstanceGenerator: whether to output the wave-number as well.
m_AddWaveNumber - Variable in class adams.data.instances.SimpleSpectralInstanceGenerator: whether to output the wave-number as well.
m_AddWaveNumber - Variable in class adams.data.spectrum.Amplitudes: whether to include the wavenumbers.
m_AdjustToVisibleData - Variable in class adams.gui.visualization.spectrum.SpectrumPanel: whether to adjust to visible data or not.
m_Algorithm - Variable in class adams.data.spectrumfilter.PLS: the PLS algorithm.
m_Algorithm - Variable in class adams.flow.transformer.SpectrumFeatureGenerator: the feature generator to use.
m_Algorithm - Variable in class adams.flow.transformer.ThreeWayDataFeatureGenerator: the algorithm to apply to the image.
m_Algorithm - Variable in class adams.flow.transformer.ThreeWayDataMerge: the algorithm to use for merging.
m_Algorithm - Variable in class adams.flow.transformer.ThreeWayDataTrain: the algorithm to build.
m_AllSpectra - Variable in class adams.data.io.input.OpusSpectrumReaderExt: whether to load all spectra.
m_AlwaysShowMarkers - Variable in class adams.gui.visualization.spectrum.SpectrumPaintlet: whether to show markers all the time.
m_Amplitude - Variable in class adams.data.spectrum.SpectrumPoint: the amplitude.
m_Amplitude - Variable in class adams.flow.transformer.SetSpectrumAmplitude: the amplitude.
m_AmplitudeIPRs - Variable in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: the interpercentiles to use for the amplitudes.
m_AmplitudePrefix - Variable in class adams.data.instances.AbstractSpectrumInstanceGenerator: the prefix for the amplitude attributes.
m_AmplitudePrefix - Variable in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: the amplitude column prefix.
m_AmplitudeRanges - Variable in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.DataCollector: the inter-percentile ranges for the amplitudes (wavenumber - IPR).
m_AmplitudeRangesPerChunk - Variable in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.DataCollector: the inter-percentile ranges for the amplitudes (list of wavenumber - lower/upper percentile) per chunk.
m_AmplitudeRows - Variable in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: the range of rows containing the amplitudes.
m_AmplitudeType - Variable in class adams.data.io.input.SoilCaresScannerSpectrumReader: the type of amplitude to read for a spectrum.
m_AntiAliasingEnabled - Variable in class adams.gui.visualization.spectrum.SimpleSpectrumPaintlet: whether anti-aliasing is enabled.
m_AntiAliasingEnabled - Variable in class adams.gui.visualization.spectrum.SpectrumPaintlet: whether anti-aliasing is enabled.
m_Apply - Variable in class adams.data.spectrumfilter.LRCoeff: apply coefficients to spectrum.
m_AtomicMove - Variable in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: whether to perform an atomic move.
m_AtomicMove - Variable in class adams.flow.standalone.rats.LoadSpectrumFileOutput: whether to perform an atomic move.
m_AttributeName - Variable in class adams.data.cleaner.instance.MinMax: the attribute name to check, uses last if left empty.
m_AttributeRange - Variable in class adams.data.spectrumanalysis.FastICA: the range of attributes to work.
m_AutoCommit - Variable in class adams.flow.transformer.BulkSampleDataDbWriter: whether to use auto-commit.
m_AutoCommit - Variable in class adams.flow.transformer.BulkSpectrumDbWriter: whether to use auto-commit.
m_Average - Variable in class adams.data.spectrumfilter.MultiplicativeScatterCorrection: the average spectrum.
m_AxisLabels - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: whether axis labeled stored (0:0x20h).
m_Backends - Variable in class adams.db.mirrored.SpectralDbBackend: the backends.
m_Base - Variable in class adams.data.evaluator.instance.MultiClassifierEvaluator: WEKA base classifier to use.
m_BaseFilter - Variable in class adams.data.multifilter.FilteredMultiSpectrumFilter: the base filter.
m_BatchFilter - Variable in class adams.data.spectrumfilter.KennardStone: Batch filter to apply before selection
m_BatchSize - Variable in class adams.flow.transformer.BulkSampleDataDbWriter: the number of records in a batch.
m_BatchSize - Variable in class adams.flow.transformer.BulkSpectrumDbWriter: the number of records in a batch.
m_BelowCountThreshold - Variable in class adams.data.multispectrumoperation.outlierremoval.CorrelationBasedThreshold: the threshold for below CC counts for rejecting spectra.
m_BelowCountThreshold - Variable in class adams.data.multispectrumoperation.outlierremoval.CosineSimilarityBasedThreshold: the threshold for below CS counts for rejecting spectra.
m_Blocks16bit - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: whether blocks are in 16bit integer (0:0x01h).
m_Buffer - Variable in class adams.data.io.input.opus.OpusBlockHelper.Block: the content of the file.
m_BufferSize - Variable in class adams.data.io.input.ZippedSpectrumReader: the buffer size to use.
m_BuildWait - Variable in class adams.data.evaluator.instance.FakeEvaluator: the build wait time in msec.
m_BulkAddStopped - Variable in class adams.db.generic.SpectrumT: whether to stop the bulk add.
m_BulkStoreStopped - Variable in class adams.db.generic.SampleDataT: whether to stop the bulk store.
m_ButtonApply - Variable in class adams.gui.tools.UpdateSampleDataPanel: the button for updating the sample data.
m_ButtonCheckAll - Variable in class adams.gui.tools.DeleteSampleDataPanel: the button for checking all.
m_ButtonCheckAll - Variable in class adams.gui.tools.ListSampleDataPanel: the button for checking all.
m_ButtonCheckNone - Variable in class adams.gui.tools.DeleteSampleDataPanel: the button for checking none.
m_ButtonCheckNone - Variable in class adams.gui.tools.ListSampleDataPanel: the button for checking none.
m_ButtonCheckSelected - Variable in class adams.gui.tools.DeleteSampleDataPanel: the button for checking the selected ones.
m_ButtonCheckSelected - Variable in class adams.gui.tools.ListSampleDataPanel: the button for checking the selected ones.
m_ButtonClose - Variable in class adams.gui.tools.DeleteSampleDataPanel: the button for closing the dialog.
m_ButtonClose - Variable in class adams.gui.tools.DeleteSpectrumPanel: the button for closing the dialog/frame.
m_ButtonClose - Variable in class adams.gui.tools.ListSampleDataPanel: the button for closing the dialog.
m_ButtonClose - Variable in class adams.gui.tools.UpdateSampleDataPanel: the button for closing the dialog.
m_ButtonConditions - Variable in class adams.gui.tools.idprovider.DatabaseSearchPanel: the button for the options.
m_ButtonDelete - Variable in class adams.gui.tools.DeleteSampleDataPanel: the button for deleting the sample values.
m_ButtonDelete - Variable in class adams.gui.tools.DeleteSpectrumPanel: the button for executing the deletion.
m_ButtonDisplay - Variable in class adams.gui.tools.ListSampleDataPanel: the button for displaying the sample data.
m_ButtonLoad - Variable in class adams.gui.tools.idprovider.ManualListPanel: the button for loading the spreadsheet.
m_ButtonLoad - Variable in class adams.gui.tools.idprovider.SpreadSheetIDPanel: the button for loading the spreadsheet.
m_ButtonRemoveReferenceValue - Variable in class adams.gui.tools.UpdateSampleDataPanel: the button for removing sample data reference values.
m_ButtonSearch - Variable in class adams.gui.tools.idprovider.DatabaseSearchPanel: the button for the search.
m_ButtonSelectAll - Variable in class adams.gui.tools.UpdateSampleDataPanel: the button for selecting all.
m_ButtonSelectInvert - Variable in class adams.gui.tools.DeleteSampleDataPanel: the button for inverting the checked ones.
m_ButtonSelectInvert - Variable in class adams.gui.tools.ListSampleDataPanel: the button for inverting the checked ones.
m_ButtonSelectInvert - Variable in class adams.gui.tools.UpdateSampleDataPanel: the button for inverting the selection.
m_ButtonSelectNone - Variable in class adams.gui.tools.UpdateSampleDataPanel: the button for selecting none.
m_BytesRead - Variable in class adams.data.io.input.SPCSpectrumReader.AbstractParser: the number of bytes read.
m_Cache - Variable in class adams.flow.transformer.SpectralAngleMapper: The LRU cache to get the storage value from.
m_CallableActor - Variable in class adams.flow.transformer.MultiSpectrumAdd: the callable actor.
m_CallableName - Variable in class adams.flow.transformer.MultiSpectrumAdd: the callable name.
m_CanAbstain - Variable in class weka.classifiers.meta.SpectrumClassifier: whether the base classifier can abstain.
m_Check - Variable in class adams.flow.transformer.PredictionCheck: the check scheme to use.
m_CheckBoxCombine - Variable in class adams.gui.visualization.spectrum.SpectrumExportDialog: whether the timeseries should be saved in the same file, if possible.
m_CheckWaveNumberAlignment - Variable in class adams.flow.transformer.SpectralAngleMapper: Whether to check wave-numbers match between spectra.
m_Chunk - Variable in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader.ChunkedSheetIterator: the next chunk.
m_ChunkSize - Variable in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.DataCollector: the chunk size.
m_ChunkSize - Variable in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: the chunk size when retrieving spectra from the database.
m_Classifier - Variable in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: WEKA classifier used for modeling.
m_Classifier - Variable in class adams.data.cleaner.instance.RemoveOutliers: the classifier to use for evaluation.
m_Classifier - Variable in class adams.data.evaluator.instance.CrossValidatedNeighborHood: the classifier to cross-validate.
m_Classifier - Variable in class adams.data.evaluator.instance.CrossValidatedPrediction: the classifier to cross-validate.
m_Classifier - Variable in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: the interval estimator to use.
m_ClassifierFirst - Variable in class adams.data.evaluator.instance.SavitzkyGolayRange: the classifier to be used on SG data with first derivative.
m_ClassifierNone - Variable in class adams.data.evaluator.instance.SavitzkyGolayRange: the classifier to be used on SG data with no derivative.
m_Classifiers - Variable in class adams.data.evaluator.instance.EnsembleEvaluator: the classifiers to use.
m_Classifiers - Variable in class adams.data.evaluator.instance.MultiClassifierEvaluator: WEKA classifiers to use.
m_Classifiers - Variable in class adams.data.postprocessor.instances.PredictionErrorIQR: the classifiers to use for internal cross-validation.
m_ClassifierSecond - Variable in class adams.data.evaluator.instance.SavitzkyGolayRange: the classifier to be used on SG data with second derivative.
m_ClassLabels - Variable in class adams.data.instances.AbstractFieldInstanceGeneratorWithClass: the nominal labels to use, in case of a nominal class.
m_ClassLabels - Variable in class adams.data.instances.AbstractSpectrumInstanceGeneratorWithClass: the nominal labels to use, in case of a nominal class.
m_ClassRange - Variable in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: the class range.
m_ClassStats - Variable in class adams.data.evaluator.instance.CrossValidatedPrediction: the attribute statistics of the class attribute.
m_ClassStats - Variable in class adams.data.evaluator.instance.SavitzkyGolayRange: the class attribute stats.
m_CleanAfterBuild - Variable in class adams.flow.transformer.Evaluator: whether to clean up after build.
m_Cleaned - Variable in class adams.flow.transformer.Cleaner.CleanJob: the cleaned data.
m_Cleaner - Variable in class adams.flow.control.InstanceCleaner: the instance cleaner to use.
m_Cleaner - Variable in class adams.flow.control.SpectrumCleaner: the spectrum cleaner to use.
m_Cleaner - Variable in class adams.flow.transformer.Cleaner.CleanJob: the cleaner to apply.
m_Cleaner - Variable in class adams.flow.transformer.Cleaner: the evaluator.
m_CleanerDetailsOutput - Variable in class adams.flow.transformer.Cleaner: the file to save the cleaner details to.
m_CleanInstancesError - Variable in class adams.data.cleaner.instance.AbstractCleaner: for storing error messages in case the cleaning of the initial Instances object failed.
m_client - Variable in class adams.data.io.output.foss.FossOutputHelper.SampleHeader: String(9): zero terminated.
m_Client - Variable in class adams.data.io.output.NIRSpectrumWriter: Client name.
m_CollectionDate - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: the collection date.
m_Color - Variable in class adams.gui.visualization.spectrum.SelectedWaveNumberPaintlet: the color to paint the point with.
m_Color - Variable in class adams.gui.visualization.spectrum.SpectrumContainer: the associated color.
m_ColorField - Variable in class adams.gui.visualization.spectrum.ReportColorSpectrumPaintlet: the report field to get the color from.
m_ColorGenerator - Variable in class adams.flow.sink.ThreeWayDataHeatmapDisplay: the generator for the color gradient.
m_ColorGenerator - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: the color generator to use.
m_ColorLookup - Variable in class adams.data.conversion.SpectrumToBufferedImage: the lookup table.
m_ColorProvider - Variable in class adams.flow.sink.SpectrumDisplay: the color provider to use.
m_ColorProvider - Variable in class adams.gui.visualization.spectrum.SpectrumContainerManager: the color provider for managing the colors.
m_ColorProvider - Variable in class adams.gui.visualization.spectrum.SpectrumPaintletStringField: the color provider to use.
m_Colors - Variable in class adams.gui.visualization.spectrum.SpectrumPaintletNumericField: the colors.
m_ColSampleDataNames - Variable in class adams.data.conversion.SpreadSheetColumnsToSampleData: the column with the sample data names.
m_ColSampleDataNames - Variable in class adams.data.conversion.SpreadSheetColumnsToSpectra: the column with the sample data names.
m_ColsSampleDataValues - Variable in class adams.data.conversion.SpreadSheetColumnsToSampleData: the columns with the sample data values.
m_ColumnAmplitude - Variable in class adams.data.conversion.SpreadSheetToSpectrum: the amplitude column.
m_ColumnData - Variable in class adams.data.conversion.SpreadSheetTo3DTensor: the data column.
m_ColumnData - Variable in class adams.data.conversion.SpreadSheetToThreeWayData: the data column.
m_ColumnID - Variable in class adams.data.conversion.SpreadSheetRowsToSampleData: the (optional) row with the sample ID.
m_ColumnID - Variable in class adams.data.conversion.SpreadSheetRowsToSpectra: the (optional) row with the sample ID.
m_ColumnMeasurementName - Variable in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: the column name that stores the reference value name.
m_ColumnMeasurementValue - Variable in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: the column name that stores the reference value.
m_Columns - Variable in class adams.data.conversion.SpreadSheetTo2DTensor: the columns to use.
m_ColumnSampleID - Variable in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: the column name to get the sample ID from.
m_ColumnSampleID - Variable in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: the column name to get the sample ID from.
m_ColumnSampleType - Variable in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: the column name that stores the sample type.
m_ColumnsAmplitude - Variable in class adams.data.conversion.SpreadSheetColumnsToSpectra: the column with amplitudes.
m_ColumnsAmplitude - Variable in class adams.data.conversion.SpreadSheetRowsToSpectra: the rows to get the amplitudes from.
m_ColumnsBoolean - Variable in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: the range of columns with boolean sample data.
m_ColumnsNumeric - Variable in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: the range of columns with numeric sample data.
m_ColumnsSampleData - Variable in class adams.data.conversion.SpreadSheetRowsToSampleData: the rows to get the sample data from.
m_ColumnsSampleData - Variable in class adams.data.conversion.SpreadSheetRowsToSpectra: the rows to get the sample data from.
m_ColumnsSampleData - Variable in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: the range of columns with the sample data.
m_ColumnWaveNumber - Variable in class adams.data.conversion.SpreadSheetColumnsToSpectra: the (optional) wavenumber column.
m_ColumnWaveNumber - Variable in class adams.data.conversion.SpreadSheetToSpectrum: the wavenumber column.
m_ColumnX - Variable in class adams.data.conversion.SpreadSheetTo3DTensor: the X column.
m_ColumnX - Variable in class adams.data.conversion.SpreadSheetToThreeWayData: the X column.
m_ColumnY - Variable in class adams.data.conversion.SpreadSheetTo3DTensor: the Y column.
m_ColumnY - Variable in class adams.data.conversion.SpreadSheetToThreeWayData: the Y column.
m_ColumnZ - Variable in class adams.data.conversion.SpreadSheetTo3DTensor: the Z column.
m_ColumnZ - Variable in class adams.data.conversion.SpreadSheetToThreeWayData: the Z column.
m_ComboBoxIDPanels - Variable in class adams.gui.tools.DeleteSampleDataPanel: the combobox for the ID panels.
m_ComboBoxIDPanels - Variable in class adams.gui.tools.ListSampleDataPanel: the comboboxes for the ID panels.
m_ComboBoxIDPanels - Variable in class adams.gui.tools.UpdateSampleDataPanel: the comboboxes for the ID panels.
m_ComboBoxType - Variable in class adams.gui.tools.UpdateSampleDataPanel: the combobox for the field data type.
m_Comment - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: the comment.
m_Comparator - Static variable in class adams.data.spectrum.MultiSpectrum: the default comparator.
m_Comparator - Static variable in class adams.data.spectrum.Spectrum: the default comparator.
m_Comparator - Static variable in class adams.data.spectrum.SpectrumUtils: comparator for finding wavenumbers.
m_Comparator - Static variable in class adams.data.threeway.L1Point: the default comparator.
m_Comparator - Static variable in class adams.data.threeway.L1PointUtils: the comparator in use.
m_Comparator - Static variable in class adams.data.threeway.ThreeWayData: the default comparator.
m_Comparator - Static variable in class adams.data.threeway.ThreeWayDataUtils: comparator for finding timestamps.
m_Component - Variable in class adams.data.conversion.WekaPredictionContainerToEvaluationContainer: the optional component to store.
m_Component - Variable in class adams.flow.transformer.Evaluator: the name of the component.
m_Components - Variable in class adams.data.spectrumanalysis.FastICA: the components.
m_Condition - Variable in class adams.data.spectrumfilter.ConditionalReportField: the condition to apply.
m_ConditionBoolean - Variable in class adams.data.multifilter.PickByReportValue: the condition for boolean fields.
m_ConditionNumericMax - Variable in class adams.data.multifilter.PickByReportValue: the condition for numeric (upper bound).
m_ConditionNumericMin - Variable in class adams.data.multifilter.PickByReportValue: the condition for numeric (lower bound).
m_Conditions - Variable in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: the spectrum retrieval conditions.
m_Conditions - Variable in class adams.data.spectrumfilter.Covariance: the spectrum retrieval conditions.
m_Conditions - Variable in class adams.data.spectrumfilter.LRCoeff: the spectrum retrieval conditions.
m_Conditions - Variable in class adams.flow.source.OrphanedSampleDataIdSupplier: the conditions for retrieving the orphaned IDs.
m_Conditions - Variable in class adams.gui.tools.idprovider.DatabaseSearchPanel: the conditions to use in the search.
m_ConditionString - Variable in class adams.data.multifilter.PickByReportValue: the condition for string fields.
m_ConfidenceLevel - Variable in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: the confidence level.
m_Configured - Variable in class adams.flow.transformer.MultiSpectrumAdd: whether the callable actor has been configured.
m_constituents - Variable in class adams.data.io.output.foss.FossOutputHelper.InstrumentHeader: 32 * 16 chars, null terminated constituent names.
m_Constituents - Variable in class adams.data.io.output.CALSpectrumWriter: constituents.
m_Constituents - Variable in class adams.data.io.output.foss.FossOutputHelper.ConstituentValues: the constituent values.
m_Conversion - Variable in class adams.data.spectrumfilter.ReportFieldFromStringValue: the conversion to apply.
m_Conversion - Variable in class adams.flow.transformer.SetEvaluationMetaData: the type of conversion.
m_Converter - Variable in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: the feature converter to use.
m_Converter - Variable in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: the feature converter to use.
m_Convertor - Variable in class adams.data.spectrumimage.Spectrogram: The conversion that does the actual work.
m_CoordinatesPaintlet - Variable in class adams.gui.visualization.spectrum.SpectrumPanel: paintlet for drawing the X-axis.
m_Correction - Variable in class adams.data.spectrumfilter.Detrend: the correction scheme to use.
m_Correction - Variable in class adams.data.spectrumfilter.MultiplicativeScatterCorrection: the correction scheme to use.
m_count - Variable in class adams.data.io.input.foss.FossHelper: number of (non deleted) spectra.
m_count - Variable in class adams.data.io.output.foss.FossOutputHelper.Generalheader: 2 BYTES: number of (non deleted) spectra.
m_CountAfter - Variable in class adams.data.postprocessor.instances.PredictionErrorIQR: the count after.
m_CountBefore - Variable in class adams.data.postprocessor.instances.PredictionErrorIQR: the count before.
m_creation_date - Variable in class adams.data.io.output.foss.FossOutputHelper.Generalheader: 2 BYTES: unsigned int.
m_CrossHairTracker - Variable in class adams.gui.visualization.spectrum.SpectrumPanel: the cross-hair paintlet.
m_CrossValidation - Variable in class adams.data.postprocessor.instances.PredictionErrorIQR: the current evaluation.
m_CrossvalidationResults - Variable in class adams.data.evaluator.instance.MultiClassifierEvaluator: the results.
m_Current - Variable in class adams.flow.transformer.SpectrumMinMax: the current input token counter.
m_CurrentAlgorithm - Variable in class adams.flow.transformer.ThreeWayDataTrain: the algorithm instance that is currently being trained.
m_CurrentEvaluation - Variable in class adams.data.cleaner.instance.RemoveOutliers: the current evaluation.
m_CurrentFile - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: the current file.
m_CurrentFilter - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the current filter.
m_CurrentFilter - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the current filter.
m_CurrentICA - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the current ICA analysis.
m_CurrentIDProvider - Variable in class adams.gui.tools.DeleteSampleDataPanel: the current panel.
m_CurrentIDProvider - Variable in class adams.gui.tools.ListSampleDataPanel: the current panel.
m_CurrentIDProvider - Variable in class adams.gui.tools.UpdateSampleDataPanel: the current panel.
m_CurrentPCA - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the current PCA analysis.
m_CurrentPLS - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the current PLS analysis.
m_CustomComparator - Variable in class adams.data.conversion.SpectraToMultiSpectrum: the custom comparator to use.
m_CustomComparator - Variable in class adams.data.spectrum.MultiSpectrum: a custom comparator.
m_CustomComparator - Variable in class adams.flow.transformer.SpectrumFileReader: the custom comparator to use.
m_Data - Variable in class adams.data.io.input.SPCSpectrumReader.AbstractParser: the binary data to analyze.
m_Data - Variable in class adams.data.threeway.L2Point: value.
m_Data - Variable in class adams.flow.standalone.rats.WSMultiSpectrumReception: the spectrum received via webservice.
m_Data - Variable in class adams.flow.standalone.rats.WSSpectrumReception: the spectrum received via webservice.
m_Data - Variable in class adams.flow.transformer.Cleaner.CleanJob: the data to clean.
m_Data - Variable in class adams.flow.transformer.Evaluator.EvaluateJob: the data to use for training.
m_Data - Variable in class adams.gui.visualization.spectrum.SpectrumTableModel: the underlying spectrum.
m_Data - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: the data on display.
m_DatabaseConnection - Variable in class adams.data.cleaner.instance.AbstractDatabaseConnectionCleaner: the database connection.
m_DatabaseConnection - Variable in class adams.data.cleaner.spectrum.AbstractDatabaseConnectionCleaner: the database connection.
m_DatabaseConnection - Variable in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.DataCollector: the database connection.
m_DatabaseConnection - Variable in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: the database connection.
m_DatabaseConnection - Variable in class adams.data.io.input.AbstractSampleDataReader: the database connection in use.
m_DatabaseConnection - Variable in class adams.flow.transformer.report.UpdateDatabaseID: the database connection in use.
m_DatabaseConnection - Variable in class adams.flow.webservice.multispectrum.SimpleRatsMultiSpectrumService: the database connection.
m_DatabaseConnection - Variable in class adams.flow.webservice.SimpleSpectralGetService: the database connection.
m_DatabaseConnection - Variable in class adams.flow.webservice.SimpleSpectralPutService: the database connection.
m_DatabaseConnection - Variable in class adams.flow.webservice.SimpleSpectralTransformService: the database connection.
m_DatabaseConnection - Variable in class adams.flow.webservice.spectrum.SimpleRatsSpectrumService: the database connection.
m_DatabaseConnection - Variable in class adams.gui.visualization.spectrum.SpectrumContainerManager: the database connection.
m_DatabaseConnection - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the database connection.
m_DatabaseConnectionUpdated - Variable in class adams.flow.control.InstanceCleaner: whether the database connection has been updated.
m_DatabaseConnectionUpdated - Variable in class adams.flow.control.SpectrumCleaner: whether the database connection has been updated.
m_DatabaseConnectionUpdated - Variable in class adams.flow.transformer.InstanceGenerator: whether the database connection has been updated.
m_DatabaseConnectionUpdated - Variable in class adams.flow.transformer.MultiSpectrumFilter: whether the database connection has been updated.
m_DatabaseConnectionUpdated - Variable in class adams.flow.transformer.MultiSpectrumOutlierDetector: whether the database connection has been updated.
m_DatabaseConnectionUpdated - Variable in class adams.flow.transformer.MultiSpectrumReportFilter: whether the database connection has been updated.
m_DatabaseID - Variable in class adams.data.spectrum.Spectrum: the database ID.
m_DatabaseID - Variable in class adams.data.threeway.ThreeWayData: database id.
m_DataImage - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: the panel for displaying the data as image.
m_DataPanel - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractThreeWayDataOverlay: the heatmap panel.
m_DataTypes - Variable in class adams.flow.transformer.BulkSampleDataDbWriter: the types of data to import.
m_date - Variable in class adams.data.io.output.foss.FossOutputHelper.SampleHeader: 2 BYTES: unsigned int. date.
m_DateFormat - Variable in class adams.data.io.input.MPSSpectrumReader: the format to use for parsing the date in the file.
m_DB - Variable in class adams.db.mirrored.SampleDataT: the non-mirrored backend.
m_DB - Variable in class adams.db.mirrored.SpectrumT: the non-mirrored backend.
m_DB - Variable in class adams.db.SampleDataF: the backend.
m_DB - Variable in class adams.db.SpectrumF: the backend.
m_DefaultColor - Variable in class adams.gui.visualization.spectrum.ReportColorSpectrumPaintlet: the default color to use if no color found in report.
m_DefaultColor - Variable in class adams.gui.visualization.spectrum.SpectrumPaintletNumericField: the default color if field is missing.
m_DefaultColor - Variable in class adams.gui.visualization.spectrum.SpectrumPaintletStringField: the default color if field is missing.
m_Definition - Variable in class adams.data.io.input.opus.OpusBlockHelper.Block: the definition the block is based on.
m_deleted - Variable in class adams.data.io.input.foss.FossHelper: number of deleted rows in this file.
m_deleted - Variable in class adams.data.io.output.foss.FossOutputHelper.Generalheader: 2 BYTES: number of (deleted) spectra.
m_deleted - Variable in class adams.data.io.output.foss.FossOutputHelper.SampleHeader: 1 BYTE??
m_deleted - Variable in class adams.data.io.output.foss.FossOutputHelper.SampleInfo: 1 BYTE?
m_Denormalize - Variable in class adams.data.io.input.SimpleEEMReader: whether to denormalize the data using the "Normalized by " value.
m_DerivativeOrder - Variable in class weka.filters.unsupervised.attribute.SavitzkyGolayRange: the order of the derivative.
m_DerivativeOrder - Variable in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: the order of the derivative.
m_Descending - Variable in class adams.data.io.output.ASCSpectrumWriter: whether to output the sample data as well.
m_Descending - Variable in class adams.data.io.output.DPTSpectrumWriter: whether to output the sample data as well.
m_Detector - Variable in class adams.data.cleaner.instance.RemoveOutliers: the outlier detector to use.
m_Detector - Variable in class adams.flow.transformer.MultiSpectrumOutlierDetector: the outlier detector to apply.
m_DialogColorGenerator - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the dialog for selecting the color provider.
m_DialogColorProvider - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the dialog for selecting the color provider.
m_DialogFilter - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the filter dialog.
m_DialogFilter - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the filter dialog.
m_DialogICA - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the ICA dialog.
m_DialogMissingValueColor - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the dialog for selecting the missing value color.
m_DialogOverlay - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the dialog for selecting an overlay.
m_DialogPaintlet - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the dialog for selecting the paintlet.
m_DialogPCA - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the PCA dialog.
m_DialogPLS - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the PLS dialog.
m_DialogSelectionProcessor - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the dialog for selecting an selection processor.
m_DontUpdateID - Variable in class adams.data.multifilter.AbstractMultiSpectrumFilter: whether to suppress updating of ID.
m_dp - Variable in class adams.data.io.input.ASCSpectrumReader.ParsedFile: vector of 2d double (double[2]) wavenumber,absorbance.
m_dp - Variable in class adams.data.io.input.DPTSpectrumReader.ParsedFile: vector of 2d double (double[2]) wavenumber,absorbance.
m_End - Variable in class adams.data.io.input.opus.OpusBlockHelper.Block: the end of the block (incl).
m_End - Variable in class weka.filters.unsupervised.attribute.SavitzkyGolayRange: the end of the range.
m_EndDate - Variable in class adams.db.AbstractSpectrumConditions: the end date of the spectra (incl.).
m_EndDate - Variable in class adams.db.OrphanedSampleDataConditions: the end date of the inserts (incl.).
m_Endpoint - Variable in class adams.flow.webservice.multispectrum.RatsMultiSpectrumServiceWS: end point for the web service
m_Endpoint - Variable in class adams.flow.webservice.SpectralGetServiceWS: end point for the web service
m_Endpoint - Variable in class adams.flow.webservice.SpectralPutServiceWS: end point for the web service
m_Endpoint - Variable in class adams.flow.webservice.SpectralTransformServiceWS: end point for the web service
m_Endpoint - Variable in class adams.flow.webservice.spectrum.RatsSpectrumServiceWS: end point for the web service
m_EOC - Variable in class adams.data.io.output.NIRSpectrumWriter: Number of EOC's per rev (???).
m_EvalMax - Variable in class adams.data.evaluator.instance.FakeEvaluator: the maximum to use for the evaluations.
m_EvalMin - Variable in class adams.data.evaluator.instance.FakeEvaluator: the minimum to use for the evaluations.
m_Evaluation - Variable in class adams.data.evaluator.instance.CrossValidatedNeighborHood: the current evaluation.
m_Evaluation - Variable in class adams.data.evaluator.instance.EnsembleEvaluator: the current evaluation.
m_Evaluation - Variable in class adams.flow.transformer.predictioncheck.Range: the evaluation to check.
m_Evaluator - Variable in class adams.flow.transformer.Evaluator.EvaluateJob: the evaluator to train.
m_Evaluator - Variable in class adams.flow.transformer.Evaluator: the evaluator.
m_EvaluatorResetVariable - Variable in class adams.flow.transformer.Evaluator: the variable to monitor for changes, triggering resets of the evaluator.
m_EvalWait - Variable in class adams.data.evaluator.instance.FakeEvaluator: the eval wait time in msec.
m_Exclude - Variable in class weka.filters.unsupervised.attribute.SegmentedDownSample: the regular expression for attributes to exclude from the splits.
m_Exclude - Variable in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: the regular expression for attributes to exclude from the splits.
m_ExcludeDummies - Variable in class adams.db.AbstractSpectrumConditions: whether to exclude spectra with dummy reports.
m_ExperimentType - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: the instrument experiment technique (2).
m_Exponent - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: the scaling exponent.
m_Exponent - Variable in class adams.data.io.input.SPCSpectrumReader.SubFileParser: the scaling exponent.
m_ExportDatasetDialog - Variable in class adams.gui.visualization.spectrum.SpectrumPanel: for exporting visible spectra to a dataset.
m_ExportDialog - Variable in class adams.gui.visualization.spectrum.SpectrumPanel: for exporting visible spectra.
m_Expression - Variable in class adams.data.spectrumfilter.AmplitudeExpression: the mathematical expression to evaluate.
m_Expression - Variable in class adams.data.spectrumfilter.WaveNumberExpression: the mathematical expression to evaluate.
m_Extract - Variable in class adams.data.spectrumfilter.ReportFieldFromStringValueWithLookup: the regexp to extract the lookup key (uses 1st group).
m_Factor - Variable in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: the maximum factor a value can be above the upper percentile or below the lower percentile before considered "un-clean".
m_Failure - Variable in class adams.data.spectrumfilter.ConditionalReportField: the failure value.
m_FFTSampleSize - Variable in class adams.data.conversion.SpectrumToBufferedImage: the FFT sample size (power of 2).
m_FFTSampleSize - Variable in class adams.data.spectrumimage.Spectrogram: the FFT sample size (power of 2).
m_field - Variable in class adams.data.spectrumoutlier.MinMax: the quant field.
m_Field - Variable in class adams.data.cleaner.spectrum.MinMax: the field in the sample data to check.
m_Field - Variable in class adams.data.instances.AbstractFieldInstanceGeneratorWithClass: the field that acts as class attribute.
m_Field - Variable in class adams.data.instances.AbstractSpectrumInstanceGeneratorWithClass: the field that acts as class attribute.
m_Field - Variable in class adams.data.multifilter.PickByReportValue: the field to use.
m_Field - Variable in class adams.data.spectrum.SpectrumComparatorByReportValue: the field to use.
m_Field - Variable in class adams.data.spectrumfilter.Covariance: reference field.
m_Field - Variable in class adams.data.spectrumoutlier.StringMatcher: the name of the reference compound.
m_Field - Variable in class adams.db.SpectrumConditionsSingle: the reference fields.
m_Field - Variable in class adams.gui.visualization.spectrum.SpectrumPaintletNumericField: the report field to get the numeric value from.
m_Field - Variable in class adams.gui.visualization.spectrum.SpectrumPaintletStringField: the report field to get the string value from.
m_FieldIPRs - Variable in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: the interpercentiles to use for the fields.
m_FieldRanges - Variable in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.DataCollector: the inter-percentile ranges for the fields (field - IPR).
m_FieldRangesPerChunk - Variable in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.DataCollector: the inter-percentile ranges for the fields (field - lower/upper percentile) per chunk.
m_Fields - Variable in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.DataCollector: the fields that were encountered.
m_Fields - Variable in class adams.data.instances.AbstractFieldInstanceGenerator: fields to add to the output data.
m_Fields - Variable in class adams.data.multireportfilter.PullUpFields: the fields to pull up from the sub-spectra and place in the top-level report.
m_Fields - Variable in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: fields to add to the output data.
m_Fields - Variable in class adams.data.spreadsheetrowgenerator.SampleDataOnlyRowGenerator: fields to add to the output data.
m_Fields - Variable in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: fields to add to the output data.
m_Fields - Variable in class adams.db.SpectrumConditionsMulti: the reference fields.
m_file_id - Variable in class adams.data.io.output.foss.FossOutputHelper.Generalheader: char[71] file id.
m_FileChooser - Variable in class adams.gui.visualization.spectrum.MultiSpectrumPanel: the file chooser to use for loading files.
m_FileChooser - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: for loading data structures from disk.
m_FileID - Variable in class adams.data.io.output.NIRSpectrumWriter: File ID.
m_FilenameGenerator - Variable in class adams.flow.standalone.rats.SaveMultiSpectrumFileOutput: the filename generator to use.
m_FilenameGenerator - Variable in class adams.flow.standalone.rats.SaveSpectrumFileOutput: the filename generator to use.
m_filter - Variable in class adams.data.spectrumfilter.Covariance: filter to apply to retrieved spectra.
m_Filter - Variable in class adams.data.cleaner.instance.IQRCleaner: the IQR filter.
m_Filter - Variable in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: the filter.
m_Filter - Variable in class adams.data.evaluator.instance.DistanceToCenter: the filter to use for filtering.
m_Filter - Variable in class adams.data.evaluator.instance.DistanceToClosest: the filter to use for filtering.
m_Filter - Variable in class adams.data.io.input.FilteredSpectrumReader: the filter to apply.
m_Filter - Variable in class adams.data.io.output.FilteredSpectrumWriter: the filter to apply.
m_Filter - Variable in class adams.data.postprocessor.instances.WekaFilter: the WEKA filter to use.
m_Filter - Variable in class adams.data.spectrumfilter.SubtractSpectrum: the filter to run.
m_Filter - Variable in class adams.data.spectrumfilter.WekaFilterToReport: the Weka filter.
m_Filter - Variable in class adams.flow.rest.TransformSpectrum: the filter to apply.
m_Filter - Variable in class adams.flow.transformer.MultiSpectrumFilter: the filter to apply.
m_Filter - Variable in class adams.flow.transformer.MultiSpectrumOutlierDetector: the filter to apply for extracting the spectrum to apply the outlier detector to.
m_Filter - Variable in class adams.flow.transformer.MultiSpectrumReportFilter: the filter to apply.
m_Filter - Variable in class weka.filters.unsupervised.attribute.RangeBasedSavitzkyGolay: the filter used internally.
m_Filter - Variable in class weka.filters.unsupervised.attribute.SegmentedDownSample: the filter used internally.
m_Filter - Variable in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: the filter used internally.
m_Filter - Variable in class weka.filters.unsupervised.attribute.SpectrumFilter: the base filter.
m_FilterAll - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: indicates whether filter is applied to all data structures.
m_FilteredInitData - Variable in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: the filtered data generated when initializing the postprocessor.
m_FilteredInitData - Variable in class adams.data.postprocessor.instances.WekaFilter: the filtered data generated when initializing the postprocessor.
m_FilterOverlayOriginalData - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: indicates whether the filtered data was overlayed over the original.
m_FilterOverlayOriginalData - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: indicates whether the filtered data was overlayed over the original.
m_First - Variable in class adams.data.spectrumfilter.AbstractStandardiseFilter: the first data point.
m_FirstPassData - Variable in class weka.filters.unsupervised.attribute.RangeBasedSavitzkyGolay: the filteed data from the first pass.
m_FirstPassData - Variable in class weka.filters.unsupervised.attribute.SegmentedDownSample: the filtered data from the first pass.
m_FirstPassData - Variable in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: the filtered data from the first pass.
m_FirstWave - Variable in class adams.flow.transformer.InstanceToSpectrum: the first wave number.
m_FirstX - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: the value of the first X.
m_FirstXPoint - Variable in class adams.data.io.output.ASCSpectrumWriter: First X WaveNumber.
m_Flip - Variable in class adams.data.spectrumoutlier.Swapped: whether to flip the halves.
m_FlowContext - Variable in class adams.data.cleaner.instance.AbstractCleaner: the flow context.
m_FlowContext - Variable in class adams.data.cleaner.spectrum.AbstractCleaner: the flow context.
m_FlowContext - Variable in class adams.data.postprocessor.instances.AbstractPostProcessor: the flow context.
m_FlowContext - Variable in class adams.data.postprocessor.instances.PredictionErrorIQR: the flow context.
m_FlowContext - Variable in class adams.data.spectrumfilter.WekaFilterToReport: the flow context.
m_Folds - Variable in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: number of fold for the cross validation.
m_Folds - Variable in class adams.data.evaluator.instance.CrossValidatedNeighborHood: the number of folds.
m_Folds - Variable in class adams.data.evaluator.instance.CrossValidatedPrediction: the number of folds.
m_Folds - Variable in class adams.data.evaluator.instance.MultiClassifierEvaluator: the number of folds.
m_Font - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: the font to use.
m_ForceCommaToPoint - Variable in class adams.data.io.input.ASCSpectrumReader.ParsedFile: whether to force replacing comma with point.
m_Format - Variable in class adams.data.conversion.ArrayToSpectrum: the format.
m_Format - Variable in class adams.data.conversion.SpreadSheetColumnsToSpectra: the format to use for the spectrum.
m_Format - Variable in class adams.data.conversion.SpreadSheetRowsToSpectra: the format to use for the spectrum.
m_Format - Variable in class adams.data.conversion.SpreadSheetToSpectrum: the format to use for the spectrum.
m_Format - Variable in class adams.data.io.input.AbstractSampleDataReader: the spectrum format to use.
m_Format - Variable in class adams.data.io.input.AbstractSpectrumReader: the form of this data.
m_Format - Variable in class adams.data.io.input.AbstractThreeWayDataReader: the form of this data.
m_Format - Variable in class adams.data.multispectrumoperation.Remove: the regular expression for the format.
m_Format - Variable in class adams.db.AbstractSpectrumConditions: the regular expression on the format type of the spectrum.
m_Format - Variable in class adams.db.SpectrumIDConditions: the regular expression on the format type of the spectrum.
m_Format - Variable in class adams.flow.condition.bool.HasSpectrum: the form of this data.
m_Format - Variable in class adams.flow.transformer.datacontainer.LoadSampleData: the format to obtain the reference data from.
m_Format - Variable in class adams.flow.transformer.DeleteSpectrum: what type of spectrum to retrieve from the database.
m_Format - Variable in class adams.flow.transformer.MultiSpectrumRemove: the regular expression for the format.
m_Format - Variable in class adams.flow.transformer.report.UpdateDatabaseID: the form of this data.
m_Format - Variable in class adams.flow.transformer.SpectrumDbReader: what type of spectrum to retrieve from the database.
m_Format - Variable in class adams.flow.webservice.Get: the spectrum format.
m_Format - Variable in class adams.gui.selection.SelectSpectrumPanel.TableModel: the FORMATs to display.
m_Formats - Variable in class adams.data.multifilter.AbstractFormatsBasedMultiSpectrumFilter: the formats to average (empty = all).
m_Formatter - Variable in class adams.gui.tools.idprovider.DatabaseSearchPanel: the formatter to use.
m_GenerateSampleIDs - Variable in class adams.flow.source.SpectrumIdSupplier: whether to return database IDs or sample IDs.
m_Generator - Variable in class adams.data.conversion.SpectrumToBufferedImage: the generator to use.
m_Generator - Variable in class adams.data.io.output.SpectrumImageWriter: the generator to use.
m_Generator - Variable in class adams.data.spectrumanalysis.AbstractWekaSpectrumAnalysis: the instance generator to use.
m_Generator - Variable in class adams.data.spectrumfilter.LRCoeff: the generator to use.
m_Generator - Variable in class adams.data.spectrumfilter.PCA: the instance generator to use.
m_Generator - Variable in class adams.data.spectrumfilter.PLS: the instance generator to use.
m_Generator - Variable in class adams.data.spectrumfilter.WekaFilterToReport: the instance generator to use.
m_Generator - Variable in class adams.data.spectrumimage.Spectrogram: the generator to use.
m_Generator - Variable in class adams.data.threewayfeatures.Histogram: determines how to generate the histogram.
m_Generator - Variable in class adams.flow.transformer.InstanceGenerator: the generator to use.
m_Generator - Variable in class adams.flow.transformer.SpreadSheetRowGenerator: the generator to use.
m_Generator - Variable in class adams.gui.visualization.spectrum.SpectrumPaintletNumericField: the color gradient generator to use.
m_GOEDialog - Variable in class adams.gui.visualization.spectrum.MultiSpectrumPanel: for choosing an appropriate reader.
m_GradientColors - Variable in class adams.data.conversion.SpectrumToBufferedImage: the gradient colors.
m_Group - Variable in class adams.data.io.input.sampleidextraction.RegExp: the regexp group to use.
m_Group - Variable in class adams.data.spectrumfilter.ReportFieldFromStringValue: the group to use as value for the target field.
m_GroupExtraction - Variable in class adams.data.io.input.ExtractIdAndTypeSpectrumReader: the group extractor.
m_GroupExtraction - Variable in class adams.data.io.input.ExtractIdAndTypeThreeWayDataReader: the group extractor.
m_Header - Variable in class adams.data.evaluator.instance.AbstractNearestNeighborBasedEvaluator: the header of the training data.
m_Header - Variable in class adams.data.evaluator.instance.EnsembleEvaluator: the header.
m_Header - Variable in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: the header.
m_Header - Variable in class adams.data.evaluator.instance.MultiClassifierEvaluator: Header of instances to process.
m_Header - Variable in class adams.data.evaluator.instance.SavitzkyGolayRange: the header of the training data.
m_HeaderContainsWaveNumber - Variable in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: whether the column header is the wave number.
m_Height - Variable in class adams.data.spectrumimage.Intensity: the image height to generate.
m_Height - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlayWithDimensions: the height of the overlay.
m_Helper - Variable in class adams.flow.transformer.MultiSpectrumAdd: the helper class.
m_HistogramSetup - Variable in class adams.gui.visualization.spectrum.SpectrumPanel: the dialog for the histogram setup.
m_ht - Variable in class adams.data.io.input.ASCSpectrumReader.ParsedFile: Name->Value, String->String. ie "Sample ID" -> "994370"
m_ICA - Variable in class adams.data.spectrumanalysis.FastICA: the Fast ICA analysis to use.
m_id - Variable in class adams.data.spectrumfilter.SubtractSpectrum
m_ID - Variable in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.InterPercentileRange: wave number or field.
m_ID - Variable in class adams.data.conversion.ArrayToSpectrum: the sample id.
m_ID - Variable in class adams.data.conversion.SpreadSheetToSpectrum: the ID to use for the spectrum.
m_ID - Variable in class adams.data.conversion.WekaPredictionContainerToEvaluationContainer: the optional ID to store.
m_ID - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: the ID to use.
m_ID - Variable in class adams.flow.condition.bool.HasSpectrum: the ID of the spectrum.
m_ID - Variable in class adams.flow.source.NewSpectrum: the ID to use.
m_ID - Variable in class adams.flow.webservice.Get: the spectrum ID.
m_IDExtraction - Variable in class adams.data.io.input.ExtractIdAndTypeSpectrumReader: the ID extractor.
m_IDExtraction - Variable in class adams.data.io.input.ExtractIdAndTypeThreeWayDataReader: the ID extractor.
m_IDPanels - Variable in class adams.gui.tools.DeleteSampleDataPanel: the ID panels.
m_IDPanels - Variable in class adams.gui.tools.ListSampleDataPanel: the ID panels.
m_IDPanels - Variable in class adams.gui.tools.UpdateSampleDataPanel: the ID panels.
m_IDs - Variable in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.DataCollector: the spectrum IDs to collected the data from.
m_IDs - Variable in class adams.gui.selection.SelectSpectrumPanel.TableModel: the IDs to display.
m_IgnoreWaveNumbers - Variable in class adams.data.io.input.SimpleEEMReader: whether to ignore the wavenumbers in the file and just use column indices.
m_ImageCache - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: for caching the generated images.
m_ImageType - Variable in class adams.data.spectrumimage.AbstractSpectrumImageGenerator: the image type to generate.
m_Implementation - Variable in class adams.flow.webservice.multispectrum.RatsMultiSpectrumServiceWS: the webservice implementation to use.
m_Implementation - Variable in class adams.flow.webservice.SpectralGetServiceWS: the webservice implementation to use.
m_Implementation - Variable in class adams.flow.webservice.SpectralPutServiceWS: the webservice implementation to use.
m_Implementation - Variable in class adams.flow.webservice.SpectralTransformServiceWS: the webservice implementation to use.
m_Implementation - Variable in class adams.flow.webservice.spectrum.RatsSpectrumServiceWS: the webservice implementation to use.
m_Index - Variable in class adams.data.io.input.SPCSpectrumReader.SubFileParser: the subfile index.
m_Index - Variable in class adams.data.multifilter.PickByIndex: the index of the spectrum to pick.
m_Index - Variable in class adams.flow.transformer.GetSpectrumAmplitude: the index.
m_Index - Variable in class adams.flow.transformer.SetSpectrumAmplitude: the index.
m_InitData - Variable in class adams.data.cleaner.instance.AbstractSerializableCleaner: the data to use for initializing the cleaner.
m_InitData - Variable in class adams.data.postprocessor.instances.AbstractSerializablePostProcessor: the data to use for initializing the postprocessor.
m_Initialized - Static variable in class adams.db.AbstractSpectralDbBackend: whether the backend was initialized.
m_Input - Variable in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader.SheetIterator: the input file.
m_InputToken - Variable in class adams.flow.control.InstanceCleaner: the input token.
m_InputToken - Variable in class adams.flow.control.SpectrumCleaner: the input token.
m_Instrument - Variable in class adams.data.conversion.SpreadSheetColumnsToSpectra: the instrument to use for the spectrum.
m_Instrument - Variable in class adams.data.conversion.SpreadSheetRowsToSpectra: the instrument to use for the spectrum.
m_Instrument - Variable in class adams.data.conversion.SpreadSheetToSpectrum: the instrument to use for the spectrum.
m_Instrument - Variable in class adams.data.io.input.AbstractSpectrumReader: the instrument this data is from.
m_Instrument - Variable in class adams.data.io.input.AbstractThreeWayDataReader: the instrument this data is from.
m_Instrument - Variable in class adams.db.AbstractSpectrumConditions: the regular expression on the name of the instrument.
m_instrument_type - Variable in class adams.data.io.output.foss.FossOutputHelper.InstrumentHeader: 2 BYTES: Instrument type.
m_InstrumentName - Variable in class adams.data.io.output.ASCSpectrumWriter: The instrument name to put in ASC header.
m_InstrumentName - Variable in class adams.data.io.output.NIRSpectrumWriter: The instrument name to put in ASC header.
m_InstrumentName - Variable in class adams.data.io.output.TrinamixSpectrumWriter: The instrument name to use.
m_Intercepts - Variable in class adams.data.spectrumfilter.amplitudetransform.ApplyMultiplicativeScatterCorrection: the intercepts.
m_Interval - Variable in class adams.flow.transformer.SpectrumMinMax: the interval when to output the min/max spectra.
m_Invert - Variable in class adams.data.spectrumfilter.KennardStone: whether to invert the selection.
m_Invert - Variable in class adams.data.spectrumfilter.Remove: whether to invert the matching sense.
m_Invert - Variable in class adams.data.spectrumfilter.SubRange: whether to invert the matching sense.
m_Invert - Variable in class adams.data.spectrumoutlier.StringMatcher: whether to invert the matching sense.
m_InvertMatching - Variable in class adams.data.io.input.ZippedSpectrumReader: invert matching sense.
m_IQR - Variable in class adams.data.cleaner.instance.IQRCleaner: the maximum value of the attribute.
m_IQRMultiplier - Variable in class adams.data.postprocessor.instances.PredictionErrorIQR: the IQR multiplier per classifier.
m_Iterations - Variable in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: number of cleaning iterations to run.
m_JobRunner - Variable in class adams.data.cleaner.instance.RemoveOutliers: the runner in use.
m_JobRunnerInstance - Variable in class adams.flow.transformer.Cleaner: the JobRunnerInstance to use.
m_JobRunnerInstance - Variable in class adams.flow.transformer.Evaluator: the JobRunnerInstance to use.
m_JobRunnerSetup - Variable in class adams.data.cleaner.instance.RemoveOutliers: the jobrunner setup.
m_KeepAttributeNames - Variable in class weka.filters.unsupervised.attribute.SpectrumFilter: whether to keep the attribute names generated by the base filter.
m_KeepFormat - Variable in class adams.data.io.input.AbstractSpectrumReader: whether to not override the format obtained from the file.
m_KeepFormat - Variable in class adams.data.io.input.AbstractThreeWayDataReader: whether to not override the format obtained from the file.
m_Key - Variable in class adams.data.io.input.OpusSpectrumReaderExt: the key in the commandline to get the sample ID from.
m_Key - Variable in class adams.flow.transformer.SetEvaluationMetaData: the key in the evaluation.
m_Last - Variable in class adams.data.spectrumfilter.AbstractStandardiseFilter: the last data point.
m_LastError - Variable in class adams.data.io.input.DPTSpectrumReader.ParsedFile: the last error that occurred.
m_LastPanel - Variable in class adams.gui.visualization.debug.objectrenderer.ThreeWayDataHeatmapRenderer: the last setup.
m_LastSpectrumPanel - Variable in class adams.gui.visualization.debug.objectrenderer.SpectrumRenderer: the last setup.
m_LastWave - Variable in class adams.flow.transformer.InstanceToSpectrum: the last wave number.
m_LastX - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: the value of the last X.
m_LastXPoint - Variable in class adams.data.io.output.ASCSpectrumWriter: Last X WaveNumber.
m_Latest - Variable in class adams.db.AbstractSpectrumConditions: whether to get latest (= reverse order).
m_Latest - Variable in class adams.db.OrphanedSampleDataConditions: whether to get latest (= reverse order).
m_Lenient - Variable in class adams.data.conversion.SpreadSheetColumnsToSampleData: whether to skip over errors.
m_Lenient - Variable in class adams.data.conversion.SpreadSheetColumnsToSpectra: whether to skip over errors.
m_Lenient - Variable in class adams.data.conversion.SpreadSheetRowsToSampleData: whether to skip over errors.
m_Lenient - Variable in class adams.data.conversion.SpreadSheetRowsToSpectra: whether to skip over errors.
m_Lenient - Variable in class adams.flow.transformer.InstanceGenerator: whether to be lenient.
m_Lenient - Variable in class adams.flow.transformer.MergeSampleDataFromMap: whether to be lenient.
m_Lenient - Variable in class adams.flow.transformer.SpreadSheetRowGenerator: whether to be lenient.
m_ListX - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: the list for selecting the X layer.
m_LoadDialog - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the dialog for loading data.
m_Loading - Variable in class adams.gui.tools.idprovider.ManualListPanel: whether IDs are currently being loaded.
m_Loading - Variable in class adams.gui.tools.idprovider.SpreadSheetIDPanel: whether a spreadsheet is currently being loaded.
m_Loadings - Variable in class adams.data.spectrumanalysis.PCA: the loadings.
m_Loadings - Variable in class adams.data.spectrumanalysis.PLS: the loadings.
m_LoadSampleData - Variable in class adams.data.instances.AbstractSpectrumBasedInstanceGenerator: whether to load the sample data if only dummy.
m_Locale - Variable in class adams.data.io.input.ASCSpectrumReader: the locale to use.
m_Locale - Variable in class adams.data.io.input.DPTSpectrumReader: the locale to use.
m_Locale - Variable in class adams.data.io.output.ASCSpectrumWriter: the locale to use.
m_Locale - Variable in class adams.data.io.output.DPTSpectrumWriter: the locale to use.
m_Log - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: the log values.
m_LogBase - Variable in class adams.data.spectrumfilter.LogTransform: the base of the log.
m_Logger - Variable in class adams.gui.tools.idprovider.AbstractIDProviderPanel: the logger.
m_Lookup - Variable in class adams.data.spectrumfilter.ReportFieldFromStringValueWithLookup: the key-value pairs.
m_LowerPercentile - Variable in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.DataCollector: the lower percentile.
m_LowerPercentile - Variable in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.InterPercentileRange: lower percentile.
m_LowerPercentile - Variable in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: the lower percentile.
m_MarkerExtent - Variable in class adams.gui.visualization.spectrum.SpectrumPaintlet: the maximum width/height of the shape to plot around the points (= data point marker), if there's enough space.
m_MarkersEnabled - Variable in class adams.gui.visualization.spectrum.SpectrumPaintlet: indicates whether marker shapes are painted or not.
m_master - Variable in class adams.data.io.output.foss.FossOutputHelper.Generalheader: char[9] master serial no.
m_Master - Variable in class adams.data.io.output.NIRSpectrumWriter: Serial Number of Master Instrument.
m_Matrix - Variable in class adams.flow.transformer.ThreeWayDataLoadingMatrix: the name of the matrix to retrieve.
m_max - Variable in class adams.data.io.input.CALSpectrumReader: maximum to load.
m_max - Variable in class adams.data.spectrumoutlier.MinMax: max.
m_Max - Variable in class adams.data.io.input.OpusSpectrumReader: maximum to load.
m_Max - Variable in class adams.data.spectrumfilter.amplitudetransform.Triangle: the maximum for the triangle.
m_Max - Variable in class adams.data.spectrumoutlier.AmplitudeRange: the maximum.
m_Max - Variable in class adams.data.threewayoutlier.ValueRange: max.
m_Max - Variable in class adams.flow.transformer.SpectrumMinMax: the maximum spectrum.
m_MaxAmplitude - Variable in class adams.data.io.input.SpecLibSpectrumReader: the maximum amplitude to allow.
m_MaxAmplitude - Variable in class adams.data.spectrum.Spectrum: point of greatest amplitude.
m_MaxAmplitude - Variable in class adams.data.spectrumfilter.Scale: the maximum amplitude to scale to.
m_MaxAmplitude - Variable in class adams.data.spectrumimage.AbstractSpectrumImageGeneratorWithRange: the maximum amplitude to use.
m_MaxAttributeNames - Variable in class adams.data.spectrumfilter.PCA: the maximum number of attribute names.
m_MaxAttributes - Variable in class adams.data.spectrumfilter.PCA: the maximum number of attributes.
m_Maximum - Variable in class adams.data.cleaner.instance.MinMax: the maximum value of the attribute.
m_Maximum - Variable in class adams.data.cleaner.spectrum.MinMax: the maximum value of the field.
m_Maximum - Variable in class adams.data.compare.SpectrumCosineSimilarity: the maximum accepted correlation coefficient.
m_MaximumValue - Variable in class adams.db.SpectrumConditionsSingle: the maximum value for the field.
m_MaximumValues - Variable in class adams.db.SpectrumConditionsMulti: the maximum value for the field(s).
m_MaxNonRemovalIterations - Variable in class adams.data.postprocessor.instances.PredictionErrorIQR: the maximum number of non-removal iterations per classifier.
m_maxPLSComponents - Variable in class adams.opt.genetic.RonWeasley
m_maxSG - Variable in class adams.opt.genetic.RonWeasley
m_MaxWaveNumber - Variable in class adams.data.io.input.SpecLibSpectrumReader: the maximum wavenumber to allow.
m_MaxWaveNumber - Variable in class adams.data.spectrum.Spectrum: point of greatest wave number.
m_MaxWaveNumber - Variable in class adams.data.spectrumfilter.SubRange: the maximum wave number.
m_MaxWaveNumber - Variable in class adams.data.spectrumoutlier.Oscillation: the maximum wave number.
m_MaxWaves - Variable in class adams.data.spectrumoutlier.MaxWaves: maximum number of wave numbers that the spectrum must contain.
m_MaxX - Variable in class adams.data.conversion.ThreeWayDataToHeatmap: the maximum x to use.
m_MaxX - Variable in class adams.data.threeway.L1Point: point of greatest x.
m_MaxX - Variable in class adams.data.threeway.ThreeWayData: point of greatest X.
m_MaxY - Variable in class adams.data.threeway.L1Point: point of greatest y.
m_MaxY - Variable in class adams.data.threeway.ThreeWayData: point of greatest Y.
m_MenuBar - Variable in class adams.gui.tools.DeleteSpectrumPanel: the menu bar, if used.
m_MenuBar - Variable in class adams.gui.visualization.spectrum.MultiSpectrumPanel: the menu bar.
m_MenuBar - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the menu bar, if used.
m_MenuBar - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the menu bar.
m_MenuItemClearData - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the clear data menu item.
m_MenuItemEnableUndo - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the toggle undo menu item.
m_MenuItemFileCloseAll - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the "close all" menu item.
m_MenuItemFileCloseCurrent - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the "close current" menu item.
m_MenuItemFileExit - Variable in class adams.gui.visualization.spectrum.MultiSpectrumPanel: the "exit" file menu item.
m_MenuItemFileOpen - Variable in class adams.gui.visualization.spectrum.MultiSpectrumPanel: the "open" file menu item.
m_MenuItemFileOpenRecent - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the "load recent" submenu.
m_MenuItemFileSaveAs - Variable in class adams.gui.visualization.spectrum.MultiSpectrumPanel: the "save as" file menu item.
m_MenuItemFileSaveAs - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the "save as" menu item.
m_MenuItemOverlayFlowOutput - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the overlay flow output menu item.
m_MenuItemProcessFilter - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the filter menu item.
m_MenuItemProcessFilterAllHeatmaps - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the filter all menu item.
m_MenuItemProcessFilterHeatmap - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the filter menu item.
m_MenuItemProcessICA - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the ica menu item.
m_MenuItemProcessPCA - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the pca menu item.
m_MenuItemProcessPLS - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the pls menu item.
m_MenuItemRedo - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the redo menu item.
m_MenuItemRefreshScripts - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the refresh scripts menu item.
m_MenuItems - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerMultiPagePane: the menu items.
m_MenuItemStartRecording - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the start recording menu item.
m_MenuItemStopExecution - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the stop execution menu item.
m_MenuItemStopRecording - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the stop recording menu item.
m_MenuItemUndo - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the undo menu item.
m_MenuItemViewAddOverlay - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the add overlay menu item.
m_MenuItemViewAntiAliasing - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the toggle anti-aliasing menu item.
m_MenuItemViewApplyAll - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: whether to apply overlay changes to all panels.
m_MenuItemViewCloseTab - Variable in class adams.gui.visualization.spectrum.MultiSpectrumPanel: the "close tab" view menu item.
m_MenuItemViewColorGenerator - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the color generator menu item.
m_MenuItemViewColorProvider - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the color provider menu item.
m_MenuItemViewMissingValueColor - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the missing value color menu item.
m_MenuItemViewNewTab - Variable in class adams.gui.visualization.spectrum.MultiSpectrumPanel: the "new tab" view menu item.
m_MenuItemViewPaintlet - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the paintlet menu item.
m_MenuItemViewRemoveOverlays - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the remove overlays menu item.
m_MenuItemViewSelectedWaveNumber - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the toggle selected GC point menu item.
m_MenuItemViewZoomIn - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the menu item "zoom in".
m_MenuItemViewZoomOut - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the menu item "zoom out".
m_MenuItemViewZoomOverview - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the toggle zoom overview menu item.
m_MenuItemWindowDuplicate - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the menuitem for duplicating theew window.
m_MenuItemWindowNew - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the menuitem for creating a new window.
m_MenuScripts - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the menu item for scripts.
m_MenuView - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the menu item for view related stuff.
m_MenuViewZoom - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the menu "zoom".
m_MenuWindow - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the menu item for window related stuff.
m_Merge - Variable in class adams.flow.transformer.MergeSampleDataFromMap: the merge type.
m_MergeReports - Variable in class adams.flow.transformer.ThreeWayDataMerge: whether to merge the reports.
m_MetaDataFields - Variable in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: meta-data fields to add to the output data.
m_MetaDataPrefix - Variable in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: the meta-data field prefix.
m_MetaDataValues - Variable in class adams.data.conversion.SpectrumToJson: the meta-data values.
m_MetaDataValues - Variable in class adams.data.io.output.JsonSpectrumWriter: the meta-data values.
m_min - Variable in class adams.data.spectrumoutlier.MinMax: min.
m_Min - Variable in class adams.data.spectrumfilter.amplitudetransform.Triangle: the minimum for the triangle.
m_Min - Variable in class adams.data.spectrumoutlier.AmplitudeRange: the minimum.
m_Min - Variable in class adams.data.threewayoutlier.ValueRange: min.
m_Min - Variable in class adams.flow.transformer.SpectrumMinMax: the minimum spectrum.
m_MinAmplitude - Variable in class adams.data.io.input.SpecLibSpectrumReader: the minimum amplitude to allow.
m_MinAmplitude - Variable in class adams.data.spectrum.Spectrum: point of smallest amplitude.
m_MinAmplitude - Variable in class adams.data.spectrumfilter.Scale: the minimum amplitude to scale to.
m_MinAmplitude - Variable in class adams.data.spectrumimage.AbstractSpectrumImageGeneratorWithRange: the minimum amplitude to use.
m_Minimum - Variable in class adams.data.cleaner.instance.MinMax: the minimum value of the attribute.
m_Minimum - Variable in class adams.data.cleaner.spectrum.MinMax: the minimum value of the field.
m_Minimum - Variable in class adams.data.compare.SpectrumCorrelation: the minimum accepted correlation coefficient.
m_Minimum - Variable in class adams.flow.transformer.predictioncheck.MinProbability: the minimum probability.
m_MinimumValue - Variable in class adams.db.SpectrumConditionsSingle: the minimum value for the field.
m_MinimumValues - Variable in class adams.db.SpectrumConditionsMulti: the minimum value for the field(s).
m_minPLSComponents - Variable in class adams.opt.genetic.RonWeasley
m_minSG - Variable in class adams.opt.genetic.RonWeasley
m_MinWaveNumber - Variable in class adams.data.io.input.SpecLibSpectrumReader: the minimum wavenumber to allow.
m_MinWaveNumber - Variable in class adams.data.spectrum.Spectrum: point of smallest wave number.
m_MinWaveNumber - Variable in class adams.data.spectrumfilter.SubRange: the minimum wave number.
m_MinWaveNumber - Variable in class adams.data.spectrumoutlier.Oscillation: the minimum wave number.
m_MinWaves - Variable in class adams.data.spectrumoutlier.MinWaves: minimum number of wave numbers that the spectrum must contain.
m_MinX - Variable in class adams.data.conversion.ThreeWayDataToHeatmap: the minimum x to use.
m_MinX - Variable in class adams.data.threeway.L1Point: point of smallest x.
m_MinX - Variable in class adams.data.threeway.ThreeWayData: point of smallest X.
m_MinY - Variable in class adams.data.threeway.L1Point: point of smallest y.
m_MinY - Variable in class adams.data.threeway.ThreeWayData: point of smallest Y.
m_Mirrors - Variable in class adams.db.mirrored.SpectralDbBackend: the database connections of the mirrors.
m_MirrorsForUrls - Variable in class adams.db.mirrored.SpectralDbBackend: the urls the mirrors are for.
m_MissingEvaluation - Variable in class adams.data.evaluator.instance.AbstractEvaluator: the value to return in case no evaluation can be performed.
m_MissingValueColor - Variable in class adams.flow.sink.ThreeWayDataHeatmapDisplay: the color for missing values.
m_MissingValueColor - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: the color to use for missing values.
m_Mode - Variable in class adams.data.io.input.JCampDX2SpectrumReader: the mode.
m_model - Variable in class adams.data.io.output.foss.FossOutputHelper.InstrumentHeader: char[21] model number.
m_Model - Variable in class adams.gui.tools.DeleteSampleDataPanel: the table model in use.
m_Model - Variable in class adams.gui.tools.ListSampleDataPanel: the table model in use.
m_Model - Variable in class adams.gui.tools.UpdateSampleDataPanel: the table model in use.
m_ModelLoader - Variable in class adams.data.spectrumfilter.WekaFilterToReport: the loader for the Weka filter.
m_ModelLoader - Variable in class adams.flow.transformer.Cleaner: the model loader.
m_ModelLoader - Variable in class adams.flow.transformer.Evaluator: the model loader.
m_ModelLoader - Variable in class adams.flow.transformer.PostProcessor: the model loader.
m_ModelLoader - Variable in class adams.flow.transformer.ThreeWayDataModelFilter: the model loader.
m_ModelResetVariable - Variable in class adams.flow.transformer.ThreeWayDataModelFilter: the variable to monitor for changes, triggering resets of the model.
m_most_recent - Variable in class adams.data.io.output.foss.FossOutputHelper.Generalheader: 2 BYTES: CHK file?
m_MultiFile - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: whether multi-file (0:0x04h).
m_MultiFilter - Variable in class weka.filters.unsupervised.attribute.SpectrumFilter: the multi-filter that does the actual work.
m_MultiPagePane - Variable in class adams.gui.visualization.spectrum.MultiSpectrumPanel: for displaying the spectra in tabs.
m_MultiPagePane - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the tabbed pane for the data structures.
m_MultWInc - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: the multiple W value increment.
m_MultZInc - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: the multiple Z value increment.
m_Name - Variable in class adams.data.io.input.opus.OpusBlockHelper.Block: the name of the block.
m_neoc - Variable in class adams.data.io.output.foss.FossOutputHelper.InstrumentHeader: 2 BYTES int, number of EOC's (??)
m_NewConnection - Variable in class adams.flow.transformer.BulkSampleDataDbWriter: whether to use a new database connection.
m_NewConnection - Variable in class adams.flow.transformer.BulkSpectrumDbWriter: whether to use a new database connection.
m_NewFormat - Variable in class adams.data.multifilter.AbstractFormatsBasedMultiSpectrumFilter: the new format to use.
m_NewFormatSeparator - Variable in class adams.data.multifilter.Fusion: the separator to use when automatically creating new format string.
m_NoAdditionalFieldsPrefix - Variable in class adams.data.instances.AbstractSpectrumInstanceGenerator: drops the prefix for the additional fields.
m_NoCopy - Variable in class adams.flow.transformer.AbstractInPlaceSpectrumTransformer: whether to skip creating a copy of the spreadsheet.
m_NoCopy - Variable in class adams.flow.transformer.Evaluator: whether to only update the container or work on a copy.
m_NoCopy - Variable in class adams.flow.transformer.PredictionCheck: whether to only update the container or work on a copy.
m_NoCopy - Variable in class adams.flow.transformer.SetEvaluationMetaData: whether to only update the container or work on a copy.
m_Noise - Variable in class adams.data.io.input.SPCSpectrumReader.SubFileParser: the peak picking noise level.
m_NonEvenX - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: whether X data is non-evenly spaced (0:0x80h).
m_NonMirroredBackend - Variable in class adams.db.mirrored.SpectralDbBackend: the default backend.
m_Normalize - Variable in class adams.data.evaluator.instance.EnsembleEvaluator: the normalization factor.
m_Normalize - Variable in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: whether to normalize.
m_Normalize - Variable in class adams.data.evaluator.instance.SavitzkyGolayRange: whether to normalize the predictions to the class attribute range.
m_NormalizeByLiveTime - Variable in class adams.data.io.input.MPSSpectrumReader: whether to normalize the amplitude by live time.
m_Notes - Variable in class adams.data.instances.AbstractSpectrumBasedInstanceGenerator: the notes to add as attributes.
m_Notes - Variable in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: the notes to add as attributes.
m_Notes - Variable in class adams.data.spectrum.MultiSpectrum: the notes for the chromatogram.
m_Notes - Variable in class adams.data.spectrum.Spectrum: the notes for the chromatogram.
m_Notes - Variable in class adams.data.threeway.ThreeWayData: the notes for the data structure.
m_Notes - Variable in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: the notes to add as attributes.
m_NrDatapoints - Variable in class adams.data.io.output.ASCSpectrumWriter: If -1 then calculate Nr of Datapoints, otherwise as specified, and fail if the number differs.
m_NthPoint - Variable in class adams.data.threewayfeatures.Flatten: the n-th point to use.
m_NthPoints - Variable in class weka.filters.unsupervised.attribute.SegmentedDownSample: the blank-separated list of number of savgol points to use.
m_num_consts - Variable in class adams.data.io.output.foss.FossOutputHelper.Generalheader: 2 BYTES: number of constituents.
m_num_points - Variable in class adams.data.io.input.foss.FossHelper: number of spectral data points.
m_num_points - Variable in class adams.data.io.input.foss.FossStdise: number of wavelengths.
m_num_points - Variable in class adams.data.io.output.foss.FossOutputHelper.Generalheader: 2 BYTES:number of spectral data points.
m_num_seg - Variable in class adams.data.io.output.foss.FossOutputHelper.InstrumentHeader: 2 BYTES integer, number of segments up to 20 (?).
m_NumAdditional - Variable in class adams.data.spectrumfilter.PadPower2: the number of additional data points to add.
m_NumAttributes - Variable in class weka.filters.unsupervised.attribute.BestBySLR: The number of attributes to choose.
m_NumberInSubset - Variable in class adams.data.spectrumfilter.KennardStone: Number of spectra to select in subset
m_NumFiles - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: the number of sub-files.
m_NumFolds - Variable in class adams.data.cleaner.instance.RemoveOutliers: the number of folds to use.
m_NumFolds - Variable in class adams.data.evaluator.instance.EnsembleEvaluator: the number of folds to use for cross-validation.
m_NumFolds - Variable in class adams.data.postprocessor.instances.PredictionErrorIQR: the number of folds per classifier.
m_NumIterations - Variable in class adams.data.postprocessor.instances.PredictionErrorIQR: the number of iterations per classifier.
m_NumNeighbors - Variable in class adams.data.evaluator.instance.CrossValidatedNeighborHood: the size of the neighborhood.
m_NumNeighbors - Variable in class adams.data.evaluator.instance.CrossValidatedPrediction: the size of the neighborhood.
m_NumNeighbors - Variable in class adams.data.evaluator.instance.DistanceToCenter: the number of neighbors to use.
m_NumPoints - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: the number of points.
m_NumPoints - Variable in class adams.data.io.input.SPCSpectrumReader.SubFileParser: the number of points.
m_NumPoints - Variable in class adams.data.spectrumfilter.AndrewsCurves: the number of data points.
m_NumPoints - Variable in class adams.data.spectrumfilter.CenterBurst: the number of data points around the burst (even number).
m_NumPoints - Variable in class weka.filters.unsupervised.attribute.SavitzkyGolayRange: the number of points (window size = numpoints*2 + 1).
m_NumPoints - Variable in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: the blank-separated list of number of savgol points to use.
m_NumScans - Variable in class adams.data.io.input.SPCSpectrumReader.SubFileParser: the number of scans.
m_numSegments - Variable in class adams.opt.genetic.RonWeasley
m_NumThreads - Variable in class adams.data.cleaner.instance.RemoveOutliers: the number of threads to use for parallel execution.
m_NumThreads - Variable in class adams.data.postprocessor.instances.PredictionErrorIQR: the number of threads to use for parallel execution.
m_NumTokensAccepted - Variable in class adams.flow.sink.spectrumdisplay.SimplePlotUpdater: the number of tokens accepted.
m_NumWPlanes - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: the number of W places in 4D data.
m_Offline - Variable in class adams.data.io.input.AbstractSampleDataReader: whether operate in offline mode, i.e., not query database.
m_Offset - Variable in class adams.data.io.input.SPCSpectrumReader.AbstractParser: the offset to use.
m_OffsetLogstc - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: the offset for LOGSTC.
m_OffsetPointersDir - Variable in class adams.data.io.input.SPCSpectrumReader.SubFileParser: whether to use the offset points directory.
m_OffsetX - Variable in class adams.data.threewayfilter.Shift: the offset for X.
m_OffsetX - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: the X offset of the overlay.
m_OffsetY - Variable in class adams.data.threewayfilter.Shift: the offset for Y.
m_OffsetY - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: the Y offset of the overlay.
m_OffsetZ - Variable in class adams.data.threewayfilter.Shift: the offset for Z.
m_OnlyDummies - Variable in class adams.db.AbstractSpectrumConditions: whether to only include spectra with dummy reports.
m_OnlyWarning - Variable in class adams.flow.transformer.MultiSpectrumOutlierDetector: whether the detection is only added as warning instead of error.
m_Operation - Variable in class adams.data.io.input.opus.OpusBlockHelper.CommandlineData: the operation.
m_Operation - Variable in class adams.data.io.input.OpusSpectrumReaderExt: the commandline in the log to use for extracting the sample ID.
m_Operation - Variable in class adams.flow.transformer.MultiSpectrumOperation: the operation to apply.
m_operator - Variable in class adams.data.io.output.foss.FossOutputHelper.SampleHeader: String(32): zero terminated. operator
m_Operator - Variable in class adams.data.io.output.NIRSpectrumWriter: Operator name.
m_OptionManager - Variable in class adams.data.spectrum.AbstractSpectrumComparator: for managing the available options.
m_Ordered - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: whether ordered (0:0x10h).
m_OutlierRemoval - Variable in class adams.data.multispectrumoperation.OutlierRemoval: the outlier removal scheme to use.
m_OutputContainer - Variable in class adams.flow.transformer.InstanceGenerator: whether to output a container.
m_OutputContainer - Variable in class adams.flow.transformer.PostProcessor: whether to output a container.
m_OutputHeader - Variable in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: the generated header.
m_OutputMultiSpectrum - Variable in class adams.flow.transformer.SpectrumFileReader: whether to generate a MultiSpectrum instead.
m_OutputReport - Variable in class adams.data.conversion.MultiSpectrumToSpectra: whether to output the "global" report in an empty spectrum.
m_OutputReport - Variable in class adams.flow.transformer.SpectrumFileWriter: whether to output the "global" report in an empty spectrum.
m_OutputSampleData - Variable in class adams.data.io.output.JCampDX2SpectrumWriter: whether to output the sample data as well.
m_OutputSampleData - Variable in class adams.data.io.output.SimpleSpectrumWriter: whether to output the sample data as well.
m_OutputSampleData - Variable in class adams.data.io.output.SimpleXYZWriter: whether to output the sample data as well.
m_OutputToken - Variable in class adams.flow.control.InstanceCleaner: the output token.
m_OutputToken - Variable in class adams.flow.control.SpectrumCleaner: the output token.
m_OverlapFactor - Variable in class adams.data.conversion.SpectrumToBufferedImage: the overlap factor (1/factor).
m_OverlapFactor - Variable in class adams.data.spectrumimage.Spectrogram: the overlap factor (1/factor).
m_Overlays - Variable in class adams.flow.sink.ThreeWayDataHeatmapDisplay: the overlays to use.
m_OverrideSerializationFile - Variable in class adams.data.cleaner.instance.AbstractSerializableCleaner: whether to override the file to serialize the setup to .
m_OverrideSerializationFile - Variable in class adams.data.cleaner.spectrum.AbstractSerializableCleaner: whether to override the file to serialize the setup to .
m_OverrideSerializationFile - Variable in class adams.data.evaluator.instance.AbstractSerializableEvaluator: whether to override the file to serialize the setup to .
m_OverrideSerializationFile - Variable in class adams.data.postprocessor.instances.AbstractSerializablePostProcessor: whether to override the file to serialize the setup to .
m_OverrideSerializationFile - Variable in class adams.data.spectrumfilter.AbstractSerializableFilter: whether to override the file to serialize the setup to .
m_Owner - Variable in class adams.flow.webservice.multispectrum.SimpleRatsMultiSpectrumService: web service object
m_Owner - Variable in class adams.flow.webservice.SimpleSpectralGetService: web service object
m_Owner - Variable in class adams.flow.webservice.SimpleSpectralPutService: web service object
m_Owner - Variable in class adams.flow.webservice.SimpleSpectralTransformService: web service object
m_Owner - Variable in class adams.flow.webservice.spectrum.SimpleRatsSpectrumService: web service object
m_Owner - Variable in class adams.gui.tools.idprovider.AbstractIDProviderPanel: the owner.
m_Owner - Variable in class adams.gui.visualization.spectrum.SpectrumContainerManager: the owning panel.
m_Owner - Variable in class adams.gui.visualization.spectrum.SpectrumPointHitDetector: the owner of this detector.
m_Owner - Variable in class adams.gui.visualization.spectrum.WaveNumberHitDetector: the owner of this detector.
m_Owner - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: the owner.
m_packing - Variable in class adams.data.io.output.foss.FossOutputHelper.Generalheader: char[30] packing info.
m_padding - Variable in class adams.data.io.output.foss.FossOutputHelper.InstrumentHeader: 94 bytes of padding.
m_padding - Variable in class adams.data.io.output.foss.FossOutputHelper.SampleHeader: 38 bytes of padding.
m_PaddingType - Variable in class adams.data.spectrumfilter.PadPower2: the type of padding to use.
m_PadLeft - Variable in class adams.data.spectrumfilter.PadPower2: whether to padd on the left.
m_PaintAll - Variable in class adams.gui.visualization.spectrum.SpectrumPaintlet: whether to paint all the data points (no optimization).
m_Paintlet - Variable in class adams.flow.sink.SpectrumDisplay: the paintlet to use.
m_Panel - Variable in class adams.flow.sink.SpectrumDisplay.DisplayPanel
m_PanelFields - Variable in class adams.gui.tools.DeleteSampleDataPanel: the fields to remove.
m_PanelFile - Variable in class adams.gui.tools.idprovider.SpreadSheetIDPanel: the file to load.
m_PanelGOEGenerator - Variable in class adams.gui.visualization.spectrum.SpectrumDatasetExportDialog: the panel for the instance generator scheme to use.
m_PanelIDProvider - Variable in class adams.gui.tools.DeleteSampleDataPanel: the panel for the ID provider panels.
m_PanelIDProvider - Variable in class adams.gui.tools.ListSampleDataPanel: the panel for the ID provider panels.
m_PanelIDProvider - Variable in class adams.gui.tools.UpdateSampleDataPanel: the panel for the ID provider panels.
m_PanelList - Variable in class adams.gui.tools.idprovider.ManualListPanel: the list of IDs.
m_PanelSampleDataButtons - Variable in class adams.gui.tools.UpdateSampleDataPanel: the panel for the buttons for the sampledata table.
m_PanelSpectrum - Variable in class adams.gui.tools.DeleteSpectrumPanel: the panel for selecting the spectra.
m_PanelSpectrum - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the panel for displaying.
m_PanelSpectrum - Variable in class adams.gui.visualization.spectrum.SpectrumPanelWithSampleData: the spectrum panel.
m_PanelZoomOverview - Variable in class adams.gui.visualization.spectrum.SpectrumPanel: the zoom overview panel.
m_ParallelAndMerge - Variable in class adams.data.spectrumfilter.MultiFilter: whether to execute the filters in parallel and merge the outputs or run them in series.
m_ParallelAndMerge - Variable in class adams.data.threewayfilter.MultiFilter: whether to execute the filters in parallel and merge the outputs or run them in series.
m_Parent - Variable in class adams.data.io.input.SPCSpectrumReader.AbstractParser: the parent parser, if any.
m_Parent - Variable in class adams.data.spectrum.MultiSpectrum: the parent.
m_Parent - Variable in class adams.data.spectrum.Spectrum: the parent.
m_Parent - Variable in class adams.data.threeway.L1Point: the parent.
m_PCA - Variable in class adams.data.spectrumanalysis.PCA: the PCA analysis to use.
m_PeakPointNum - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: the peak point number.
m_PlotUpdater - Variable in class adams.flow.sink.SpectrumDisplay: the plot updater to use.
m_PLS - Variable in class adams.data.spectrumanalysis.PLS: the PLS analysis to use.
m_Point - Variable in class adams.gui.visualization.spectrum.SelectedWaveNumberPaintlet: the point to paint.
m_points_per_segment - Variable in class adams.data.io.output.foss.FossOutputHelper.InstrumentHeader: 40 BYTES int[20], points per sement.. ?
m_Polynomial - Variable in class adams.data.spectrumfilter.StandardiseByInterpolation
m_PolynomialOrder - Variable in class weka.filters.unsupervised.attribute.SavitzkyGolayRange: the polynomial order.
m_PolynomialOrder - Variable in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: the polynomial order.
m_Port - Variable in class adams.flow.webservice.Get: the port instance.
m_Port - Variable in class adams.flow.webservice.Put: the port instance.
m_Port - Variable in class adams.flow.webservice.Transform: the port instance.
m_PostProcessor - Variable in class adams.flow.transformer.PostProcessor: the postprocessor.
m_PostProcessor - Variable in class adams.flow.transformer.ThreeWayDataTrain: the post-processor.
m_PostProcessorDetailsOutput - Variable in class adams.flow.transformer.PostProcessor: the file to save the cleaner details to.
m_PreferJobRunner - Variable in class adams.flow.transformer.Cleaner: whether to offload training into a JobRunnerInstance.
m_PreferJobRunner - Variable in class adams.flow.transformer.Evaluator: whether to offload training into a JobRunnerInstance.
m_PreFilter - Variable in class adams.data.cleaner.instance.AbstractCleaner: the pre-filter to use.
m_PreFilter - Variable in class adams.data.cleaner.spectrum.AbstractCleaner: the pre-filter to use.
m_PreFilter - Variable in class adams.data.multispectrumoperation.outlierremoval.CorrelationBasedThreshold: the prefilter to apply before computing the correlation coefficient.
m_PreFilter - Variable in class adams.data.multispectrumoperation.outlierremoval.CosineSimilarityBasedThreshold: the prefilter to apply before computing the cosine similarity.
m_PreFilter - Variable in class adams.data.multispectrumoperation.outlierremoval.MeanSpectrumCosineSimilarityBasedThreshold: the prefilter to apply before computing the cosine similarity.
m_PreFilter - Variable in class adams.data.spectrumfilter.KennardStone: Pre filter to apply before selection
m_PreFilter - Variable in class adams.data.spectrumfilter.multiplicativescattercorrection.AbstractMultiplicativeScatterCorrection: the filter to apply to the spectra internally.
m_PreFilter - Variable in class adams.data.spectrumfilter.MultiplicativeScatterCorrection: the filter to apply to the spectra internally.
m_PreFilters - Variable in class adams.data.multifilter.FilteredMultiSpectrumFilter: the "pre" filters.
m_Prefix - Variable in class adams.data.instances.FieldInstanceGenerator: the prefix to use.
m_Prefix - Variable in class adams.data.spectrumfilter.WekaFilterToReport: the prefix for the report.
m_Prefix - Variable in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: the prefix to use for the fields.
m_PrefixNew - Variable in class weka.filters.unsupervised.attribute.SpectrumFilter: the new prefix.
m_PrefixOld - Variable in class weka.filters.unsupervised.attribute.SpectrumFilter: the old prefix.
m_PrettyPrinting - Variable in class adams.data.conversion.SpectrumToJson: whether to use pretty-printing.
m_PrettyPrinting - Variable in class adams.data.io.output.JsonSpectrumWriter: whether to use pretty-printing.
m_product_code - Variable in class adams.data.io.output.foss.FossOutputHelper.SampleHeader: 2 BYTES: unsigned int. code.
m_ProductCode - Variable in class adams.data.io.output.ASCSpectrumWriter: Either the Field name with the product code in it, or the actual product code.
m_ProductCode - Variable in class adams.data.io.output.NIRSpectrumWriter: Either the Field name with the product code in it, or the actual product code.
m_ProductCode - Variable in class adams.flow.transformer.InstanceToSpectrum: Either the attribute name with the product code in it, or the actual product code.
m_ProductCodeFromAttribute - Variable in class adams.flow.transformer.InstanceToSpectrum: Get the product code from the attribute named ProductCode in the Instance?
m_ProductCodeFromField - Variable in class adams.data.io.output.ASCSpectrumWriter: Get the product code from the Field named ProductCode in the Report?
m_ProductCodeFromField - Variable in class adams.data.io.output.NIRSpectrumWriter: Get the product code from the Field named ProductCode in the Report?
m_Properties - Static variable in class adams.db.AbstractSpectralDbBackend: the properties with the defaults.
m_Properties - Static variable in class adams.gui.tools.DeleteSampleDataPanel: the properties.
m_Properties - Static variable in class adams.gui.tools.ListSampleDataPanel: the properties.
m_Properties - Static variable in class adams.gui.tools.UpdateSampleDataPanel: the properties.
m_Properties - Static variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: the setup for the panel.
m_Properties - Static variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the setup for the panel.
m_Queue - Variable in class adams.flow.transformer.SpectrumFeatureGenerator: the generated objects.
m_Queue - Variable in class adams.flow.transformer.SpectrumInfo: the tokens to output.
m_Queue - Variable in class adams.flow.transformer.ThreeWayDataFeatureGenerator: the generated objects.
m_QueueFailed - Variable in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: the name of the queue in the internal storage for failed files.
m_QueueFailed - Variable in class adams.flow.standalone.rats.LoadSpectrumFileOutput: the name of the queue in the internal storage for failed files.
m_QueueSpectra - Variable in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: the name of the queue in the internal storage for spectra.
m_QueueSpectra - Variable in class adams.flow.standalone.rats.LoadSpectrumFileOutput: the name of the queue in the internal storage for spectra.
m_QueueSuccessful - Variable in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: the name of the queue in the internal storage for successful files.
m_QueueSuccessful - Variable in class adams.flow.standalone.rats.LoadSpectrumFileOutput: the name of the queue in the internal storage for successful files.
m_Random - Variable in class adams.data.evaluator.instance.FakeEvaluator: for generating the random numbers.
m_Random - Variable in class adams.data.postprocessor.instances.PredictionErrorIQR: the random number generator in use.
m_Range - Variable in class adams.data.cleaner.instance.IQRCleaner: the attribute range to work on.
m_Range - Variable in class adams.data.spectrumfilter.Remove: the range of amplitudes to remove.
m_Range - Variable in class adams.flow.transformer.predictioncheck.Range: the allowed range.
m_Ranges - Variable in class adams.data.spectrumfilter.amplitudetransform.ApplyMultiplicativeScatterCorrection: the ranges.
m_Ranges - Variable in class adams.data.spectrumfilter.detrend.RangeBased: the ranges to calculate the intercept/slope for.
m_Ranges - Variable in class adams.data.spectrumfilter.multiplicativescattercorrection.RangeBased: the ranges to calculate the intercept/slope for.
m_Ranges - Variable in class weka.filters.unsupervised.attribute.RangeBasedSavitzkyGolay: the ranges to use.
m_RangeX - Variable in class adams.data.threewayfilter.Crop: the range for X.
m_RangeY - Variable in class adams.data.threewayfilter.Crop: the range for Y.
m_RangeZ - Variable in class adams.data.threewayfilter.Crop: the range for Z.
m_RatInput - Variable in class adams.flow.webservice.multispectrum.RatsMultiSpectrumServiceWS: the associated rat input.
m_RatInput - Variable in class adams.flow.webservice.spectrum.RatsSpectrumServiceWS: the associated rat input.
m_Raw - Variable in class adams.data.io.input.opus.OpusBlockHelper.CommandlineData: the raw string.
m_RawTrainingData - Variable in class adams.data.evaluator.instance.DistanceToCenter: the raw training data.
m_RawTrainingData - Variable in class adams.data.evaluator.instance.DistanceToClosest: the raw training data.
m_Reader - Variable in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: the spreadsheet reader to use.
m_Reader - Variable in class adams.data.io.input.ExtractIdAndTypeSpectrumReader: the base reader.
m_Reader - Variable in class adams.data.io.input.ExtractIdAndTypeThreeWayDataReader: the base reader.
m_Reader - Variable in class adams.data.io.input.FilteredSpectrumReader: the underlying reader.
m_Reader - Variable in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: the spreadsheet reader.
m_Reader - Variable in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: the spreadsheet reader.
m_Reader - Variable in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: the spreadsheet reader to use.
m_Reader - Variable in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader.SheetIterator: the reader.
m_Reader - Variable in class adams.data.io.input.ThreeWayHeatmapReader: the reader to use.
m_Reader - Variable in class adams.data.io.input.ZippedSpectrumReader: the base reader to use.
m_Reader - Variable in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: the sprectrum reader to use.
m_Reader - Variable in class adams.flow.standalone.rats.LoadSpectrumFileOutput: the sprectrum reader to use.
m_RecentFilesHandler - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the recent files handler.
m_RecentFilesHandler - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the recent files handler.
m_ref_count - Variable in class adams.data.io.input.foss.FossHelper: number of reference values per spectra.
m_ref_names - Variable in class adams.data.io.input.foss.FossHelper: reference names.
m_Reference - Variable in class adams.data.threeway.ThreeWayData: 'reference' values.
m_ReferencesStorage - Variable in class adams.flow.transformer.SpectralAngleMapper: Storage of the reference spectra.
m_ReferenceValuePrefix - Variable in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: the reference value field prefix.
m_ReferenceValues - Variable in class adams.data.conversion.SpectrumToJson: the reference values.
m_ReferenceValues - Variable in class adams.data.io.output.JsonSpectrumWriter: the reference values.
m_ReferenceValues - Variable in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: reference value fields to add to the output data.
m_RefRegExp - Variable in class weka.core.converters.CALSpectrumLoader: the references to load.
m_RegExp - Variable in class adams.data.io.input.sampleidextraction.RegExp: regexp to extract sample ID from file name.
m_RegExp - Variable in class adams.data.io.input.ZippedSpectrumReader: the regular expression that the filenames must match to be extracted.
m_RegExp - Variable in class adams.data.spectrumfilter.ReportFieldFromStringValue: the regular expression to apply.
m_RegExp - Variable in class adams.data.spectrumfilter.WekaFilterToReport: the regular expression for the attribute names to transfer.
m_RegExp - Variable in class adams.data.spectrumoutlier.StringMatcher: the regular expression that the value must match.
m_RegExp - Variable in class adams.gui.visualization.spectrum.SpectrumPaintletStringField: the regular expression to apply (extracts first group).
m_RejectedTokensActor - Variable in class adams.flow.control.InstanceCleaner: the actor for the rejected tokens.
m_RejectedTokensActor - Variable in class adams.flow.control.SpectrumCleaner: the actor for the rejected tokens.
m_RejectionMessagesActor - Variable in class adams.flow.control.InstanceCleaner: the actor for the rejection messages.
m_RejectionMessagesActor - Variable in class adams.flow.control.SpectrumCleaner: the actor for the rejection messages.
m_RelDiff - Variable in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: the relative difference.
m_Reloadable - Variable in class adams.gui.visualization.spectrum.SpectrumContainerManager: whether the spectrums can be reloaded from the database (fake ones can't be reloaded!).
m_Remove - Variable in class weka.classifiers.meta.SpectrumClassifier: The filter for removing sample ID/database ID.
m_Remove - Variable in class weka.clusterers.SpectrumClusterer: The filter for removing sample ID/database ID.
m_RemoveUnused - Variable in class weka.filters.unsupervised.attribute.RangeBasedSavitzkyGolay: Whether unused attributes are left out of the output.
m_RemoveUnused - Variable in class weka.filters.unsupervised.attribute.SegmentedDownSample: Whether unused attributes are left out of the output.
m_RemoveUnused - Variable in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: Whether unused attributes are left out of the output.
m_RemoveWithMissing - Variable in class adams.data.cleaner.instance.IQRCleaner: whether to remove instances with missing values.
m_ReportField - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: the report value.
m_Reports - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the sample data reports.
m_ReportTable - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: the report of the data.
m_RequiredField - Variable in class adams.db.SpectrumConditionsSingle: the field that us required to be present in report.
m_RequiredFields - Variable in class adams.db.SpectrumConditionsMulti: the fields that are required to be present in report.
m_ResetEvaluator - Variable in class adams.flow.transformer.Evaluator: whether we need to reset the evaluator.
m_ResetModel - Variable in class adams.flow.transformer.ThreeWayDataModelFilter: whether we need to reset the model.
m_Resolution - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: the resolution.
m_RowFinder - Variable in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: for locating the rows to import.
m_RowFinder - Variable in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: for locating the rows to import.
m_RowFinder - Variable in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: the row finder to use.
m_RowID - Variable in class adams.data.conversion.SpreadSheetColumnsToSampleData: the (optional) row with the sample ID.
m_RowID - Variable in class adams.data.conversion.SpreadSheetColumnsToSpectra: the (optional) row with the sample ID.
m_RowSampleDataNames - Variable in class adams.data.conversion.SpreadSheetRowsToSampleData: the column with the sample data names.
m_RowSampleDataNames - Variable in class adams.data.conversion.SpreadSheetRowsToSpectra: the column with the sample data names.
m_RowsAmplitude - Variable in class adams.data.conversion.SpreadSheetColumnsToSpectra: the rows to get the amplitudes from.
m_RowsAmplitude - Variable in class adams.data.conversion.SpreadSheetRowsToSpectra: the rows with amplitudes.
m_RowsSampleData - Variable in class adams.data.conversion.SpreadSheetColumnsToSampleData: the rows to get the sample data from.
m_RowsSampleData - Variable in class adams.data.conversion.SpreadSheetColumnsToSpectra: the rows to get the sample data from.
m_RowsSampleDataValues - Variable in class adams.data.conversion.SpreadSheetRowsToSampleData: the rows with sample data values.
m_RowWaveNumber - Variable in class adams.data.conversion.SpreadSheetRowsToSpectra: the (optional) wavenumber row.
m_sample_id - Variable in class adams.data.io.output.foss.FossOutputHelper.SampleInfo: String(13): zero terminated.
m_sample_id1 - Variable in class adams.data.io.output.foss.FossOutputHelper.SampleHeader: SampleID #1.
m_sample_id2 - Variable in class adams.data.io.output.foss.FossOutputHelper.SampleHeader: SampleID #2.
m_sample_id3 - Variable in class adams.data.io.output.foss.FossOutputHelper.SampleHeader: SampleID #3.
m_sample_no - Variable in class adams.data.io.output.foss.FossOutputHelper.SampleHeader: String(13): zero terminated.
m_SampleData - Variable in class adams.data.spectrum.MultiSpectrum: the report.
m_SampleData - Variable in class adams.data.spectrum.Spectrum: Sample Data.
m_SampleDataColumns - Variable in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: the range of columns containing sample data.
m_SampleDataF - Variable in class adams.flow.transformer.BulkSampleDataDbWriter: the instance that is currently running a bulk store.
m_SampleDataFormat - Variable in class adams.data.spectrumfilter.ChangeFormat: the format to get the sample data from.
m_SampleDataLabelsColumn - Variable in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: the column containing the labels for the sample data values.
m_SampleDataNamesInHeader - Variable in class adams.data.conversion.SpreadSheetRowsToSampleData: whether the sample data names are in the header row.
m_SampleDataNamesInHeader - Variable in class adams.data.conversion.SpreadSheetRowsToSpectra: whether the sample data names are in the header row.
m_SampleDataRows - Variable in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: the range of rows containing the sample data.
m_SampleID - Variable in class adams.data.io.input.OpusSpectrumReader: where to get sample id from. see param defs
m_SampleID - Variable in class adams.data.multispectrumoperation.Remove: the regular expression for the sample ID.
m_SampleID - Variable in class adams.flow.transformer.MultiSpectrumRemove: the regular expression for the sample ID.
m_SampleID - Variable in class adams.gui.selection.SelectSpectrumPanel.TableModel: the NAMEs to display.
m_SampleID1 - Variable in class adams.data.io.output.NIRSpectrumWriter: SampleID 1.
m_SampleID2 - Variable in class adams.data.io.output.NIRSpectrumWriter: SampleID 2.
m_SampleID3 - Variable in class adams.data.io.output.NIRSpectrumWriter: SampleID 3.
m_SampleIDColumn - Variable in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: the column containing the sample ID.
m_SampleIDExtraction - Variable in class adams.data.io.input.ASCIIXYSpectrumReader: scheme for extracting sample ID from file name.
m_SampleIDLocation - Variable in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: the sample ID location.
m_SampleIDregex - Variable in class adams.flow.transformer.InstanceToSpectrum: Regex to find sample id. e.g "sampleID"
m_SampleIDRegExp - Variable in class adams.db.AbstractSpectrumConditions: the regular expression on the name of the spectrum.
m_SampleIDRegExp - Variable in class adams.db.SpectrumIDConditions: the regular expression on the name of the spectrum.
m_SampleIDRow - Variable in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: the row containing the sample ID.
m_SampleType - Variable in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: the sample type regular expression.
m_SampleType - Variable in class adams.data.multispectrumoperation.Remove: the regular expression for the sample type.
m_SampleType - Variable in class adams.flow.transformer.MultiSpectrumRemove: the regular expression for the sample type.
m_SampleTypeRegExp - Variable in class adams.db.AbstractSpectrumConditions: the regular expression on the sample type of the spectrum.
m_SampleTypeRegExp - Variable in class adams.db.SpectrumIDConditions: the regular expression on the type of the spectrum.
m_Scale - Variable in class adams.data.spectrumfilter.Covariance: display absolute values.
m_Scale - Variable in class adams.data.spectrumfilter.LRCoeff: display absolute values.
m_Scores - Variable in class adams.data.spectrumanalysis.PCA: the scores.
m_Scores - Variable in class adams.data.spectrumanalysis.PLS: the scores.
m_ScriptingDialog - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the dialog for managing scripts.
m_Search - Variable in class adams.data.evaluator.instance.AbstractNearestNeighborBasedEvaluator: the nearest neighbor algorithm to use.
m_SearchIDs - Variable in class adams.gui.tools.DeleteSampleDataPanel: the search panel for the IDs.
m_SearchIDs - Variable in class adams.gui.tools.ListSampleDataPanel: the search panel for the IDs.
m_SearchIDs - Variable in class adams.gui.tools.UpdateSampleDataPanel: the search panel for the IDs.
m_Searching - Variable in class adams.gui.tools.idprovider.DatabaseSearchPanel: whether the search is currently happening.
m_SearchPanel - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: for searching the fields in the reports.
m_SearchPanel - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: the search panel for the data report.
m_SearchPanel - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the search panel for the heatmap report.
m_SearchSampleData - Variable in class adams.gui.tools.ListSampleDataPanel: the search panel for the sample data.
m_SearchSampleData - Variable in class adams.gui.tools.UpdateSampleDataPanel: the search panel for the sample data.
m_Seed - Variable in class adams.data.cleaner.instance.RemoveOutliers: the seed value.
m_Seed - Variable in class adams.data.evaluator.instance.CrossValidatedNeighborHood: the seed value.
m_Seed - Variable in class adams.data.evaluator.instance.CrossValidatedPrediction: the seed value.
m_Seed - Variable in class adams.data.evaluator.instance.EnsembleEvaluator: the seed value.
m_Seed - Variable in class adams.data.evaluator.instance.FakeEvaluator: the seed.
m_Seed - Variable in class adams.data.evaluator.instance.MultiClassifierEvaluator: the seed value.
m_Seed - Variable in class adams.data.postprocessor.instances.PredictionErrorIQR: the seed value.
m_Segments - Variable in class adams.data.io.output.NIRSpectrumWriter: Segment points.
m_SelectedWaveNumberPaintlet - Variable in class adams.gui.visualization.spectrum.SpectrumPanel: paintlet for drawing the selected wave number.
m_Separator - Variable in class adams.data.io.input.ASCIIXYSpectrumReader: the separator to use.
m_Separator - Variable in class adams.data.io.input.SimpleXYZReader: the column separator.
m_Separator - Variable in class adams.data.io.output.ASCIIXYSpectrumWriter: the separator to use.
m_Separator - Variable in class adams.data.io.output.SimpleXYZWriter: the column separator.
m_sequence - Variable in class adams.data.io.output.foss.FossOutputHelper.SampleHeader: 2 BYTE?
m_sequence - Variable in class adams.data.io.output.foss.FossOutputHelper.SampleInfo: 2 BYTE?
m_serial - Variable in class adams.data.io.output.foss.FossOutputHelper.InstrumentHeader: char[9] serial number.
m_Serial - Variable in class adams.data.io.output.NIRSpectrumWriter: Serial Number of Instrument.
m_SerializableObjectHelper - Variable in class adams.data.cleaner.instance.AbstractSerializableCleaner: the helper class for serializing.
m_SerializableObjectHelper - Variable in class adams.data.cleaner.spectrum.AbstractSerializableCleaner: the helper class for serializing.
m_SerializableObjectHelper - Variable in class adams.data.evaluator.instance.AbstractSerializableEvaluator: the helper class for serializing.
m_SerializableObjectHelper - Variable in class adams.data.postprocessor.instances.AbstractSerializablePostProcessor: the helper class for serializing.
m_SerializableObjectHelper - Variable in class adams.data.spectrumfilter.AbstractSerializableFilter: the helper class for serializing.
m_SerializationFile - Variable in class adams.data.cleaner.instance.AbstractSerializableCleaner: the file to serialize the setup to .
m_SerializationFile - Variable in class adams.data.cleaner.spectrum.AbstractSerializableCleaner: the file to serialize the setup to .
m_SerializationFile - Variable in class adams.data.evaluator.instance.AbstractSerializableEvaluator: the file to serialize the setup to .
m_SerializationFile - Variable in class adams.data.postprocessor.instances.AbstractSerializablePostProcessor: the file to serialize the setup to .
m_SerializationFile - Variable in class adams.data.spectrumfilter.AbstractSerializableFilter: the file to serialize the setup to .
m_Service - Variable in class adams.flow.webservice.Get: the service instance.
m_Service - Variable in class adams.flow.webservice.Put: the service instance.
m_Service - Variable in class adams.flow.webservice.Transform: the service instance.
m_Sheets - Variable in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader.MultiSheetIterator: the list of sheets.
m_Sheets - Variable in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader.SingleSheetIterator: the list of sheets.
m_ShowReportTable - Variable in class adams.flow.sink.ThreeWayDataHeatmapDisplay: whether to show the report table.
m_ShowSidePanel - Variable in class adams.flow.sink.SpectrumDisplay: whether to show the side panel or not.
m_Singleton - Static variable in class adams.db.AbstractSpectralDbBackend: the singleton.
m_SkipFields - Variable in class adams.flow.transformer.BulkSampleDataDbWriter: whether to skip fields.
m_SkipFieldsRegExp - Variable in class adams.flow.transformer.BulkSampleDataDbWriter: the fields to ignore.
m_Slopes - Variable in class adams.data.spectrumfilter.amplitudetransform.ApplyMultiplicativeScatterCorrection: the slopes.
m_SortOnInsertTimestamp - Variable in class adams.db.AbstractSpectrumConditions: whether to sort by insert timestamp.
m_SortOnSampleID - Variable in class adams.db.AbstractSpectrumConditions: whether to sort by sample ID.
m_Source - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: the source.
m_Source - Variable in class adams.data.spectrumfilter.ReportFieldFromStringValue: the source field.
m_Source - Variable in class adams.data.spectrumfilter.ReportFieldFromStringValueWithLookup: the report field to read from.
m_Sources - Variable in class adams.data.spectrumanalysis.FastICA: the sources.
m_spacing_mode - Variable in class adams.data.io.output.foss.FossOutputHelper.InstrumentHeader: 2 BYTES int spacing mode: 00=TILFIL, 01=EQUALSPC, 02=FILFIL, 03=SIN.
m_Spectra - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: the parsed spectrum.
m_spectra_head_size - Variable in class adams.data.io.input.foss.FossHelper: size of spectrum header (static).
m_spectra_size - Variable in class adams.data.io.input.foss.FossHelper: size of spectra data.
m_spectra_tail_size - Variable in class adams.data.io.input.foss.FossHelper: size of spectrum tail (static).
m_SpectralData - Variable in class adams.flow.transformer.InstanceToSpectrum: Regex to find spectral data. e.g "amplitude
m_Spectrum - Variable in class adams.data.io.input.SPCSpectrumReader.SubFileParser: the parsed spectrum.
m_Spectrum - Variable in class adams.data.io.output.foss.FossOutputHelper.DataBlock: The Spectrum.
m_SpectrumBlockType - Variable in class adams.data.io.input.OpusSpectrumReaderExt: the hex mask for the spectrum to extract.
m_SpectrumColumns - Variable in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: the range of columns to load spectra from.
m_SpectrumF - Variable in class adams.flow.transformer.BulkSpectrumDbWriter: the instance that is currently running a bulk store.
m_SpectrumFileChooser - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the file chooser for importing data.
m_SpectrumFormat - Variable in class adams.data.spectrumfilter.ChangeFormat: the format of the spectrum to load from the database.
m_SpectrumIn - Variable in class adams.flow.webservice.multispectrum.MultiUpload: input spectrum
m_SpectrumIn - Variable in class adams.flow.webservice.Put: input spectrum
m_SpectrumIn - Variable in class adams.flow.webservice.spectrum.Upload: input spectrum
m_SpectrumIn - Variable in class adams.flow.webservice.Transform: input spectrum
m_SpectrumPaintlet - Variable in class adams.gui.visualization.spectrum.SpectrumPanel: paintlet for drawing the spectrum.
m_SpectrumPointHitDetector - Variable in class adams.gui.visualization.spectrum.SpectrumPanel: for detecting hits.
m_SpectrumType - Variable in class adams.data.io.input.SoilCaresScannerSpectrumReader: the type of spectrum to read.
m_SplitPane - Variable in class adams.gui.tools.DeleteSampleDataPanel: the split pane.
m_SplitPane - Variable in class adams.gui.tools.ListSampleDataPanel: the split pane.
m_SplitPane - Variable in class adams.gui.tools.UpdateSampleDataPanel: the split pane.
m_SplitPaneAll - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: the split pane for X-list and split pane on right.
m_SplitPaneRight - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: the split pane for image/spreadsheet and report.
m_standardised - Variable in class adams.data.io.output.foss.FossOutputHelper.SampleHeader: 2 BYTE??
m_Standardize - Variable in class adams.data.multifilter.Average: for aligning the spectra.
m_start - Variable in class adams.data.io.input.CALSpectrumReader: starting spectrum.
m_Start - Variable in class adams.data.io.input.opus.OpusBlockHelper.Block: the start of the block (incl).
m_Start - Variable in class adams.data.io.input.OpusSpectrumReader: starting spectrum.
m_Start - Variable in class adams.data.spectrumfilter.Rebase: the new starting point for wave numbers.
m_Start - Variable in class weka.filters.unsupervised.attribute.SavitzkyGolayRange: the start of the range.
m_StartDate - Variable in class adams.db.AbstractSpectrumConditions: the start date of the spectra (incl.).
m_StartDate - Variable in class adams.db.OrphanedSampleDataConditions: the start date of the inserts (incl.).
m_Statistic - Variable in class adams.data.evaluator.instance.CrossValidatedNeighborHood: the measure to output as evaluation.
m_Statistic - Variable in class adams.data.evaluator.instance.CrossValidatedPrediction: the measure to output as evaluation.
m_Statistic - Variable in class adams.flow.transformer.threewaydatamerge.CollapseX: the type of statistic to calculate.
m_StatusBar - Variable in class adams.gui.tools.DeleteSampleDataPanel: the status bar.
m_StatusBar - Variable in class adams.gui.tools.ListSampleDataPanel: the status bar.
m_StatusBar - Variable in class adams.gui.tools.UpdateSampleDataPanel: the status bar.
m_StatusBar - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the status bar.
m_StatusBar - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the status bar.
m_Step - Variable in class adams.data.spectrumfilter.AbstractStandardiseFilter: the step.
m_Stopped - Variable in class adams.data.cleaner.instance.RemoveOutliers: whether the execution was stopped.
m_Stopped - Variable in class adams.data.evaluator.instance.CrossValidatedNeighborHood: whether the execution was stopped.
m_Stopped - Variable in class adams.data.evaluator.instance.EnsembleEvaluator: whether the execution was stopped.
m_Stopped - Variable in class adams.data.evaluator.instance.MultiClassifierEvaluator: whether the execution was stopped.
m_Stopped - Variable in class adams.data.io.input.AbstractSpectrumReader: whether reading was stopped.
m_Stopped - Variable in class adams.data.io.input.AbstractThreeWayDataReader: whether reading was stopped.
m_Stopped - Variable in class adams.data.postprocessor.instances.PredictionErrorIQR: whether the execution was stopped.
m_StorageName - Variable in class adams.flow.transformer.MergeSampleDataFromMap: the name of the stored value.
m_StorageName - Variable in class adams.flow.transformer.MultiSpectrumAdd: the name of the stored value.
m_StoreWaveNo - Variable in class adams.flow.transformer.BulkSpectrumDbWriter: whether to store the wave numbers as well.
m_StoreWaveNo - Variable in class adams.flow.transformer.SpectrumDbWriter: whether to store the wave numbers as well.
m_Streams - Variable in class adams.data.io.input.UnscramblerSpectrumReader: the streams to close at the end.
m_SubGenerators - Variable in class adams.data.threewayfeatures.MultiThreeWayDataFeatureGenerator: the generators to use.
m_SubHeaders - Variable in class adams.data.threewayfeatures.MultiThreeWayDataFeatureGenerator: the sub-headers.
m_Success - Variable in class adams.data.spectrumfilter.ConditionalReportField: the success value.
m_TabbedPane - Variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the tabbed pane for the data to display.
m_TabbedPane - Variable in class adams.gui.visualization.spectrum.SpectrumPanelWithSampleData: the tabbed pane.
m_TabCounter - Variable in class adams.gui.visualization.spectrum.MultiSpectrumPanel: the counter for the tabs.
m_Table - Variable in class adams.data.spectrumfilter.ReportFieldFromStringValueWithLookup: the lookup table.
m_TableIDs - Variable in class adams.gui.tools.DeleteSampleDataPanel: the table with the spectra.
m_TableIDs - Variable in class adams.gui.tools.ListSampleDataPanel: the table with the spectra.
m_TableIDs - Variable in class adams.gui.tools.UpdateSampleDataPanel: the table with the spectra.
m_TableManager - Static variable in class adams.db.generic.SampleDataT: the table manager.
m_TableManager - Static variable in class adams.db.generic.SpectrumT: the table manager.
m_TableManager - Static variable in class adams.db.h2.SampleDataT: the table manager.
m_TableManager - Static variable in class adams.db.h2.SpectrumT: the table manager.
m_TableManager - Static variable in class adams.db.mirrored.SampleDataT: the table manager.
m_TableManager - Static variable in class adams.db.mirrored.SpectrumT: the table manager.
m_TableManager - Static variable in class adams.db.mssql.SampleDataT: the table manager.
m_TableManager - Static variable in class adams.db.mssql.SpectrumT: the table manager.
m_TableManager - Static variable in class adams.db.mysql.SampleDataT: the table manager.
m_TableManager - Static variable in class adams.db.mysql.SpectrumT: the table manager.
m_TableManager - Static variable in class adams.db.postgresql.SampleDataT: the table manager.
m_TableManager - Static variable in class adams.db.postgresql.SpectrumT: the table manager.
m_TableManager - Static variable in class adams.db.SampleDataF: the facade manager.
m_TableManager - Static variable in class adams.db.SpectrumF: the facade manager.
m_TableManager - Static variable in class adams.db.sqlite.SampleDataT: the table manager.
m_TableManager - Static variable in class adams.db.sqlite.SpectrumT: the table manager.
m_TableSampleData - Variable in class adams.gui.tools.ListSampleDataPanel: the sample data overview table.
m_TableSampleData - Variable in class adams.gui.tools.UpdateSampleDataPanel: the sample data table.
m_TableSampleData - Variable in class adams.gui.visualization.spectrum.SpectrumPanelWithSampleData: the sample data table.
m_Target - Variable in class adams.data.spectrumfilter.ConditionalReportField: the target field.
m_Target - Variable in class adams.data.spectrumfilter.ReportFieldFromStringValue: the target field.
m_Target - Variable in class adams.data.spectrumfilter.ReportFieldFromStringValueWithLookup: the report field to store the result in.
m_Text - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: the fixed text.
m_TextColor - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: the color of the text.
m_TextColumn - Variable in class adams.gui.tools.idprovider.SpreadSheetIDPanel: the column to get the ID from.
m_TextFormat - Variable in class adams.gui.tools.idprovider.ManualListPanel: the spectrum format.
m_TextFormat - Variable in class adams.gui.tools.idprovider.SpreadSheetIDPanel: the spectrum format.
m_TextFrom - Variable in class adams.gui.tools.idprovider.DatabaseSearchPanel: the from date.
m_TextName - Variable in class adams.gui.tools.UpdateSampleDataPanel: the text field for the field name.
m_TextRegexp - Variable in class adams.gui.tools.ListSampleDataPanel: the regexp field for limiting the sample data fields.
m_TextTo - Variable in class adams.gui.tools.idprovider.DatabaseSearchPanel: the to date.
m_TextValue - Variable in class adams.gui.tools.UpdateSampleDataPanel: the text field for the field value.
m_Threshold - Variable in class adams.data.multispectrumoperation.outlierremoval.CorrelationBasedThreshold: the threshold.
m_Threshold - Variable in class adams.data.multispectrumoperation.outlierremoval.CosineSimilarityBasedThreshold: the threshold.
m_Threshold - Variable in class adams.data.multispectrumoperation.outlierremoval.MeanSpectrumCosineSimilarityBasedThreshold: the threshold.
m_Threshold - Variable in class adams.data.spectrumoutlier.Oscillation: the threshold for the the correlation coefficient.
m_time - Variable in class adams.data.io.output.foss.FossOutputHelper.Generalheader: 4 BYTES: long int.
m_time - Variable in class adams.data.io.output.foss.FossOutputHelper.SampleHeader: sample time.
m_Timestamp - Variable in class adams.data.io.output.NIRSpectrumWriter: the timestamp to use in the file.
m_TolerateHeaderChanges - Variable in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: whether to tolerate header changes.
m_ToolTipMaxColumns - Variable in class adams.gui.visualization.spectrum.SpectrumPanel: the maximum number of columns for the tooltip.
m_ToolTipMaxRows - Variable in class adams.gui.visualization.spectrum.SpectrumPanel: the maximum number of rows for the tooltip.
m_Trace - Variable in class adams.data.io.input.OpusSpectrumReader: trace of data that was retrieved from byte array.
m_TrainingData - Variable in class adams.data.evaluator.instance.AbstractNearestNeighborBasedEvaluator: the training data.
m_TrainingData - Variable in class adams.data.evaluator.instance.EnsembleEvaluator: the training data.
m_TrainingData - Variable in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: the training data.
m_TrainingData - Variable in class adams.data.evaluator.instance.MultiClassifierEvaluator: Instances for training bags.
m_TrainingData - Variable in class adams.data.evaluator.instance.SavitzkyGolayRange: the training data.
m_TransferPrefix - Variable in class adams.data.conversion.MultiSpectrumToSpectra: the (optional) prefix for fields from the multi-spectrum.
m_TransferPrefix - Variable in class adams.flow.transformer.MultiSpectrumFilter: the (optional) prefix for fields from the multi-spectrum.
m_TransferRegExp - Variable in class adams.data.conversion.MultiSpectrumToSpectra: the regular expression for field names to transfer.
m_TransferRegExp - Variable in class adams.flow.transformer.MultiSpectrumFilter: the regular expression for field names to transfer.
m_TransferReport - Variable in class adams.data.conversion.MultiSpectrumToSpectra: whether to transfer the multi-spectrum's report into the sub-spectra.
m_TransferReport - Variable in class adams.flow.transformer.MultiSpectrumFilter: whether to transfer the multi-spectrum's report into the sub-spectra.
m_Transformer - Variable in class adams.data.spectrumfilter.AmplitudeTransform: the transformer to apply.
m_type - Variable in class adams.data.io.output.foss.FossOutputHelper.Generalheader: 2 BYTES: Use 1st BYTE. 01=.NIR, 02=.CAL.
m_Type - Variable in class adams.data.conversion.SpectrumToArray: the data to output.
m_Type - Variable in class adams.data.io.input.opus.OpusBlockHelper.Block: the type of the block.
m_Type - Variable in class adams.data.io.input.opus.OpusBlockHelper.CommandlineData: the type of the commandline.
m_Type - Variable in class adams.data.io.input.ScioLabExportSpectrumReader: the type of spectrum to read.
m_Type - Variable in class adams.flow.transformer.GetSpectrumAmplitude: how to retrieve the amplitude.
m_Type - Variable in class adams.flow.transformer.SetSpectrumAmplitude: how to retrieve the amplitude.
m_Type - Variable in class adams.flow.transformer.SpectrumInfo: the type of information to generate.
m_UniqueXs - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: whether each subfile has unique X array (0:0x40h).
m_Unsigned - Variable in class adams.data.io.input.FitsLibsReader: whether the data is unsigned.
m_UpdateContainerColor - Variable in class adams.gui.visualization.spectrum.ReportColorSpectrumPaintlet: whether to update the color of the container.
m_UpdateInterval - Variable in class adams.flow.sink.spectrumdisplay.SimplePlotUpdater: the interval of tokens processed after which to update the display.
m_UpdateWaveNumbers - Variable in class adams.data.spectrumfilter.Rebase: whether to introduce new step size between points.
m_Updating - Variable in class adams.db.mirrored.SampleDataT: object for blocking polling/removal of fully processed.
m_Updating - Variable in class adams.db.mirrored.SpectrumT: object for blocking polling/removal of fully processed.
m_UpperPercentile - Variable in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.DataCollector: the upper percentile.
m_UpperPercentile - Variable in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.InterPercentileRange: upper percentile.
m_UpperPercentile - Variable in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: the upper percentile.
m_UseAbsoluteError - Variable in class adams.data.postprocessor.instances.PredictionErrorIQR: whether to use absolute errors.
m_UseAbsoluteSource - Variable in class adams.data.io.input.AbstractSpectrumReader: whether to use absolute filename for the source report field or just the file's name.
m_UseAbsoluteSource - Variable in class adams.data.io.input.AbstractThreeWayDataReader: whether to use absolute filename for the source report field or just the file's name.
m_UseAmplitude - Variable in class adams.data.spectrum.SpectrumPointComparator: whether to compare amplitude or wave number.
m_UseCompression - Variable in class adams.data.io.output.SimpleSpectrumWriter: whether to use compression.
m_UseCompression - Variable in class adams.data.io.output.SimpleXYZWriter: whether to use compression.
m_UseCustomComparator - Variable in class adams.data.conversion.SpectraToMultiSpectrum: whether to use a custom comparator.
m_UseCustomComparator - Variable in class adams.flow.transformer.SpectrumFileReader: whether to use a custom comparator.
m_UseData - Variable in class adams.data.threeway.L2PointComparator: whether to compare data as well as z.
m_UseEvaluatorResetVariable - Variable in class adams.flow.transformer.Evaluator: whether to use a variable to monitor for changes, triggering resets of the evaluator.
m_UseFilenameAsID - Variable in class adams.data.io.input.AbstractJCampSpectrumReader: whether to use the filename as ID.
m_UseFilenameAsID - Variable in class adams.data.io.input.JCampDX2SpectrumReader: whether to use the filename as ID.
m_UseFilenameAsSampleID - Variable in class adams.data.io.input.RelabSpectrumReader: whether to use the (uppercase) filename as sample ID.
m_UseModelResetVariable - Variable in class adams.flow.transformer.ThreeWayDataModelFilter: whether to use a variable to monitor for changes, triggering resets of the model.
m_UseModifiedAlgorithm - Variable in class adams.flow.transformer.SpectralAngleMapper: Whether to use the modified algorithm described in Oshigami et al.
m_UseReferenceAndMetaData - Variable in class adams.data.conversion.SpectrumToJson: whether to output speficied reference and meta-data values.
m_UseReferenceAndMetaData - Variable in class adams.data.io.output.JsonSpectrumWriter: whether to output speficied reference and meta-data values.
m_UseStoreTable - Variable in class adams.data.spectrumfilter.AbstractDatabaseFilter: whether to load the sample data if missing.
m_UseY - Variable in class adams.data.threeway.L1PointComparator: whether to compare Y as well.
m_Validate - Variable in class adams.data.io.input.JCampDX2SpectrumReader: whether the reader validates.
m_Value - Variable in class adams.flow.transformer.SetEvaluationMetaData: the value in the evaluation.
m_Values - Variable in class adams.data.io.input.opus.OpusBlockHelper.CommandlineData: the data.
m_VariableName - Variable in class adams.flow.transformer.SpectrumFeatureGenerator: the variable to listen to.
m_VariableName - Variable in class adams.flow.transformer.ThreeWayDataFeatureGenerator: the variable to listen to.
m_Variance - Variable in class adams.data.spectrumfilter.PCA: the variance to cover.
m_Version - Variable in class adams.data.conversion.WekaPredictionContainerToEvaluationContainer: the optional version to store.
m_Version - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: the version (1).
m_Version - Variable in class adams.flow.transformer.Evaluator: the version of the component.
m_Visible - Variable in class adams.gui.visualization.spectrum.SpectrumContainer: whether the spectrum is visible.
m_WaitPoll - Variable in class adams.flow.standalone.rats.WSMultiSpectrumReception: the waiting period in msec before polling again.
m_WaitPoll - Variable in class adams.flow.standalone.rats.WSSpectrumReception: the waiting period in msec before polling again.
m_wave - Variable in class adams.data.io.output.foss.FossOutputHelper.InstrumentHeader: start float[7], inc float[7], end float[7] but looking at
m_WaveColumns - Variable in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: the range of columns containing wave amplitudes.
m_WaveEnds - Variable in class adams.data.io.output.NIRSpectrumWriter: Segment ends.
m_WaveNoInc - Variable in class adams.data.conversion.ArrayToSpectrum: the wave number increment.
m_WaveNoStart - Variable in class adams.data.conversion.ArrayToSpectrum: the starting wave number.
m_WaveNumber - Variable in class adams.data.spectrum.SpectrumPoint: the wave number.
m_WaveNumber - Variable in class adams.flow.transformer.GetSpectrumAmplitude: the wave number.
m_WaveNumber - Variable in class adams.flow.transformer.SetSpectrumAmplitude: the wave number.
m_WaveNumberAsSuffix - Variable in class adams.data.instances.SimpleInstanceGenerator: whether to use the wave number as suffix.
m_WaveNumberAsSuffix - Variable in class adams.data.instances.SimpleSpectralInstanceGenerator: whether to use the wave number as suffix.
m_WaveNumberColumn - Variable in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: the column with the wave numbers.
m_WaveNumberPrefix - Variable in class adams.data.instances.AbstractSpectrumInstanceGenerator: the prefix for the wave-numbers attributes.
m_WaveNumberRegExp - Variable in class adams.data.conversion.SpreadSheetColumnsToSpectra: the regular expression to extract the wave number from the header (first group is used).
m_WaveNumberRegExp - Variable in class adams.data.conversion.SpreadSheetRowsToSpectra: the regular expression to extract the wave number from the header (first group is used).
m_WaveNumberRegExp - Variable in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: the regular expression to extract the wave number from the header (first group is used).
m_WaveNumbers - Variable in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.DataCollector: the wave numbers that were encountered.
m_WaveNumbersInHeader - Variable in class adams.data.conversion.SpreadSheetRowsToSpectra: whether the wavenumbers are in the header row.
m_WaveNumbersInHeader - Variable in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: whether to use the wave numbers in the header.
m_WaveNumberStarts - Variable in class adams.data.multifilter.Fusion: the starting points for the wave numbers in the merged spectrum (use -1 for the next available one).
m_WaveNumberStepSize - Variable in class adams.data.spectrumfilter.PadPower2: the step size between wave numbers (<= 0 to use average).
m_WaveNumberStepSizes - Variable in class adams.data.multifilter.Fusion: the step sizes for the wave numbers.
m_WaveStarts - Variable in class adams.data.io.output.NIRSpectrumWriter: Segment starting.
m_WaveStep - Variable in class adams.data.spectrumfilter.Rebase: the difference between two wave numbers.
m_WaveStep - Variable in class adams.flow.transformer.InstanceToSpectrum: the wave number step.
m_WaveSteps - Variable in class adams.data.io.output.NIRSpectrumWriter: Increments.
m_WAxis - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: the label of the W axis.
m_WAxis - Variable in class adams.data.io.input.SPCSpectrumReader.SubFileParser: the W axis value.
m_WebService - Variable in class adams.flow.standalone.rats.WSMultiSpectrumReception: the webservice to run.
m_WebService - Variable in class adams.flow.standalone.rats.WSSpectrumReception: the webservice to run.
m_Width - Variable in class adams.data.spectrumimage.Intensity: the image width to generate.
m_Width - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlayWithDimensions: the width of the overlay.
m_Window - Variable in class adams.data.sampledata.SignalToNoiseRatio: smoothing window for savitsky golay
m_WindowSize - Variable in class adams.data.spectrumoutlier.Oscillation: the LOWESS window size.
m_WindowSizeFirst - Variable in class adams.data.evaluator.instance.SavitzkyGolayRange: the window size for for SG with first derivative.
m_WindowSizeNone - Variable in class adams.data.evaluator.instance.SavitzkyGolayRange: the window size for for SG with no derivative.
m_WindowSizeSecond - Variable in class adams.data.evaluator.instance.SavitzkyGolayRange: the window size for for SG with second derivative.
m_Wrap - Variable in class adams.data.postprocessor.instances.WekaFilter: whether to wrap the filter in a SpectrumFilter.
m_Writer - Variable in class adams.data.io.output.FilteredSpectrumWriter: the underlying writer.
m_Writer - Variable in class adams.data.io.output.SpreadSheetSpectrumWriter: the spreadsheet writer to use.
m_Writer - Variable in class adams.flow.standalone.rats.SaveMultiSpectrumFileOutput: the sprectrum writer to use.
m_Writer - Variable in class adams.flow.standalone.rats.SaveSpectrumFileOutput: the sprectrum writer to use.
m_X - Variable in class adams.data.io.input.SimpleEEMReader: the X value to use for the 3-way data.
m_X - Variable in class adams.data.threeway.L1Point: x.
m_X - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlay: the X position of the overlay.
m_XAxis - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: the label of the X axis.
m_Y - Variable in class adams.data.threeway.L1Point: y.
m_Y - Variable in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlay: the Y position of the overlay.
m_YasIEEE32bit - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: whether Y values are stored in IEEE 32bit floats.
m_YasIEEE32bit - Variable in class adams.data.io.input.SPCSpectrumReader.SubFileParser: whether Y values are stored in IEEE 32bit floats.
m_YAxis - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: the label of the Y axis.
m_Z - Variable in class adams.data.threeway.L2Point: z.
m_ZAxis - Variable in class adams.data.io.input.SPCSpectrumReader.FileParser: the label of the Z axis.
m_ZAxis - Variable in class adams.data.io.input.SPCSpectrumReader.SubFileParser: the Z axis value.
m_ZAxisEnd - Variable in class adams.data.io.input.SPCSpectrumReader.SubFileParser: the Z axis end value.
m_Zoom - Variable in class adams.flow.sink.ThreeWayDataHeatmapDisplay: the zoom level.
m_ZoomOverview - Variable in class adams.flow.sink.SpectrumDisplay: whether to display the zoom overview.
main(String[]) - Static method in class adams.data.io.input.AniMLSpectrumReader: Runs the reader from the command-line.
main(String[]) - Static method in class adams.data.io.input.ASCIIXYSpectrumReader: Runs the reader from the command-line.
main(String[]) - Static method in class adams.data.io.input.ASCSpectrumReader: Runs the reader from the command-line.
main(String[]) - Static method in class adams.data.io.input.CALSpectrumReader: Runs the reader from the command-line.
main(String[]) - Static method in class adams.data.io.input.CMLSpectrumReader: Runs the reader from the command-line.
main(String[]) - Static method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Runs the reader from the command-line.
main(String[]) - Static method in class adams.data.io.input.DPTSpectrumReader: Runs the reader from the command-line.
main(String[]) - Static method in class adams.data.io.input.ExtractIdAndTypeSpectrumReader: Runs the reader from the command-line.
main(String[]) - Static method in class adams.data.io.input.foss.FossHelper: Test.
main(String[]) - Static method in class adams.data.io.input.foss.FossStdise: TEST args0 foss std file to read.
main(String[]) - Static method in class adams.data.io.input.JCampDX2SpectrumReader: Runs the reader from the command-line.
main(String[]) - Static method in class adams.data.io.input.JCampDXSpectrumReader: Runs the reader from the command-line.
main(String[]) - Static method in class adams.data.io.input.JsonSpectrumReader: Runs the reader from the command-line.
main(String[]) - Static method in class adams.data.io.input.MPSSpectrumReader: Runs the reader from the command-line.
main(String[]) - Static method in class adams.data.io.input.NIRSpectrumReader: Runs the reader from the command-line.
main(String[]) - Static method in class adams.data.io.input.OpusSpectrumReader: Runs the reader from the command-line.
main(String[]) - Static method in class adams.data.io.input.OpusSpectrumReaderExt: Runs the reader from the command-line.
main(String[]) - Static method in class adams.data.io.input.RelabSpectrumReader: Runs the reader from the command-line.
main(String[]) - Static method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Runs the reader from the command-line.
main(String[]) - Static method in class adams.data.io.input.ScioLabExportSpectrumReader: Runs the reader from the command-line.
main(String[]) - Static method in class adams.data.io.input.SimpleSpectrumReader: Runs the reader from the command-line.
main(String[]) - Static method in class adams.data.io.input.SoilCaresScannerSpectrumReader: Runs the reader from the command-line.
main(String[]) - Static method in class adams.data.io.input.SPASpectrumReader: Runs the reader from the command-line.
main(String[]) - Static method in class adams.data.io.input.SPCSpectrumReader: Runs the reader from the command-line.
main(String[]) - Static method in class adams.data.io.input.SpecLibSpectrumReader: Runs the reader from the command-line.
main(String[]) - Static method in class adams.data.io.input.UnscramblerSpectrumReader: Runs the reader from the command-line.
main(String[]) - Static method in class adams.data.io.input.ZippedSpectrumReader: Runs the reader from the command-line.
main(String[]) - Static method in class weka.classifiers.meta.SpectrumClassifier: Main method for executing this classifier.
main(String[]) - Static method in class weka.clusterers.SpectrumClusterer: Main method for executing this clusterer.
main(String[]) - Static method in class weka.core.converters.CALSpectrumLoader: Main method.
main(String[]) - Static method in class weka.filters.unsupervised.attribute.BestBySLR: Runs the filter with the given parameters.
main(String[]) - Static method in class weka.filters.unsupervised.attribute.SpectrumFilter: Main method for testing this class.
manageScripts() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Executes a script.
MANUAL_FORMAT - Static variable in class adams.gui.tools.idprovider.ManualListPanel
ManualListPanel - Class in adams.gui.tools.idprovider: Allows the user to specify the IDs manually.
ManualListPanel(IDConsumer) - Constructor for class adams.gui.tools.idprovider.ManualListPanel: Initializes the panel with the owner.
markerExtentTipText() - Method in class adams.gui.visualization.spectrum.SpectrumPaintlet: Returns the tip text for this property.
markersDisabledTipText() - Method in class adams.gui.visualization.spectrum.SpectrumPaintlet: Returns the tip text for this property.
masterTipText() - Method in class adams.data.io.output.NIRSpectrumWriter: Returns the tip text for this property.
matrixTipText() - Method in class adams.flow.transformer.ThreeWayDataLoadingMatrix: Returns the tip text for this property.
Max - Class in adams.data.threewayfeatures: Simply determines the largest data value.
Max() - Constructor for class adams.data.threewayfeatures.Max
MAX_AMPLITUDE - adams.flow.transformer.SpectrumInfo.InfoType: the largets amplitude.
MAX_AMPLITUDE - Static variable in class adams.data.statistics.SpectrumStatistic
MAX_DELTA_WAVE_NUMBER - Static variable in class adams.data.statistics.SpectrumStatistic
MAX_NUM_SPECTRUMS_CACHED - Static variable in interface adams.db.SpectrumIntf
MAX_WAVE - adams.flow.transformer.SpectrumInfo.InfoType: the largets wave number.
maxAmplitudeTipText() - Method in class adams.data.io.input.SpecLibSpectrumReader: Returns the tip text for this property.
maxAmplitudeTipText() - Method in class adams.data.spectrumfilter.Scale: Returns the tip text for this property.
maxAmplitudeTipText() - Method in class adams.data.spectrumimage.AbstractSpectrumImageGeneratorWithRange: Returns the tip text for this property.
maxAttributeNamesTipText() - Method in class adams.data.spectrumfilter.PCA: Returns the tip text for this property.
maxAttributesTipText() - Method in class adams.data.spectrumfilter.PCA: Returns the tip text for this property.
maximumTipText() - Method in class adams.data.cleaner.instance.MinMax: Returns the tip text for this property.
maximumTipText() - Method in class adams.data.cleaner.spectrum.MinMax: Returns the tip text for this property.
maximumTipText() - Method in class adams.data.compare.SpectrumCosineSimilarity: Returns the tip text for this property.
maximumValuesTipText() - Method in class adams.db.SpectrumConditionsMulti: Returns the tip text for this property.
maximumValueTipText() - Method in class adams.db.SpectrumConditionsSingle: Returns the tip text for this property.
maxNonRemovalIterationsTipText() - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Returns the tip text for this property.
maxNumRows() - Method in class adams.gui.core.spreadsheettable.ExportSpectra: Returns the maximum number of rows that the plugin requires.
maxNumRows() - Method in class adams.gui.visualization.instances.instancestable.ExportSpectra: Returns the maximum number of rows that the plugin requires.
maxPLSTipText() - Method in class adams.opt.genetic.RonWeasley: Returns the tip text for this property.
maxSGTipText() - Method in class adams.opt.genetic.RonWeasley: Returns the tip text for this property.
maxTipText() - Method in class adams.data.io.input.CALSpectrumReader: Returns the tip text for this property.
maxTipText() - Method in class adams.data.io.input.OpusSpectrumReader: Returns the tip text for this property.
maxTipText() - Method in class adams.data.spectrumfilter.amplitudetransform.Triangle: Returns the tip text for this property.
maxTipText() - Method in class adams.data.spectrumoutlier.MinMax: Returns the tip text for this property.
maxTipText() - Method in class adams.data.threewayoutlier.ValueRange: Returns the tip text for this property.
maxWaveNumberTipText() - Method in class adams.data.io.input.SpecLibSpectrumReader: Returns the tip text for this property.
maxWaveNumberTipText() - Method in class adams.data.spectrumfilter.SubRange: Returns the tip text for this property.
maxWaveNumberTipText() - Method in class adams.data.spectrumoutlier.Oscillation: Returns the tip text for this property.
MaxWaves - Class in adams.data.spectrumoutlier: Detects spectra that have too many wave numbers.
MaxWaves() - Constructor for class adams.data.spectrumoutlier.MaxWaves
maxWavesTipText() - Method in class adams.data.spectrumoutlier.MaxWaves: Returns the tip text for this property.
maxXTipText() - Method in class adams.data.conversion.ThreeWayDataToHeatmap: Returns the tip text for this property.
Mean - Class in adams.data.multifilter: Averages spectra into a single one.
Mean - Class in adams.data.spectrumfilter.detrend: Performs the correction using simply the mean.
Mean - Class in adams.data.threewayfeatures: Determines the mean of all the data values.
Mean() - Constructor for class adams.data.multifilter.Mean
Mean() - Constructor for class adams.data.spectrumfilter.detrend.Mean
Mean() - Constructor for class adams.data.threewayfeatures.Mean
MEAN - adams.flow.transformer.threewaydatamerge.CollapseX.StatisticType
MEAN_AMPLITUDE - Static variable in class adams.data.statistics.SpectrumStatistic
MEAN_DELTA_WAVE_NUMBER - Static variable in class adams.data.statistics.SpectrumStatistic
MeanSpectrumCosineSimilarityBasedThreshold - Class in adams.data.multispectrumoperation.outlierremoval: Calculates the mean spectrum from the incoming spectra and then calculates the cosine similarity between the mean spectrum and the spectra.
MeanSpectrumCosineSimilarityBasedThreshold() - Constructor for class adams.data.multispectrumoperation.outlierremoval.MeanSpectrumCosineSimilarityBasedThreshold
Median - Class in adams.data.multifilter: Averages spectra into a single one using the median.
Median - Class in adams.data.threewayfeatures: Determines the median of all the data values.
Median() - Constructor for class adams.data.multifilter.Median
Median() - Constructor for class adams.data.threewayfeatures.Median
MEDIAN - adams.flow.transformer.threewaydatamerge.CollapseX.StatisticType
MEDIAN_AMPLITUDE - Static variable in class adams.data.statistics.SpectrumStatistic
MEDIAN_DELTA_WAVE_NUMBER - Static variable in class adams.data.statistics.SpectrumStatistic
merge(Spectrum, Spectrum) - Static method in class adams.data.spectrum.SpectrumUtils: Merges the two spectrums.
merge(L1Point, L1Point) - Static method in class adams.data.threeway.L1PointUtils: Merges the two level 1 points.
merge(ThreeWayData[]) - Method in class adams.flow.transformer.threewaydatamerge.AbstractThreeWayDataMerge: Merges the data containers into a single one.
merge(List<Spectrum>) - Static method in class adams.data.spectrum.SpectrumUtils: Merges the given spectrums.
MERGE_CURRENT_WITH_OTHER - adams.flow.transformer.MergeSampleDataFromMap.MergeType
MERGE_OTHER_WITH_CURRENT - adams.flow.transformer.MergeSampleDataFromMap.MergeType
mergeReportsTipText() - Method in class adams.flow.transformer.ThreeWayDataMerge: Returns the tip text for this property.
MergeSampleDataFromMap - Class in adams.flow.transformer: Merges the passing through spectrum/sample data objects with the referenced map of sample data objects in storage (the map uses the sample ID as key).

See also:
adams.data.conversion.SampleDataArrayToMap

Input/output:
- accepts:
   adams.data.spectrum.Spectrum
   adams.data.sampledata.SampleData
- generates:
   adams.data.spectrum.Spectrum
   adams.data.sampledata.SampleData
MergeSampleDataFromMap() - Constructor for class adams.flow.transformer.MergeSampleDataFromMap
MergeSampleDataFromMap.MergeType - Enum in adams.flow.transformer: the type of merge operation to perform.
mergeTipText() - Method in class adams.flow.transformer.MergeSampleDataFromMap: Returns the tip text for this property.
mergeWith(SpectrumDisplay.DisplayPanel) - Method in class adams.flow.sink.SpectrumDisplay.DisplayPanel
message - Variable in class nz.ac.waikato.adams.webservice.rats.multispectrum.UploadResponse
message - Variable in class nz.ac.waikato.adams.webservice.rats.spectrum.UploadResponse
message - Variable in class nz.ac.waikato.adams.webservice.spectral.get.GetResponse
message - Variable in class nz.ac.waikato.adams.webservice.spectral.put.PutResponse
message - Variable in class nz.ac.waikato.adams.webservice.spectral.transform.TransformResponse
METADATA - Static variable in class adams.data.io.input.SoilCaresScannerSpectrumReader: the name of the metadata file.
metaDataFieldsTipText() - Method in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: Returns the tip text for this property.
metaDataPrefixTipText() - Method in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: Returns the tip text for this property.
metaDataValuesTipText() - Method in class adams.data.conversion.SpectrumToJson: Returns the tip text for this property.
metaDataValuesTipText() - Method in class adams.data.io.output.JsonSpectrumWriter: Returns the tip text for this property.
Min - Class in adams.data.threewayfeatures: Simply determines the smallest data value.
Min() - Constructor for class adams.data.threewayfeatures.Min
MIN_AMPLITUDE - adams.flow.transformer.SpectrumInfo.InfoType: the smallest amplitude.
MIN_AMPLITUDE - Static variable in class adams.data.statistics.SpectrumStatistic
MIN_DELTA_WAVE_NUMBER - Static variable in class adams.data.statistics.SpectrumStatistic
MIN_WAVE - adams.flow.transformer.SpectrumInfo.InfoType: the smallest wave number.
minAmplitudeTipText() - Method in class adams.data.io.input.SpecLibSpectrumReader: Returns the tip text for this property.
minAmplitudeTipText() - Method in class adams.data.spectrumfilter.Scale: Returns the tip text for this property.
minAmplitudeTipText() - Method in class adams.data.spectrumimage.AbstractSpectrumImageGeneratorWithRange: Returns the tip text for this property.
minimumTipText() - Method in class adams.data.cleaner.instance.MinMax: Returns the tip text for this property.
minimumTipText() - Method in class adams.data.cleaner.spectrum.MinMax: Returns the tip text for this property.
minimumTipText() - Method in class adams.data.compare.SpectrumCorrelation: Returns the tip text for this property.
minimumTipText() - Method in class adams.flow.transformer.predictioncheck.MinProbability: Returns the tip text for this property.
minimumValuesTipText() - Method in class adams.db.SpectrumConditionsMulti: Returns the tip text for this property.
minimumValueTipText() - Method in class adams.db.SpectrumConditionsSingle: Returns the tip text for this property.
MinMax - Class in adams.data.cleaner.instance: Checks an attribute in the Instance whether the value is within a certain range.
MinMax - Class in adams.data.cleaner.spectrum: Checks a field in the sample data whether the value is within a certain range.
MinMax - Class in adams.data.spectrumoutlier: Detects data containers where a report value is too high/low.
MinMax() - Constructor for class adams.data.cleaner.instance.MinMax
MinMax() - Constructor for class adams.data.cleaner.spectrum.MinMax
MinMax() - Constructor for class adams.data.spectrumoutlier.MinMax
minNumRows() - Method in class adams.gui.core.spreadsheettable.ExportSpectra: Returns the minimum number of rows that the plugin requires.
minNumRows() - Method in class adams.gui.visualization.instances.instancestable.ExportSpectra: Returns the minimum number of rows that the plugin requires.
minPLSTipText() - Method in class adams.opt.genetic.RonWeasley: Returns the tip text for this property.
MinProbability - Class in adams.flow.transformer.predictioncheck: Ensures that the highest probability on the class distribution is at least the specified value.
Adds a new boolean evaluation to the container with the name 'minprobability.passed'.
MinProbability() - Constructor for class adams.flow.transformer.predictioncheck.MinProbability
minSGTipText() - Method in class adams.opt.genetic.RonWeasley: Returns the tip text for this property.
minTipText() - Method in class adams.data.spectrumfilter.amplitudetransform.Triangle: Returns the tip text for this property.
minTipText() - Method in class adams.data.spectrumoutlier.MinMax: Returns the tip text for this property.
minTipText() - Method in class adams.data.threewayoutlier.ValueRange: Returns the tip text for this property.
minus(Spectrum, Spectrum) - Static method in class adams.data.spectrum.SpectrumUtils: Returns a spectrum that contains all the points that are in "a" but not in "b".
minWaveNumberTipText() - Method in class adams.data.io.input.SpecLibSpectrumReader: Returns the tip text for this property.
minWaveNumberTipText() - Method in class adams.data.spectrumfilter.SubRange: Returns the tip text for this property.
minWaveNumberTipText() - Method in class adams.data.spectrumoutlier.Oscillation: Returns the tip text for this property.
MinWaves - Class in adams.data.spectrumoutlier: Detects spectra that have too few wave numbers.
MinWaves() - Constructor for class adams.data.spectrumoutlier.MinWaves
minWavesTipText() - Method in class adams.data.spectrumoutlier.MinWaves: Returns the tip text for this property.
minXTipText() - Method in class adams.data.conversion.ThreeWayDataToHeatmap: Returns the tip text for this property.
mirrorsForUrlsTipText() - Method in class adams.db.mirrored.SpectralDbBackend: Returns the tip text for this property.
mirrorsTipText() - Method in class adams.db.mirrored.SpectralDbBackend: Returns the tip text for this property.
missingEvaluationTipText() - Method in class adams.data.evaluator.instance.AbstractEvaluator: Returns the tip text for this property.
missingEvaluationTipText() - Method in interface adams.data.evaluator.instance.Evaluator: Returns the tip text for this property.
missingValueColorTipText() - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Returns the tip text for this property.
modelActorTipText() - Method in class adams.data.spectrumfilter.WekaFilterToReport: Returns the tip text for this property.
modelActorTipText() - Method in class adams.flow.transformer.Cleaner: Returns the tip text for this property.
modelActorTipText() - Method in class adams.flow.transformer.Evaluator: Returns the tip text for this property.
modelActorTipText() - Method in class adams.flow.transformer.PostProcessor: Returns the tip text for this property.
modelActorTipText() - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Returns the tip text for this property.
modelFileTipText() - Method in class adams.data.spectrumfilter.WekaFilterToReport: Returns the tip text for this property.
modelFileTipText() - Method in class adams.flow.transformer.Cleaner: Returns the tip text for this property.
modelFileTipText() - Method in class adams.flow.transformer.Evaluator: Returns the tip text for this property.
modelFileTipText() - Method in class adams.flow.transformer.PostProcessor: Returns the tip text for this property.
modelFileTipText() - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Returns the tip text for this property.
modelLoadingTypeTipText() - Method in class adams.data.spectrumfilter.WekaFilterToReport: Returns the tip text for this property.
modelLoadingTypeTipText() - Method in class adams.flow.transformer.Cleaner: Returns the tip text for this property.
modelLoadingTypeTipText() - Method in class adams.flow.transformer.Evaluator: Returns the tip text for this property.
modelLoadingTypeTipText() - Method in class adams.flow.transformer.PostProcessor: Returns the tip text for this property.
modelLoadingTypeTipText() - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Returns the tip text for this property.
modelResetVariableTipText() - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Returns the tip text for this property.
modelStorageTipText() - Method in class adams.data.spectrumfilter.WekaFilterToReport: Returns the tip text for this property.
modelStorageTipText() - Method in class adams.flow.transformer.Cleaner: Returns the tip text for this property.
modelStorageTipText() - Method in class adams.flow.transformer.Evaluator: Returns the tip text for this property.
modelStorageTipText() - Method in class adams.flow.transformer.PostProcessor: Returns the tip text for this property.
modelStorageTipText() - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Returns the tip text for this property.
modeTipText() - Method in class adams.data.io.input.JCampDX2SpectrumReader: Returns the tip text for this property.
modifiedListener(boolean) - Method in class adams.data.spectrum.Spectrum: Method that gets notified about changes in the collection of data points.
modifiedListener(boolean) - Method in class adams.data.threeway.L1Point: Method that gets notified about changes in the collection of data points.
modifiedListener(boolean) - Method in class adams.data.threeway.ThreeWayData: Method that gets notified about changes in the collection of data points.
modifiedTipText() - Method in class adams.flow.transformer.SpectralAngleMapper: Gets the tip-text for the modified option.
moveFile(File, File, StorageQueueHandler) - Method in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: Moves the file and adds it to the queue if successful.
moveFile(File, File, StorageQueueHandler) - Method in class adams.flow.standalone.rats.LoadSpectrumFileOutput: Moves the file and adds it to the queue if successful.
MPSSpectrumHandler - Class in adams.gui.tools.previewbrowser: Displays the following spectrum types: mps

Valid options are:
MPSSpectrumHandler() - Constructor for class adams.gui.tools.previewbrowser.MPSSpectrumHandler
MPSSpectrumReader - Class in adams.data.io.input: Reads XRF spectra in MPS format.
MPSSpectrumReader() - Constructor for class adams.data.io.input.MPSSpectrumReader
MultiClassifierEvaluator - Class in adams.data.evaluator.instance: Multi-classifier based evaluator.
MultiClassifierEvaluator() - Constructor for class adams.data.evaluator.instance.MultiClassifierEvaluator
MultiColumnSpreadSheetSampleDataReader - Class in adams.data.io.input: Reads sample data from a spreadsheet (format depends on reader), reference values stored in the specified range of columns and the column headers representing the reference value names.
MultiColumnSpreadSheetSampleDataReader() - Constructor for class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader
MultiFilter - Class in adams.data.spectrumfilter: A meta-filter that runs multiple filters over the data.
The filter can be executed in two ways:
1. in series (the default):
Each filter runs on the data the previous filter generated.
2. in parallel:
Each filter is run on the original input data and the generated
outputs are merged into a single spectrum again.
MultiFilter - Class in adams.data.threewayfilter: A meta-filter that runs multiple filters over the data.
The filter can be executed in two ways:
1. in series (the default):
Each filter runs on the data the previous filter generated.
2. in parallel:
Each filter is run on the original input data and the generated
outputs are merged into a single 3-way data structure again.
MultiFilter() - Constructor for class adams.data.spectrumfilter.MultiFilter
MultiFilter() - Constructor for class adams.data.threewayfilter.MultiFilter
MultiplicativeScatterCorrection - Class in adams.data.spectrumfilter: Performs Multiplicative Scatter Correction.
Assumes that all spectra have the same wave numbers.
The 'pre-filter' gets only applied internally.
Intercept and slope get stored in the report, for each defined range (using prefixes Intercept. and Slope.)
MultiplicativeScatterCorrection() - Constructor for class adams.data.spectrumfilter.MultiplicativeScatterCorrection
Multiply - Class in adams.data.multifilter: Multiplies the amplitudes of two spectra with each other.
Multiply() - Constructor for class adams.data.multifilter.Multiply
MultiSheetIterator(MultiSheetSpreadSheetReader, File) - Constructor for class adams.data.io.input.RowWiseSpreadSheetSpectrumReader.MultiSheetIterator: Initializes the iterator.
MultiSpectrum - Class in adams.data.spectrum: For storing multiple spectra.
MultiSpectrum - Class in nz.ac.waikato.adams.webservice.rats.multispectrum: Java class for MultiSpectrum complex type.
MultiSpectrum() - Constructor for class adams.data.spectrum.MultiSpectrum: Default constructor.
MultiSpectrum() - Constructor for class nz.ac.waikato.adams.webservice.rats.multispectrum.MultiSpectrum
MultiSpectrumAdd - Class in adams.flow.transformer: Adds a value obtained from either the callable actor or from storage.
Callable actor takes precedent over storage, i.e., only if the callable actor cannot be located, is the storage name used.
MultiSpectrumAdd() - Constructor for class adams.flow.transformer.MultiSpectrumAdd
MultiSpectrumFilter - Class in adams.flow.transformer: Generates a single spectrum from a multi-spectrum using the specified filter.
For some filters that use several spectra, the order of the spectra is important.
MultiSpectrumFilter() - Constructor for class adams.flow.transformer.MultiSpectrumFilter
MultiSpectrumOperation - Class in adams.flow.transformer
MultiSpectrumOperation() - Constructor for class adams.flow.transformer.MultiSpectrumOperation
MultiSpectrumOutlierDetector - Class in adams.flow.transformer: Uses the specified multi-spectrum filter to obtain a single spectrum from the multi-spectrum and applies the outlier detector to it.
Any resulting detections get added to the multi-spectrum itself.
MultiSpectrumOutlierDetector() - Constructor for class adams.flow.transformer.MultiSpectrumOutlierDetector
MultiSpectrumPanel - Class in adams.gui.visualization.spectrum: A panel for viewing spectra in pages.
MultiSpectrumPanel() - Constructor for class adams.gui.visualization.spectrum.MultiSpectrumPanel
MultiSpectrumRemove - Class in adams.flow.transformer: Removes all spectra from the multi-spectrum that match the criteria.
MultiSpectrumRemove() - Constructor for class adams.flow.transformer.MultiSpectrumRemove
MultiSpectrumReportFilter - Class in adams.flow.transformer: Generates a single spectrum from a multi-spectrum using the specified filter.
MultiSpectrumReportFilter() - Constructor for class adams.flow.transformer.MultiSpectrumReportFilter
MultiSpectrumToSpectra - Class in adams.data.conversion: Generates an array of knir.data.spectrum.Spectrum from the incoming knir.data.spectrum.MultiSpectrum.
One can either transfer the data (all or partial) from the 'global' report to the sub-spectra or output the 'global' report as a separate (= first) spectrum with no spectral data points.

See also:
knir.data.conversion.SpectraToMultiSpectrum
MultiSpectrumToSpectra() - Constructor for class adams.data.conversion.MultiSpectrumToSpectra
MultiThreeWayDataFeatureGenerator - Class in adams.data.threewayfeatures: Applies multiple generators to the same 3-way data and merges the generated a feature vectors side-by-side.
MultiThreeWayDataFeatureGenerator() - Constructor for class adams.data.threewayfeatures.MultiThreeWayDataFeatureGenerator
MultiUpload - Class in adams.flow.webservice.multispectrum: Uploads a MultiSpectrum.
MultiUpload() - Constructor for class adams.flow.webservice.multispectrum.MultiUpload

N

names() - Method in class adams.flow.container.CleaningContainer: Returns all value names that can be used (theoretically).
names() - Method in class adams.flow.container.EvaluationContainer: Returns all value names that can be used (theoretically).
names() - Method in class adams.flow.container.PostProcessingContainer: Returns all value names that can be used (theoretically).
names() - Method in class adams.flow.container.ThreeWayDataModelContainer: Returns all value names that can be used (theoretically).
newComparator() - Method in class adams.data.spectrum.MultiSpectrum: Returns a new instance of the default comparator.
newComparator() - Method in class adams.data.spectrum.Spectrum: Returns a new instance of the default comparator.
newComparator() - Method in class adams.data.threeway.L1Point: Returns a new instance of the default comparator.
newComparator() - Method in class adams.data.threeway.ThreeWayData: Returns a new instance of the default comparator.
newConnectionTipText() - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Returns the tip text for this property.
newConnectionTipText() - Method in class adams.flow.transformer.BulkSpectrumDbWriter: Returns the tip text for this property.
newContainer(Comparable) - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: Returns a new container containing the given payload.
newContainer(Comparable) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataContainerManager: Returns a new container containing the given payload.
newContainerManager() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Returns the container manager to use.
newDataPoint(double, double) - Method in class adams.data.spectrumfilter.Autocorrelation: Creates a new DataPoint from the X/Y data.
newDataPoint(double, double) - Method in class adams.data.spectrumfilter.SAX: Creates a new data point from the X and Y values.
newDataPoint(int, double) - Method in class adams.data.spectrumfilter.Histogram: Creates a new data point from the X and Y values.
newDataPoint(DataPoint, double) - Method in class adams.data.spectrumfilter.FastWavelet: Creates a new DataPoint based on the old one and the new X value.
newDataPoint(DataPoint, double) - Method in class adams.data.spectrumfilter.SavitzkyGolay: Creates a new DataPoint based on the old one and the new X value.
newDataPoint(DataPoint, double) - Method in class adams.data.spectrumfilter.SimpleSavitzkyGolay: Creates a new DataPoint based on the old one and the new Y-value.
newDataPoint(Point2D) - Method in class adams.data.spectrumfilter.LOWESS: Creates a new DataPoint from the smoothed one.
newDataPoint(List<DataPoint>, int, double) - Method in class adams.data.spectrumfilter.FastWavelet: Creates a new DataPoint based on the index and the new X value.
newDataPoint(List<DataPoint>, int, double) - Method in class adams.data.spectrumfilter.FFT: Creates a new DataPoint based on the index and the new Y value.
newFormatSeparatorTipText() - Method in class adams.data.multifilter.Fusion: Returns the tip text for this property.
newFormatTipText() - Method in class adams.data.multifilter.AbstractFormatsBasedMultiSpectrumFilter: Returns the tip text for this property.
newFormatTipText() - Method in class adams.data.multifilter.Add: Returns the tip text for this property.
newFormatTipText() - Method in class adams.data.multifilter.Atan2: Returns the tip text for this property.
newFormatTipText() - Method in class adams.data.multifilter.Average: Returns the tip text for this property.
newFormatTipText() - Method in class adams.data.multifilter.Divide: Returns the tip text for this property.
newFormatTipText() - Method in class adams.data.multifilter.Fusion: Returns the tip text for this property.
newFormatTipText() - Method in class adams.data.multifilter.Mean: Returns the tip text for this property.
newFormatTipText() - Method in class adams.data.multifilter.Median: Returns the tip text for this property.
newFormatTipText() - Method in class adams.data.multifilter.Multiply: Returns the tip text for this property.
newFormatTipText() - Method in class adams.data.multifilter.Subtract: Returns the tip text for this property.
newImage(int, int) - Method in class adams.data.spectrumimage.AbstractSpectrumImageGenerator: Creates a new image.
newInstance() - Method in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: Returns a new instance of the report class in use.
newInstance() - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Returns a new instance of the report class in use.
newInstance() - Method in class adams.data.io.input.SimpleCSVSampleDataReader: Returns a new instance of the report class in use.
newInstance() - Method in class adams.data.io.input.SimpleJsonSampleDataReader: Returns a new instance of the report class in use.
newInstance() - Method in class adams.data.io.input.SimpleSampleDataReader: Returns a new instance of the report class in use.
newInstance() - Method in class adams.data.io.input.SpecLibSampleDataReader: Returns a new instance of the report class in use.
newJob(int, int[], Instances, Instances) - Method in class adams.opt.genetic.RonWeasley: Creates a new Job instance.
newOptionManager() - Method in class adams.data.spectrum.AbstractSpectrumComparator: Returns a new instance of the option manager.
newPanel() - Method in class adams.flow.sink.SpectrumDisplay: Creates the panel to display in the dialog.
newPanel() - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Creates the panel to display in the dialog.
newPanel() - Method in class adams.gui.selection.SelectSpectrumDialog: Returns a new instance of the panel to use in the GUI.
newPanel() - Method in class adams.gui.visualization.spectrum.SampleDataFactory.Dialog: Returns a new tabbed pane instance.
newPanel(ThreeWayData) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Creates a new panel and configures it.
newPoint() - Method in class adams.data.spectrum.MultiSpectrum: Returns a new instance of a DataContainer point.
newPoint() - Method in class adams.data.spectrum.Spectrum: Returns a new instance of a sequence point.
newPoint() - Method in class adams.data.threeway.L1Point: Returns a new instance of a DataContainer point.
newPoint() - Method in class adams.data.threeway.ThreeWayData: Returns a new instance of a DataContainer point.
newReport() - Method in class adams.flow.transformer.SetSampleDataValue: Creates a new, empty report if the MutableReportHandler is missing one.
newReportFileChooser() - Method in class adams.gui.visualization.spectrum.SampleDataFactory.Table: Returns the file chooser to use for exporting the reports.
NewSpectrum - Class in adams.flow.source: Creates an empty spectrum.
NewSpectrum() - Constructor for class adams.flow.source.NewSpectrum
newTab() - Method in class adams.gui.visualization.spectrum.MultiSpectrumPanel: Adds a new tab.
newTab(ThreeWayData, String) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Adds a new tab using the heatmap and adds the comment to the log.
newTable(ReportFactory.Model) - Method in class adams.gui.visualization.spectrum.SampleDataFactory.Panel: Creates a new table.
newTableModel() - Method in class adams.gui.selection.SelectSpectrumPanel: Returns an empty table model.
newWindow(boolean) - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Opens a new window.
newZoomPaintlet() - Method in class adams.gui.visualization.spectrum.SpectrumZoomOverviewPanel: Creates a new zoom paintlet.
next() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader.ChunkedSheetIterator: Returns the next element in the iteration.
next() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader.MultiSheetIterator: Returns the next element in the iteration.
next() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader.SingleSheetIterator: Returns the next element in the iteration.
NIRSpectrumHandler - Class in adams.gui.tools.previewbrowser: Displays the following spectrum types: nir

Valid options are:
NIRSpectrumHandler() - Constructor for class adams.gui.tools.previewbrowser.NIRSpectrumHandler
NIRSpectrumReader - Class in adams.data.io.input: Reads spectra in FOSS NIR format.
NIRSpectrumReader() - Constructor for class adams.data.io.input.NIRSpectrumReader
NIRSpectrumWriter - Class in adams.data.io.output: Writer that stores spectrums in the FOSS .nir Format.
NIRSpectrumWriter() - Constructor for class adams.data.io.output.NIRSpectrumWriter
noAdditionalFieldsPrefixTipText() - Method in class adams.data.instances.AbstractSpectrumInstanceGenerator: Returns the tip text for this property.
noCopyTipText() - Method in class adams.flow.transformer.AbstractInPlaceSpectrumTransformer: Returns the tip text for this property.
noCopyTipText() - Method in class adams.flow.transformer.Evaluator: Returns the tip text for this property.
noCopyTipText() - Method in class adams.flow.transformer.PredictionCheck: Returns the tip text for this property.
noCopyTipText() - Method in class adams.flow.transformer.SetEvaluationMetaData: Returns the tip text for this property.
Noise_bySmoothing(Spectrum) - Method in class adams.data.sampledata.SignalToNoiseRatio: Return the RMSE noise value, as a distance from the smoothed spectrum
NONE - adams.gui.visualization.spectrum.SpectrumPaintlet.MarkerShape: nothing.
nonMirroredBackendTipText() - Method in class adams.db.mirrored.SpectralDbBackend: Returns the tip text for this property.
normalizeByLiveTimeTipText() - Method in class adams.data.io.input.MPSSpectrumReader: Returns the tip text for this property.
normalizeTipText() - Method in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: Returns the tip text for this property.
normalizeTipText() - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Returns the tip text for this property.
notesTipText() - Method in class adams.data.instances.AbstractSpectrumBasedInstanceGenerator: Returns the tip text for this property.
notesTipText() - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Returns the tip text for this property.
notesTipText() - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Returns the tip text for this property.
Npps_offset - Static variable in class adams.data.io.input.foss.FossHelper
NPT - Static variable in class adams.data.io.input.opus.OpusBlockHelper: the NPT character sequence.
NSeg_offset - Static variable in class adams.data.io.input.foss.FossHelper
nthPointsTipText() - Method in class weka.filters.unsupervised.attribute.SegmentedDownSample: Returns the tip text for this property.
nthPointTipText() - Method in class adams.data.threewayfeatures.Flatten: Returns the tip text for this property.
Null - Class in adams.gui.visualization.threewaydata.heatmapviewer.overlay: Dummy overlay, does nothing.
Null() - Constructor for class adams.gui.visualization.threewaydata.heatmapviewer.overlay.Null
NullEvaluator - Class in adams.data.evaluator.instance: Dummy evaluator, which always return 1.0 as evaluation result.
NullEvaluator() - Constructor for class adams.data.evaluator.instance.NullEvaluator
NUM_WAVES - adams.flow.transformer.SpectrumInfo.InfoType: the number of waves.
numAdditionalTipText() - Method in class adams.data.spectrumfilter.PadPower2: Returns the tip text for this property.
numAttributesTipText() - Method in class weka.filters.unsupervised.attribute.BestBySLR: Returns the tip text for this property.
numatts - Variable in class adams.opt.genetic.RonWeasley
number - Variable in class nz.ac.waikato.adams.webservice.rats.multispectrum.Wave
number - Variable in class nz.ac.waikato.adams.webservice.rats.spectrum.Wave
number - Variable in class nz.ac.waikato.adams.webservice.spectral.get.Wave
number - Variable in class nz.ac.waikato.adams.webservice.spectral.put.Wave
number - Variable in class nz.ac.waikato.adams.webservice.spectral.transform.Wave
NUMBER_OF_POINTS - Static variable in class adams.data.statistics.SpectrumStatistic
numberInSubsetTipText() - Method in class adams.data.spectrumfilter.KennardStone: Tip text for this property
NUMERIC - nz.ac.waikato.adams.webservice.rats.multispectrum.DataType
NUMERIC - nz.ac.waikato.adams.webservice.rats.spectrum.DataType
NUMERIC - nz.ac.waikato.adams.webservice.spectral.get.DataType
NUMERIC - nz.ac.waikato.adams.webservice.spectral.put.DataType
NUMERIC - nz.ac.waikato.adams.webservice.spectral.transform.DataType
numFoldsTipText() - Method in class adams.data.cleaner.instance.RemoveOutliers: Returns the tip text for this property.
numFoldsTipText() - Method in class adams.data.evaluator.instance.EnsembleEvaluator: Returns the tip text for this property.
numFoldsTipText() - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Returns the tip text for this property.
numIterationsTipText() - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Returns the tip text for this property.
numNeighborsTipText() - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Returns the tip text for this property.
numNeighborsTipText() - Method in class adams.data.evaluator.instance.CrossValidatedPrediction: Returns the tip text for this property.
numNeighborsTipText() - Method in class adams.data.evaluator.instance.DistanceToCenter: Returns the tip text for this property.
numPointsTipText() - Method in class adams.data.spectrumfilter.AndrewsCurves: Returns the tip text for this property.
numPointsTipText() - Method in class adams.data.spectrumfilter.CenterBurst: Returns the tip text for this property.
numPointsTipText() - Method in class weka.filters.unsupervised.attribute.SavitzkyGolayRange: Returns the tip text for this property.
numPointsTipText() - Method in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: Returns the tip text for this property.
numThreadsTipText() - Method in class adams.data.cleaner.instance.RemoveOutliers: Returns the tip text for this property.
numThreadsTipText() - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Returns the tip text for this property.
nz.ac.waikato.adams.webservice.rats.multispectrum - package nz.ac.waikato.adams.webservice.rats.multispectrum
nz.ac.waikato.adams.webservice.rats.spectrum - package nz.ac.waikato.adams.webservice.rats.spectrum
nz.ac.waikato.adams.webservice.spectral.get - package nz.ac.waikato.adams.webservice.spectral.get
nz.ac.waikato.adams.webservice.spectral.put - package nz.ac.waikato.adams.webservice.spectral.put
nz.ac.waikato.adams.webservice.spectral.transform - package nz.ac.waikato.adams.webservice.spectral.transform

O

ObjectFactory - Class in nz.ac.waikato.adams.webservice.rats.multispectrum: This object contains factory methods for each Java content interface and Java element interface generated in the nz.ac.waikato.adams.webservice.rats.multispectrum package.
ObjectFactory - Class in nz.ac.waikato.adams.webservice.rats.spectrum: This object contains factory methods for each Java content interface and Java element interface generated in the nz.ac.waikato.adams.webservice.rats.spectrum package.
ObjectFactory - Class in nz.ac.waikato.adams.webservice.spectral.get: This object contains factory methods for each Java content interface and Java element interface generated in the nz.ac.waikato.adams.webservice.spectral.get package.
ObjectFactory - Class in nz.ac.waikato.adams.webservice.spectral.put: This object contains factory methods for each Java content interface and Java element interface generated in the nz.ac.waikato.adams.webservice.spectral.put package.
ObjectFactory - Class in nz.ac.waikato.adams.webservice.spectral.transform: This object contains factory methods for each Java content interface and Java element interface generated in the nz.ac.waikato.adams.webservice.spectral.transform package.
ObjectFactory() - Constructor for class nz.ac.waikato.adams.webservice.rats.multispectrum.ObjectFactory: Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: nz.ac.waikato.adams.webservice.rats.multispectrum
ObjectFactory() - Constructor for class nz.ac.waikato.adams.webservice.rats.spectrum.ObjectFactory: Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: nz.ac.waikato.adams.webservice.rats.spectrum
ObjectFactory() - Constructor for class nz.ac.waikato.adams.webservice.spectral.get.ObjectFactory: Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: nz.ac.waikato.adams.webservice.spectral.get
ObjectFactory() - Constructor for class nz.ac.waikato.adams.webservice.spectral.put.ObjectFactory: Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: nz.ac.waikato.adams.webservice.spectral.put
ObjectFactory() - Constructor for class nz.ac.waikato.adams.webservice.spectral.transform.ObjectFactory: Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: nz.ac.waikato.adams.webservice.spectral.transform
offlineTipText() - Method in class adams.data.io.input.AbstractSampleDataReader: Returns the tip text for this property.
offset - Variable in class adams.data.io.input.opus.OpusBlockHelper.BlockDefinition: the offset.
offsetTipText() - Method in class adams.data.spectrumfilter.EquiDistance: Returns the tip text for this property.
offsetXTipText() - Method in class adams.data.threewayfilter.Shift: Returns the tip text for this property.
offsetXTipText() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Returns the tip text for this property.
offsetYTipText() - Method in class adams.data.threewayfilter.Shift: Returns the tip text for this property.
offsetYTipText() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Returns the tip text for this property.
offsetZTipText() - Method in class adams.data.threewayfilter.Shift: Returns the tip text for this property.
onlyDummiesTipText() - Method in class adams.db.AbstractSpectrumConditions: Returns the tip text for this property.
onlyWarningTipText() - Method in class adams.flow.transformer.MultiSpectrumOutlierDetector: Returns the tip text for this property.
OpenContainingFolder - Class in adams.gui.visualization.threewaydata.heatmapviewer.multipageaction: Opens the folder in the system's file browser that this flow is stored in.
OpenContainingFolder() - Constructor for class adams.gui.visualization.threewaydata.heatmapviewer.multipageaction.OpenContainingFolder
OPERATION_MEASURESAMPLE - Static variable in class adams.data.io.input.opus.OpusBlockHelper: the operation containing the sample ID.
operationTipText() - Method in class adams.data.io.input.OpusSpectrumReaderExt: Returns the tip text for this property.
operationTipText() - Method in class adams.flow.transformer.MultiSpectrumOperation: Returns the tip text for this property.
operatorTipText() - Method in class adams.data.io.output.NIRSpectrumWriter: Returns the tip text for this property.
OPTION_OUTPUTDIR - Static variable in class adams.data.io.input.AbstractSpectrumReader
OpusBlockHelper - Class in adams.data.io.input.opus: Analyzer for Opus file blocks in the header.
OpusBlockHelper() - Constructor for class adams.data.io.input.opus.OpusBlockHelper
OpusBlockHelper.Block - Class in adams.data.io.input.opus: Convenience class for handling blocks.
OpusBlockHelper.BlockDefinition - Class in adams.data.io.input.opus: Container class for Opus block definitions in the header.
OpusBlockHelper.CommandlineData - Class in adams.data.io.input.opus: Encapsulates and parses a commandline string.
OpusSpectrumExtHandler - Class in adams.gui.tools.previewbrowser: Displays the following spectrum types: *

Valid options are:
OpusSpectrumExtHandler() - Constructor for class adams.gui.tools.previewbrowser.OpusSpectrumExtHandler
OpusSpectrumHandler - Class in adams.gui.tools.previewbrowser: Displays the following spectrum types: *

Valid options are:
OpusSpectrumHandler() - Constructor for class adams.gui.tools.previewbrowser.OpusSpectrumHandler
OpusSpectrumReader - Class in adams.data.io.input: Reads spectra in OPUS format.
OpusSpectrumReader() - Constructor for class adams.data.io.input.OpusSpectrumReader
OpusSpectrumReaderExt - Class in adams.data.io.input: Reads spectra in OPUS format (extended version).
OpusSpectrumReaderExt() - Constructor for class adams.data.io.input.OpusSpectrumReaderExt
OrphanedSampleDataConditions - Class in adams.db: Allows the retrieval of sample IDs of orphaned sample data, ie no spectrum available.
OrphanedSampleDataConditions() - Constructor for class adams.db.OrphanedSampleDataConditions
OrphanedSampleDataIdSupplier - Class in adams.flow.source: Retrieves sample IDs of sample data that have no spectra associated.
OrphanedSampleDataIdSupplier() - Constructor for class adams.flow.source.OrphanedSampleDataIdSupplier
Oscillation - Class in adams.data.spectrumoutlier: Detects spectra that have an oscillating signal.
Computes the correlation coefficient between original spectrum and a LOWESS-smoothed one, using the defined wave number range.
If the correlation coefficient falls below the specified threshold, it is considered an outlier.
Oscillation() - Constructor for class adams.data.spectrumoutlier.Oscillation
OutlierRemoval - Class in adams.data.multispectrumoperation: Applies the specified outlier removal scheme to the multi-spectrum to remove potential outliers.
OutlierRemoval() - Constructor for class adams.data.multispectrumoperation.OutlierRemoval
outlierRemovalTipText() - Method in class adams.data.multispectrumoperation.OutlierRemoval: Returns the tip text for this property.
output() - Method in class adams.flow.control.InstanceCleaner: Returns the generated token.
output() - Method in class adams.flow.control.SpectrumCleaner: Returns the generated token.
output() - Method in class adams.flow.standalone.rats.WSMultiSpectrumReception: Returns the received data.
output() - Method in class adams.flow.standalone.rats.WSSpectrumReception: Returns the received data.
output() - Method in class adams.flow.transformer.SpectrumFeatureGenerator: Returns the generated token.
output() - Method in class adams.flow.transformer.SpectrumInfo: Returns the generated token.
output() - Method in class adams.flow.transformer.ThreeWayDataFeatureGenerator: Returns the generated token.
outputArrayTipText() - Method in class adams.flow.source.OrphanedSampleDataIdSupplier: Returns the tip text for this property.
outputArrayTipText() - Method in class adams.flow.transformer.SampleDataFileReader: Returns the tip text for this property.
outputContainerTipText() - Method in class adams.flow.transformer.InstanceGenerator: Returns the tip text for this property.
outputContainerTipText() - Method in class adams.flow.transformer.PostProcessor: Returns the tip text for this property.
outputContainerTipText() - Method in class adams.flow.transformer.SpectrumDbWriter: Returns the tip text for this property.
outputMultiSpectrumTipText() - Method in class adams.flow.transformer.SpectrumFileReader: Returns the tip text for this property.
outputReportTipText() - Method in class adams.data.conversion.MultiSpectrumToSpectra: Returns the tip text for this property.
outputReportTipText() - Method in class adams.flow.transformer.SpectrumFileWriter: Returns the tip text for this property.
outputSampleDataTipText() - Method in class adams.data.io.output.JCampDX2SpectrumWriter: Returns the tip text for this property.
outputSampleDataTipText() - Method in class adams.data.io.output.SimpleSpectrumWriter: Returns the tip text for this property.
outputSampleDataTipText() - Method in class adams.data.io.output.SimpleXYZWriter: Returns the tip text for this property.
outputTipText() - Method in class adams.flow.sink.SpectrumImageWriter: Returns the tip text for this property.
overlapFactorTipText() - Method in class adams.data.conversion.SpectrumToBufferedImage: Returns the tip text for this property.
overlapFactorTipText() - Method in class adams.data.spectrumimage.Spectrogram: Returns the tip text for this property.
overlaysTipText() - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Returns the tip text for this property.
overrideSerializedFileTipText() - Method in class adams.data.cleaner.instance.AbstractSerializableCleaner: Returns the tip text for this property.
overrideSerializedFileTipText() - Method in class adams.data.cleaner.spectrum.AbstractSerializableCleaner: Returns the tip text for this property.
overrideSerializedFileTipText() - Method in class adams.data.evaluator.instance.AbstractSerializableEvaluator: Returns the tip text for this property.
overrideSerializedFileTipText() - Method in class adams.data.postprocessor.instances.AbstractSerializablePostProcessor: Returns the tip text for this property.
overrideSerializedFileTipText() - Method in class adams.data.spectrumfilter.AbstractSerializableFilter: Returns the tip text for this property.
overwriteExistingTipText() - Method in interface adams.flow.transformer.SpectrumDatabaseWriter: Returns the tip text for this property.
overwriteExistingTipText() - Method in class adams.flow.transformer.SpectrumDbWriter: Returns the tip text for this property.
OwnedByRatsMultiSpectrumServiceWS - Interface in adams.flow.webservice.multispectrum: Interface for classes that are owned by RatsMultiSpectrumServiceWS.
OwnedByRatsSpectrumServiceWS - Interface in adams.flow.webservice.spectrum: Interface for classes that are owned by RatsSpectrumServiceWS.
OwnedBySpectralGetServiceWS - Interface in adams.flow.webservice: Interface for classes that are owned by SpectralGetServiceWS.
OwnedBySpectralPutServiceWS - Interface in adams.flow.webservice: Interface for classes that are owned by SpectralPutServiceWS.
OwnedBySpectralTransformServiceWS - Interface in adams.flow.webservice: Interface for classes that are owned by SpectralTransformServiceWS.

P

pad(Spectrum, int, boolean, float, float) - Static method in class adams.data.spectrum.SpectrumUtils: Pads the spectrum either on left or right to have at least the specified number of points.
paddingTypeTipText() - Method in class adams.data.spectrumfilter.PadPower2: Returns the tip text for this property.
padLeftTipText() - Method in class adams.data.spectrumfilter.PadPower2: Returns the tip text for this property.
PadPower2 - Class in adams.data.spectrumfilter: Pads the spectrum to a power of 2 number of wave numbers.
PadPower2() - Constructor for class adams.data.spectrumfilter.PadPower2
paintAllTipText() - Method in class adams.gui.visualization.spectrum.SpectrumPaintlet: Returns the tip text for this property.
paintletTipText() - Method in class adams.flow.sink.SpectrumDisplay: Returns the tip text for this property.
paintOverlay(ImagePanel.PaintPanel, Graphics) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractThreeWayDataOverlay: Paints the overlay over the image.
Panel() - Constructor for class adams.gui.visualization.spectrum.HistogramFactory.Panel
Panel() - Constructor for class adams.gui.visualization.spectrum.SampleDataFactory.Panel: Initializes the tabbed pane with not reports.
ParafacLossHistory - Class in adams.flow.transformer.threewaydatatrain: Turns the PARAFAC loss history into a spreadsheet.
ParafacLossHistory() - Constructor for class adams.flow.transformer.threewaydatatrain.ParafacLossHistory
PARALLEL_6250 - adams.data.io.output.foss.FossOutputHelper.InstrumentHeader.InstrumentType
PARALLEL_6250V - adams.data.io.output.foss.FossOutputHelper.InstrumentHeader.InstrumentType
parallelAndMergeTipText() - Method in class adams.data.spectrumfilter.MultiFilter: Returns the tip text for this property.
parallelAndMergeTipText() - Method in class adams.data.threewayfilter.MultiFilter: Returns the tip text for this property.
parse() - Method in class adams.data.io.input.opus.OpusBlockHelper.CommandlineData: Parses the commandline.
parse() - Method in class adams.data.io.input.SPCSpectrumReader.AbstractParser: Parses the data.
parse(File) - Method in class adams.data.io.input.ASCSpectrumReader.ParsedFile: Parses the given file.
parse(String) - Method in class adams.data.io.input.ASCSpectrumReader.ParsedFile: Parses the given string.
parse(String) - Method in class adams.data.spectrum.SpectrumPoint: Parses a string and instantiates a sequence point of it.
parse(List<String>) - Method in class adams.data.io.input.DPTSpectrumReader.ParsedFile: Parses the given lines.
parseData() - Method in class adams.data.io.input.SPCSpectrumReader.AbstractParser: Parses the spectral data.
parseData() - Method in class adams.data.io.input.SPCSpectrumReader.FileParser: Parses the spectral data.
parseData() - Method in class adams.data.io.input.SPCSpectrumReader.SubFileParser: Parses the spectral data.
ParsedFile() - Constructor for class adams.data.io.input.ASCSpectrumReader.ParsedFile
ParsedFile() - Constructor for class adams.data.io.input.DPTSpectrumReader.ParsedFile
parseFooter() - Method in class adams.data.io.input.SPCSpectrumReader.AbstractParser: Parses the footer data (if any).
parseFooter() - Method in class adams.data.io.input.SPCSpectrumReader.FileParser: Parses the footer data (if any).
parseHeader() - Method in class adams.data.io.input.SPCSpectrumReader.AbstractParser: Parses the header data.
parseHeader() - Method in class adams.data.io.input.SPCSpectrumReader.FileParser: Parses the header data.
parseHeader() - Method in class adams.data.io.input.SPCSpectrumReader.SubFileParser: Parses the header data.
parseProperties(Properties) - Static method in class adams.data.sampledata.SampleData: Parses the properties (generated with the toProperties() method) and generates a sample data object from it.
parseProperties(Properties) - Static method in class adams.data.threewayreport.ThreeWayReport: Parses the properties (generated with the toProperties() method) and generates a sample data object from it.
parseReport(String) - Static method in class adams.data.sampledata.SampleData: Parses the string generated by the toString() method.
parseReport(String) - Static method in class adams.data.threewayreport.ThreeWayReport: Parses the string generated by the toString() method.
parseWaveNo(String, Map<String, Float>) - Method in class adams.data.io.input.ScioLabExportSpectrumReader: Parses/collects the wave number strings (eg '2 + 740') and their float representation.
PASSED - Static variable in class adams.flow.transformer.predictioncheck.MinProbability: the suffix for the passed flag.
PassThrough - Class in adams.data.cleaner.instance: Dummy cleaner that flags everything as clean.
PassThrough - Class in adams.data.cleaner.spectrum: Dummy cleaner that flags everything as clean.
PassThrough - Class in adams.data.multireportfilter: Dummy filter, does nothing.
PassThrough - Class in adams.data.multispectrumoperation.outlierremoval: Dummy, just passes through the data.
PassThrough - Class in adams.data.multispectrumoperation: Does nothing, passes through the data.
PassThrough - Class in adams.data.spectrumfilter.amplitudetransform: Dummy transformer, which only returns a copy of the data point.
PassThrough - Class in adams.flow.transformer.predictioncheck: Does nothing, just passes the container through.
PassThrough - Class in adams.flow.transformer.threewaydatatrain: Does nothing.
PassThrough() - Constructor for class adams.data.cleaner.instance.PassThrough
PassThrough() - Constructor for class adams.data.cleaner.spectrum.PassThrough
PassThrough() - Constructor for class adams.data.multireportfilter.PassThrough
PassThrough() - Constructor for class adams.data.multispectrumoperation.outlierremoval.PassThrough
PassThrough() - Constructor for class adams.data.multispectrumoperation.PassThrough
PassThrough() - Constructor for class adams.data.spectrumfilter.amplitudetransform.PassThrough
PassThrough() - Constructor for class adams.flow.transformer.predictioncheck.PassThrough
PassThrough() - Constructor for class adams.flow.transformer.threewaydatatrain.PassThrough
pca() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Performs PCA on the visible spectra.
PCA - Class in adams.data.spectrumanalysis: Performs principal components analysis.
PCA - Class in adams.data.spectrumfilter: Turns the spectra internally into instances and transforms them using principal component analysis (PCA).
The generated output is then converted back into spectra.
Only works as batch filter, not in single spectrum mode.
PCA() - Constructor for class adams.data.spectrumanalysis.PCA
PCA() - Constructor for class adams.data.spectrumfilter.PCA
PCATipText() - Method in class adams.data.spectrumanalysis.PCA: Returns the tip text for this property.
performBuild(Instances) - Method in class adams.data.evaluator.instance.AbstractEvaluator: Builds the evaluator.
performBuild(Instances) - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Builds the evaluator.
performBuild(Instances) - Method in class adams.data.evaluator.instance.CrossValidatedPrediction: Builds the evaluator.
performBuild(Instances) - Method in class adams.data.evaluator.instance.DistanceToCenter: Builds the evaluator.
performBuild(Instances) - Method in class adams.data.evaluator.instance.DistanceToClosest: Builds the evaluator.
performBuild(Instances) - Method in class adams.data.evaluator.instance.EnsembleEvaluator: Builds the evaluator.
performBuild(Instances) - Method in class adams.data.evaluator.instance.FakeEvaluator: Builds the evaluator.
performBuild(Instances) - Method in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: Builds the evaluator.
performBuild(Instances) - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Builds the evaluator.
performBuild(Instances) - Method in class adams.data.evaluator.instance.NullEvaluator: Builds the evaluator.
performBuild(Instances) - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Builds the evaluator.
performCheck(Spectrum) - Method in class adams.data.cleaner.spectrum.AbstractCleaner: Performs the actual check.
performCheck(Spectrum) - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Performs the check.
performCheck(Spectrum) - Method in class adams.data.cleaner.spectrum.MinMax: Performs the actual check.
performCheck(Spectrum) - Method in class adams.data.cleaner.spectrum.PassThrough: Performs the actual check.
performCheck(Instance) - Method in class adams.data.cleaner.instance.AbstractCleaner: Performs the actual check.
performCheck(Instance) - Method in class adams.data.cleaner.instance.IQRCleaner: Performs the actual check.
performCheck(Instance) - Method in class adams.data.cleaner.instance.MinMax: Performs the actual check.
performCheck(Instance) - Method in class adams.data.cleaner.instance.PassThrough: Performs the actual check.
performCheck(Instance) - Method in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: Performs the actual check.
performCheck(Instance) - Method in class adams.data.cleaner.instance.RemoveOutliers: Performs the actual check.
performClean(Instances) - Method in class adams.data.cleaner.instance.AbstractCleaner: Performs the actual check.
performClean(Instances) - Method in class adams.data.cleaner.instance.IQRCleaner: Clean Instances
performClean(Instances) - Method in class adams.data.cleaner.instance.MinMax: Clean Instances.
performClean(Instances) - Method in class adams.data.cleaner.instance.PassThrough: Return original Instances.
performClean(Instances) - Method in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: Clean Instances.
performClean(Instances) - Method in class adams.data.cleaner.instance.RemoveOutliers: Performs the actual check.
performEvaluate(Instance) - Method in class adams.data.evaluator.instance.AbstractEvaluator: Performs the actual evaluation.
performEvaluate(Instance) - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Performs the actual evaluation.
performEvaluate(Instance) - Method in class adams.data.evaluator.instance.CrossValidatedPrediction: Performs the actual evaluation.
performEvaluate(Instance) - Method in class adams.data.evaluator.instance.DistanceToCenter: Performs the actual evaluation.
performEvaluate(Instance) - Method in class adams.data.evaluator.instance.DistanceToClosest: Performs the actual evaluation.
performEvaluate(Instance) - Method in class adams.data.evaluator.instance.EnsembleEvaluator: Performs the actual evaluation.
performEvaluate(Instance) - Method in class adams.data.evaluator.instance.FakeEvaluator: Performs the actual evaluation.
performEvaluate(Instance) - Method in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: Performs the actual evaluation.
performEvaluate(Instance) - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Get predictions for each of the models.
performEvaluate(Instance) - Method in class adams.data.evaluator.instance.NullEvaluator: Performs the actual evaluation.
performEvaluate(Instance) - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Performs the actual evaluation.
performMultiEvaluate(Instance) - Method in class adams.data.evaluator.instance.AbstractEvaluator: Performs the actual evaluation, allowing return of multiple evaluation metrics.
performMultiEvaluate(Instance) - Method in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: Performs the actual evaluation, allowing return of multiple evaluation metrics.
performMultiEvaluate(Instance) - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Performs the actual evaluation, allowing return of multiple evaluation metrics.
performPostProcess(Instance) - Method in class adams.data.postprocessor.instances.AbstractPostProcessor: Performs the actual postprocessing.
performPostProcess(Instance) - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Performs the actual postprocessing.
performPostProcess(Instance) - Method in class adams.data.postprocessor.instances.WekaFilter: Performs the actual postprocessing.
performPostProcess(Instances) - Method in class adams.data.postprocessor.instances.AbstractPostProcessor: Performs the actual postprocessing.
performPostProcess(Instances) - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Performs the actual postprocessing.
performPostProcess(Instances) - Method in class adams.data.postprocessor.instances.WekaFilter: Performs the actual postprocessing.
PickByIndex - Class in adams.data.multifilter: Extracts the specified sub-spectrum.
PickByIndex() - Constructor for class adams.data.multifilter.PickByIndex
PickByReportValue - Class in adams.data.multifilter: Extracts the first sub-spectrum that matches the condition for the field.
PickByReportValue() - Constructor for class adams.data.multifilter.PickByReportValue
PLACEHOLDER_AMPLITUDE - Static variable in class adams.data.spectrumfilter.AmplitudeExpression: the placeholder for the amplitude.
PLACEHOLDER_AMPLITUDE - Static variable in class adams.data.spectrumfilter.WaveNumberExpression: the placeholder for the amplitude.
PLACEHOLDER_INDEX - Static variable in class adams.data.spectrumfilter.AmplitudeExpression: the placeholder for the index.
PLACEHOLDER_INDEX - Static variable in class adams.data.spectrumfilter.WaveNumberExpression: the placeholder for the index.
PLACEHOLDER_SIZE - Static variable in class adams.data.spectrumfilter.AmplitudeExpression: the placeholder for the total number of wave numbers.
PLACEHOLDER_SIZE - Static variable in class adams.data.spectrumfilter.WaveNumberExpression: the placeholder for the total number of wave numbers.
PLACEHOLDER_WAVENUMBER - Static variable in class adams.data.spectrumfilter.AmplitudeExpression: the placeholder for the wave number.
PLACEHOLDER_WAVENUMBER - Static variable in class adams.data.spectrumfilter.WaveNumberExpression: the placeholder for the wave number.
PLF - Static variable in class adams.data.io.input.opus.OpusBlockHelper: the PLF character sequence.
plotUpdaterTipText() - Method in class adams.flow.sink.SpectrumDisplay: Returns the tip text for this property.
pls() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Performs PLS on the visible spectra.
PLS - Class in adams.data.spectrumanalysis: Performs partial least squares analysis.
PLS - Class in adams.data.spectrumfilter: Turns the spectra internally into instances and transforms them using the specified PLS algorithm.
PLS() - Constructor for class adams.data.spectrumanalysis.PLS
PLS() - Constructor for class adams.data.spectrumfilter.PLS
PLSTipText() - Method in class adams.data.spectrumanalysis.PLS: Returns the tip text for this property.
pointsToString(Spectrum, boolean) - Method in class adams.db.generic.SpectrumT: Turns the spectrum points into a string to be stored in the database.
polynomialOrderTipText() - Method in class weka.filters.unsupervised.attribute.SavitzkyGolayRange: Returns the tip text for this property.
polynomialOrderTipText() - Method in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: Returns the tip text for this property.
polynomialTipText() - Method in class adams.data.spectrumfilter.StandardiseByInterpolation: Returns the tip text for this property.
postAdd(SpectrumContainer) - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: A post-hook for the add-method, after the container got added to the internal list and the notifications got sent.
postProcess() - Method in class adams.data.io.input.SPCSpectrumReader.AbstractParser: For post-processing the data.
postProcess() - Method in class adams.data.io.input.SPCSpectrumReader.FileParser: For post-processing the data.
postProcess() - Method in class adams.data.io.input.SPCSpectrumReader.SubFileParser: For post-processing the data.
postProcess(double[][]) - Method in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: Post-processes the confidence levels if necessary.
postProcess(ThreeWayDataModelContainer) - Method in class adams.flow.transformer.threewaydatatrain.AbstractThreeWayDataTrainPostProcessor: Post-processes the container.
postProcess(Instance) - Method in class adams.data.postprocessor.instances.AbstractPostProcessor: Performs the processing.
postProcess(Instances) - Method in class adams.data.postprocessor.instances.AbstractPostProcessor: Performs the processing.
postProcessCheck() - Method in class adams.flow.transformer.Cleaner.CleanJob: Checks whether all post-conditions have been met.
postProcessCheck() - Method in class adams.flow.transformer.Evaluator.EvaluateJob: Checks whether all post-conditions have been met.
postProcessData() - Method in class adams.data.io.input.AbstractSpectrumReader: Performs some post-processing.
postProcessData() - Method in class adams.data.io.input.AbstractThreeWayDataReader: Performs some post-processing.
postProcessHeader(HeaderDefinition) - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Post-processes the header, adding fields and notes.
postProcessHeader(HeaderDefinition) - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Post-processes the header, adding fields and notes.
postProcessHeader(Spectrum) - Method in class adams.data.instances.AbstractSpectrumBasedInstanceGenerator: Adds IDs, notes, additional fields to header.
postProcessHeader(Spectrum) - Method in class adams.data.instances.AbstractSpectrumInstanceGenerator: Adds IDs, notes, additional fields to header.
postProcessHeader(Spectrum) - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Adds IDs, notes, additional fields to header.
PostProcessingContainer - Class in adams.flow.container: Container used by post-processors.
PostProcessingContainer() - Constructor for class adams.flow.container.PostProcessingContainer: Default constructor.
PostProcessingContainer(Instance, Instance, AbstractPostProcessor) - Constructor for class adams.flow.container.PostProcessingContainer: Initializes the container with the WEKA instance and the post-processor.
PostProcessingContainer(Instances, Instances, AbstractPostProcessor) - Constructor for class adams.flow.container.PostProcessingContainer: Initializes the container with the WEKA instances and the post-processor.
PostProcessingContainerToWekaInstanceContainer - Class in adams.data.conversion: Converts a adams.flow.container.PostProcessingContainer container to a adams.data.instance.WekaInstanceContainer one.
PostProcessingContainerToWekaInstanceContainer() - Constructor for class adams.data.conversion.PostProcessingContainerToWekaInstanceContainer
PostProcessor - Class in adams.flow.transformer: Post-processes the input Instances or, after the post-processor has been initialized with Instances, also input Instance objects.
The actual post-processor in use gets output when container output enabled.
PostProcessor() - Constructor for class adams.flow.transformer.PostProcessor
PostProcessorDetails<T> - Interface in adams.data.postprocessor: Interface for post-processors that provide details about their internals after they have been built.
postProcessorDetailsOutputTipText() - Method in class adams.flow.transformer.PostProcessor: Returns the tip text for this property.
PostProcessorModelLoader - Class in adams.flow.core: Model loader for AbstractPostProcessor objects.
PostProcessorModelLoader() - Constructor for class adams.flow.core.PostProcessorModelLoader
postProcessorTipText() - Method in class adams.flow.transformer.PostProcessor: Returns the tip text for this property.
postProcessorTipText() - Method in class adams.flow.transformer.ThreeWayDataTrain: Returns the tip text for this property.
postProcessOutput(Spectrum, Row) - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: For adding IDs, notes, additional fields to the data.
postProcessOutput(Spectrum, Instance) - Method in class adams.data.instances.AbstractSpectrumBasedInstanceGenerator: Adds the IDs, notes, additional fields to the data.
postProcessOutput(Spectrum, Instance) - Method in class adams.data.instances.AbstractSpectrumInstanceGenerator: Adds the IDs, notes, additional fields to the data.
postProcessRow(Spectrum, List<Object>) - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Post-processes the generated row, adding notes and fields.
postProcessRow(ThreeWayData, List<Object>) - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Post-processes the generated row, adding notes and fields.
postProcessRows(Spectrum, List<Object>[]) - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Post-processes the generated rows, adding notes and fields.
postProcessRows(ThreeWayData, List<Object>[]) - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Post-processes the generated rows, adding notes and fields.
postUpdate() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Hook method, called after the update was performed.
preAdd(SpectrumContainer) - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: A pre-hook for the add method, before a container gets added to the internal list.
preCheck(Spectrum) - Method in class adams.data.cleaner.spectrum.AbstractCleaner: Performs the some pre-checks whether the data is actually suitable.
preCheck(Spectrum) - Method in class adams.data.cleaner.spectrum.AbstractSerializableCleaner: Performs the some pre-checks whether the data is actually suitable.
preCheck(Instance) - Method in class adams.data.cleaner.instance.AbstractCleaner: Performs the pre-checks whether the data is actually suitable.
preCheck(Instance) - Method in class adams.data.cleaner.instance.AbstractSerializableCleaner: Performs the some pre-checks whether the data is actually suitable.
preCheck(Instance) - Method in class adams.data.evaluator.instance.AbstractEvaluator: Performs the some pre-checks whether the data is actually suitable.
preCheck(Instance) - Method in class adams.data.evaluator.instance.AbstractSerializableEvaluator: Performs the some pre-checks whether the data is actually suitable.
preCheck(Instance) - Method in class adams.data.postprocessor.instances.AbstractPostProcessor: Performs some pre-checks whether the data is actually suitable.
preCheck(Instance) - Method in class adams.data.postprocessor.instances.AbstractSerializablePostProcessor: Performs some pre-checks whether the data is actually suitable.
preCheck(Instances) - Method in class adams.data.cleaner.instance.AbstractCleaner: Performs the some pre-checks whether the data is actually suitable.
preCheck(Instances) - Method in class adams.data.cleaner.instance.AbstractSerializableCleaner: Performs the some pre-checks whether the data is actually suitable.
preCheck(Instances) - Method in class adams.data.cleaner.instance.RemoveOutliers: Performs the some pre-checks whether the data is actually suitable.
preCheck(Instances) - Method in class adams.data.evaluator.instance.AbstractEvaluator: Performs the some pre-checks whether the data is actually suitable.
preCheck(Instances) - Method in class adams.data.postprocessor.instances.AbstractPostProcessor: Performs some pre-checks whether the data is actually suitable.
preCheck(Instances) - Method in class adams.data.postprocessor.instances.AbstractSerializablePostProcessor: Performs the some pre-checks whether the data is actually suitable.
preCheck(Instances) - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Performs some pre-checks whether the data is actually suitable.
PredictionCheck - Class in adams.flow.transformer: Applies the specified check scheme to the incoming evaluation container.
PredictionCheck() - Constructor for class adams.flow.transformer.PredictionCheck
PredictionErrorIQR - Class in adams.data.postprocessor.instances: Post-processor that removes outliers using a coarse IQR approach on the predictions errors of one or more classifiers.

parameters:
- list of classifiers
- foreach classifier; number or folds, an IQR multiplier, number of iterations or number of consecutive non-removal iterations before stop.

algorithm:
foreach classifier
loop
do xval, get predictions, remove all examples where error > percentile75+IQR*multiplier of errors
stop if done num_iterations, or consecutive zero removals
PredictionErrorIQR() - Constructor for class adams.data.postprocessor.instances.PredictionErrorIQR
preferJobRunnerTipText() - Method in class adams.flow.transformer.Cleaner: Returns the tip text for this property.
preferJobRunnerTipText() - Method in class adams.flow.transformer.Evaluator: Returns the tip text for this property.
preFilter(Spectrum) - Method in class adams.data.cleaner.spectrum.AbstractCleaner: Performs the filtering.
preFilter(Instance) - Method in class adams.data.cleaner.instance.AbstractCleaner: Performs the filtering.
preFilter(Instances) - Method in class adams.data.cleaner.instance.AbstractCleaner: Performs the filtering.
preFiltersTipText() - Method in class adams.data.multifilter.FilteredMultiSpectrumFilter: Returns the tip text for this property.
preFilterTipText() - Method in class adams.data.cleaner.instance.AbstractCleaner: Returns the tip text for this property.
preFilterTipText() - Method in class adams.data.cleaner.spectrum.AbstractCleaner: Returns the tip text for this property.
preFilterTipText() - Method in class adams.data.multispectrumoperation.outlierremoval.CorrelationBasedThreshold: Returns the tip text for this property.
preFilterTipText() - Method in class adams.data.multispectrumoperation.outlierremoval.CosineSimilarityBasedThreshold: Returns the tip text for this property.
preFilterTipText() - Method in class adams.data.multispectrumoperation.outlierremoval.MeanSpectrumCosineSimilarityBasedThreshold: Returns the tip text for this property.
preFilterTipText() - Method in class adams.data.spectrumfilter.KennardStone: Tip text for this property
preFilterTipText() - Method in class adams.data.spectrumfilter.multiplicativescattercorrection.AbstractMultiplicativeScatterCorrection: Returns the tip text for this property.
preFilterTipText() - Method in class adams.data.spectrumfilter.MultiplicativeScatterCorrection: Returns the tip text for this property.
PREFIX_AMPLITUDE - Static variable in class adams.data.columnfinder.AmplitudeFinder: the prefix for a spectral attribute.
PREFIX_AMPLITUDE - Static variable in class adams.data.instances.ArffUtils
PREFIX_AMPLITUDE - Static variable in class weka.filters.unsupervised.attribute.RangeBasedSavitzkyGolay: the prefix for a spectral attribute.
PREFIX_AMPLITUDE - Static variable in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: the prefix for a spectral attribute.
PREFIX_AMPLITUDE - Static variable in class weka.filters.unsupervised.attribute.SpectrumFilter: the prefix for a spectral attribute.
PREFIX_INFO - Static variable in class adams.data.io.input.SimpleEEMReader
PREFIX_INTERCEPT - Static variable in class adams.data.spectrumfilter.MultiplicativeScatterCorrection
PREFIX_NORMALIZED_BY - Static variable in class adams.data.io.input.SimpleEEMReader
PREFIX_OPUS - Static variable in class adams.data.io.input.OpusSpectrumReaderExt
PREFIX_SAMPLE_RAW - Static variable in class adams.data.io.input.ScioLabExportSpectrumReader
PREFIX_SLOPE - Static variable in class adams.data.spectrumfilter.MultiplicativeScatterCorrection
PREFIX_SPECTRUM - Static variable in class adams.data.io.input.ScioLabExportSpectrumReader
PREFIX_TRACE - Static variable in class adams.data.io.input.OpusSpectrumReader: the prefix for the trace values in the report.
PREFIX_WAVE_NUMBER - Static variable in class adams.data.instances.ArffUtils
PREFIX_WR_RAW - Static variable in class adams.data.io.input.ScioLabExportSpectrumReader
prefixNewTipText() - Method in class weka.filters.unsupervised.attribute.SpectrumFilter: Returns the tip text for this property.
prefixOldTipText() - Method in class weka.filters.unsupervised.attribute.SpectrumFilter: Returns the tip text for this property.
prefixTipText() - Method in class adams.data.instances.FieldInstanceGenerator: Returns the tip text for this property.
prefixTipText() - Method in class adams.data.spectrumfilter.WekaFilterToReport: Returns the tip text for this property.
prefixTipText() - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Returns the tip text for this property.
prepareUpdate() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Updates the axes with the min/max of the new data.
preProcessCheck() - Method in class adams.flow.transformer.Cleaner.CleanJob: Checks whether all pre-conditions have been met.
preProcessCheck() - Method in class adams.flow.transformer.Evaluator.EvaluateJob: Checks whether all pre-conditions have been met.
preRun() - Method in class adams.opt.genetic.RonWeasley: Some more initializations.
preSet(int, SpectrumContainer) - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: A pre-hook for the set method, before the container replaces the item currently occupying the position.
prettyPrintingTipText() - Method in class adams.data.conversion.SpectrumToJson: Returns the tip text for this property.
prettyPrintingTipText() - Method in class adams.data.io.output.JsonSpectrumWriter: Returns the tip text for this property.
process() - Method in class adams.flow.transformer.Cleaner.CleanJob: Does the actual execution of the job.
process() - Method in class adams.flow.transformer.Evaluator.EvaluateJob: Does the actual execution of the job.
process(Instances) - Method in class weka.filters.unsupervised.attribute.BestBySLR
process(Instances) - Method in class weka.filters.unsupervised.attribute.RangeBasedSavitzkyGolay: Processes the given data (may change the provided dataset) and returns the modified version.
process(Instances) - Method in class weka.filters.unsupervised.attribute.SegmentedDownSample: Processes the given data (may change the provided dataset) and returns the modified version.
process(Instances) - Method in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: Processes the given data (may change the provided dataset) and returns the modified version.
process(Instances) - Method in class weka.filters.unsupervised.attribute.SpectrumFilter: processes the given instances (may change the provided instances) and returns the modified version.
processBatchData(DataContainer[]) - Method in class adams.data.spectrumfilter.KennardStone
processBatchData(Spectrum[]) - Method in class adams.data.spectrumfilter.PCA: Performs the actual batch filtering.
processBatchData(Spectrum[]) - Method in class adams.data.spectrumfilter.PLS: Performs the actual batch filtering.
processData(DataContainer) - Method in class adams.data.spectrumfilter.KennardStone
processData(DataContainer) - Method in class adams.data.spectrumoutlier.MinMax: Performs the actual detection.
processData(DataContainer) - Method in class adams.data.spectrumoutlier.StringMatcher: Performs the actual detection.
processData(MultiSpectrum) - Method in class adams.data.multifilter.AbstractBinaryFormatsBasedMultiSpectrumFilter: Performs the actual filtering.
processData(MultiSpectrum) - Method in class adams.data.multifilter.AbstractMultiSpectrumFilter: Performs the actual filtering.
processData(MultiSpectrum) - Method in class adams.data.multifilter.Average: Performs the actual filtering.
processData(MultiSpectrum) - Method in class adams.data.multifilter.FilteredMultiSpectrumFilter: Performs the actual filtering.
processData(MultiSpectrum) - Method in class adams.data.multifilter.Fusion: Performs the actual filtering.
processData(MultiSpectrum) - Method in class adams.data.multifilter.Mean: Performs the actual filtering.
processData(MultiSpectrum) - Method in class adams.data.multifilter.Median: Performs the actual filtering.
processData(MultiSpectrum) - Method in class adams.data.multifilter.PickByIndex: Performs the actual filtering.
processData(MultiSpectrum) - Method in class adams.data.multifilter.PickByReportValue: Performs the actual filtering.
processData(MultiSpectrum) - Method in class adams.data.multireportfilter.AbstractMultiSpectrumReportFilter: Performs the actual filtering.
processData(MultiSpectrum) - Method in class adams.data.multireportfilter.DistributeSampleData: Performs the actual filtering.
processData(MultiSpectrum) - Method in class adams.data.multireportfilter.PassThrough: Performs the actual filtering.
processData(MultiSpectrum) - Method in class adams.data.multireportfilter.PullUpFields: Performs the actual filtering.
processData(MultiSpectrum, List<Spectrum>) - Method in class adams.data.multifilter.AbstractBinaryFormatsBasedMultiSpectrumFilter: Performs the actual filtering of the selected spectra.
processData(MultiSpectrum, List<Spectrum>) - Method in class adams.data.multifilter.Add: Performs the actual filtering of the selected spectra.
processData(MultiSpectrum, List<Spectrum>) - Method in class adams.data.multifilter.Atan2: Performs the actual filtering of the selected spectra.
processData(MultiSpectrum, List<Spectrum>) - Method in class adams.data.multifilter.Divide: Performs the actual filtering of the selected spectra.
processData(MultiSpectrum, List<Spectrum>) - Method in class adams.data.multifilter.Multiply: Performs the actual filtering of the selected spectra.
processData(MultiSpectrum, List<Spectrum>) - Method in class adams.data.multifilter.Subtract: Performs the actual filtering of the selected spectra.
processData(Spectrum) - Method in class adams.data.sampledata.SignalToNoiseRatio
processData(Spectrum) - Method in class adams.data.spectrumfilter.AmplitudeExpression: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.AmplitudeTransform: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.AndrewsCurves: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.CenterBurst: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.ChangeFormat: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.ConditionalReportField: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.Covariance: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.Detrend: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.EquiDistance: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.LogTransform: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.LRCoeff: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.MultiFilter: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.MultiplicativeScatterCorrection: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.PadPower2: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.PCA: Does nothing.
processData(Spectrum) - Method in class adams.data.spectrumfilter.PLS: Does nothing.
processData(Spectrum) - Method in class adams.data.spectrumfilter.Rebase: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.Remove: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.ReportFieldFromStringValue: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.ReportFieldFromStringValueWithLookup: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.Reverse: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.RowNorm: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.RowZeroMin: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.Scale: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.StandardiseByInterpolation: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.SubRange: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.SubtractSpectrum: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.WaveNumberExpression: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.WekaFilterToReport: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumfilter.ZeroCenterBurst: Performs the actual filtering.
processData(Spectrum) - Method in class adams.data.spectrumoutlier.AmplitudeRange: Performs the actual detection.
processData(Spectrum) - Method in class adams.data.spectrumoutlier.Flatliner: Performs the actual detection.
processData(Spectrum) - Method in class adams.data.spectrumoutlier.MaxWaves: Performs the actual detection.
processData(Spectrum) - Method in class adams.data.spectrumoutlier.MinWaves: Performs the actual detection.
processData(Spectrum) - Method in class adams.data.spectrumoutlier.Oscillation: Performs the actual detection.
processData(Spectrum) - Method in class adams.data.spectrumoutlier.Swapped: Performs the actual detection.
processData(ThreeWayData) - Method in class adams.data.threewayfilter.Crop: Performs the actual filtering.
processData(ThreeWayData) - Method in class adams.data.threewayfilter.MultiFilter: Performs the actual filtering.
processData(ThreeWayData) - Method in class adams.data.threewayfilter.Shift: Performs the actual filtering.
processData(ThreeWayData) - Method in class adams.data.threewayoutlier.ValueRange: Performs the actual detection.
processDataParallel(Spectrum) - Method in class adams.data.spectrumfilter.MultiFilter: Performs the actual filtering - parallel application of filters and merging of results.
processDataParallel(ThreeWayData) - Method in class adams.data.threewayfilter.MultiFilter: Performs the actual filtering - parallel application of filters and merging of results.
processHeader() - Method in class adams.data.io.input.foss.FossHelper: Process the data from the cal file header.
processHit(MouseEvent, Double) - Method in class adams.gui.visualization.spectrum.WaveNumberHitDetector: Performs the action when a hit is detected.
processHit(MouseEvent, List<SpectrumPoint>) - Method in class adams.gui.visualization.spectrum.SpectrumPointHitDetector: Performs the action when a hit is detected.
processRow(SpreadSheetTablePopupMenuItemHelper.TableState) - Method in class adams.gui.core.spreadsheettable.ExportSpectra: Processes the specified row.
processRow(InstancesTablePopupMenuItemHelper.TableState) - Method in class adams.gui.visualization.instances.instancestable.ExportSpectra: Processes the specified row.
processTipText(PlotPanel, Point, String) - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Processes the given tip text.
product_code - Variable in class adams.data.io.input.foss.FossHelper.FossFields: product code field.
productCodeFromFieldTipText() - Method in class adams.data.io.output.ASCSpectrumWriter: Returns the tip text for this property.
productCodeFromFieldTipText() - Method in class adams.data.io.output.NIRSpectrumWriter: Returns the tip text for this property.
productCodeTipText() - Method in class adams.data.io.output.ASCSpectrumWriter: Returns the tip text for this property.
productCodeTipText() - Method in class adams.data.io.output.NIRSpectrumWriter: Returns the tip text for this property.
productCodeTipText() - Method in class adams.flow.transformer.InstanceToSpectrum: Returns the tip text for this property.
promptParameters(SpreadSheetTable) - Method in class adams.gui.core.spreadsheettable.ExportSpectra: Prompts the user for parameters.
promptParameters(InstancesTable) - Method in class adams.gui.visualization.instances.instancestable.ExportSpectra: Prompts the user for parameters.
prop - Variable in class nz.ac.waikato.adams.webservice.rats.multispectrum.Properties
prop - Variable in class nz.ac.waikato.adams.webservice.rats.spectrum.Properties
prop - Variable in class nz.ac.waikato.adams.webservice.spectral.get.Properties
prop - Variable in class nz.ac.waikato.adams.webservice.spectral.put.Properties
prop - Variable in class nz.ac.waikato.adams.webservice.spectral.transform.Properties
Properties - Class in nz.ac.waikato.adams.webservice.rats.multispectrum: Java class for Properties complex type.
Properties - Class in nz.ac.waikato.adams.webservice.rats.spectrum: Java class for Properties complex type.
Properties - Class in nz.ac.waikato.adams.webservice.spectral.get: Java class for Properties complex type.
Properties - Class in nz.ac.waikato.adams.webservice.spectral.put: Java class for Properties complex type.
Properties - Class in nz.ac.waikato.adams.webservice.spectral.transform: Java class for Properties complex type.
Properties() - Constructor for class nz.ac.waikato.adams.webservice.rats.multispectrum.Properties
Properties() - Constructor for class nz.ac.waikato.adams.webservice.rats.spectrum.Properties
Properties() - Constructor for class nz.ac.waikato.adams.webservice.spectral.get.Properties
Properties() - Constructor for class nz.ac.waikato.adams.webservice.spectral.put.Properties
Properties() - Constructor for class nz.ac.waikato.adams.webservice.spectral.transform.Properties
Property - Class in nz.ac.waikato.adams.webservice.rats.multispectrum: Java class for Property complex type.
Property - Class in nz.ac.waikato.adams.webservice.rats.spectrum: Java class for Property complex type.
Property - Class in nz.ac.waikato.adams.webservice.spectral.get: Java class for Property complex type.
Property - Class in nz.ac.waikato.adams.webservice.spectral.put: Java class for Property complex type.
Property - Class in nz.ac.waikato.adams.webservice.spectral.transform: Java class for Property complex type.
Property() - Constructor for class nz.ac.waikato.adams.webservice.rats.multispectrum.Property
Property() - Constructor for class nz.ac.waikato.adams.webservice.rats.spectrum.Property
Property() - Constructor for class nz.ac.waikato.adams.webservice.spectral.get.Property
Property() - Constructor for class nz.ac.waikato.adams.webservice.spectral.put.Property
Property() - Constructor for class nz.ac.waikato.adams.webservice.spectral.transform.Property
props - Variable in class nz.ac.waikato.adams.webservice.rats.multispectrum.MultiSpectrum
props - Variable in class nz.ac.waikato.adams.webservice.rats.multispectrum.Spectrum
props - Variable in class nz.ac.waikato.adams.webservice.rats.spectrum.Spectrum
props - Variable in class nz.ac.waikato.adams.webservice.spectral.get.Spectrum
props - Variable in class nz.ac.waikato.adams.webservice.spectral.put.Spectrum
props - Variable in class nz.ac.waikato.adams.webservice.spectral.transform.Spectrum
pruneBackup() - Method in class adams.flow.transformer.Cleaner: Removes entries from the backup.
pruneBackup() - Method in class adams.flow.transformer.Evaluator: Removes entries from the backup.
pruneBackup() - Method in class adams.flow.transformer.MultiSpectrumAdd: Removes entries from the backup.
pruneBackup() - Method in class adams.flow.transformer.PostProcessor: Removes entries from the backup.
pruneBackup() - Method in class adams.flow.transformer.SpectrumFeatureGenerator: Removes entries from the backup.
pruneBackup() - Method in class adams.flow.transformer.SpectrumMinMax: Removes entries from the backup.
pruneBackup() - Method in class adams.flow.transformer.ThreeWayDataFeatureGenerator: Removes entries from the backup.
pruneBackup() - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Removes entries from the backup.
PullUpFields - Class in adams.data.multireportfilter: Distributes the sample data among all the sub-spectra, never overwrites already existing values.
PullUpFields() - Constructor for class adams.data.multireportfilter.PullUpFields
put(String, String) - Method in class adams.flow.rest.PutSampleData: Stores the upload spectrum (in JSON format) in the database.
put(String, String, String) - Method in class adams.flow.rest.PutSpectrum: Stores the upload spectrum (in JSON format) in the database.
put(String, String, String) - Method in class adams.flow.rest.TransformSpectrum: Filters the upload spectrum (in JSON format) with the filter and returns the output of the filter again (in JSON format).
put(PutRequest) - Method in class adams.flow.webservice.SimpleSpectralPutService: Downloads a spectrum.
put(PutRequest) - Method in interface nz.ac.waikato.adams.webservice.spectral.put.SpectralPutService
Put - Class in adams.flow.webservice: Stores a spectrum.
Put() - Constructor for class adams.flow.webservice.Put
putBooleanLittleEndian(byte[], int, boolean) - Static method in class adams.data.io.output.foss.FossOutputHelper: Put byte of boolean into array.
putDate(byte[], int, Calendar) - Static method in class adams.data.io.output.foss.FossOutputHelper: Put bytes of date into array, Little Endian.
putDate(byte[], int, Date) - Static method in class adams.data.io.output.foss.FossOutputHelper: Put bytes of date into array, Little Endian.
putFloatLittleEndian(byte[], int, float) - Static method in class adams.data.io.output.foss.FossOutputHelper: Put bytes of float into array, Little Endian, IEEE754.
putIntLittleEndian(byte[], int, int) - Static method in class adams.data.io.output.foss.FossOutputHelper: Put bytes of integer into array, Little Endian.
PutRequest - Class in nz.ac.waikato.adams.webservice.spectral.put: Java class for putRequest complex type.
PutRequest() - Constructor for class nz.ac.waikato.adams.webservice.spectral.put.PutRequest
PutResponse - Class in nz.ac.waikato.adams.webservice.spectral.put: Java class for putResponse complex type.
PutResponse() - Constructor for class nz.ac.waikato.adams.webservice.spectral.put.PutResponse
PutSampleData - Class in adams.flow.rest: REST plugin for uploading sample data.
PutSampleData() - Constructor for class adams.flow.rest.PutSampleData
PutSpectrum - Class in adams.flow.rest: REST plugin for uploading spectra.
PutSpectrum() - Constructor for class adams.flow.rest.PutSpectrum
PutSpectrumHelper - Class in adams.flow.core: Helper class for converting spectra.
PutSpectrumHelper() - Constructor for class adams.flow.core.PutSpectrumHelper
putTime(byte[], int, Calendar) - Static method in class adams.data.io.output.foss.FossOutputHelper: Put bytes of time (in seconds since epoch) into array, Little Endian.
putTime(byte[], int, Date) - Static method in class adams.data.io.output.foss.FossOutputHelper: Put bytes of time (in seconds since epoch) into array, Little Endian.
putZeroTerminatedString(byte[], int, String, int) - Static method in class adams.data.io.output.foss.FossOutputHelper: Put String into array, terminate string with 0.

Q

queryDatabase() - Method in class adams.flow.source.OrphanedSampleDataIdSupplier: Performs the actual database query.
queryDatabase() - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Performs the actual database query.
queryDatabase() - Method in class adams.flow.transformer.BulkSpectrumDbWriter: Performs the actual database query.
queryDatabase() - Method in class adams.flow.transformer.SpectrumDbReader: Executes the flow item.
queueFailedTipText() - Method in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: Returns the tip text for this property.
queueFailedTipText() - Method in class adams.flow.standalone.rats.LoadSpectrumFileOutput: Returns the tip text for this property.
queueSpectraTipText() - Method in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: Returns the tip text for this property.
queueSpectraTipText() - Method in class adams.flow.standalone.rats.LoadSpectrumFileOutput: Returns the tip text for this property.
queueSuccessfulTipText() - Method in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: Returns the tip text for this property.
queueSuccessfulTipText() - Method in class adams.flow.standalone.rats.LoadSpectrumFileOutput: Returns the tip text for this property.

R

Range - Class in adams.flow.transformer.predictioncheck: Ensures that the specified (numeric) evaluator results are within a specified range.
Adds a new boolean evaluation to the container, with the same name as the checked one, but appended with the suffix '.passed'.
E.g., when checking the evaluation 'sqr', 'sqr..passed' will get added, either with 'true' or 'false' as value.
Range() - Constructor for class adams.flow.transformer.predictioncheck.Range
RANGE - adams.data.evaluator.instance.CrossValidatedPrediction.StatisticType
RangeBased - Class in adams.data.spectrumfilter.detrend: Performs the correction using slopes/intercepts calculated for the defined ranges.
RangeBased - Class in adams.data.spectrumfilter.multiplicativescattercorrection: Performs the correction using slopes/intercepts calculated for the defined ranges.
RangeBased() - Constructor for class adams.data.spectrumfilter.detrend.RangeBased
RangeBased() - Constructor for class adams.data.spectrumfilter.multiplicativescattercorrection.RangeBased
RangeBasedSavitzkyGolay - Class in weka.filters.unsupervised.attribute: Configures a weka.filters.unsupervised.attribute.PartitionedMultiFilter, using the supplied ranges and the number of points to configure the weka.filters.unsupervised.attribute.SavitzkyGolay2 filter to apply to that subset.
RangeBasedSavitzkyGolay() - Constructor for class weka.filters.unsupervised.attribute.RangeBasedSavitzkyGolay
rangeCheck(float) - Method in class adams.data.spectrumimage.AbstractSpectrumImageGeneratorWithRange: Makes sure that the amplitude is within the defined ranges.
rangesTipText() - Method in class adams.data.spectrumfilter.detrend.RangeBased: Returns the tip text for this property.
rangesTipText() - Method in class adams.data.spectrumfilter.multiplicativescattercorrection.RangeBased: Returns the tip text for this property.
rangesTipText() - Method in class weka.filters.unsupervised.attribute.RangeBasedSavitzkyGolay: Returns the tip text for this property.
rangeTipText() - Method in class adams.data.spectrumfilter.Remove: Returns the tip text for this property.
rangeTipText() - Method in class adams.flow.transformer.predictioncheck.Range: Returns the tip text for this property.
rangeXTipText() - Method in class adams.data.threewayfilter.Crop: Returns the tip text for this property.
rangeYTipText() - Method in class adams.data.threewayfilter.Crop: Returns the tip text for this property.
rangeZTipText() - Method in class adams.data.threewayfilter.Crop: Returns the tip text for this property.
RatsMultiSpectrumHelper - Class in adams.flow.core: Helper class for converting spectra.
RatsMultiSpectrumHelper() - Constructor for class adams.flow.core.RatsMultiSpectrumHelper
RatsMultiSpectrumService - Interface in nz.ac.waikato.adams.webservice.rats.multispectrum: This class was generated by Apache CXF 3.6.6 2025-09-19T23:39:59.728+12:00 Generated source version: 3.6.6
RatsMultiSpectrumServicePort - Static variable in class nz.ac.waikato.adams.webservice.rats.multispectrum.RatsMultiSpectrumServiceService
RatsMultiSpectrumServiceService - Class in nz.ac.waikato.adams.webservice.rats.multispectrum: This class was generated by Apache CXF 3.6.6 2025-09-19T23:39:59.762+12:00 Generated source version: 3.6.6
RatsMultiSpectrumServiceService() - Constructor for class nz.ac.waikato.adams.webservice.rats.multispectrum.RatsMultiSpectrumServiceService
RatsMultiSpectrumServiceService(URL) - Constructor for class nz.ac.waikato.adams.webservice.rats.multispectrum.RatsMultiSpectrumServiceService
RatsMultiSpectrumServiceService(URL, QName) - Constructor for class nz.ac.waikato.adams.webservice.rats.multispectrum.RatsMultiSpectrumServiceService
RatsMultiSpectrumServiceWS - Class in adams.flow.webservice.multispectrum: Webservice for RATS Spectrum.
RatsMultiSpectrumServiceWS() - Constructor for class adams.flow.webservice.multispectrum.RatsMultiSpectrumServiceWS
RatsSpectrumHelper - Class in adams.flow.core: Helper class for converting spectra.
RatsSpectrumHelper() - Constructor for class adams.flow.core.RatsSpectrumHelper
RatsSpectrumService - Interface in nz.ac.waikato.adams.webservice.rats.spectrum: This class was generated by Apache CXF 3.6.6 2025-09-19T23:39:57.280+12:00 Generated source version: 3.6.6
RatsSpectrumServicePort - Static variable in class nz.ac.waikato.adams.webservice.rats.spectrum.RatsSpectrumServiceService
RatsSpectrumServiceService - Class in nz.ac.waikato.adams.webservice.rats.spectrum: This class was generated by Apache CXF 3.6.6 2025-09-19T23:39:57.316+12:00 Generated source version: 3.6.6
RatsSpectrumServiceService() - Constructor for class nz.ac.waikato.adams.webservice.rats.spectrum.RatsSpectrumServiceService
RatsSpectrumServiceService(URL) - Constructor for class nz.ac.waikato.adams.webservice.rats.spectrum.RatsSpectrumServiceService
RatsSpectrumServiceService(URL, QName) - Constructor for class nz.ac.waikato.adams.webservice.rats.spectrum.RatsSpectrumServiceService
RatsSpectrumServiceWS - Class in adams.flow.webservice.spectrum: Webservice for RATS Spectrum.
RatsSpectrumServiceWS() - Constructor for class adams.flow.webservice.spectrum.RatsSpectrumServiceWS
rawDump(double[]) - Method in class adams.data.io.input.foss.FossStdise: Testing: output raw bytes.
read(BufferedReader) - Method in class adams.data.io.input.SimpleSpectrumReader: Reads its content from the given reader.
read(String) - Method in class adams.data.io.input.SimpleSpectrumReader: Reads its content from the given file.
readBin(ZipFile, ZipArchiveEntry) - Method in class adams.data.io.input.UnscramblerSpectrumReader: Reads the binary file all as floats and returns them.
readBlocks(byte[], List<OpusBlockHelper.BlockDefinition>) - Static method in class adams.data.io.input.opus.OpusBlockHelper: Creates blocks from the definitions.
readData() - Method in class adams.data.io.input.AbstractJCampSpectrumReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.ASCIIXYSpectrumReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.ASCSpectrumReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.CALSpectrumReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.DPTSpectrumReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.ExtractIdAndTypeSpectrumReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.ExtractIdAndTypeThreeWayDataReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.FilteredSpectrumReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.FitsLibsReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.JCampDX2SpectrumReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.JCampDXSpectrumReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.JsonSpectrumReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.MPSSpectrumReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.OpusSpectrumReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.OpusSpectrumReaderExt: Performs the actual reading.
readData() - Method in class adams.data.io.input.RelabSpectrumReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.ScioLabExportSpectrumReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.SimpleEEMReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.SimpleSpectrumReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.SimpleXYZReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.SoilCaresScannerSpectrumReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.SPASpectrumReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.SPCSpectrumReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.SpecLibSampleDataReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.SpecLibSpectrumReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.ThreeWayHeatmapReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.TrinamixSpectrumJsonReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.TrinamixSpectrumReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.UnscramblerSpectrumReader: Performs the actual reading.
readData() - Method in class adams.data.io.input.ZippedSpectrumReader: Performs the actual reading.
readDefinitions(byte[], MessageCollection) - Static method in class adams.data.io.input.opus.OpusBlockHelper: Parses the opus header and returns the blocks definitions.
readDefinitions(File, MessageCollection) - Static method in class adams.data.io.input.opus.OpusBlockHelper: Parses the opus header and returns the blocks definitions.
readerTipText() - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Returns the tip text for this property.
readerTipText() - Method in class adams.data.io.input.ExtractIdAndTypeSpectrumReader: Returns the tip text for this property.
readerTipText() - Method in class adams.data.io.input.ExtractIdAndTypeThreeWayDataReader: Returns the tip text for this property.
readerTipText() - Method in class adams.data.io.input.FilteredSpectrumReader: Returns the tip text for this property.
readerTipText() - Method in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: Returns the tip text for this property.
readerTipText() - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Returns the tip text for this property.
readerTipText() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Returns the tip text for this property.
readerTipText() - Method in class adams.data.io.input.ThreeWayHeatmapReader: Returns the tip text for this property.
readerTipText() - Method in class adams.data.io.input.ZippedSpectrumReader: Returns the tip text for this property.
readerTipText() - Method in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: Returns the tip text for this property.
readerTipText() - Method in class adams.flow.standalone.rats.LoadSpectrumFileOutput: Returns the tip text for this property.
readFloat(byte[], int) - Method in class adams.data.io.input.SPASpectrumReader: Reads a float (4bytes).
readInt(byte[], int) - Method in class adams.data.io.input.SPASpectrumReader: Reads an integer (4bytes).
readMetaData(ZipFile, ZipEntry) - Method in class adams.data.io.input.SoilCaresScannerSpectrumReader: Reads the meta-data from the zip file.
readShort(byte[], int) - Method in class adams.data.io.input.SPASpectrumReader: Reads a short (2bytes).
readSpectrum(ZipFile, ZipEntry) - Method in class adams.data.io.input.SoilCaresScannerSpectrumReader: Reads the spectrum from the specified zip entry.
readString(byte[], int) - Method in class adams.data.io.input.SPASpectrumReader: Reads a string starting at the offset till encountering a null byte or EOF.
readXML(ZipFile, ZipArchiveEntry) - Method in class adams.data.io.input.UnscramblerSpectrumReader: Parses the zip entry as XML.
Rebase - Class in adams.data.spectrumfilter: Shifts all wave numbers (left or right), so that the first wave number is at the specified starting point.
Rebase() - Constructor for class adams.data.spectrumfilter.Rebase
redo() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: performs a redo if possible.
REF_REGEXP - Static variable in class weka.core.converters.CALSpectrumLoader
reference_count - Static variable in class adams.data.io.input.foss.FossHelper
reference_name_num - Static variable in class adams.data.io.input.foss.FossHelper
reference_name_width - Static variable in class adams.data.io.input.foss.FossHelper
reference_offset - Static variable in class adams.data.io.input.foss.FossHelper
referencesTipText() - Method in class adams.flow.transformer.SpectralAngleMapper: Gets the tip-text for the references option.
referenceValuePrefixTipText() - Method in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: Returns the tip text for this property.
referenceValuesTipText() - Method in class adams.data.conversion.SpectrumToJson: Returns the tip text for this property.
referenceValuesTipText() - Method in class adams.data.io.output.JsonSpectrumWriter: Returns the tip text for this property.
referenceValuesTipText() - Method in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: Returns the tip text for this property.
refRegExpTipText() - Method in class weka.core.converters.CALSpectrumLoader: Returns the tip text for this property.
refresh() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Regenerates the image of the current heatmap and redisplays it.
refreshIfNecessary() - Method in class adams.gui.selection.SelectSpectrumPanel: Does a refresh if data hasn't been displayed.
refreshScripts() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: re-builds the "Scripts" menu.
RegExp - Class in adams.data.io.input.sampleidextraction: Uses the specified group from a regular expression as sample ID.
RegExp() - Constructor for class adams.data.io.input.sampleidextraction.RegExp
regExpTipText() - Method in class adams.data.io.input.sampleidextraction.RegExp: Returns the tip text for this property.
regExpTipText() - Method in class adams.data.io.input.ZippedSpectrumReader: Returns the tip text for this property.
regExpTipText() - Method in class adams.data.spectrumfilter.ReportFieldFromStringValue: Returns the tip text for this property.
regExpTipText() - Method in class adams.data.spectrumfilter.WekaFilterToReport: Returns the tip text for this property.
regExpTipText() - Method in class adams.data.spectrumoutlier.StringMatcher: Returns the tip text for this property.
regExpTipText() - Method in class adams.gui.visualization.spectrum.SpectrumPaintletStringField: Returns the tip text for this property.
rejectedTokensActorTipText() - Method in class adams.flow.control.InstanceCleaner: Returns the tip text for this property.
rejectedTokensActorTipText() - Method in class adams.flow.control.SpectrumCleaner: Returns the tip text for this property.
rejectionMessagesActorTipText() - Method in class adams.flow.control.InstanceCleaner: Returns the tip text for this property.
rejectionMessagesActorTipText() - Method in class adams.flow.control.SpectrumCleaner: Returns the tip text for this property.
RelabSpectrumHandler - Class in adams.gui.tools.previewbrowser: Displays the following spectrum types: asc

Valid options are:
RelabSpectrumHandler() - Constructor for class adams.gui.tools.previewbrowser.RelabSpectrumHandler
RelabSpectrumReader - Class in adams.data.io.input: Reads spectra in Relab ASCII format.

http://www.planetary.brown.edu/relabdata/
RelabSpectrumReader() - Constructor for class adams.data.io.input.RelabSpectrumReader
RELAXED - adams.data.io.input.JCampDX2SpectrumReader.ReaderMode
reldiffTipText() - Method in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: Returns the tip text for this property.
remove(int) - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: Removes the container at the specified position.
remove(int, boolean) - Method in class adams.db.generic.SpectrumT: Removes the spectrum and its sample data.
remove(int, boolean) - Method in class adams.db.mirrored.SpectrumT: Removes the spectrum and its sample data.
remove(int, boolean) - Method in class adams.db.SpectrumF: Removes the spectrum and its sample data.
remove(int, boolean) - Method in interface adams.db.SpectrumIntf: Removes the spectrum and its sample data.
remove(DataProvider, Spectrum) - Method in class adams.flow.transformer.SpectrumDbWriter: Removes the container from the database.
remove(Token) - Method in class adams.flow.transformer.DeleteSpectrum: Removes the container from the database.
remove(String) - Method in class adams.db.mirrored.SampleDataT: Removes the report from the database.
remove(String) - Method in class adams.db.SampleDataF: Removes the report from the database.
remove(String, boolean) - Method in class adams.db.generic.SpectrumT: Removes the spectrum and its sample data.
remove(String, boolean) - Method in class adams.db.mirrored.SpectrumT: Removes the spectrum and its sample data.
remove(String, boolean) - Method in class adams.db.SpectrumF: Removes the spectrum and its sample data.
remove(String, boolean) - Method in interface adams.db.SpectrumIntf: Removes the spectrum and its sample data.
remove(String, AbstractField) - Method in class adams.db.mirrored.SampleDataT: Removes the report field from the database.
remove(String, AbstractField) - Method in class adams.db.SampleDataF: Removes the report field from the database.
remove(String, String, boolean) - Method in class adams.db.generic.SpectrumT: Removes the spectrum and its sample data.
remove(String, String, boolean) - Method in class adams.db.mirrored.SpectrumT: Removes the spectrum and its sample data.
remove(String, String, boolean) - Method in class adams.db.SpectrumF: Removes the spectrum and its sample data.
remove(String, String, boolean) - Method in interface adams.db.SpectrumIntf: Removes the spectrum and its sample data.
Remove - Class in adams.data.multispectrumoperation: Removes all spectra from the multi-spectrum that match the criteria.
Remove - Class in adams.data.spectrumfilter: Removes a range of amplitudes from a spectrum.
The matching sense can be inverted as well, i.e., removing everything else but the defined range of amplitudes.
Remove() - Constructor for class adams.data.multispectrumoperation.Remove
Remove() - Constructor for class adams.data.spectrumfilter.Remove
removeContainers(int[]) - Method in class adams.gui.visualization.spectrum.SpectrumContainerTable: Removes the containers from the table.
RemoveMisclassifiedCleaner - Class in adams.data.cleaner.instance: Removes instances that are misclassified by the given relative difference, unless they are within the absolute difference.
RemoveMisclassifiedCleaner() - Constructor for class adams.data.cleaner.instance.RemoveMisclassifiedCleaner
removeOutliers(MultiSpectrum, MessageCollection) - Method in class adams.data.multispectrumoperation.outlierremoval.AbstractOutlierRemoval: Performs the outlier removal.
RemoveOutliers - Class in adams.data.cleaner.instance: Cross-validates the specified classifier on the incoming data and applies the outlier detector to the actual vs predicted data to remove the outliers.
NB: only works on full dataset, not instance by instance.
RemoveOutliers() - Constructor for class adams.data.cleaner.instance.RemoveOutliers
removeOverlays() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Removes all overlays.
removeReferenceValues() - Method in class adams.gui.tools.UpdateSampleDataPanel: Removes any selected reference values from the database.
removeUnusedTipText() - Method in class weka.filters.unsupervised.attribute.RangeBasedSavitzkyGolay: Returns the tip text for this property.
removeUnusedTipText() - Method in class weka.filters.unsupervised.attribute.SegmentedDownSample: Returns the tip text for this property.
removeUnusedTipText() - Method in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: Returns the tip text for this property.
removeWithMissingTipText() - Method in class adams.data.cleaner.instance.IQRCleaner: Returns the tip text for this property.
REPLACE - adams.flow.transformer.MergeSampleDataFromMap.MergeType
ReportColorSpectrumPaintlet - Class in adams.gui.visualization.spectrum: Paintlet for painting the spectral data using the color stored in the report.
ReportColorSpectrumPaintlet() - Constructor for class adams.gui.visualization.spectrum.ReportColorSpectrumPaintlet
ReportFieldFromStringValue - Class in adams.data.spectrumfilter: Sets a report field with the value extracted from another string field via a regular expression.
ReportFieldFromStringValue() - Constructor for class adams.data.spectrumfilter.ReportFieldFromStringValue
ReportFieldFromStringValueWithLookup - Class in adams.data.spectrumfilter: Extracts the first group from the regular expression matched against the report field value and uses this value as key in the provided lookup table generated from the specified key-value pairs.
ReportFieldFromStringValueWithLookup() - Constructor for class adams.data.spectrumfilter.ReportFieldFromStringValueWithLookup
reportFieldTipText() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Returns the tip text for this property.
ReportToSampleData - Class in adams.data.conversion: Converts a Report into a SampleData object.
ReportToSampleData() - Constructor for class adams.data.conversion.ReportToSampleData
requiredFieldsTipText() - Method in class adams.db.SpectrumConditionsMulti: Returns the tip text for this property.
requiredFieldTipText() - Method in class adams.db.SpectrumConditionsSingle: Returns the tip text for this property.
reset() - Method in class adams.data.cleaner.instance.AbstractCleaner: Resets the scheme.
reset() - Method in class adams.data.cleaner.instance.AbstractSerializableCleaner: Resets the scheme.
reset() - Method in class adams.data.cleaner.instance.IQRCleaner: Resets the scheme.
reset() - Method in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: Resets the scheme.
reset() - Method in class adams.data.cleaner.spectrum.AbstractCleaner: Resets the scheme.
reset() - Method in class adams.data.cleaner.spectrum.AbstractSerializableCleaner: Resets the scheme.
reset() - Method in class adams.data.conversion.SpectrumToBufferedImage: Resets the object.
reset() - Method in class adams.data.evaluator.instance.AbstractSerializableEvaluator: Resets the scheme.
reset() - Method in class adams.data.multifilter.AbstractMultiSpectrumFilter: Resets the filter.
reset() - Method in class adams.data.multireportfilter.AbstractMultiSpectrumReportFilter: Resets the filter.
reset() - Method in class adams.data.postprocessor.instances.AbstractSerializablePostProcessor: Resets the scheme.
reset() - Method in class adams.data.spectrum.AbstractSpectrumComparator: Resets the scheme.
reset() - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Resets the scheme, i.e., the header information.
reset() - Method in class adams.data.spectrumfilter.AbstractSerializableFilter: Resets the scheme.
reset() - Method in class adams.data.spectrumfilter.MultiplicativeScatterCorrection: Resets the scheme.
reset() - Method in class adams.data.spectrumfilter.ReportFieldFromStringValueWithLookup: Resets the scheme.
reset() - Method in class adams.data.spectrumfilter.WekaFilterToReport: Resets the scheme.
reset() - Method in class adams.data.spectrumimage.Spectrogram: Resets the object.
reset() - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Resets the generator (but does not clear the input data!).
reset() - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Resets the scheme, i.e., the header information.
reset() - Method in class adams.flow.control.InstanceCleaner: Resets the scheme.
reset() - Method in class adams.flow.control.SpectrumCleaner: Resets the scheme.
reset() - Method in class adams.flow.sink.spectrumdisplay.SimplePlotUpdater: Resets the object.
reset() - Method in class adams.flow.transformer.Cleaner: Resets the scheme.
reset() - Method in class adams.flow.transformer.Evaluator: Resets the scheme.
reset() - Method in class adams.flow.transformer.InstanceGenerator: Resets the scheme.
reset() - Method in class adams.flow.transformer.MultiSpectrumAdd: Resets the scheme.
reset() - Method in class adams.flow.transformer.MultiSpectrumFilter: Resets the scheme.
reset() - Method in class adams.flow.transformer.MultiSpectrumOutlierDetector: Resets the scheme.
reset() - Method in class adams.flow.transformer.MultiSpectrumReportFilter: Resets the scheme.
reset() - Method in class adams.flow.transformer.PostProcessor: Resets the scheme.
reset() - Method in class adams.flow.transformer.report.UpdateDatabaseID: Resets the scheme.
reset() - Method in class adams.flow.transformer.SpectrumFeatureGenerator: Resets the scheme.
reset() - Method in class adams.flow.transformer.SpectrumMinMax: Resets the scheme.
reset() - Method in class adams.flow.transformer.ThreeWayDataFeatureGenerator: Resets the scheme.
reset() - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Resets the scheme.
reset() - Method in class adams.flow.webservice.Get: Resets the scheme.
reset() - Method in class adams.flow.webservice.Put: Resets the scheme.
reset() - Method in class adams.flow.webservice.Transform: Resets the scheme.
reset() - Method in class adams.gui.visualization.spectrum.SpectrumPaintletNumericField: Resets the scheme.
reset() - Method in class weka.filters.unsupervised.attribute.RangeBasedSavitzkyGolay: resets the filter, i.e., m_NewBatch to true and m_FirstBatchDone to false.
reset() - Method in class weka.filters.unsupervised.attribute.SegmentedDownSample: resets the filter, i.e., m_NewBatch to true and m_FirstBatchDone to false.
reset() - Method in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: resets the filter, i.e., m_NewBatch to true and m_FirstBatchDone to false.
resetDetector() - Method in class adams.data.spectrumoutlier.AmplitudeRange: Resets the detector, i.e., flags it as "not trained".
resetFilter() - Method in class adams.data.spectrumfilter.MultiplicativeScatterCorrection: Resets the filter, i.e., flags it as "not trained".
restoreState(Hashtable<String, Object>) - Method in class adams.flow.transformer.Cleaner: Restores the state of the actor before the variables got updated.
restoreState(Hashtable<String, Object>) - Method in class adams.flow.transformer.Evaluator: Restores the state of the actor before the variables got updated.
restoreState(Hashtable<String, Object>) - Method in class adams.flow.transformer.MultiSpectrumAdd: Restores the state of the actor before the variables got updated.
restoreState(Hashtable<String, Object>) - Method in class adams.flow.transformer.PostProcessor: Restores the state of the actor before the variables got updated.
restoreState(Hashtable<String, Object>) - Method in class adams.flow.transformer.SpectrumFeatureGenerator: Restores the state of the actor before the variables got updated.
restoreState(Hashtable<String, Object>) - Method in class adams.flow.transformer.SpectrumMinMax: Restores the state of the actor before the variables got updated.
restoreState(Hashtable<String, Object>) - Method in class adams.flow.transformer.ThreeWayDataFeatureGenerator: Restores the state of the actor before the variables got updated.
restoreState(Hashtable<String, Object>) - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Restores the state of the actor before the variables got updated.
resultsetToSpectrum(ResultSet, boolean) - Method in class adams.db.generic.SpectrumT: Turns a ResultSet into a spectrum.
retrieveSerializationSetup() - Method in class adams.data.cleaner.instance.IQRCleaner: Returns the member variables to serialize to a file.
retrieveSerializationSetup() - Method in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: Returns the member variables to serialize to a file.
retrieveSerializationSetup() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Returns the member variables to serialize to a file.
retrieveSerializationSetup() - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Returns the member variables to serialize to a file.
retrieveSerializationSetup() - Method in class adams.data.evaluator.instance.CrossValidatedPrediction: Returns the member variables to serialize to a file.
retrieveSerializationSetup() - Method in class adams.data.evaluator.instance.DistanceToCenter: Returns the member variables to serialize to a file.
retrieveSerializationSetup() - Method in class adams.data.evaluator.instance.DistanceToClosest: Returns the member variables to serialize to a file.
retrieveSerializationSetup() - Method in class adams.data.evaluator.instance.EnsembleEvaluator: Returns the member variables to serialize to a file.
retrieveSerializationSetup() - Method in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: Returns the member variables to serialize to a file.
retrieveSerializationSetup() - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Returns the member variables to serialize to a file.
retrieveSerializationSetup() - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Returns the member variables to serialize to a file.
retrieveSerializationSetup() - Method in class adams.data.postprocessor.instances.WekaFilter: Returns the member variables to serialize to a file.
reusePreview(File[], PreviewPanel) - Method in class adams.gui.tools.previewbrowser.AbstractSpectrumHandler: Returns the preview for the specified files.
Reverse - Class in adams.data.spectrumfilter: A filter that reverses the order of the amplitudes by making the wave numbers negative.
Reverse() - Constructor for class adams.data.spectrumfilter.Reverse
RGB - adams.data.spectrumimage.ImageType
RonWeasley - Class in adams.opt.genetic: Ron Weasley.
RonWeasley() - Constructor for class adams.opt.genetic.RonWeasley
RonWeasley.RonWeasleyJob - Class in adams.opt.genetic: A job class specific to Ron Weasley.
RonWeasleyJob(RonWeasley, int, int[], Instances, Instances) - Constructor for class adams.opt.genetic.RonWeasley.RonWeasleyJob: Initializes the job.
ROW - adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader.SampleIDLocation
rowFinderTipText() - Method in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: Returns the tip text for this property.
rowFinderTipText() - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Returns the tip text for this property.
rowFinderTipText() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Returns the tip text for this property.
rowIDTipText() - Method in class adams.data.conversion.SpreadSheetColumnsToSampleData: Returns the tip text for this property.
rowIDTipText() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Returns the tip text for this property.
RowNorm - Class in adams.data.spectrumfilter: A filter that returns only every n-th wave number.
RowNorm() - Constructor for class adams.data.spectrumfilter.RowNorm
rowSampleDataNamesTipText() - Method in class adams.data.conversion.SpreadSheetRowsToSampleData: Returns the tip text for this property.
rowSampleDataNamesTipText() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns the tip text for this property.
rowsAmplitudeTipText() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Returns the tip text for this property.
rowsAmplitudeTipText() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns the tip text for this property.
rowsSampleDataTipText() - Method in class adams.data.conversion.SpreadSheetColumnsToSampleData: Returns the tip text for this property.
rowsSampleDataTipText() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Returns the tip text for this property.
rowsSampleDataValuesTipText() - Method in class adams.data.conversion.SpreadSheetRowsToSampleData: Returns the tip text for this property.
rowWaveNumberTipText() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns the tip text for this property.
RowWiseSpreadSheetSampleDataReader - Class in adams.data.io.input: Reads a sample data file from a spreadsheet (format depends on reader), one reference value per row.
RowWiseSpreadSheetSampleDataReader() - Constructor for class adams.data.io.input.RowWiseSpreadSheetSampleDataReader
RowWiseSpreadSheetSpectrumReader - Class in adams.data.io.input: Reads spectra from rows in a spreadsheet obtained with the specified spreadsheet reader.
Sample ID and sample data columns get removed automatically from the range of wave columns.
RowWiseSpreadSheetSpectrumReader() - Constructor for class adams.data.io.input.RowWiseSpreadSheetSpectrumReader
RowWiseSpreadSheetSpectrumReader.ChunkedSheetIterator - Class in adams.data.io.input: Iterator for chunked spreadsheet readers.
RowWiseSpreadSheetSpectrumReader.MultiSheetIterator - Class in adams.data.io.input: Iterator for multi-sheet readers.
RowWiseSpreadSheetSpectrumReader.SheetIterator - Class in adams.data.io.input: Ancestor for sheet iterators.
RowWiseSpreadSheetSpectrumReader.SingleSheetIterator - Class in adams.data.io.input: Iterator for single-sheet readers.
RowZeroMin - Class in adams.data.spectrumfilter: Make row min = 0.
RowZeroMin() - Constructor for class adams.data.spectrumfilter.RowZeroMin
runReader(Class, Class, String[]) - Static method in class adams.data.io.input.AbstractSpectrumReader: Runs the reader from commandline.

S

sample_id - Variable in class adams.data.io.input.CALSpectrumReader: where to get sample id from. see param defs
SAMPLE_ID - Static variable in class adams.data.instances.ArffUtils
SAMPLE_ID - Static variable in class adams.data.sampledata.SampleData: field name for the sample ID.
SAMPLE_ID - Static variable in class adams.data.threewayreport.ThreeWayReport: field name for the sample ID.
SAMPLE_RAW - adams.data.io.input.ScioLabExportSpectrumReader.SpectrumType
sample_type - Variable in class adams.data.io.input.CALSpectrumReader: where to get sample type from. see param defs
SAMPLE_TYPE - Static variable in class adams.data.sampledata.SampleData: field name for the sample type.
SAMPLE_TYPE - Static variable in class adams.data.threewayreport.ThreeWayReport: field name for the sample type.
SampleData - Class in adams.data.sampledata: Read and store data from the Sample Report.
SampleData - Class in adams.gui.visualization.spectrum.containerlistpopup: Displays the sample data.
SampleData() - Constructor for class adams.data.sampledata.SampleData
SampleData() - Constructor for class adams.gui.visualization.spectrum.containerlistpopup.SampleData
SampleDataArrayToMap - Class in adams.data.conversion: Converts the incoming sample data array into a map using the sample ID as key.
SampleDataArrayToMap() - Constructor for class adams.data.conversion.SampleDataArrayToMap
sampleDataColumnsTipText() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Returns the tip text for this property.
SampleDataContainerDisplayIDGenerator - Class in adams.gui.visualization.spectrum: Class for generating display IDs.
SampleDataContainerDisplayIDGenerator() - Constructor for class adams.gui.visualization.spectrum.SampleDataContainerDisplayIDGenerator
SampleDataDatabaseReader - Interface in adams.flow.transformer: Indicator interface for database readers for sample data.
SampleDataDatabaseWriter - Interface in adams.flow.transformer: Indicator interface for database writers for sample data.
SampleDataDbReader - Class in adams.flow.transformer: Loads sample data from the database and passes it on.
SampleDataDbReader() - Constructor for class adams.flow.transformer.SampleDataDbReader
SampleDataDbWriter - Class in adams.flow.transformer: Writes sample data to the database if possible and passes the ID of the saved report on.
SampleDataDbWriter() - Constructor for class adams.flow.transformer.SampleDataDbWriter
SampleDataDisplay - Class in adams.flow.sink: Displays sample data.
SampleDataDisplay() - Constructor for class adams.flow.sink.SampleDataDisplay
SampleDataF - Class in adams.db: Facade for sample data.
SampleDataF(AbstractDatabaseConnection, String) - Constructor for class adams.db.SampleDataF: Constructor.
SampleDataFactory - Class in adams.gui.visualization.spectrum: A factory for GUI components for sample data.
SampleDataFactory() - Constructor for class adams.gui.visualization.spectrum.SampleDataFactory
SampleDataFactory.Dialog - Class in adams.gui.visualization.spectrum: A specialized dialog that displays reports.
SampleDataFactory.Panel - Class in adams.gui.visualization.spectrum: A specialized panel that displays reports.
SampleDataFactory.Table<ReportProviderByID> - Class in adams.gui.visualization.spectrum: A specialized table for displaying a SampleData.
SampleDataFileChooser - Class in adams.gui.chooser: A specialized JFileChooser that lists all available file Readers and Writers for sampledata reports.
SampleDataFileChooser() - Constructor for class adams.gui.chooser.SampleDataFileChooser: Constructs a FileChooser pointing to the user's default directory.
SampleDataFileChooser(File) - Constructor for class adams.gui.chooser.SampleDataFileChooser: Constructs a FileChooser using the given File as the path.
SampleDataFileChooser(String) - Constructor for class adams.gui.chooser.SampleDataFileChooser: Constructs a FileChooser using the given path.
SampleDataFileReader - Class in adams.flow.transformer: Loads a file containing sample data from disk with a specified reader and passes it on.
SampleDataFileReader() - Constructor for class adams.flow.transformer.SampleDataFileReader
SampleDataFileWriter - Class in adams.flow.transformer: Saves a quantitation report to disk with the specified writer and passes the absolute filename on.
As filename/directory name (depending on the writer) the database ID of the report is used (below the specified output directory).
SampleDataFileWriter() - Constructor for class adams.flow.transformer.SampleDataFileWriter
sampleDataFormatTipText() - Method in class adams.data.spectrumfilter.ChangeFormat: Returns the tip text for this property.
SampleDataIntf - Interface in adams.db: Interface for sample data reports table.
sampleDataLabelsColumnTipText() - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Returns the tip text for this property.
sampleDataNamesInHeaderTipText() - Method in class adams.data.conversion.SpreadSheetRowsToSampleData: Returns the tip text for this property.
sampleDataNamesInHeaderTipText() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns the tip text for this property.
SampleDataOnlyRowGenerator - Class in adams.data.spreadsheetrowgenerator: Outputs only sample data values.
SampleDataOnlyRowGenerator() - Constructor for class adams.data.spreadsheetrowgenerator.SampleDataOnlyRowGenerator
SampleDataReader - Interface in adams.data.io.input: Indicator interface for readers that process sample data.
SampleDataReportFilter - Class in adams.data.sampledata: Ensures that all important sample data values are kept when applying a report filter.
SampleDataReportFilter() - Constructor for class adams.data.sampledata.SampleDataReportFilter
sampleDataRowsTipText() - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Returns the tip text for this property.
SampleDataT - Class in adams.db.generic: A class for handling the sample data reports table.
SampleDataT - Class in adams.db.h2: H2 implementation.
SampleDataT - Class in adams.db.mirrored: Allows mirroring to another database.
SampleDataT - Class in adams.db.mssql: H2 implementation.
SampleDataT - Class in adams.db.mysql: MySQL implementation.
SampleDataT - Class in adams.db.postgresql: PostgreSQL implementation.
SampleDataT - Class in adams.db.sqlite: SQLite implementation.
SampleDataT(AbstractDatabaseConnection) - Constructor for class adams.db.generic.SampleDataT: Constructor.
SampleDataT(AbstractDatabaseConnection) - Constructor for class adams.db.h2.SampleDataT: Constructor.
SampleDataT(AbstractDatabaseConnection) - Constructor for class adams.db.mssql.SampleDataT: Constructor.
SampleDataT(AbstractDatabaseConnection) - Constructor for class adams.db.mysql.SampleDataT: Constructor.
SampleDataT(AbstractDatabaseConnection) - Constructor for class adams.db.postgresql.SampleDataT: Constructor.
SampleDataT(AbstractDatabaseConnection) - Constructor for class adams.db.sqlite.SampleDataT: Constructor.
SampleDataT(AbstractDatabaseConnection, SampleDataIntf) - Constructor for class adams.db.mirrored.SampleDataT: Initializes the mirror.
SampleDataValueDbWriter - Class in adams.flow.transformer: Stores the specified values from the sample data passing through in the database.
SampleDataValueDbWriter() - Constructor for class adams.flow.transformer.SampleDataValueDbWriter
SampleDataWriter - Interface in adams.data.io.output: Indicator interface for readers that process sample data.
SampleHeader() - Constructor for class adams.data.io.output.foss.FossOutputHelper.SampleHeader
sampleID1TipText() - Method in class adams.data.io.output.NIRSpectrumWriter: Returns the tip text for this property.
sampleID2TipText() - Method in class adams.data.io.output.NIRSpectrumWriter: Returns the tip text for this property.
sampleID3TipText() - Method in class adams.data.io.output.NIRSpectrumWriter: Returns the tip text for this property.
sampleIDColumnTipText() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Returns the tip text for this property.
SampleIDExtraction - Interface in adams.data.io.input.sampleidextraction: Interface for classes that extract the sample ID from the filename.
sampleIDExtractionTipText() - Method in class adams.data.io.input.ASCIIXYSpectrumReader: Returns the tip text for this property.
sampleIDExtractionTipText() - Method in interface adams.data.io.input.SpectrumReaderWithSampleIDExtraction: Returns the tip text for this property.
sampleIDLocationTipText() - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Returns the tip text for this property.
SampleIDRegExpSupporter - Interface in adams.db: Interface for condition classes that support regular expressions for the Sample ID.
sampleIDRegExpTipText() - Method in class adams.db.AbstractSpectrumConditions: Returns the tip text for this property.
sampleIDRegExpTipText() - Method in class adams.db.SpectrumIDConditions: Returns the tip text for this property.
sampleIDRowTipText() - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Returns the tip text for this property.
SampleIdSource - Interface in adams.flow.source: Interface for ID sources that output either database IDs (= integers) or sample IDs (= strings).
sampleIDTipText() - Method in class adams.data.io.input.OpusSpectrumReader: Returns the tip text for this property.
sampleIDTipText() - Method in class adams.data.multispectrumoperation.Remove: Returns the tip text for this property.
sampleIDTipText() - Method in class adams.flow.transformer.InstanceToSpectrum: Returns the tip text for this property.
sampleIDTipText() - Method in class adams.flow.transformer.MultiSpectrumRemove: Returns the tip text for this property.
SampleInfo() - Constructor for class adams.data.io.output.foss.FossOutputHelper.SampleInfo
SampleTypeRegExpSupporter - Interface in adams.db: Interface for condition classes that support regular expressions for the sample type.
sampleTypeRegExpTipText() - Method in class adams.db.AbstractSpectrumConditions: Returns the tip text for this property.
sampleTypeRegExpTipText() - Method in class adams.db.SpectrumIDConditions: Returns the tip text for this property.
sampleTypeTipText() - Method in class adams.data.multispectrumoperation.Remove: Returns the tip text for this property.
sampleTypeTipText() - Method in class adams.flow.transformer.MultiSpectrumRemove: Returns the tip text for this property.
saveAs() - Method in class adams.gui.visualization.spectrum.MultiSpectrumPanel: Displays a dialog for saving a spectrum to a file.
saveAs() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Saves the current heatmap to disk.
SaveMultiSpectrumFileOutput - Class in adams.flow.standalone.rats: Writes the input spectrum to the file that the filename generator produces.
SaveMultiSpectrumFileOutput() - Constructor for class adams.flow.standalone.rats.SaveMultiSpectrumFileOutput
SaveSpectrumFileOutput - Class in adams.flow.standalone.rats: Writes the input spectrum to the file that the filename generator produces.
SaveSpectrumFileOutput() - Constructor for class adams.flow.standalone.rats.SaveSpectrumFileOutput
SaveVisible - Class in adams.gui.visualization.spectrum.plotpopup: Allows the user to save the visible spectra.
SaveVisible() - Constructor for class adams.gui.visualization.spectrum.plotpopup.SaveVisible
saveVisibleSpectra() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Saves the visible spectra to a directory.
SavitzkyGolay - Class in adams.data.spectrumfilter: A filter that applies Savitzky-Golay smoothing.

For more information see:

A.
SavitzkyGolay() - Constructor for class adams.data.spectrumfilter.SavitzkyGolay
SavitzkyGolayBased - Class in adams.data.spectrumbaseline: A baseline correction scheme that uses SavitzkyGolay smoothing to determine the baseline.

For more information see:

A.
SavitzkyGolayBased - Class in adams.data.spectrumsmoothing: A Savitzky-Golay based smoothing algorithm.
It uses a Savitzky-Golay filter with derivative order 0 and adding of mass-spec data turned on.

For more information on Savitzky-Golay see:

A.
SavitzkyGolayBased() - Constructor for class adams.data.spectrumbaseline.SavitzkyGolayBased
SavitzkyGolayBased() - Constructor for class adams.data.spectrumsmoothing.SavitzkyGolayBased
SavitzkyGolayRange - Class in adams.data.evaluator.instance: This evaluator builds three classifiers:
- on Savitzky-Golay filtered data with no derivative
- on Savitzky-Golay filtered data with first derivative
- on Savitzky-Golay filtered data with second derivative
Each instance under evaluation will be pushed through the three classifiers separately and the range of the three predictions is then output as evaluation result.
SavitzkyGolayRange - Class in weka.filters.unsupervised.attribute: Range definition for a SavitzkyGolay filter setup.
SavitzkyGolayRange() - Constructor for class adams.data.evaluator.instance.SavitzkyGolayRange
SavitzkyGolayRange() - Constructor for class weka.filters.unsupervised.attribute.SavitzkyGolayRange
SAX - Class in adams.data.spectrumfilter: Performs Symbolic Aggregate approXimation (SAX).
The data must be normalized using knir.data.filter.RowNorm beforehand.
For more information see:

Chiu, B., Keogh, E., Lonardi, S. (2003).
SAX() - Constructor for class adams.data.spectrumfilter.SAX
SC - adams.data.io.input.SoilCaresScannerSpectrumReader.SpectrumType
Scale - Class in adams.data.spectrumfilter: Scales the amplitudes to a given maximum.
Scale() - Constructor for class adams.data.spectrumfilter.Scale
scaleTipText() - Method in class adams.data.spectrumfilter.Covariance: Returns the tip text for this property.
scaleTipText() - Method in class adams.data.spectrumfilter.LRCoeff: Returns the tip text for this property.
ScioLabExportSpectrumReader - Class in adams.data.io.input: Reads the CSV export from the SCiO Lab web site.
ScioLabExportSpectrumReader() - Constructor for class adams.data.io.input.ScioLabExportSpectrumReader
ScioLabExportSpectrumReader.SpectrumType - Enum in adams.data.io.input: Determines the type of spectrum to load.
search() - Method in class adams.gui.tools.idprovider.DatabaseSearchPanel: Performs the search and updates the table.
search(String, boolean) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Performs a search.
search(String, boolean) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Performs a search.
searchTipText() - Method in class adams.data.evaluator.instance.AbstractNearestNeighborBasedEvaluator: Returns the tip text for this property.
seedTipText() - Method in class adams.data.cleaner.instance.RemoveOutliers: Returns the tip text for this property.
seedTipText() - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Returns the tip text for this property.
seedTipText() - Method in class adams.data.evaluator.instance.CrossValidatedPrediction: Returns the tip text for this property.
seedTipText() - Method in class adams.data.evaluator.instance.EnsembleEvaluator: Returns the tip text for this property.
seedTipText() - Method in class adams.data.evaluator.instance.FakeEvaluator: Returns the tip text for this property.
seedTipText() - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Returns the tip text for this property.
seedTipText() - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Returns the tip text for this property.
SegmentedDownSample - Class in weka.filters.unsupervised.attribute: Configures a weka.filters.unsupervised.attribute.PartitionedMultiFilter2, using the supplied number of splits and the nth points to configure the weka.filters.unsupervised.attribute.DownSample filter to apply to the subsets.
SegmentedDownSample() - Constructor for class weka.filters.unsupervised.attribute.SegmentedDownSample
SegmentedDownSampleNthPoints - Class in adams.core.discovery.genetic: SegmentedDownSample nthPoints handler.
SegmentedDownSampleNthPoints() - Constructor for class adams.core.discovery.genetic.SegmentedDownSampleNthPoints
SegmentedSavitzkyGolay - Class in weka.filters.unsupervised.attribute: Configures a weka.filters.unsupervised.attribute.PartitionedMultiFilter, using the supplied number of splits and the number of points to configure the weka.filters.unsupervised.attribute.SavitzkyGolay2 filter to apply to the subsets.
SegmentedSavitzkyGolay() - Constructor for class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay
SegmentedSavitzkyGolayDerivativeOrder - Class in adams.core.discovery.genetic: SegmentedSavitzkyGolay numPoints handler.
SegmentedSavitzkyGolayDerivativeOrder() - Constructor for class adams.core.discovery.genetic.SegmentedSavitzkyGolayDerivativeOrder
SegmentedSavitzkyGolayNumPoints - Class in adams.core.discovery.genetic: SegmentedSavitzkyGolay numPoints handler.
SegmentedSavitzkyGolayNumPoints() - Constructor for class adams.core.discovery.genetic.SegmentedSavitzkyGolayNumPoints
segments_offset - Static variable in class adams.data.io.input.foss.FossStdise: start of segment data.
segmentsTipText() - Method in class adams.opt.genetic.RonWeasley: Returns the tip text for this property.
segmentWidthsTipText() - Method in class adams.data.io.output.NIRSpectrumWriter: Returns the tip text for this property.
select(SpectrumPanel, float) - Static method in class adams.gui.visualization.spectrum.WaveNumberHitDetector: Selects a wave number.
selectColorGenerator() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Lets the user select a new color generator.
selectColorProvider() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Lets the user select a new color provider.
SelectedWaveNumberPaintlet - Class in adams.gui.visualization.spectrum: Paintlet for highlighting a selected SpectrumPoint point on a panel.
SelectedWaveNumberPaintlet() - Constructor for class adams.gui.visualization.spectrum.SelectedWaveNumberPaintlet
selectMissingValueColor() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Shows a color dialog for selecting the color representing missing values.
selectOverlay() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Lets the user select an overlay from a dialog.
selectPaintlet() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Lets the user select a new paintlet.
selectSelectionProcessor() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Lets the user select a selection processor from a dialog.
SelectSpectrumDialog - Class in adams.gui.selection: Dialog for loading spectrum data from the database and displaying it.
SelectSpectrumDialog(Dialog) - Constructor for class adams.gui.selection.SelectSpectrumDialog: Creates a modal dialog.
SelectSpectrumDialog(Dialog, String) - Constructor for class adams.gui.selection.SelectSpectrumDialog: Creates a modal dialog.
SelectSpectrumDialog(Frame) - Constructor for class adams.gui.selection.SelectSpectrumDialog: Creates a modal dialog.
SelectSpectrumDialog(Frame, String) - Constructor for class adams.gui.selection.SelectSpectrumDialog: Creates a modal dialog.
SelectSpectrumPanel - Class in adams.gui.selection: A panel that lists all the spectrums currently in the database.
SelectSpectrumPanel() - Constructor for class adams.gui.selection.SelectSpectrumPanel
SelectSpectrumPanel.TableModel - Class in adams.gui.selection: A simple table model for displaying the database IDs and Names.
selectWaveNumber() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Selects the spectrum point based on the wave number.
SelectWaveNumber - Class in adams.gui.scripting: Action parameters:
SelectWaveNumber() - Constructor for class adams.gui.scripting.SelectWaveNumber
SEPARATOR - Static variable in class adams.data.io.input.MPSSpectrumReader: the separator.
SEPARATOR - Static variable in class adams.data.spectrum.Spectrum: the separator for multiple spectra in a single file.
separatorTipText() - Method in class adams.data.io.input.ASCIIXYSpectrumReader: Returns the tip text for this property.
separatorTipText() - Method in class adams.data.io.input.SimpleXYZReader: Returns the tip text for this property.
separatorTipText() - Method in class adams.data.io.output.ASCIIXYSpectrumWriter: Returns the tip text for this property.
separatorTipText() - Method in class adams.data.io.output.SimpleXYZWriter: Returns the tip text for this property.
SER_4250 - adams.data.io.output.foss.FossOutputHelper.InstrumentHeader.InstrumentType
SER_51A - adams.data.io.output.foss.FossOutputHelper.InstrumentHeader.InstrumentType
serializationFileTipText() - Method in class adams.data.cleaner.instance.AbstractSerializableCleaner: Returns the tip text for this property.
serializationFileTipText() - Method in class adams.data.cleaner.spectrum.AbstractSerializableCleaner: Returns the tip text for this property.
serializationFileTipText() - Method in class adams.data.evaluator.instance.AbstractSerializableEvaluator: Returns the tip text for this property.
serializationFileTipText() - Method in class adams.data.postprocessor.instances.AbstractSerializablePostProcessor: Returns the tip text for this property.
serializationFileTipText() - Method in class adams.data.spectrumfilter.AbstractSerializableFilter: Returns the tip text for this property.
serialNoTipText() - Method in class adams.data.io.output.NIRSpectrumWriter: Returns the tip text for this property.
SERVICE - Static variable in class nz.ac.waikato.adams.webservice.rats.multispectrum.RatsMultiSpectrumServiceService
SERVICE - Static variable in class nz.ac.waikato.adams.webservice.rats.spectrum.RatsSpectrumServiceService
SERVICE - Static variable in class nz.ac.waikato.adams.webservice.spectral.get.SpectralGetServiceService
SERVICE - Static variable in class nz.ac.waikato.adams.webservice.spectral.put.SpectralPutServiceService
SERVICE - Static variable in class nz.ac.waikato.adams.webservice.spectral.transform.SpectralTransformServiceService
SESSION_FILE - Static variable in class adams.gui.visualization.spectrum.SpectrumExplorer: the file to store the recent files in.
SESSION_FILE - Static variable in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: the file to store the recent files in.
SESSION_FILENAME - Static variable in class adams.gui.tools.DeleteSampleDataPanel: the name of the session file.
SESSION_FILENAME - Static variable in class adams.gui.tools.ListSampleDataPanel: the name of the session file.
SESSION_FILENAME - Static variable in class adams.gui.tools.UpdateSampleDataPanel: the name of the session file.
set(int, Actor) - Method in class adams.flow.control.InstanceCleaner: Sets the actor at the given position.
set(int, Actor) - Method in class adams.flow.control.SpectrumCleaner: Sets the actor at the given position.
setAbsdiff(double) - Method in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: Sets the absolute difference.
setAbsolute(boolean) - Method in class adams.data.spectrumfilter.Covariance: Set absolute?
setAbsolute(boolean) - Method in class adams.data.spectrumfilter.LRCoeff: Set absolute?
setAbsolute(boolean) - Method in class adams.flow.transformer.SpectrumDiff: Sets whether to compute absolute difference or with sign.
setAccessoryName(String) - Method in class adams.data.io.output.ASCSpectrumWriter: Set accessory name.
setAction(String) - Method in class adams.flow.webservice.Transform: Sets the action (callable actor on the server side) to execute.
setAction(String) - Method in class nz.ac.waikato.adams.webservice.spectral.transform.TransformRequest: Sets the value of the action property.
setAddCommandLines(boolean) - Method in class adams.data.io.input.OpusSpectrumReaderExt: Sets whether to add the other command-lines to the report.
setAddDatabaseID(boolean) - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Sets whether to add the database ID.
setAddDatabaseID(boolean) - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Sets whether the database ID is added to the data or not.
setAddID(boolean) - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Sets whether to add the ID.
setAdditionalFields(Field[]) - Method in class adams.data.instances.AbstractSpectrumInstanceGenerator: Sets the additional fields to add.
setAddLog(boolean) - Method in class adams.data.io.input.OpusSpectrumReaderExt: Sets whether to add the entire log to the report.
setAddRawMetaData(boolean) - Method in class adams.data.io.input.JCampDX2SpectrumReader: Sets whether to add the raw meta-data to the report.
setAddRawMetaData(boolean) - Method in class adams.data.io.input.JCampDXSpectrumReader: Sets whether to add the raw meta-data to the report.
setAddSampleID(boolean) - Method in class adams.data.instances.AbstractSpectrumBasedInstanceGenerator: Sets whether the sample ID is added to the data or not.
setAddSampleID(boolean) - Method in interface adams.data.instances.InstanceGeneratorWithSampleID: Sets whether the sample ID is added to the data or not.
setAddSampleID(boolean) - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Sets whether the sample ID is added to the data or not.
setAddTraceToReport(boolean) - Method in class adams.data.io.input.OpusSpectrumReader: Sets whether to add the trace to the report.
setAddWaveNumber(boolean) - Method in class adams.data.instances.SimpleInstanceGenerator: Sets whether the wave number gets added to the output data as well.
setAddWaveNumber(boolean) - Method in class adams.data.instances.SimpleSpectralInstanceGenerator: Sets whether the wave number gets added to the output data as well.
setAddWaveNumber(boolean) - Method in class adams.data.spectrum.Amplitudes: Sets whether to add the wave numbers as well (preceding the amplitude).
setAdjustToVisibleData(boolean) - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Sets whether the display is adjusted to only the visible data or everything currently loaded.
setAlgorithm(AbstractPLS) - Method in class adams.data.spectrumfilter.PLS: Sets PLS algorithm to use.
setAlgorithm(AbstractSpectrumFeatureGenerator) - Method in class adams.flow.transformer.SpectrumFeatureGenerator: Sets the algorithm to use.
setAlgorithm(AbstractThreeWayDataFeatureGenerator) - Method in class adams.flow.transformer.ThreeWayDataFeatureGenerator: Sets the algorithm to use.
setAlgorithm(AbstractThreeWayDataMerge) - Method in class adams.flow.transformer.ThreeWayDataMerge: Sets the algorithm to use.
setAlgorithm(AbstractAlgorithm) - Method in class adams.flow.transformer.ThreeWayDataTrain: Sets the algorithm to use.
setAllSpectra(boolean) - Method in class adams.data.io.input.OpusSpectrumReaderExt: Sets whether to load all spectra.
setAlwaysShowMarkers(boolean) - Method in class adams.gui.visualization.spectrum.SpectrumPaintlet: Sets whether to always draw markers.
setAmplitude(float) - Method in class adams.data.spectrum.SpectrumPoint: Sets the amplitude.
setAmplitude(float) - Method in class adams.flow.transformer.SetSpectrumAmplitude: Sets the amplitude to set.
setAmplitude(float) - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.Wave: Sets the value of the amplitude property.
setAmplitude(float) - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.Wave: Sets the value of the amplitude property.
setAmplitude(float) - Method in class nz.ac.waikato.adams.webservice.spectral.get.Wave: Sets the value of the amplitude property.
setAmplitude(float) - Method in class nz.ac.waikato.adams.webservice.spectral.put.Wave: Sets the value of the amplitude property.
setAmplitude(float) - Method in class nz.ac.waikato.adams.webservice.spectral.transform.Wave: Sets the value of the amplitude property.
setAmplitudePrefix(String) - Method in class adams.data.instances.AbstractSpectrumInstanceGenerator: Sets the prefix for the wave number attributes.
setAmplitudePrefix(String) - Method in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: Sets the column prefix for the amplitudes.
setAmplitudeRows(Range) - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Sets the range of rows containing the amplitudes.
setAmplitudeType(SoilCaresScannerSpectrumReader.AmplitudeType) - Method in class adams.data.io.input.SoilCaresScannerSpectrumReader: Sets the type of amplitude to read.
setAntiAliasingEnabled(boolean) - Method in class adams.gui.visualization.spectrum.SimpleSpectrumPaintlet: Sets whether to use anti-aliasing.
setAntiAliasingEnabled(boolean) - Method in class adams.gui.visualization.spectrum.SpectrumPaintlet: Sets whether to use anti-aliasing.
setAntiAliasingEnabled(boolean) - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Sets whether to use anti-aliasing.
setApply(boolean) - Method in class adams.data.spectrumfilter.LRCoeff: Set apply coeff to spectrum?
setAscending(boolean) - Method in class adams.data.spectrum.AbstractSpectrumComparator: Sets whether to sort in ascending manner.
setAtomicMove(boolean) - Method in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: Sets whether to attempt atomic move operation.
setAtomicMove(boolean) - Method in class adams.flow.standalone.rats.LoadSpectrumFileOutput: Sets whether to attempt atomic move operation.
setAttributeName(String) - Method in class adams.data.cleaner.instance.MinMax: Sets the name of the attribute to work on.
setAttributeRange(Range) - Method in class adams.data.cleaner.instance.IQRCleaner: Sets the attribute range to work on.
setAttributeRange(WekaAttributeRange) - Method in class adams.data.spectrumanalysis.FastICA: Sets the attribute range parameter.
setAutoCommit(boolean) - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Sets whether to use auto-commit for bulk transaction.
setAutoCommit(boolean) - Method in class adams.flow.transformer.BulkSpectrumDbWriter: Sets whether to use auto-commit for bulk transaction.
setBackends(SpectralDbBackend[]) - Method in class adams.db.mirrored.SpectralDbBackend: Sets the backends to use.
setBase(Classifier) - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Set the base classifier to be used.
setBaseFilter(AbstractMultiSpectrumFilter) - Method in class adams.data.multifilter.FilteredMultiSpectrumFilter: Sets the base filter.
setBatchFilter(BatchFilter) - Method in class adams.data.spectrumfilter.KennardStone: Set the batch filter to apply before selection
setBatchSize(int) - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Sets the batch size to use.
setBatchSize(int) - Method in class adams.flow.transformer.BulkSpectrumDbWriter: Sets the batch size to use.
setBelowCountThreshold(int) - Method in class adams.data.multispectrumoperation.outlierremoval.CorrelationBasedThreshold: Sets the number of spectra below threshold that trigger rejection of the spectrum.
setBelowCountThreshold(int) - Method in class adams.data.multispectrumoperation.outlierremoval.CosineSimilarityBasedThreshold: Sets the number of spectra below threshold that trigger rejection of the spectrum.
setBufferSize(int) - Method in class adams.data.io.input.ZippedSpectrumReader: Sets the buffer size for the stream.
setBuildWait(int) - Method in class adams.data.evaluator.instance.FakeEvaluator: Sets the time in msec to wait when calling buildClassifier.
setCache(BaseString) - Method in class adams.flow.transformer.SpectralAngleMapper: Sets the name of the LRU cache to use.
setCallableName(CallableActorReference) - Method in class adams.flow.transformer.MultiSpectrumAdd: Sets the name of the callable actor to use.
setCheck(AbstractPredictionCheck) - Method in class adams.flow.transformer.PredictionCheck: Sets the check to use.
setCheckWaveNumberAlignment(boolean) - Method in class adams.flow.transformer.SpectralAngleMapper: Sets whether wave-number alignment should be checked.
setChunkSize(int) - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Sets the chunk size to use for loading data from the database.
setClassifier(Classifier) - Method in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: Sets the classifier.
setClassifier(Classifier) - Method in class adams.data.cleaner.instance.RemoveOutliers: Sets the classifier.
setClassifier(Classifier) - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Sets the classifier to use.
setClassifier(Classifier) - Method in class adams.data.evaluator.instance.CrossValidatedPrediction: Sets the classifier to use.
setClassifier(Classifier) - Method in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: Sets the interval estimator to use.
setClassifier(Classifier) - Method in interface adams.data.evaluator.instance.WekaClassifierBasedEvaluator: Sets the classifier to use.
setClassifierFirst(Classifier) - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Sets the classifier to be used in conjunction with Savitzky-Golay filter with first derivative.
setClassifierNone(Classifier) - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Sets the classifier to be used in conjunction with Savitzky-Golay filter with no derivative.
setClassifiers(Classifier[]) - Method in class adams.data.evaluator.instance.EnsembleEvaluator: Sets the classifiers to use.
setClassifiers(Classifier[]) - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Set the classifiers to be used.
setClassifiers(Classifier[]) - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Sets the classifiers to use internally.
setClassifierSecond(Classifier) - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Sets the classifier to be used in conjunction with Savitzky-Golay filter with second derivative.
setClassLabels(BaseString[]) - Method in class adams.data.instances.AbstractFieldInstanceGeneratorWithClass: Sets the labels for a nominal class attribute.
setClassLabels(BaseString[]) - Method in class adams.data.instances.AbstractSpectrumInstanceGeneratorWithClass: Sets the labels for a nominal class attribute.
setClassLabels(BaseString[]) - Method in interface adams.data.instances.InstanceGeneratorWithClassLabels: Sets the labels for a nominal class attribute.
setCleanAfterBuild(boolean) - Method in class adams.flow.transformer.Evaluator: Sets whether to discard the internal evaluator again after building it.
setCleaner(AbstractCleaner) - Method in class adams.flow.control.InstanceCleaner: Sets the cleaner.
setCleaner(AbstractCleaner) - Method in class adams.flow.transformer.Cleaner: Sets the cleaner to use.
setCleaner(AbstractCleaner) - Method in class adams.flow.control.SpectrumCleaner: Sets the cleaner.
setCleanerDetailsOutput(PlaceholderFile) - Method in class adams.flow.transformer.Cleaner: Sets the file for the cleaner details.
setClient(String) - Method in class adams.data.io.output.NIRSpectrumWriter: Set client.
setColor(Color) - Method in class adams.gui.visualization.spectrum.SelectedWaveNumberPaintlet: Sets the color to paint the point with.
setColor(Color) - Method in class adams.gui.visualization.spectrum.SpectrumContainer: Sets the color to use.
setColorField(Field) - Method in class adams.gui.visualization.spectrum.ReportColorSpectrumPaintlet: Sets the report field that contains the color.
setColorGenerator(ColorGradientGenerator) - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Sets the generator for the color gradient.
setColorGenerator(ColorGradientGenerator) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Sets the generator for the color gradient.
setColorProvider(ColorProvider) - Method in class adams.flow.sink.SpectrumDisplay: Sets the color provider to use.
setColorProvider(ColorProvider) - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: Sets the color provider to use.
setColorProvider(ColorProvider) - Method in class adams.gui.visualization.spectrum.SpectrumPaintletStringField: Sets the color provider to use.
setColSampleDataNames(SpreadSheetColumnIndex) - Method in class adams.data.conversion.SpreadSheetColumnsToSampleData: Sets the column that contains the sample data names.
setColSampleDataNames(SpreadSheetColumnIndex) - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Sets the column that contains the sample data names.
setColsSampleDataValues(SpreadSheetColumnRange) - Method in class adams.data.conversion.SpreadSheetColumnsToSampleData: Sets the columns to get the sample data values from.
setColumnAmplitude(SpreadSheetColumnIndex) - Method in class adams.data.conversion.SpreadSheetToSpectrum: Sets the column with the amplitude information.
setColumnData(SpreadSheetColumnIndex) - Method in class adams.data.conversion.SpreadSheetTo3DTensor: Sets the data column.
setColumnData(SpreadSheetColumnIndex) - Method in class adams.data.conversion.SpreadSheetToThreeWayData: Sets the data column.
setColumnID(SpreadSheetColumnIndex) - Method in class adams.data.conversion.SpreadSheetRowsToSampleData: Sets the (optional) column that contains the sample ID.
setColumnID(SpreadSheetColumnIndex) - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Sets the (optional) column that contains the sample ID.
setColumnMeasurementName(String) - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Sets the name of the column with the reference value name.
setColumnMeasurementValue(String) - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Sets the name of the column with the reference value.
setColumns(SpreadSheetColumnRange) - Method in class adams.data.conversion.SpreadSheetTo2DTensor: Sets the columns of the matrix.
setColumnSampleID(SpreadSheetColumnIndex) - Method in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: Sets the column with the sample ID.
setColumnSampleID(String) - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Sets the name of the column with the sample ID.
setColumnSampleType(String) - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Sets the name of the column with the sample type.
setColumnsAmplitude(SpreadSheetColumnRange) - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Sets the columns with the amplitude information.
setColumnsAmplitude(SpreadSheetColumnRange) - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Sets the columns with amplitude information.
setColumnsBoolean(SpreadSheetColumnRange) - Method in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: Sets the range of columns with boolean reference values.
setColumnsNumeric(SpreadSheetColumnRange) - Method in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: Sets the range of columns with numeric reference values.
setColumnsSampleData(SpreadSheetColumnRange) - Method in class adams.data.conversion.SpreadSheetRowsToSampleData: Sets the columns with sampledata.
setColumnsSampleData(SpreadSheetColumnRange) - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Sets the columns with sampledata.
setColumnsSampleData(SpreadSheetColumnRange) - Method in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: Sets the range of columns with the reference values.
setColumnWaveNumber(SpreadSheetColumnIndex) - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Sets the column with the wavenumber information.
setColumnWaveNumber(SpreadSheetColumnIndex) - Method in class adams.data.conversion.SpreadSheetToSpectrum: Sets the column with the wavenumber information.
setColumnX(SpreadSheetColumnIndex) - Method in class adams.data.conversion.SpreadSheetTo3DTensor: Sets the X column.
setColumnX(SpreadSheetColumnIndex) - Method in class adams.data.conversion.SpreadSheetToThreeWayData: Sets the X column.
setColumnY(SpreadSheetColumnIndex) - Method in class adams.data.conversion.SpreadSheetTo3DTensor: Sets the X column.
setColumnY(SpreadSheetColumnIndex) - Method in class adams.data.conversion.SpreadSheetToThreeWayData: Sets the X column.
setColumnZ(SpreadSheetColumnIndex) - Method in class adams.data.conversion.SpreadSheetTo3DTensor: Sets the Z column.
setColumnZ(SpreadSheetColumnIndex) - Method in class adams.data.conversion.SpreadSheetToThreeWayData: Sets the Z column.
setCombine(boolean) - Method in class adams.gui.visualization.spectrum.SpectrumExportDialog: Sets whether the files should get combined if possible.
setComponent(String) - Method in class adams.data.conversion.WekaPredictionContainerToEvaluationContainer: Sets the component to use for the evaluation.
setComponent(String) - Method in class adams.flow.transformer.Evaluator: Sets the component identifier to use.
setCondition(BooleanCondition) - Method in class adams.data.spectrumfilter.ConditionalReportField: Sets the condition to evaluate.
setConditionBoolean(boolean) - Method in class adams.data.multifilter.PickByReportValue: Sets whether the boolean field must be true or false.
setConditionNumericMax(double) - Method in class adams.data.multifilter.PickByReportValue: Sets the upper bound that numeric fields must match.
setConditionNumericMin(double) - Method in class adams.data.multifilter.PickByReportValue: Sets the lower bound that numeric fields must match.
setConditions(AbstractConditions) - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Sets the conditions container to use for retrieving the spectra.
setConditions(AbstractConditions) - Method in class adams.data.spectrumfilter.Covariance: Sets the conditions container to use for retrieving the spectra.
setConditions(AbstractConditions) - Method in class adams.data.spectrumfilter.LRCoeff: Sets the conditions container to use for retrieving the spectra.
setConditions(OrphanedSampleDataConditions) - Method in class adams.flow.source.OrphanedSampleDataIdSupplier: Sets whether to output the items as array or as single strings.
setConditionString(BaseRegExp) - Method in class adams.data.multifilter.PickByReportValue: Sets the regular expression to apply to string fields.
setConfidenceLevel(double) - Method in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: Sets the confidence level to use.
setConstituents(Field[]) - Method in class adams.data.io.output.CALSpectrumWriter: Sets the constituents.
setContainerManager(SpectrumContainerManager) - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Sets the manager for handling the containers.
setConversion(Conversion) - Method in class adams.data.spectrumfilter.ReportFieldFromStringValue: Sets the conversion to apply to the extracted string value.
setConversion(Conversion) - Method in class adams.flow.transformer.SetEvaluationMetaData: Sets the type of conversion to perform on the value before storing it in the evaluation container.
setConverter(AbstractFeatureConverter) - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Sets the feature converter to use.
setConverter(AbstractFeatureConverter) - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Sets the feature converter to use.
setCorrection(AbstractDetrend) - Method in class adams.data.spectrumfilter.Detrend: Sets the correction scheme to use.
setCorrection(AbstractMultiplicativeScatterCorrection) - Method in class adams.data.spectrumfilter.MultiplicativeScatterCorrection: Sets the correction scheme to use.
setCurrentFile(File) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Sets the current file.
setCustomComparator(AbstractSpectrumComparator) - Method in class adams.data.conversion.SpectraToMultiSpectrum: Sets the custom comparator.
setCustomComparator(AbstractSpectrumComparator) - Method in class adams.data.spectrum.MultiSpectrum: Sets the custom comparator to use.
setCustomComparator(AbstractSpectrumComparator) - Method in class adams.flow.transformer.SpectrumFileReader: Sets the custom comparator.
setData(double) - Method in class adams.data.threeway.L2Point: Sets the value.
setData(MultiSpectrum) - Method in class adams.flow.standalone.rats.WSMultiSpectrumReception: For setting the data received from the webservice.
setData(Spectrum) - Method in class adams.data.statistics.SpectrumStatistic: Sets the data to use as basis for the calculations.
setData(Spectrum) - Method in class adams.flow.standalone.rats.WSSpectrumReception: For setting the data received from the webservice.
setData(Spectrum) - Method in class adams.gui.visualization.spectrum.SpectrumContainer: Sets the spectrum.
setData(ThreeWayData) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Sets the data to display.
setData(Instances) - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Set training data.
setDatabaseConnection(AbstractDatabaseConnection) - Method in class adams.data.cleaner.instance.AbstractDatabaseConnectionCleaner: Sets the database connection object to use.
setDatabaseConnection(AbstractDatabaseConnection) - Method in class adams.data.cleaner.spectrum.AbstractDatabaseConnectionCleaner: Sets the database connection object to use.
setDatabaseConnection(AbstractDatabaseConnection) - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Sets the database connection object to use.
setDatabaseConnection(AbstractDatabaseConnection) - Method in class adams.data.io.input.AbstractSampleDataReader: Sets the database connection object to use.
setDatabaseConnection(AbstractDatabaseConnection) - Method in class adams.gui.selection.SelectSpectrumDialog: Sets the database connection object to use.
setDatabaseConnection(AbstractDatabaseConnection) - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: Sets the database connection object to use.
setDatabaseConnection(AbstractDatabaseConnection) - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Sets the database connection object to use.
setDatabaseID(int) - Method in class adams.data.spectrum.Spectrum: Sets the database ID of the sequence.
setDatabaseID(int) - Method in class adams.data.threeway.ThreeWayData: Set the database ID.
setDataPaintlet(Paintlet) - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Sets the paintlet to use for painting the data.
setDataPanel(ThreeWayDataHeatmapPanel) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractThreeWayDataOverlay: Sets the data panel this overlay is for.
setDataPoints(int) - Method in class adams.data.io.output.ASCSpectrumWriter: Set number of data points. -1 means use as many as in spectrum.
setDataTypes(DataType[]) - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Sets the data types to import.
setDateFormat(DateFormatString) - Method in class adams.data.io.input.MPSSpectrumReader: Sets the date format for parsing the MPSSpectrumReader.KEY_TIME_MEASURED field.
setDefaultColor(Color) - Method in class adams.gui.visualization.spectrum.ReportColorSpectrumPaintlet: Sets the default color to use when no color information in the report.
setDefaultColor(Color) - Method in class adams.gui.visualization.spectrum.SpectrumPaintletNumericField: Sets the default color to use when then report field is missing or invalid.
setDefaultColor(Color) - Method in class adams.gui.visualization.spectrum.SpectrumPaintletStringField: Sets the default color to use when then report field is missing or invalid.
setDenormalize(boolean) - Method in class adams.data.io.input.SimpleEEMReader: Sets whether to denormalize the amplitudes using the 'Normalized by ' value.
setDerivativeOrder(int) - Method in class weka.filters.unsupervised.attribute.SavitzkyGolayRange: Sets the order of the derivative.
setDerivativeOrder(int) - Method in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: Sets the order of the derivative.
setDescending(boolean) - Method in class adams.data.io.output.ASCSpectrumWriter: Sets whether to output spectrum points by descending x-axis.
setDescending(boolean) - Method in class adams.data.io.output.DPTSpectrumWriter: Sets whether to output spectrum points by descending x-axis.
setDetector(AbstractOutlierDetector) - Method in class adams.flow.transformer.MultiSpectrumOutlierDetector: Sets the outlier detector to use.
setDetector(AbstractOutlierDetector) - Method in class adams.data.cleaner.instance.RemoveOutliers: Sets the detector.
setDontUpdateID(boolean) - Method in class adams.data.multifilter.AbstractMultiSpectrumFilter: Sets whether ID update is suppressed.
setEnd(int) - Method in class weka.filters.unsupervised.attribute.SavitzkyGolayRange: Sets the last amplitude.
setEndDate(BaseDateTime) - Method in class adams.db.AbstractSpectrumConditions: Sets the end date.
setEndDate(BaseDateTime) - Method in class adams.db.OrphanedSampleDataConditions: Sets the end date.
setEndPoints(BaseFloat[]) - Method in class adams.data.io.output.NIRSpectrumWriter: Set end points.
setEOC(Integer) - Method in class adams.data.io.output.NIRSpectrumWriter: Set number of EOC's per rev
setEvalMax(float) - Method in class adams.data.evaluator.instance.FakeEvaluator: Sets the maximum value to output.
setEvalMin(float) - Method in class adams.data.evaluator.instance.FakeEvaluator: Sets the minimum value to output.
setEvaluation(String) - Method in class adams.flow.transformer.predictioncheck.Range: Sets the evaluation to check.
SetEvaluationMetaData - Class in adams.flow.transformer: Adds the specified value under the listed key in the evaluation container.
SetEvaluationMetaData() - Constructor for class adams.flow.transformer.SetEvaluationMetaData
setEvaluator(AbstractEvaluator) - Method in class adams.flow.transformer.Evaluator: Sets the evaluator to use.
setEvaluatorResetVariable(VariableName) - Method in class adams.flow.transformer.Evaluator: Sets the variable to monitor for changes in order to reset the evaluator.
setEvalWait(int) - Method in class adams.data.evaluator.instance.FakeEvaluator: Sets the time in msec to wait when calling classifyInstance.
setExclude(BaseRegExp) - Method in class weka.filters.unsupervised.attribute.SegmentedDownSample: Sets the regular expression that identifies attributes to be excluded from the splits.
setExclude(BaseRegExp) - Method in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: Sets the regular expression that identifies attributes to be excluded from the splits.
setExcludeDummies(boolean) - Method in class adams.db.AbstractSpectrumConditions: Sets whether to exclude spectra with reports flagged as dummies or not.
setExpression(MathematicalExpressionText) - Method in class adams.data.spectrumfilter.AmplitudeExpression: Sets the mathematical expression to evaluate.
setExpression(MathematicalExpressionText) - Method in class adams.data.spectrumfilter.WaveNumberExpression: Sets the mathematical expression to evaluate.
setExtract(BaseRegExp) - Method in class adams.data.spectrumfilter.ReportFieldFromStringValueWithLookup: Sets the regexp for extracting the substring to use in the lookup.
setFactor(double) - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Sets the factor to multiply the inter-percentile range with.
setFailure(String) - Method in class adams.data.spectrumfilter.ConditionalReportField: Sets the failure value, ie the value to use when the condition evaluates to true.
setFFTSampleSize(int) - Method in class adams.data.conversion.SpectrumToBufferedImage: Sets the FFT sample size (power of 2).
setFFTSampleSize(int) - Method in class adams.data.spectrumimage.Spectrogram: Sets the FFT sample size (power of 2).
setField(Field) - Method in class adams.data.cleaner.spectrum.MinMax: Sets the field to use.
setField(Field) - Method in class adams.data.instances.AbstractFieldInstanceGeneratorWithClass: Sets the field to act as class attribute.
setField(Field) - Method in class adams.data.instances.AbstractSpectrumInstanceGeneratorWithClass: Sets the field to act as class attribute.
setField(Field) - Method in interface adams.data.instances.InstanceGeneratorWithTargetField: Sets the field to act as class attribute.
setField(Field) - Method in class adams.data.multifilter.PickByReportValue: Sets the field to inspect.
setField(Field) - Method in class adams.data.spectrum.SpectrumComparatorByReportValue: Sets the field to inspect.
setField(Field) - Method in class adams.data.spectrumfilter.Covariance: Set Field.
setField(Field) - Method in class adams.data.spectrumoutlier.MinMax: Sets the field.
setField(Field) - Method in class adams.data.spectrumoutlier.StringMatcher: Sets the reference, i.e., the class.
setField(Field) - Method in class adams.db.SpectrumConditionsSingle: Sets the field to require.
setField(Field) - Method in class adams.flow.transformer.DeleteSampleDataValueByExpression: Sets the field to delete from the report.
setField(Field) - Method in class adams.flow.transformer.GetSampleDataValue: Sets the field to retrieve from the report.
setField(Field) - Method in class adams.flow.transformer.SetSampleDataValue: Sets the field to retrieve from the report.
setField(Field) - Method in class adams.gui.visualization.spectrum.SpectrumPaintletNumericField: Sets the numeric field to determine the color with.
setField(Field) - Method in class adams.gui.visualization.spectrum.SpectrumPaintletStringField: Sets the string field to determine the color with.
setFields(Field[]) - Method in class adams.data.instances.AbstractFieldInstanceGenerator: Sets the targets to add.
setFields(Field[]) - Method in class adams.data.multireportfilter.PullUpFields: Sets the fields to pull up.
setFields(Field[]) - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Sets the targets to add.
setFields(Field[]) - Method in class adams.data.spreadsheetrowgenerator.SampleDataOnlyRowGenerator: Sets the fields to add.
setFields(Field[]) - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Sets the targets to add.
setFields(Field[]) - Method in class adams.db.SpectrumConditionsMulti: Sets the fields to require.
setFields(Field[]) - Method in class adams.flow.transformer.DeleteDbSampleDataValue: Sets the fields to delete from the report.
setFields(Field[]) - Method in class adams.flow.transformer.DeleteSampleDataValue: Sets the fields to delete from the report.
setFields(Field[]) - Method in class adams.flow.transformer.SampleDataValueDbWriter: Sets the fields to store in the database.
setFileID(String) - Method in class adams.data.io.output.NIRSpectrumWriter: Set file id.
setFilenameGenerator(AbstractFilenameGenerator) - Method in class adams.flow.standalone.rats.SaveMultiSpectrumFileOutput: Sets the filename generator to use.
setFilenameGenerator(AbstractFilenameGenerator) - Method in class adams.flow.standalone.rats.SaveSpectrumFileOutput: Sets the filename generator to use.
setFilter(Filter) - Method in class adams.data.io.input.FilteredSpectrumReader: Sets the filter to apply to the data that was read.
setFilter(Filter) - Method in class adams.data.io.output.FilteredSpectrumWriter: Sets the filter to apply to the data that was read.
setFilter(Filter) - Method in class adams.data.spectrumfilter.SubtractSpectrum: Sets the filter to run.
setFilter(Filter) - Method in class adams.flow.rest.TransformSpectrum: Sets the filter to use.
setFilter(Filter<Spectrum>) - Method in class adams.data.spectrumfilter.Covariance: Set filter.
setFilter(AbstractMultiSpectrumFilter) - Method in class adams.flow.transformer.MultiSpectrumFilter: Sets the filter to use.
setFilter(AbstractMultiSpectrumFilter) - Method in class adams.flow.transformer.MultiSpectrumOutlierDetector: Sets the filter to use.
setFilter(AbstractMultiSpectrumReportFilter) - Method in class adams.flow.transformer.MultiSpectrumReportFilter: Sets the filter to use.
setFilter(Filter) - Method in class adams.data.cleaner.instance.IQRCleaner: Sets the IQR filter.
setFilter(Filter) - Method in class adams.data.evaluator.instance.DistanceToCenter: Sets the filter to use.
setFilter(Filter) - Method in class adams.data.evaluator.instance.DistanceToClosest: Sets the filter to use.
setFilter(Filter) - Method in class adams.data.postprocessor.instances.WekaFilter: Sets the filter to use.
setFilter(Filter) - Method in class weka.filters.unsupervised.attribute.SpectrumFilter: Sets the base filter.
setFirst(double) - Method in class adams.data.spectrumfilter.AbstractStandardiseFilter: Sets the start data point
setFirstWave(float) - Method in class adams.flow.transformer.InstanceToSpectrum: Sets the starting point for the wave numbers.
setFirstXPoint(Double) - Method in class adams.data.io.output.ASCSpectrumWriter: Set first X wavenumber.
setFlip(boolean) - Method in class adams.data.spectrumoutlier.Swapped: Sets whether to swap left and right half for the comparison.
setFlowContent(Actor) - Method in class adams.data.cleaner.spectrum.AbstractCleaner: Sets the flow context.
setFlowContext(Actor) - Method in class adams.data.cleaner.instance.AbstractCleaner: Sets the flow context.
setFlowContext(Actor) - Method in class adams.data.postprocessor.instances.AbstractPostProcessor: Sets the flow context.
setFlowContext(Actor) - Method in class adams.data.spectrumfilter.WekaFilterToReport: Sets the flow context.
setFolds(int) - Method in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: Sets the folds.
setFolds(int) - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Sets the number of folds.
setFolds(int) - Method in class adams.data.evaluator.instance.CrossValidatedPrediction: Sets the number of folds.
setFolds(int) - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Sets the number of folds to use (>= 2).
setFont(Font) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Sets the font for the text.
setFormat(BaseRegExp) - Method in class adams.data.multispectrumoperation.Remove: Sets the regular expression that the format of a spectrum must match in order to get removed.
setFormat(BaseRegExp) - Method in class adams.db.AbstractSpectrumConditions: Sets the regular expression for the format.
setFormat(BaseRegExp) - Method in class adams.db.SpectrumIDConditions: Sets the regular expression for the format.
setFormat(BaseRegExp) - Method in class adams.flow.transformer.MultiSpectrumRemove: Sets the regular expression that the format of a spectrum must match in order to get removed.
setFormat(String) - Method in class adams.data.conversion.ArrayToSpectrum: Sets the format.
setFormat(String) - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Sets the format to use for the spectrum.
setFormat(String) - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Sets the format to use for the spectrum.
setFormat(String) - Method in class adams.data.conversion.SpreadSheetToSpectrum: Sets the format to use for the spectrum.
setFormat(String) - Method in class adams.data.io.input.AbstractSampleDataReader: Sets the format of spectrum to use.
setFormat(String) - Method in class adams.data.io.input.AbstractSpectrumReader: Sets the format string of the data (always converted to upper case).
setFormat(String) - Method in class adams.data.io.input.AbstractThreeWayDataReader: Sets the format string of the data (always converted to upper case).
setFormat(String) - Method in class adams.data.spectrum.Spectrum: Sets the data format (always converted to upper case).
setFormat(String) - Method in class adams.flow.condition.bool.HasSpectrum: Sets the format string of the data (always converted to upper case).
setFormat(String) - Method in class adams.flow.transformer.datacontainer.LoadSampleData: Sets the format of the spectrum to obtain the reference data from.
setFormat(String) - Method in class adams.flow.transformer.DeleteSpectrum: Sets the format of spectrum to retrieve from the database.
setFormat(String) - Method in class adams.flow.transformer.report.UpdateDatabaseID: Sets the format string of the data (always converted to upper case).
setFormat(String) - Method in class adams.flow.transformer.SpectrumDbReader: Sets the format of spectrum to retrieve from the database.
setFormat(String) - Method in class adams.flow.webservice.Get: Sets the format of the spectrum to retrieve
setFormat(String) - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.Spectrum: Sets the value of the format property.
setFormat(String) - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.Spectrum: Sets the value of the format property.
setFormat(String) - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.UploadRequest: Sets the value of the format property.
setFormat(String) - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.UploadResponse: Sets the value of the format property.
setFormat(String) - Method in class nz.ac.waikato.adams.webservice.spectral.get.GetRequest: Sets the value of the format property.
setFormat(String) - Method in class nz.ac.waikato.adams.webservice.spectral.get.GetResponse: Sets the value of the format property.
setFormat(String) - Method in class nz.ac.waikato.adams.webservice.spectral.get.Spectrum: Sets the value of the format property.
setFormat(String) - Method in class nz.ac.waikato.adams.webservice.spectral.put.PutRequest: Sets the value of the format property.
setFormat(String) - Method in class nz.ac.waikato.adams.webservice.spectral.put.PutResponse: Sets the value of the format property.
setFormat(String) - Method in class nz.ac.waikato.adams.webservice.spectral.put.Spectrum: Sets the value of the format property.
setFormat(String) - Method in class nz.ac.waikato.adams.webservice.spectral.transform.Spectrum: Sets the value of the format property.
setFormat(String) - Method in class nz.ac.waikato.adams.webservice.spectral.transform.TransformRequest: Sets the value of the format property.
setFormat(String) - Method in class nz.ac.waikato.adams.webservice.spectral.transform.TransformResponse: Sets the value of the format property.
setFormats(BaseString[]) - Method in class adams.data.multifilter.AbstractFormatsBasedMultiSpectrumFilter: Sets the formats of the spectra to use.
setGenerateSampleIDs(boolean) - Method in interface adams.flow.source.SampleIdSource: Sets whether to generate database IDs or sample IDs.
setGenerateSampleIDs(boolean) - Method in class adams.flow.source.SpectrumIdSupplier: Sets whether to generate database IDs or sample IDs.
setGenerator(AbstractInstanceGenerator) - Method in class adams.data.spectrumanalysis.AbstractWekaSpectrumAnalysis: Sets the instance generator.
setGenerator(AbstractInstanceGenerator) - Method in class adams.data.spectrumfilter.LRCoeff: Sets the generator to use.
setGenerator(AbstractInstanceGenerator) - Method in class adams.data.spectrumfilter.PCA: Sets the instance generator to use.
setGenerator(AbstractInstanceGenerator) - Method in class adams.data.spectrumfilter.PLS: Sets the instance generator to use.
setGenerator(AbstractInstanceGenerator) - Method in class adams.data.spectrumfilter.WekaFilterToReport: Sets the generator to use.
setGenerator(AbstractInstanceGenerator) - Method in class adams.flow.transformer.InstanceGenerator: Sets the generator to use.
setGenerator(AbstractInstanceGenerator) - Method in class adams.gui.visualization.spectrum.SpectrumDatasetExportDialog: Sets the generator to use.
setGenerator(AbstractSpectrumImageGenerator) - Method in class adams.data.io.output.SpectrumImageWriter: Sets the generator to use.
setGenerator(AbstractSpreadSheetRowGenerator) - Method in class adams.flow.transformer.SpreadSheetRowGenerator: Sets the generator to use.
setGenerator(ArrayHistogram) - Method in class adams.data.threewayfeatures.Histogram: Sets the histogram generator.
setGenerator(ColorGradientGenerator) - Method in class adams.data.conversion.SpectrumToBufferedImage: Sets the color generator.
setGenerator(ColorGradientGenerator) - Method in class adams.data.spectrumimage.Spectrogram: Sets the color generator.
setGenerator(ColorGradientGenerator) - Method in class adams.gui.visualization.spectrum.SpectrumPaintletNumericField: Sets the color gradient generator to use.
setGetProductCodeFromAttribute(Boolean) - Method in class adams.flow.transformer.InstanceToSpectrum: Set product code from instance attribute?
setGroup(int) - Method in class adams.data.io.input.sampleidextraction.RegExp: Sets the regular expression group that contains the sample ID from the file name (w/o path).
setGroup(String) - Method in class adams.data.spectrumfilter.ReportFieldFromStringValue: Sets the group expression for generating the value to be stored.
setGroupExtraction(GroupExtractor) - Method in class adams.data.io.input.ExtractIdAndTypeSpectrumReader: Sets the scheme for extracting the sample type.
setGroupExtraction(GroupExtractor) - Method in class adams.data.io.input.ExtractIdAndTypeThreeWayDataReader: Sets the scheme for extracting the sample type.
setHeaderContainsWaveNumber(boolean) - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Sets whether to extract the wave number from the header columns.
setHeight(int) - Method in class adams.data.spectrumimage.Intensity: Sets the height of the image.
setHeight(int) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlayWithDimensions: Sets the height of the overlay.
setICA(FastICA) - Method in class adams.data.spectrumanalysis.FastICA: Sets the ICA analysis.
setId(String) - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.MultiSpectrum: Sets the value of the id property.
setId(String) - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.Spectrum: Sets the value of the id property.
setId(String) - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.UploadRequest: Sets the value of the id property.
setId(String) - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.UploadResponse: Sets the value of the id property.
setId(String) - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.Spectrum: Sets the value of the id property.
setId(String) - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.UploadRequest: Sets the value of the id property.
setId(String) - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.UploadResponse: Sets the value of the id property.
setId(String) - Method in class nz.ac.waikato.adams.webservice.spectral.get.GetRequest: Sets the value of the id property.
setId(String) - Method in class nz.ac.waikato.adams.webservice.spectral.get.GetResponse: Sets the value of the id property.
setId(String) - Method in class nz.ac.waikato.adams.webservice.spectral.get.Spectrum: Sets the value of the id property.
setId(String) - Method in class nz.ac.waikato.adams.webservice.spectral.put.PutRequest: Sets the value of the id property.
setId(String) - Method in class nz.ac.waikato.adams.webservice.spectral.put.PutResponse: Sets the value of the id property.
setId(String) - Method in class nz.ac.waikato.adams.webservice.spectral.put.Spectrum: Sets the value of the id property.
setId(String) - Method in class nz.ac.waikato.adams.webservice.spectral.transform.Spectrum: Sets the value of the id property.
setId(String) - Method in class nz.ac.waikato.adams.webservice.spectral.transform.TransformRequest: Sets the value of the id property.
setId(String) - Method in class nz.ac.waikato.adams.webservice.spectral.transform.TransformResponse: Sets the value of the id property.
setID(String) - Method in class adams.data.conversion.ArrayToSpectrum: Sets the sample ID.
setID(String) - Method in class adams.data.conversion.SpreadSheetToSpectrum: Sets the ID to use for the spectrum.
setID(String) - Method in class adams.data.conversion.WekaPredictionContainerToEvaluationContainer: Sets the ID to use for the evaluation (to be used instead of component).
setID(String) - Method in class adams.data.sampledata.SampleData: Sets the ID.
setID(String) - Method in class adams.data.spectrum.Spectrum: Sets the ID of the spectrum.
setID(String) - Method in class adams.data.threeway.ThreeWayData: Sets the ID of the chromatogram.
setID(String) - Method in class adams.data.threewayreport.ThreeWayReport: Sets the ID.
setID(String) - Method in class adams.flow.condition.bool.HasSpectrum: Sets the ID to look, if not obtained from the passing through ID handler.
setID(String) - Method in class adams.flow.source.NewSpectrum: Sets the ID to use for the spectrum.
setID(String) - Method in class adams.flow.webservice.Get: Sets the ID of the spectrum to retrieve
setID(String) - Method in class adams.gui.visualization.spectrum.SpectrumContainer: Sets the ID to use for display.
setID(String) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataContainer: Sets the container's ID.
setIDExtraction(IDExtractor) - Method in class adams.data.io.input.ExtractIdAndTypeSpectrumReader: Sets the sample ID extractor to use.
setIDExtraction(IDExtractor) - Method in class adams.data.io.input.ExtractIdAndTypeThreeWayDataReader: Sets the sample ID extractor to use.
setIdfield(String) - Method in class adams.data.io.input.CALSpectrumReader: Set id field.
setIDs(String[]) - Method in class adams.gui.tools.DeleteSampleDataPanel: Updates the model with the specified IDs.
setIDs(String[]) - Method in interface adams.gui.tools.idprovider.IDConsumer: Updates the model with the specified IDs.
setIDs(String[]) - Method in class adams.gui.tools.ListSampleDataPanel: Updates the model with the specified IDs.
setIDs(String[]) - Method in class adams.gui.tools.UpdateSampleDataPanel: Updates the model with the specified IDs.
setIgnoreWaveNumbers(boolean) - Method in class adams.data.io.input.SimpleEEMReader: Sets whether to ignore the wave numbers and use row/col indices instead.
setImageType(ImageType) - Method in class adams.data.spectrumimage.AbstractSpectrumImageGenerator: Sets the type of image to generate.
setImplementation(RatsMultiSpectrumService) - Method in class adams.flow.webservice.multispectrum.RatsMultiSpectrumServiceWS: Sets the webservice implementation to use.
setImplementation(RatsSpectrumService) - Method in class adams.flow.webservice.spectrum.RatsSpectrumServiceWS: Sets the webservice implementation to use.
setImplementation(SpectralGetService) - Method in class adams.flow.webservice.SpectralGetServiceWS: Sets the webservice implementation to use.
setImplementation(SpectralPutService) - Method in class adams.flow.webservice.SpectralPutServiceWS: Sets the webservice implementation to use.
setImplementation(SpectralTransformService) - Method in class adams.flow.webservice.SpectralTransformServiceWS: Sets the webservice implementation to use.
setIncrements(BaseFloat[]) - Method in class adams.data.io.output.NIRSpectrumWriter: Set increments.
setIndex(Index) - Method in class adams.data.multifilter.PickByIndex: Sets the index of the spectrum to select.
setIndex(Index) - Method in class adams.flow.transformer.GetSpectrumAmplitude: Sets the index of the amplitude to retrieve.
setIndex(Index) - Method in class adams.flow.transformer.SetSpectrumAmplitude: Sets the index of the amplitude to set.
setInstrument(BaseRegExp) - Method in class adams.db.AbstractSpectrumConditions: Sets the regular expression for the instrument name.
setInstrument(String) - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Sets the instrument to use for the spectrum.
setInstrument(String) - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Sets the instrument to use for the spectrum.
setInstrument(String) - Method in class adams.data.conversion.SpreadSheetToSpectrum: Sets the instrument to use for the spectrum.
setInstrument(String) - Method in class adams.data.io.input.AbstractSpectrumReader: Sets the instrument's name.
setInstrument(String) - Method in class adams.data.io.input.AbstractThreeWayDataReader: Sets the instrument's name.
setInstrumentName(String) - Method in class adams.data.io.output.ASCSpectrumWriter: Set instrument name.
setInstrumentName(String) - Method in class adams.data.io.output.NIRSpectrumWriter: Set instrument name.
setInstrumentName(String) - Method in class adams.data.io.output.TrinamixSpectrumWriter: Set instrument name.
setInterval(int) - Method in class adams.flow.transformer.SpectrumMinMax: Sets the interval (ie number of spectra processed) when to output the min/max spectra.
setInvert(boolean) - Method in class adams.data.spectrumfilter.KennardStone: Set whether to return the remaining spectra are returned rather than the chosen ones.
setInvert(boolean) - Method in class adams.data.spectrumfilter.Remove: Whether to invert the matching sense.
setInvert(boolean) - Method in class adams.data.spectrumfilter.SubRange: Whether to invert the matching sense.
setInvert(boolean) - Method in class adams.data.spectrumoutlier.StringMatcher: Sets whether to invert the matching sense.
setInvertMatching(boolean) - Method in class adams.data.io.input.ZippedSpectrumReader: Sets whether to invert the matching sense of the regular expression.
setIqr(double) - Method in class adams.data.cleaner.instance.IQRCleaner: Sets the IQR multiplier.
setIQRMultiplier(BaseDouble[]) - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Sets the IQR multipliers per classifier.
setIterations(int) - Method in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: Sets the iterations.
setKeepAttributeNames(boolean) - Method in class weka.filters.unsupervised.attribute.SpectrumFilter: Sets whether to keep the attribute names generated by the base filter.
setKeepFormat(boolean) - Method in class adams.data.io.input.AbstractSpectrumReader: Sets whether to keep the format obtained from the file.
setKeepFormat(boolean) - Method in class adams.data.io.input.AbstractThreeWayDataReader: Sets whether to keep the format obtained from the file.
setKey(String) - Method in class adams.data.io.input.OpusSpectrumReaderExt: Sets the command-line key from which to retrieve the sample ID.
setKey(String) - Method in class adams.flow.transformer.SetEvaluationMetaData: Sets the key to use for storing the value.
setKey(String) - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.Property: Sets the value of the key property.
setKey(String) - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.Property: Sets the value of the key property.
setKey(String) - Method in class nz.ac.waikato.adams.webservice.spectral.get.Property: Sets the value of the key property.
setKey(String) - Method in class nz.ac.waikato.adams.webservice.spectral.put.Property: Sets the value of the key property.
setKey(String) - Method in class nz.ac.waikato.adams.webservice.spectral.transform.Property: Sets the value of the key property.
setLast(double) - Method in class adams.data.spectrumfilter.AbstractStandardiseFilter: Sets the last data point
setLastWave(float) - Method in class adams.flow.transformer.InstanceToSpectrum: Sets the end point for the wave numbers.
setLastXPoint(Double) - Method in class adams.data.io.output.ASCSpectrumWriter: Set last X wavenumber.
setLatest(boolean) - Method in class adams.db.AbstractSpectrumConditions: Sets whether to get only the latest ones (= reverse order).
setLatest(boolean) - Method in class adams.db.OrphanedSampleDataConditions: Sets whether to get only the latest ones (= reverse order).
setLenient(boolean) - Method in class adams.data.conversion.SpreadSheetColumnsToSampleData: Sets whether to skip over errors.
setLenient(boolean) - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Sets whether to skip over errors.
setLenient(boolean) - Method in class adams.data.conversion.SpreadSheetRowsToSampleData: Sets whether to skip over errors.
setLenient(boolean) - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Sets whether to skip over errors.
setLenient(boolean) - Method in class adams.flow.transformer.InstanceGenerator: Sets whether lenient, ie whether errors only get logged rather than returned (and possibly causing the flow to stop).
setLenient(boolean) - Method in class adams.flow.transformer.MergeSampleDataFromMap: Sets whether to use lenient mode (missing IDs in map won't cause error).
setLenient(boolean) - Method in class adams.flow.transformer.SpreadSheetRowGenerator: Sets whether lenient, ie whether errors only get logged rather than returned (and possibly causing the flow to stop).
setLoadSampleData(boolean) - Method in class adams.data.instances.AbstractSpectrumBasedInstanceGenerator: Sets whether to load the sample data via the sample ID if only dummy report available.
setLocale(Locale) - Method in class adams.data.io.input.ASCSpectrumReader: Sets the locale to use.
setLocale(Locale) - Method in class adams.data.io.input.DPTSpectrumReader: Sets the locale to use.
setLocale(Locale) - Method in class adams.data.io.output.ASCSpectrumWriter: Sets the locale to use.
setLocale(Locale) - Method in class adams.data.io.output.DPTSpectrumWriter: Sets the locale to use.
setLogBase(String) - Method in class adams.data.spectrumfilter.LogTransform: Sets the base of the log ("e" or a positive number greater than 1).
setLoggingLevel(LoggingLevel) - Method in class adams.data.evaluator.instance.AbstractSerializableEvaluator
setLoggingLevel(LoggingLevel) - Method in class adams.data.spectrumfilter.WekaFilterToReport: Sets the logging level.
setLoggingLevel(LoggingLevel) - Method in class adams.flow.transformer.Cleaner: Sets the logging level.
setLoggingLevel(LoggingLevel) - Method in class adams.flow.transformer.Evaluator: Sets the logging level.
setLoggingLevel(LoggingLevel) - Method in class adams.flow.transformer.PostProcessor: Sets the logging level.
setLoggingLevel(LoggingLevel) - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Sets the logging level.
setLookup(BaseKeyValuePair[]) - Method in class adams.data.spectrumfilter.ReportFieldFromStringValueWithLookup: Sets the key-value pairs that make up the lookup table.
setLowerPercentile(double) - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Sets the lower percentile.
setMarkerExtent(int) - Method in class adams.gui.visualization.spectrum.SpectrumPaintlet: Sets the extent (width and height of the shape around the plotted point). 0 turns the plotting off.
setMarkersDisabled(boolean) - Method in class adams.gui.visualization.spectrum.SpectrumPaintlet: Sets whether to draw markers or not.
setMaster(String) - Method in class adams.data.io.output.NIRSpectrumWriter: Set serial no of master.
setMatrix(String) - Method in class adams.flow.transformer.ThreeWayDataLoadingMatrix: Sets the name of the loading matrix to retrieve.
setMax(double) - Method in class adams.data.spectrumoutlier.MinMax: Sets the max.
setMax(double) - Method in class adams.data.threewayoutlier.ValueRange: Sets the max.
setMax(float) - Method in class adams.data.spectrumfilter.amplitudetransform.Triangle: Sets the maximum for the triangle.
setMax(int) - Method in class adams.data.io.input.CALSpectrumReader: Sets the nth point setting.
setMax(int) - Method in class adams.data.io.input.OpusSpectrumReader: Sets the nth point setting.
setMaxAmplitude(double) - Method in class adams.data.spectrumfilter.Scale: Sets the maximum amplitude to scale to.
setMaxAmplitude(float) - Method in class adams.data.io.input.SpecLibSpectrumReader: Sets the largest allowed amplitude.
setMaxAmplitude(float) - Method in class adams.data.spectrumimage.AbstractSpectrumImageGeneratorWithRange: Sets the maximum amplitude to assume.
setMaxAttributeNames(int) - Method in class adams.data.spectrumfilter.PCA: Sets the maximum number of attribute names.
setMaxAttributes(int) - Method in class adams.data.spectrumfilter.PCA: Sets the maximum attributes.
setMaximum(double) - Method in class adams.data.cleaner.instance.MinMax: Sets maximum value the field is allowed to have (incl).
setMaximum(double) - Method in class adams.data.cleaner.spectrum.MinMax: Sets maximum value the field is allowed to have (incl).
setMaximum(double) - Method in class adams.data.compare.SpectrumCosineSimilarity: Sets the maximum for the cosine similarity.
setMaximumValue(BaseDouble) - Method in class adams.db.SpectrumConditionsSingle: Sets the maximum value to the fields.
setMaximumValues(BaseDouble[]) - Method in class adams.db.SpectrumConditionsMulti: Sets the maximum values to the fields.
setMaxNonRemovalIterations(BaseInteger[]) - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Sets the maximum number of non-removal iterations per classifier.
setMaxPLS(int) - Method in class adams.opt.genetic.RonWeasley: Set max pls components
setMaxSG(int) - Method in class adams.opt.genetic.RonWeasley: Set max sg smoothing window
setMaxWaveNumber(double) - Method in class adams.data.spectrumfilter.SubRange: Sets the maximum wave number to include in the output.
setMaxWaveNumber(double) - Method in class adams.data.spectrumoutlier.Oscillation: Sets the maximum wave number to include in the output.
setMaxWaveNumber(float) - Method in class adams.data.io.input.SpecLibSpectrumReader: Sets the largest allowed wavenumber.
setMaxWaves(int) - Method in class adams.data.spectrumoutlier.MaxWaves: Sets the maximum number of wave numbers.
setMaxX(double) - Method in class adams.data.conversion.ThreeWayDataToHeatmap: Sets the maximum X layer to use.
setMerge(MergeReport.MergeType) - Method in class adams.flow.transformer.MergeSampleDataFromMap: Sets the merge type.
setMergeReports(boolean) - Method in class adams.flow.transformer.ThreeWayDataMerge: Sets whether to merge the reports into a single one and use in the outgoing data.
setMessage(String) - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.UploadResponse: Sets the value of the message property.
setMessage(String) - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.UploadResponse: Sets the value of the message property.
setMessage(String) - Method in class nz.ac.waikato.adams.webservice.spectral.get.GetResponse: Sets the value of the message property.
setMessage(String) - Method in class nz.ac.waikato.adams.webservice.spectral.put.PutResponse: Sets the value of the message property.
setMessage(String) - Method in class nz.ac.waikato.adams.webservice.spectral.transform.TransformResponse: Sets the value of the message property.
setMetaDataFields(Field[]) - Method in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: Sets the meta-data fields to add.
setMetaDataPrefix(String) - Method in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: Sets the column prefix for the meta-data values.
setMetaDataValues(Field[]) - Method in class adams.data.conversion.SpectrumToJson: Sets the meta-data values to output.
setMetaDataValues(Field[]) - Method in class adams.data.io.output.JsonSpectrumWriter: Sets the meta-data values to output.
setMin(double) - Method in class adams.data.spectrumoutlier.MinMax: Sets the minimum.
setMin(double) - Method in class adams.data.threewayoutlier.ValueRange: Sets the minimum.
setMin(float) - Method in class adams.data.spectrumfilter.amplitudetransform.Triangle: Sets the minimum for the triangle.
setMinAmplitude(double) - Method in class adams.data.spectrumfilter.Scale: Sets the minimum amplitude to scale to.
setMinAmplitude(float) - Method in class adams.data.io.input.SpecLibSpectrumReader: Sets the smallest allowed amplitude.
setMinAmplitude(float) - Method in class adams.data.spectrumimage.AbstractSpectrumImageGeneratorWithRange: Sets the minimum amplitude to assume.
setMinimum(double) - Method in class adams.data.cleaner.instance.MinMax: Sets the minimum value the field can have (incl.).
setMinimum(double) - Method in class adams.data.cleaner.spectrum.MinMax: Sets the minimum value the field can have (incl.).
setMinimum(double) - Method in class adams.data.compare.SpectrumCorrelation: Sets the minimum for the correlation coefficient.
setMinimum(double) - Method in class adams.flow.transformer.predictioncheck.MinProbability: Sets the minimum probability (included) that the highest probability in the class distribution must achieve.
setMinimumValue(BaseDouble) - Method in class adams.db.SpectrumConditionsSingle: Sets the minimum value for the field.
setMinimumValues(BaseDouble[]) - Method in class adams.db.SpectrumConditionsMulti: Sets the minimum values to the fields.
setMinPLS(int) - Method in class adams.opt.genetic.RonWeasley: Set minimum pls components
setMinSG(int) - Method in class adams.opt.genetic.RonWeasley: Set minimum sg
setMinWaveNumber(double) - Method in class adams.data.spectrumfilter.SubRange: Sets the minimum wave number to include in the output.
setMinWaveNumber(double) - Method in class adams.data.spectrumoutlier.Oscillation: Sets the minimum wave number to include in the detection.
setMinWaveNumber(float) - Method in class adams.data.io.input.SpecLibSpectrumReader: Sets the smallest allowed wavenumber.
setMinWaves(int) - Method in class adams.data.spectrumoutlier.MinWaves: Sets the minimum number of wave numbers.
setMinX(double) - Method in class adams.data.conversion.ThreeWayDataToHeatmap: Sets the minimum X layer to use.
setMirrors(AbstractDatabaseConnection[]) - Method in class adams.db.mirrored.SpectralDbBackend: Sets the mirror connections to use.
setMirrorsForUrls(JdbcUrl[]) - Method in class adams.db.mirrored.SpectralDbBackend: Sets the URLs that the mirrors are for.
setMissingEvaluation(float) - Method in class adams.data.evaluator.instance.AbstractEvaluator: Sets the replacement string for missing evaluations.
setMissingEvaluation(float) - Method in interface adams.data.evaluator.instance.Evaluator: Sets the replacement string for missing evaluations.
setMissingValueColor(Color) - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Sets the color for missing values.
setMissingValueColor(Color) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Sets the color to use for missing values.
setMode(JCampDX2SpectrumReader.ReaderMode) - Method in class adams.data.io.input.JCampDX2SpectrumReader: Sets the reader mode.
setModelActor(CallableActorReference) - Method in class adams.data.spectrumfilter.WekaFilterToReport: Sets the filter source actor.
setModelActor(CallableActorReference) - Method in class adams.flow.transformer.Cleaner: Sets the filter source actor.
setModelActor(CallableActorReference) - Method in class adams.flow.transformer.Evaluator: Sets the filter source actor.
setModelActor(CallableActorReference) - Method in class adams.flow.transformer.PostProcessor: Sets the filter source actor.
setModelActor(CallableActorReference) - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Sets the filter source actor.
setModelFile(PlaceholderFile) - Method in class adams.data.spectrumfilter.WekaFilterToReport: Sets the file to load the model from.
setModelFile(PlaceholderFile) - Method in class adams.flow.transformer.Cleaner: Sets the file to load the model from.
setModelFile(PlaceholderFile) - Method in class adams.flow.transformer.Evaluator: Sets the file to load the model from.
setModelFile(PlaceholderFile) - Method in class adams.flow.transformer.PostProcessor: Sets the file to load the model from.
setModelFile(PlaceholderFile) - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Sets the file to load the model from.
setModelLoadingType(AbstractModelLoader.ModelLoadingType) - Method in class adams.data.spectrumfilter.WekaFilterToReport: Sets the loading type.
setModelLoadingType(AbstractModelLoader.ModelLoadingType) - Method in class adams.flow.transformer.Cleaner: Sets the loading type.
setModelLoadingType(AbstractModelLoader.ModelLoadingType) - Method in class adams.flow.transformer.Evaluator: Sets the loading type.
setModelLoadingType(AbstractModelLoader.ModelLoadingType) - Method in class adams.flow.transformer.PostProcessor: Sets the loading type.
setModelLoadingType(AbstractModelLoader.ModelLoadingType) - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Sets the loading type.
setModelResetVariable(VariableName) - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Sets the variable to monitor for changes in order to reset the model.
setModelStorage(StorageName) - Method in class adams.data.spectrumfilter.WekaFilterToReport: Sets the filter storage item.
setModelStorage(StorageName) - Method in class adams.flow.transformer.Cleaner: Sets the filter storage item.
setModelStorage(StorageName) - Method in class adams.flow.transformer.Evaluator: Sets the filter storage item.
setModelStorage(StorageName) - Method in class adams.flow.transformer.PostProcessor: Sets the filter storage item.
setModelStorage(StorageName) - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Sets the filter storage item.
setModified(boolean) - Method in class adams.flow.transformer.SpectralAngleMapper: Sets whether to use the modified algorithm.
setNewConnection(boolean) - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Sets whether to use a new connection for this update.
setNewConnection(boolean) - Method in class adams.flow.transformer.BulkSpectrumDbWriter: Sets whether to use a new connection for this update.
setNewFormat(String) - Method in class adams.data.multifilter.AbstractFormatsBasedMultiSpectrumFilter: Sets the new format for the generated spectrum.
setNewFormatSeparator(String) - Method in class adams.data.multifilter.Fusion: Sets the separator to use when automatically generating a new format string.
setNoAdditionalFieldsPrefix(boolean) - Method in class adams.data.instances.AbstractSpectrumInstanceGenerator: Sets whether to drop the prefix for the additional fields.
setNoCopy(boolean) - Method in class adams.flow.transformer.AbstractInPlaceSpectrumTransformer: Sets whether to skip creating a copy of the spectrum before processing it.
setNoCopy(boolean) - Method in class adams.flow.transformer.Evaluator: Sets whether to skip creating a copy of the container before updating it.
setNoCopy(boolean) - Method in class adams.flow.transformer.PredictionCheck: Sets whether to skip creating a copy of the data before processing it.
setNoCopy(boolean) - Method in class adams.flow.transformer.SetEvaluationMetaData: Sets whether to skip creating a copy of the container before updating it.
setNonMirroredBackend(SpectralDbBackend) - Method in class adams.db.mirrored.SpectralDbBackend: Sets the backend to use for non-mirrored connections.
setNormalize(boolean) - Method in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: Sets whether to normalize the confidence intervals using the class range.
setNormalize(boolean) - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Sets whether to normalize the predictions to the class attribute range.
setNormalizeByLiveTime(boolean) - Method in class adams.data.io.input.MPSSpectrumReader: Sets whether to normalize the amplitudes with the MPSSpectrumReader.KEY_LIVE_TIME field.
setNotes(BaseString[]) - Method in class adams.data.instances.AbstractSpectrumBasedInstanceGenerator: Sets the notes to add as attributes.
setNotes(BaseString[]) - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Sets the notes to add as attributes.
setNotes(BaseString[]) - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Sets the notes to add as attributes.
setNthPoint(int) - Method in class adams.data.threewayfeatures.Flatten: Sets the nth point setting.
setNthPoints(String) - Method in class weka.filters.unsupervised.attribute.SegmentedDownSample: Sets the blank-separated list number of points to use for the savitzky-golay window (>= 1).
setNumAdditional(int) - Method in class adams.data.spectrumfilter.PadPower2: Sets the number of additional wave numbers to add (beyond the power of 2).
setNumAttributes(int) - Method in class weka.filters.unsupervised.attribute.BestBySLR: Set the number of attributes.
setNumber(float) - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.Wave: Sets the value of the number property.
setNumber(float) - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.Wave: Sets the value of the number property.
setNumber(float) - Method in class nz.ac.waikato.adams.webservice.spectral.get.Wave: Sets the value of the number property.
setNumber(float) - Method in class nz.ac.waikato.adams.webservice.spectral.put.Wave: Sets the value of the number property.
setNumber(float) - Method in class nz.ac.waikato.adams.webservice.spectral.transform.Wave: Sets the value of the number property.
setNumberInSubset(int) - Method in class adams.data.spectrumfilter.KennardStone: Set the number of spectra to select in subset
setNumDeleted(int) - Method in class adams.data.io.input.foss.FossHelper.FossFields: Sets the number of previously deleted.
setNumFolds(int) - Method in class adams.data.cleaner.instance.RemoveOutliers: Sets the number of folds to use.
setNumFolds(int) - Method in class adams.data.evaluator.instance.EnsembleEvaluator: Sets the number of folds.
setNumFolds(BaseInteger[]) - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Sets the number of cross-validation folds per classifier.
setNumIterations(BaseInteger[]) - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Sets the number of iterations per classifier.
setNumNeighbors(int) - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Sets the number of neighbors to use in the neighborhood.
setNumNeighbors(int) - Method in class adams.data.evaluator.instance.CrossValidatedPrediction: Sets the number of neighbors to use in the neighborhood.
setNumNeighbors(int) - Method in class adams.data.evaluator.instance.DistanceToCenter: Sets the number of neighbors to use in the neighborhood.
setNumPoints(int) - Method in class adams.data.spectrumfilter.AndrewsCurves: Sets the number of points to generate.
setNumPoints(int) - Method in class adams.data.spectrumfilter.CenterBurst: Sets the number of points to use.
setNumPoints(int) - Method in class weka.filters.unsupervised.attribute.SavitzkyGolayRange: Sets the number of points for the window (window = numPoints*2 + 1).
setNumPoints(String) - Method in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: Sets the blank-separated list number of points to use for the savitzky-golay window (>= 1).
setNumThreads(int) - Method in class adams.data.cleaner.instance.RemoveOutliers: Sets the number of threads to use for cross-validation.
setNumThreads(int) - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Sets the number of threads to use for cross-validation.
setOffline(boolean) - Method in class adams.data.io.input.AbstractSampleDataReader: Sets whether to work in offline mode, i.e., not query the database.
setOffsetX(int) - Method in class adams.data.threewayfilter.Shift: Sets the offset for X.
setOffsetX(int) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Sets the X offset for the text.
setOffsetY(int) - Method in class adams.data.threewayfilter.Shift: Sets the offset for Y.
setOffsetY(int) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Sets the Y offset of the text.
setOffsetZ(int) - Method in class adams.data.threewayfilter.Shift: Sets the offset for Z.
setOnlyDummies(boolean) - Method in class adams.db.AbstractSpectrumConditions: Sets whether to include only spectra with reports flagged as dummies or not.
setOnlyWarning(boolean) - Method in class adams.flow.transformer.MultiSpectrumOutlierDetector: Sets whether the detections are added as error or warning.
setOperation(AbstractMultiSpectrumOperation) - Method in class adams.flow.transformer.MultiSpectrumOperation: Sets the multi-spectrum operation to apply.
setOperation(String) - Method in class adams.data.io.input.OpusSpectrumReaderExt: Sets the command-line operation from which to retrieve the sample ID.
setOperator(String) - Method in class adams.data.io.output.NIRSpectrumWriter: Set operator.
setOptions(String[]) - Method in class weka.core.converters.CALSpectrumLoader: Sets the OptionHandler's options using the given list.
setOptions(String[]) - Method in class weka.filters.unsupervised.attribute.BestBySLR: Parses a given list of options.
setOptions(String[]) - Method in class weka.filters.unsupervised.attribute.RangeBasedSavitzkyGolay: Parses a list of options for this object.
setOptions(String[]) - Method in class weka.filters.unsupervised.attribute.SegmentedDownSample: Parses a list of options for this object.
setOptions(String[]) - Method in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: Parses a list of options for this object.
setOptions(String[]) - Method in class weka.filters.unsupervised.attribute.SpectrumFilter: Parses a list of options for this object.
setOutlierRemoval(AbstractOutlierRemoval) - Method in class adams.data.multispectrumoperation.OutlierRemoval: Sets the outlier removal scheme to apply.
setOutput(double[]) - Method in class adams.flow.transformer.SpectralAngleMapper: Sets the output token to the given array of angles.
setOutputContainer(boolean) - Method in class adams.flow.transformer.InstanceGenerator: Sets whether to output a container with the instance alongside the report or just the instance.
setOutputContainer(boolean) - Method in class adams.flow.transformer.PostProcessor: Sets whether to output a container.
setOutputMultiSpectrum(boolean) - Method in class adams.flow.transformer.SpectrumFileReader: Sets whether to output a MultiSpectrum instead.
setOutputReport(boolean) - Method in class adams.data.conversion.MultiSpectrumToSpectra: Sets whether to output the global report of the multi-spectrum as separate (= first) report-only spectrum (ie no spectral data).
setOutputReport(boolean) - Method in class adams.flow.transformer.SpectrumFileWriter: Sets whether to output the global report of the multi-spectrum as separate (= first) report-only spectrum (ie no spectral data).
setOutputSampleData(boolean) - Method in class adams.data.io.output.JCampDX2SpectrumWriter: Sets whether to output the sample data as well.
setOutputSampleData(boolean) - Method in class adams.data.io.output.SimpleSpectrumWriter: Sets whether to output the sample data as well.
setOutputSampleData(boolean) - Method in class adams.data.io.output.SimpleXYZWriter: Sets whether to output the sample data as well.
setOverlapFactor(int) - Method in class adams.data.conversion.SpectrumToBufferedImage: Sets the overlap factor (1/factor).
setOverlapFactor(int) - Method in class adams.data.spectrumimage.Spectrogram: Sets the overlap factor (1/factor).
setOverlays(AbstractThreeWayDataOverlay[]) - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Sets the overlays to use.
setOverrideSerializedFile(boolean) - Method in class adams.data.cleaner.instance.AbstractSerializableCleaner: Sets whether to override an existing serialized setup.
setOverrideSerializedFile(boolean) - Method in class adams.data.cleaner.spectrum.AbstractSerializableCleaner: Sets whether to override an existing serialized setup.
setOverrideSerializedFile(boolean) - Method in class adams.data.evaluator.instance.AbstractSerializableEvaluator: Sets whether to override an existing serialized setup.
setOverrideSerializedFile(boolean) - Method in class adams.data.postprocessor.instances.AbstractSerializablePostProcessor: Sets whether to override an existing serialized setup.
setOverrideSerializedFile(boolean) - Method in class adams.data.spectrumfilter.AbstractSerializableFilter: Sets whether to override an existing serialized setup.
setOverwriteExisting(boolean) - Method in interface adams.flow.transformer.SpectrumDatabaseWriter: Sets whether to remove existing containers.
setOwner(RatsMultiSpectrumServiceWS) - Method in interface adams.flow.webservice.multispectrum.OwnedByRatsMultiSpectrumServiceWS: Sets the owner.
setOwner(RatsMultiSpectrumServiceWS) - Method in class adams.flow.webservice.multispectrum.SimpleRatsMultiSpectrumService: Sets the owner of this webservice.
setOwner(SpectralGetServiceWS) - Method in interface adams.flow.webservice.OwnedBySpectralGetServiceWS: Sets the owner.
setOwner(SpectralGetServiceWS) - Method in class adams.flow.webservice.SimpleSpectralGetService: Sets the owner of this webservice.
setOwner(SpectralPutServiceWS) - Method in interface adams.flow.webservice.OwnedBySpectralPutServiceWS: Sets the owner.
setOwner(SpectralPutServiceWS) - Method in class adams.flow.webservice.SimpleSpectralPutService: Sets the owner of this webservice.
setOwner(SpectralTransformServiceWS) - Method in interface adams.flow.webservice.OwnedBySpectralTransformServiceWS: Sets the owner.
setOwner(SpectralTransformServiceWS) - Method in class adams.flow.webservice.SimpleSpectralTransformService: Sets the owner of this webservice.
setOwner(RatsSpectrumServiceWS) - Method in interface adams.flow.webservice.spectrum.OwnedByRatsSpectrumServiceWS: Sets the owner.
setOwner(RatsSpectrumServiceWS) - Method in class adams.flow.webservice.spectrum.SimpleRatsSpectrumService: Sets the owner of this webservice.
setPaddingType(PaddingType) - Method in class adams.data.spectrumfilter.PadPower2: Sets the type of padding.
setPadLeft(boolean) - Method in class adams.data.spectrumfilter.PadPower2: Sets whether to pad on the left rather than on the right.
setPaintAll(boolean) - Method in class adams.gui.visualization.spectrum.SpectrumPaintlet: Sets whether to draw markers or not.
setPaintlet(AbstractSpectrumPaintlet) - Method in class adams.flow.sink.SpectrumDisplay: Sets the paintlet to use.
setParallelAndMerge(boolean) - Method in class adams.data.spectrumfilter.MultiFilter: Sets whether filters are executed in series or parallel.
setParallelAndMerge(boolean) - Method in class adams.data.threewayfilter.MultiFilter: Sets whether filters are executed in series or parallel.
setParent(DataContainer) - Method in class adams.data.spectrum.MultiSpectrum: Sets the container this point belongs to.
setParent(DataContainer) - Method in class adams.data.spectrum.Spectrum: Sets the container this point belongs to.
setParent(DataContainer) - Method in class adams.data.threeway.L1Point: Sets the parent this point belongs to.
setPCA(PCA) - Method in class adams.data.spectrumanalysis.PCA: Sets the PCA analysis.
setPixel(BufferedImage, int, int, int) - Method in class adams.data.spectrumimage.AbstractSpectrumImageGenerator: Sets the pixel in the image.
setPlotUpdater(AbstractPlotUpdater) - Method in class adams.flow.sink.SpectrumDisplay: Sets the plot updater to use.
setPLS(PLS) - Method in class adams.data.spectrumanalysis.PLS: Sets the PLS analysis.
setPoint(SpectrumPoint) - Method in class adams.gui.visualization.spectrum.SelectedWaveNumberPaintlet: Sets the point to highlight, automatically repaints the panel.
setPolynomial(int) - Method in class adams.data.spectrumfilter.StandardiseByInterpolation: Sets the polynomial for interpolation
setPolynomialOrder(int) - Method in class weka.filters.unsupervised.attribute.SavitzkyGolayRange: Sets the polynomial order.
setPolynomialOrder(int) - Method in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: Sets the polynomial order.
setPostProcessor(AbstractPostProcessor) - Method in class adams.flow.transformer.PostProcessor: Sets the post-processor to use.
setPostProcessor(AbstractThreeWayDataTrainPostProcessor) - Method in class adams.flow.transformer.ThreeWayDataTrain: Sets the post-processor to use on the model.
setPostProcessorDetailsOutput(PlaceholderFile) - Method in class adams.flow.transformer.PostProcessor: Sets the file for the post-processor details.
setPreferJobRunner(boolean) - Method in class adams.flow.transformer.Cleaner: Sets whether to offload processing to a JobRunner instance if available.
setPreferJobRunner(boolean) - Method in class adams.flow.transformer.Evaluator: Sets whether to offload processing to a JobRunner instance if available.
setPreFilter(Filter) - Method in class adams.data.cleaner.spectrum.AbstractCleaner: Sets the filter to use for pre-filtering the data.
setPreFilter(Filter) - Method in class adams.data.multispectrumoperation.outlierremoval.CorrelationBasedThreshold: Sets the pre-filter to use.
setPreFilter(Filter) - Method in class adams.data.multispectrumoperation.outlierremoval.CosineSimilarityBasedThreshold: Sets the pre-filter to use.
setPreFilter(Filter) - Method in class adams.data.multispectrumoperation.outlierremoval.MeanSpectrumCosineSimilarityBasedThreshold: Sets the pre-filter to use.
setPreFilter(Filter) - Method in class adams.data.spectrumfilter.KennardStone: Set the filter to apply before selection
setPreFilter(Filter<Spectrum>) - Method in class adams.data.spectrumfilter.multiplicativescattercorrection.AbstractMultiplicativeScatterCorrection: Sets the prefilter to use.
setPreFilter(Filter<Spectrum>) - Method in class adams.data.spectrumfilter.MultiplicativeScatterCorrection: Sets the prefilter to use.
setPreFilter(Filter) - Method in class adams.data.cleaner.instance.AbstractCleaner: Sets the filter to use for pre-filtering the data.
setPreFilters(AbstractMultiSpectrumFilter[]) - Method in class adams.data.multifilter.FilteredMultiSpectrumFilter: Sets the pre-filters.
setPrefix(String) - Method in class adams.data.instances.FieldInstanceGenerator: Sets the prefix for the attribute names.
setPrefix(String) - Method in class adams.data.spectrumfilter.WekaFilterToReport: Sets the prefix for the report fields.
setPrefix(String) - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Sets the (optional) prefix for the feature names.
setPrefixNew(String) - Method in class weka.filters.unsupervised.attribute.SpectrumFilter: Sets the (new) attribute prefix to use.
setPrefixOld(String) - Method in class weka.filters.unsupervised.attribute.SpectrumFilter: Sets the (old) attribute prefix to look for.
setPrettyPrinting(boolean) - Method in class adams.data.conversion.SpectrumToJson: Sets whether to use pretty-printing or not.
setPrettyPrinting(boolean) - Method in class adams.data.io.output.JsonSpectrumWriter: Sets whether to use pretty-printing or not.
setProductCode(String) - Method in class adams.data.io.output.ASCSpectrumWriter: Set product code.
setProductCode(String) - Method in class adams.data.io.output.NIRSpectrumWriter: Set product code.
setProductCode(String) - Method in class adams.flow.transformer.InstanceToSpectrum: Set product code.
setProductCodeFromField(Boolean) - Method in class adams.data.io.output.ASCSpectrumWriter: Set product code from instance attribute?
setProductCodeFromField(Boolean) - Method in class adams.data.io.output.NIRSpectrumWriter: Set product code from instance attribute?
setProps(Properties) - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.MultiSpectrum: Sets the value of the props property.
setProps(Properties) - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.Spectrum: Sets the value of the props property.
setProps(Properties) - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.Spectrum: Sets the value of the props property.
setProps(Properties) - Method in class nz.ac.waikato.adams.webservice.spectral.get.Spectrum: Sets the value of the props property.
setProps(Properties) - Method in class nz.ac.waikato.adams.webservice.spectral.put.Spectrum: Sets the value of the props property.
setProps(Properties) - Method in class nz.ac.waikato.adams.webservice.spectral.transform.Spectrum: Sets the value of the props property.
setQueueFailed(StorageName) - Method in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: Sets the name for the queue in the internal storage for failed files.
setQueueFailed(StorageName) - Method in class adams.flow.standalone.rats.LoadSpectrumFileOutput: Sets the name for the queue in the internal storage for failed files.
setQueueSpectra(StorageName) - Method in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: Sets the name for the queue in the internal storage for failed files.
setQueueSpectra(StorageName) - Method in class adams.flow.standalone.rats.LoadSpectrumFileOutput: Sets the name for the queue in the internal storage for failed files.
setQueueSuccessful(StorageName) - Method in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: Sets the name for the queue in the internal storage for successful files.
setQueueSuccessful(StorageName) - Method in class adams.flow.standalone.rats.LoadSpectrumFileOutput: Sets the name for the queue in the internal storage for successful files.
setRange(BaseInterval) - Method in class adams.flow.transformer.predictioncheck.Range: Sets the allowed range of the numeric value.
setRange(String) - Method in class adams.data.spectrumfilter.Remove: Sets the range of amplitudes to remove.
setRanges(BaseInterval[]) - Method in class adams.data.spectrumfilter.detrend.RangeBased: Sets the wave number ranges.
setRanges(BaseInterval[]) - Method in class adams.data.spectrumfilter.multiplicativescattercorrection.RangeBased: Sets the wave number ranges.
setRanges(SavitzkyGolayRange[]) - Method in class weka.filters.unsupervised.attribute.RangeBasedSavitzkyGolay: Sets the ranges to use.
setRangeX(BaseInterval) - Method in class adams.data.threewayfilter.Crop: Sets the range for X.
setRangeY(BaseInterval) - Method in class adams.data.threewayfilter.Crop: Sets the range for Y.
setRangeZ(BaseInterval) - Method in class adams.data.threewayfilter.Crop: Sets the range for Z.
setRatInput(RatInput) - Method in class adams.flow.webservice.multispectrum.RatsMultiSpectrumServiceWS: Sets the Rat input associated with this webservice.
setRatInput(RatInput) - Method in class adams.flow.webservice.spectrum.RatsSpectrumServiceWS: Sets the Rat input associated with this webservice.
setReader(AbstractSpectrumReader) - Method in class adams.data.io.input.ExtractIdAndTypeSpectrumReader: Sets the base reader to use.
setReader(AbstractSpectrumReader) - Method in class adams.data.io.input.FilteredSpectrumReader: Sets the underlying reader.
setReader(AbstractSpectrumReader) - Method in class adams.data.io.input.ZippedSpectrumReader: Sets the reader to use.
setReader(AbstractSpectrumReader) - Method in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: Sets the reader to use.
setReader(AbstractSpectrumReader) - Method in class adams.flow.standalone.rats.LoadSpectrumFileOutput: Sets the reader to use.
setReader(AbstractThreeWayDataReader) - Method in class adams.data.io.input.ExtractIdAndTypeThreeWayDataReader: Sets the base reader to use.
setReader(AbstractThreeWayDataReader) - Method in class adams.data.io.input.ThreeWayHeatmapReader: Sets the reader to use.
setReader(SpreadSheetReader) - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Sets the spreadsheet reader to use.
setReader(SpreadSheetReader) - Method in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: Sets the spreadsheet reader to use.
setReader(SpreadSheetReader) - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Sets the spreadsheet reader to use.
setReader(SpreadSheetReader) - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Sets the spreadsheet reader to use.
setReferences(StorageName) - Method in class adams.flow.transformer.SpectralAngleMapper: Sets the name of the storage location for reference spectra.
setReferenceValuePrefix(String) - Method in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: Sets the column prefix for the reference values.
setReferenceValues(Field[]) - Method in class adams.data.conversion.SpectrumToJson: Sets the reference values to output.
setReferenceValues(Field[]) - Method in class adams.data.io.output.JsonSpectrumWriter: Sets the reference values to output.
setReferenceValues(Field[]) - Method in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: Sets the reference value fields to add.
setRefRegExp(BaseRegExp) - Method in class weka.core.converters.CALSpectrumLoader: Sets the regexp to use for matching the reference names to include in the dataset.
setRegExp(BaseRegExp) - Method in class adams.data.io.input.sampleidextraction.RegExp: Sets the regular expression to use for extracting the sample ID from the file name (w/o path).
setRegExp(BaseRegExp) - Method in class adams.data.io.input.ZippedSpectrumReader: Sets the regular expression that the filenames must match.
setRegExp(BaseRegExp) - Method in class adams.data.spectrumfilter.ReportFieldFromStringValue: Sets the regular expression to apply for identifying the group(s) to extract from the string.
setRegExp(BaseRegExp) - Method in class adams.data.spectrumfilter.WekaFilterToReport: Sets the regular expression that the Instance attribute names must match in order to get transferred into the report.
setRegExp(BaseRegExp) - Method in class adams.data.spectrumoutlier.StringMatcher: Sets the regular expression to match the strings against.
setRegExp(BaseRegExp) - Method in class adams.gui.visualization.spectrum.SpectrumPaintletStringField: Sets regular expression to apply to the string field; the string obtained from the first group is associated with a color.
setRejectedTokensActor(Actor) - Method in class adams.flow.control.InstanceCleaner: Sets the actor to send the rejected tokens to.
setRejectedTokensActor(Actor) - Method in class adams.flow.control.SpectrumCleaner: Sets the actor to send the rejected tokens to.
setRejectionMessagesActor(Actor) - Method in class adams.flow.control.InstanceCleaner: Sets the actor to send the rejection messages to.
setRejectionMessagesActor(Actor) - Method in class adams.flow.control.SpectrumCleaner: Sets the actor to send the rejection messages to.
setReldiff(double) - Method in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: Sets the relative difference.
setReloadable(boolean) - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: Sets whether the spectrums are reloadable (from the database) or not.
setRemoveUnused(boolean) - Method in class weka.filters.unsupervised.attribute.RangeBasedSavitzkyGolay: Sets whether unused attributes (ones that are not covered by any of the ranges) are removed from the output.
setRemoveUnused(boolean) - Method in class weka.filters.unsupervised.attribute.SegmentedDownSample: Sets whether unused attributes (ones that are not covered by any of the ranges) are removed from the output.
setRemoveUnused(boolean) - Method in class weka.filters.unsupervised.attribute.SegmentedSavitzkyGolay: Sets whether unused attributes (ones that are not covered by any of the ranges) are removed from the output.
setRemoveWithMissing(boolean) - Method in class adams.data.cleaner.instance.IQRCleaner: Sets whether to remove instances with missing values.
setReport(SampleData) - Method in class adams.data.spectrum.MultiSpectrum: Set sample data.
setReport(SampleData) - Method in class adams.data.spectrum.Spectrum: Set sample data.
setReport(ThreeWayReport) - Method in class adams.data.threeway.ThreeWayData: Set the report (reference values).
setReportField(Field) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Sets the report field to output.
setReportVisible(boolean) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Sets the visibility state of the report table.
setRequestData(MultiSpectrum) - Method in class adams.flow.webservice.multispectrum.MultiUpload: Sets the data for the request, if any.
setRequestData(Spectrum) - Method in class adams.flow.webservice.Put: Sets the data for the request, if any.
setRequestData(Spectrum) - Method in class adams.flow.webservice.spectrum.Upload: Sets the data for the request, if any.
setRequestData(Spectrum) - Method in class adams.flow.webservice.Transform: Sets the data for the request, if any.
setRequiredField(Field) - Method in class adams.db.SpectrumConditionsSingle: Sets the required field.
setRequiredFields(Field[]) - Method in class adams.db.SpectrumConditionsMulti: Sets the required fields.
setRowFinder(RowFinder) - Method in class adams.data.io.input.MultiColumnSpreadSheetSampleDataReader: Sets the row finder to use for locating the rows to import.
setRowFinder(RowFinder) - Method in class adams.data.io.input.RowWiseSpreadSheetSampleDataReader: Sets the row finder to use for locating the rows to import.
setRowFinder(RowFinder) - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Sets the row finder to use for filtering the rows.
setRowID(SpreadSheetRowIndex) - Method in class adams.data.conversion.SpreadSheetColumnsToSampleData: Sets the (optional) row that contains the sample ID.
setRowID(SpreadSheetRowIndex) - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Sets the (optional) row that contains the sample ID.
setRowSampleDataNames(SpreadSheetRowIndex) - Method in class adams.data.conversion.SpreadSheetRowsToSampleData: Sets the row that contains the sample data names.
setRowSampleDataNames(SpreadSheetRowIndex) - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Sets the row that contains the sample data names.
setRowsAmplitude(SpreadSheetRowRange) - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Sets the rows with amplitude information.
setRowsAmplitude(SpreadSheetRowRange) - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Sets the rows with the amplitude information.
setRowsSampleData(SpreadSheetRowRange) - Method in class adams.data.conversion.SpreadSheetColumnsToSampleData: Sets the rows with sampledata.
setRowsSampleData(SpreadSheetRowRange) - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Sets the rows with sampledata.
setRowsSampleDataValues(SpreadSheetRowRange) - Method in class adams.data.conversion.SpreadSheetRowsToSampleData: Sets the rows with the sample data values.
setRowWaveNumber(SpreadSheetRowIndex) - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Sets the row with the wavenumber information.
setSampleDataColumns(SpreadSheetColumnRange) - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Sets the columns containing the sample data.
setSampleDataFormat(String) - Method in class adams.data.spectrumfilter.ChangeFormat: Sets the format for the sample data.
setSampleDataLabelsColumn(SpreadSheetColumnIndex) - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Sets the column containing the labels for the sample data values.
setSampleDataNamesInHeader(boolean) - Method in class adams.data.conversion.SpreadSheetRowsToSampleData: Sets whether the wave numbers are in the header.
setSampleDataNamesInHeader(boolean) - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Sets whether the wave numbers are in the header.
setSampleDataRows(Range) - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Sets the range of rows containing the sample data.
SetSampleDataValue - Class in adams.flow.transformer: Sets a value in the sample data.
SetSampleDataValue() - Constructor for class adams.flow.transformer.SetSampleDataValue
setSampleID(BaseRegExp) - Method in class adams.data.multispectrumoperation.Remove: Sets the regular expression that the sample ID of a spectrum must match in order to get removed.
setSampleID(BaseRegExp) - Method in class adams.flow.transformer.MultiSpectrumRemove: Sets the regular expression that the sample ID of a spectrum must match in order to get removed.
setSampleID(String) - Method in class adams.data.io.input.OpusSpectrumReader: Set id field.
setSampleID(String) - Method in class adams.flow.transformer.InstanceToSpectrum: Get sample id regex.
setSampleID1(String) - Method in class adams.data.io.output.NIRSpectrumWriter: Set sample id1.
setSampleID2(String) - Method in class adams.data.io.output.NIRSpectrumWriter: Set sample id2.
setSampleID3(String) - Method in class adams.data.io.output.NIRSpectrumWriter: Set sample id3.
setSampleIDColumn(SpreadSheetColumnIndex) - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Sets the column containing the sample ID.
setSampleIDExtraction(SampleIDExtraction) - Method in class adams.data.io.input.ASCIIXYSpectrumReader: Sets the scheme for extracting the sample ID from the filename.
setSampleIDExtraction(SampleIDExtraction) - Method in interface adams.data.io.input.SpectrumReaderWithSampleIDExtraction: Sets the scheme for extracting the sample ID from the filename.
setSampleIDLocation(ColumnWiseSpreadSheetSpectrumReader.SampleIDLocation) - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Sets whether the sample ID is located.
setSampleIDRegExp(BaseRegExp) - Method in class adams.db.AbstractSpectrumConditions: Sets the regular expression for the spectrum name.
setSampleIDRegExp(BaseRegExp) - Method in interface adams.db.SampleIDRegExpSupporter: Sets the regular expression to use on the sample ID.
setSampleIDRegExp(BaseRegExp) - Method in class adams.db.SpectrumIDConditions: Sets the regular expression for the spectrum name.
setSampleIDRow(Index) - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Sets the row that contains the sample ID.
setSampleType(BaseRegExp) - Method in class adams.data.multispectrumoperation.Remove: Sets the regular expression that the sample Type of a spectrum must match in order to get removed.
setSampleType(BaseRegExp) - Method in class adams.flow.transformer.MultiSpectrumRemove: Sets the regular expression that the sample type of a spectrum must match in order to get removed.
setSampleTypeRegExp(BaseRegExp) - Method in class adams.db.AbstractSpectrumConditions: Sets the regular expression for the sample type.
setSampleTypeRegExp(BaseRegExp) - Method in interface adams.db.SampleTypeRegExpSupporter: Sets the regular expression to use on the sample type.
setSampleTypeRegExp(BaseRegExp) - Method in class adams.db.SpectrumIDConditions: Sets the regular expression for the sample type.
setScale(boolean) - Method in class adams.data.spectrumfilter.Covariance: Set scale?
setScale(boolean) - Method in class adams.data.spectrumfilter.LRCoeff: Set scale?
setSearch(NearestNeighbourSearch) - Method in class adams.data.evaluator.instance.AbstractNearestNeighborBasedEvaluator: Sets the nearest neighbor search algorithm.
setSearchPanelVisible(boolean) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Sets whether to display the search panel or not.
setSeed(long) - Method in class adams.data.cleaner.instance.RemoveOutliers: Sets the seed value.
setSeed(long) - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Sets the seed value for cross-validation.
setSeed(long) - Method in class adams.data.evaluator.instance.CrossValidatedPrediction: Sets the seed value for cross-validation.
setSeed(long) - Method in class adams.data.evaluator.instance.EnsembleEvaluator: Sets the seed value.
setSeed(long) - Method in class adams.data.evaluator.instance.FakeEvaluator: Sets the seed value for the random values.
setSeed(long) - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Sets the seed value.
setSeed(long) - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Sets the seed value.
setSegments(int) - Method in class adams.opt.genetic.RonWeasley: Set number of s-g segments to optimise
setSegmentWidths(BaseInteger[]) - Method in class adams.data.io.output.NIRSpectrumWriter: Set segments.
setSeparator(String) - Method in class adams.data.io.input.ASCIIXYSpectrumReader: Sets the separator to use.
setSeparator(String) - Method in class adams.data.io.input.SimpleXYZReader: Sets the string to use as separator for the columns, use '\t' for tab.
setSeparator(String) - Method in class adams.data.io.output.ASCIIXYSpectrumWriter: Sets the separator to use between X and Y columns.
setSeparator(String) - Method in class adams.data.io.output.SimpleXYZWriter: Sets the string to use as separator for the columns, use '\t' for tab.
setSerializationFile(PlaceholderFile) - Method in class adams.data.cleaner.instance.AbstractSerializableCleaner: Sets the file to serialize to.
setSerializationFile(PlaceholderFile) - Method in class adams.data.cleaner.spectrum.AbstractSerializableCleaner: Sets the file to serialize to.
setSerializationFile(PlaceholderFile) - Method in class adams.data.evaluator.instance.AbstractSerializableEvaluator: Sets the file to serialize to.
setSerializationFile(PlaceholderFile) - Method in class adams.data.postprocessor.instances.AbstractSerializablePostProcessor: Sets the file to serialize to.
setSerializationFile(PlaceholderFile) - Method in class adams.data.spectrumfilter.AbstractSerializableFilter: Sets the file to serialize to.
setSerializationSetup(Object[]) - Method in class adams.data.cleaner.instance.IQRCleaner: Updates the member variables with the provided objects obtained from deserialization.
setSerializationSetup(Object[]) - Method in class adams.data.cleaner.instance.RemoveMisclassifiedCleaner: Updates the member variables with the provided objects obtained from deserialization.
setSerializationSetup(Object[]) - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Updates the member variables with the provided objects obtained from deserialization.
setSerializationSetup(Object[]) - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Updates the member variables with the provided objects obtained from deserialization.
setSerializationSetup(Object[]) - Method in class adams.data.evaluator.instance.CrossValidatedPrediction: Updates the member variables with the provided objects obtained from deserialization.
setSerializationSetup(Object[]) - Method in class adams.data.evaluator.instance.DistanceToCenter: Updates the member variables with the provided objects obtained from deserialization.
setSerializationSetup(Object[]) - Method in class adams.data.evaluator.instance.DistanceToClosest: Updates the member variables with the provided objects obtained from deserialization.
setSerializationSetup(Object[]) - Method in class adams.data.evaluator.instance.EnsembleEvaluator: Updates the member variables with the provided objects obtained from deserialization.
setSerializationSetup(Object[]) - Method in class adams.data.evaluator.instance.IntervalEstimatorEvaluator: Updates the member variables with the provided objects obtained from deserialization.
setSerializationSetup(Object[]) - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Updates the member variables with the provided objects obtained from deserialization.
setSerializationSetup(Object[]) - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Updates the member variables with the provided objects obtained from deserialization.
setSerializationSetup(Object[]) - Method in class adams.data.postprocessor.instances.WekaFilter: Updates the member variables with the provided objects obtained from deserialization.
setSerialNo(String) - Method in class adams.data.io.output.NIRSpectrumWriter: Set serial no.
setSetupLoadedOrGenerated(boolean) - Method in class adams.data.cleaner.instance.AbstractSerializableCleaner: Sets whether the setup was loaded/generated.
setSetupLoadedOrGenerated(boolean) - Method in class adams.data.cleaner.spectrum.AbstractSerializableCleaner: Sets whether the setup was loaded/generated.
setSetupLoadedOrGenerated(boolean) - Method in class adams.data.evaluator.instance.AbstractSerializableEvaluator: Sets whether the setup was loaded/generated.
setSetupLoadedOrGenerated(boolean) - Method in class adams.data.postprocessor.instances.AbstractSerializablePostProcessor: Sets whether the setup was loaded/generated.
setSetupLoadedOrGenerated(boolean) - Method in class adams.data.spectrumfilter.AbstractSerializableFilter: Sets whether the setup was loaded/generated.
setShowReportTable(boolean) - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Sets whether the report value is visible.
setShowSidePanel(boolean) - Method in class adams.flow.sink.SpectrumDisplay: Sets whether to show the side panel or not.
setSkipFields(boolean) - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Sets whether to skip fields.
setSkipFieldsRegExp(BaseRegExp) - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Sets the regular expression for identifying fields to skip (if enabled).
setSortOnInsertTimestamp(boolean) - Method in class adams.db.AbstractSpectrumConditions: Sets whether to sort on SampleData.INSERT_TIMESTAMP instead of auto ID.
setSortOnSampleID(boolean) - Method in class adams.db.AbstractSpectrumConditions: Sets whether to sort on SampleData.SAMPLE_ID instead of auto ID.
setSource(Field) - Method in class adams.data.spectrumfilter.ReportFieldFromStringValue: Sets the source field in the report to get the string to apply the regular expression to.
setSource(Field) - Method in class adams.data.spectrumfilter.ReportFieldFromStringValueWithLookup: Sets the source field to use.
setSource(InputStream) - Method in class weka.core.converters.CALSpectrumLoader: Does nothing.
setSpectralDataAttributes(String) - Method in class adams.flow.transformer.InstanceToSpectrum: Set which attributes to use for spectral data.
setSpectrum(MultiSpectrum) - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.UploadRequest: Sets the value of the spectrum property.
setSpectrum(Spectrum) - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.UploadRequest: Sets the value of the spectrum property.
setSpectrum(Spectrum) - Method in class nz.ac.waikato.adams.webservice.spectral.get.GetResponse: Sets the value of the spectrum property.
setSpectrum(Spectrum) - Method in class nz.ac.waikato.adams.webservice.spectral.put.PutRequest: Sets the value of the spectrum property.
setSpectrum(Spectrum) - Method in class nz.ac.waikato.adams.webservice.spectral.transform.TransformRequest: Sets the value of the spectrum property.
setSpectrum(Spectrum) - Method in class nz.ac.waikato.adams.webservice.spectral.transform.TransformResponse: Sets the value of the spectrum property.
SetSpectrumAmplitude - Class in adams.flow.transformer: Sets the amplitude for the specified wave number.
Can either be used to replace an existing spectrum point or simply to insert another one.
SetSpectrumAmplitude() - Constructor for class adams.flow.transformer.SetSpectrumAmplitude
SetSpectrumAmplitude.UpdateType - Enum in adams.flow.transformer: Defines how to set the amplitude.
setSpectrumBlockType(String) - Method in class adams.data.io.input.OpusSpectrumReaderExt: Sets the block type of the spectrum to extract.
setSpectrumColumns(SpreadSheetColumnRange) - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Sets the columns containing spectral data.
setSpectrumFormat(String) - Method in class adams.data.spectrumfilter.ChangeFormat: Sets the format for the spectrum.
setSpectrumType(SoilCaresScannerSpectrumReader.SpectrumType) - Method in class adams.data.io.input.SoilCaresScannerSpectrumReader: Sets the type of spectrum to read.
setStandardize(StandardiseByInterpolation) - Method in class adams.data.multifilter.Average: Sets the filter to use for standardizing the spectra.
setStart(float) - Method in class adams.data.spectrumfilter.Rebase: Sets the new starting point for the wave numbers.
setStart(int) - Method in class adams.data.io.input.CALSpectrumReader: Sets the start point setting.
setStart(int) - Method in class adams.data.io.input.OpusSpectrumReader: Sets the start point setting.
setStart(int) - Method in class weka.filters.unsupervised.attribute.SavitzkyGolayRange: Sets the first amplitude.
setStartDate(BaseDateTime) - Method in class adams.db.AbstractSpectrumConditions: Sets the start date.
setStartDate(BaseDateTime) - Method in class adams.db.OrphanedSampleDataConditions: Sets the start date.
setStartPoints(BaseFloat[]) - Method in class adams.data.io.output.NIRSpectrumWriter: Set start points.
setStatistic(CrossValidatedPrediction.StatisticType) - Method in class adams.data.evaluator.instance.CrossValidatedPrediction: Sets the statistic to use as evaluation output.
setStatistic(EvaluationStatistic) - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Sets the statistic to use as evaluation output.
setStatistic(CollapseX.StatisticType) - Method in class adams.flow.transformer.threewaydatamerge.CollapseX: Sets the type of statistic to calculate.
setStep(double) - Method in class adams.data.spectrumfilter.AbstractStandardiseFilter: Sets the step
setStorageName(StorageName) - Method in class adams.flow.transformer.MergeSampleDataFromMap: Sets the name of the stored map with the sample data objects.
setStorageName(StorageName) - Method in class adams.flow.transformer.MultiSpectrumAdd: Sets the name of the stored value.
setStoreWaveNo(boolean) - Method in class adams.flow.transformer.BulkSpectrumDbWriter: Sets whether to store the wave numbers as well.
setStoreWaveNo(boolean) - Method in class adams.flow.transformer.SpectrumDbWriter: Sets whether to store the wave numbers as well.
setSubGenerators(AbstractThreeWayDataFeatureGenerator[]) - Method in class adams.data.threewayfeatures.MultiThreeWayDataFeatureGenerator: Sets the generators to use.
setSuccess(boolean) - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.UploadResponse: Sets the value of the success property.
setSuccess(boolean) - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.UploadResponse: Sets the value of the success property.
setSuccess(boolean) - Method in class nz.ac.waikato.adams.webservice.spectral.get.GetResponse: Sets the value of the success property.
setSuccess(boolean) - Method in class nz.ac.waikato.adams.webservice.spectral.put.PutResponse: Sets the value of the success property.
setSuccess(boolean) - Method in class nz.ac.waikato.adams.webservice.spectral.transform.TransformResponse: Sets the value of the success property.
setSuccess(String) - Method in class adams.data.spectrumfilter.ConditionalReportField: Sets the success value, ie the value to use when the condition evaluates to true.
setTarget(Field) - Method in class adams.data.spectrumfilter.ConditionalReportField: Sets the target field in the report to store the result in.
setTarget(Field) - Method in class adams.data.spectrumfilter.ReportFieldFromStringValue: Sets the target field in the report to store the result in.
setTarget(Field) - Method in class adams.data.spectrumfilter.ReportFieldFromStringValueWithLookup: Sets the target field to use for the result.
setText(String) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Sets the fixed text to output.
setTextColor(Color) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Sets the color for the text.
setThreshold(double) - Method in class adams.data.multispectrumoperation.outlierremoval.CorrelationBasedThreshold: Sets the threshold to use.
setThreshold(double) - Method in class adams.data.multispectrumoperation.outlierremoval.CosineSimilarityBasedThreshold: Sets the threshold to use.
setThreshold(double) - Method in class adams.data.multispectrumoperation.outlierremoval.MeanSpectrumCosineSimilarityBasedThreshold: Sets the threshold to use.
setThreshold(double) - Method in class adams.data.spectrumoutlier.Oscillation: Sets the threshold for the correlation coefficient.
setTimestamp(BaseDateTime) - Method in class adams.data.io.output.NIRSpectrumWriter: Set the timestamp to use in the file.
setTolerateHeaderChanges(boolean) - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Sets whether to tolerate header changes and merely re-generating the header instead of throwing an exception.
setTransferPrefix(String) - Method in class adams.data.conversion.MultiSpectrumToSpectra: Sets the (optional) prefix for report fields that get transferred.
setTransferPrefix(String) - Method in class adams.flow.transformer.MultiSpectrumFilter: Sets the (optional) prefix for report fields that get transferred.
setTransferRegExp(BaseRegExp) - Method in class adams.data.conversion.MultiSpectrumToSpectra: Sets the regular expression that the field names must match in order to get transferred.
setTransferRegExp(BaseRegExp) - Method in class adams.flow.transformer.MultiSpectrumFilter: Sets the regular expression that the field names must match in order to get transferred.
setTransferReport(boolean) - Method in class adams.data.conversion.MultiSpectrumToSpectra: Sets whether to transfer the report values from the multi-spectrum into the sub-spectra.
setTransferReport(boolean) - Method in class adams.flow.transformer.MultiSpectrumFilter: Sets whether to transfer the report values from the multi-spectrum into the sub-spectra.
setTransformer(AbstractAmplitudeTransformer) - Method in class adams.data.spectrumfilter.AmplitudeTransform: Sets the transformer to use.
setType(SpectrumToArray.DataType) - Method in class adams.data.conversion.SpectrumToArray: Sets the type of data to output.
setType(ScioLabExportSpectrumReader.SpectrumType) - Method in class adams.data.io.input.ScioLabExportSpectrumReader: Sets the type of spectrum to read.
setType(GetSpectrumAmplitude.RetrievalType) - Method in class adams.flow.transformer.GetSpectrumAmplitude: Sets how to retrieve the amplitude.
setType(SetSpectrumAmplitude.UpdateType) - Method in class adams.flow.transformer.SetSpectrumAmplitude: Sets how to retrieve the amplitude.
setType(SpectrumInfo.InfoType) - Method in class adams.flow.transformer.SpectrumInfo: Sets the type of information to generate.
setType(String) - Method in class adams.data.spectrum.Spectrum: Sets the sample type.
setType(DataType) - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.Property: Sets the value of the type property.
setType(DataType) - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.Property: Sets the value of the type property.
setType(DataType) - Method in class nz.ac.waikato.adams.webservice.spectral.get.Property: Sets the value of the type property.
setType(DataType) - Method in class nz.ac.waikato.adams.webservice.spectral.put.Property: Sets the value of the type property.
setType(DataType) - Method in class nz.ac.waikato.adams.webservice.spectral.transform.Property: Sets the value of the type property.
setTypefield(String) - Method in class adams.data.io.input.CALSpectrumReader: Set type field.
setUnsigned(boolean) - Method in class adams.data.io.input.FitsLibsReader: Sets whether the numbers are to be interpreted as unsigned.
setUp() - Method in class adams.flow.control.InstanceCleaner: Initializes the sub-actors for flow execution.
setUp() - Method in class adams.flow.control.SpectrumCleaner: Initializes the sub-actors for flow execution.
setUp() - Method in class adams.flow.transformer.Cleaner: Initializes the item for flow execution.
setUp() - Method in class adams.flow.transformer.Evaluator: Initializes the item for flow execution.
setUp() - Method in class adams.flow.transformer.MultiSpectrumAdd: Initializes the item for flow execution.
setUp() - Method in class adams.flow.transformer.SetEvaluationMetaData: Initializes the item for flow execution.
setUpCallableActor() - Method in class adams.flow.transformer.MultiSpectrumAdd: Configures the callable actor.
setUpCleaner() - Method in class adams.flow.transformer.Cleaner: Configures the cleaner.
setUpdateContainerColor(boolean) - Method in class adams.gui.visualization.spectrum.ReportColorSpectrumPaintlet: Sets whether to update the container's color with the color determined by this paintlet.
setUpdateInterval(int) - Method in class adams.flow.sink.spectrumdisplay.SimplePlotUpdater: Sets the number of tokens after which the display is being updated.
setUpdateWaveNumbers(boolean) - Method in class adams.data.spectrumfilter.Rebase: Sets whether to update the wave numbers using the specified step size.
SetupDialog(Dialog, Dialog.ModalityType) - Constructor for class adams.gui.visualization.spectrum.HistogramFactory.SetupDialog: Initializes the dialog.
SetupDialog(Frame, boolean) - Constructor for class adams.gui.visualization.spectrum.HistogramFactory.SetupDialog: Initializes the dialog.
setUpEvaluator() - Method in class adams.flow.transformer.Evaluator: Loads the evaluator from the evaluator file.
setUpModel() - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Tries to obtain the algorithm model.
setUpperPercentile(double) - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Sets the upper percentile.
setUpPostProcessor() - Method in class adams.flow.transformer.PostProcessor: Configures the postprocessor.
setupScriptlet(AbstractScriptlet) - Method in class adams.gui.scripting.SpectralCommandProcessor: Performs further setups of the scriptlet.
setUseAbsoluteError(boolean) - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Sets whether to use an absolute error (ie no direction).
setUseAbsoluteSource(boolean) - Method in class adams.data.io.input.AbstractSpectrumReader: Sets whether to use absolute source filename rather than just name.
setUseAbsoluteSource(boolean) - Method in class adams.data.io.input.AbstractThreeWayDataReader: Sets whether to use absolute source filename rather than just name.
setUseCompression(boolean) - Method in class adams.data.io.output.SimpleSpectrumWriter: Sets whether to use compression.
setUseCompression(boolean) - Method in class adams.data.io.output.SimpleXYZWriter: Sets whether to use compression.
setUseCustomComparator(boolean) - Method in class adams.data.conversion.SpectraToMultiSpectrum: Sets whether to use a custom comparator.
setUseCustomComparator(boolean) - Method in class adams.flow.transformer.SpectrumFileReader: Sets whether to use a custom comparator.
setUseEvaluatorResetVariable(boolean) - Method in class adams.flow.transformer.Evaluator: Sets whether to use a variable to monitor for changes in order to reset the evaluator.
setUseFilenameAsID(boolean) - Method in class adams.data.io.input.AbstractJCampSpectrumReader: Sets whether to use the filename as ID.
setUseFilenameAsID(boolean) - Method in class adams.data.io.input.JCampDX2SpectrumReader: Sets whether to use the filename as ID.
setUseFilenameAsSampleID(boolean) - Method in class adams.data.io.input.RelabSpectrumReader: Sets whether to use the filename (without path, uppercase) in the sample id as well.
setUseModelResetVariable(boolean) - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Sets whether to use a variable to monitor for changes in order to reset the model.
setUseReferenceAndMetaData(boolean) - Method in class adams.data.conversion.SpectrumToJson: Sets whether only the specified reference and meta-data report values are output (in separate sections).
setUseReferenceAndMetaData(boolean) - Method in class adams.data.io.output.JsonSpectrumWriter: Sets whether only the specified reference and meta-data report values are output (in separate sections).
setUseStoreTable(boolean) - Method in class adams.data.spectrumfilter.AbstractDatabaseFilter: Sets whether to read from the active or store table.
setValidate(boolean) - Method in class adams.data.io.input.JCampDX2SpectrumReader: Sets whether to use a validating parser.
setValue(PropertyPath.PropertyContainer, int) - Method in class adams.core.discovery.genetic.SegmentedSavitzkyGolayDerivativeOrder: Sets the integer value in the property container.
setValue(PropertyPath.PropertyContainer, int[]) - Method in class adams.core.discovery.genetic.SegmentedDownSampleNthPoints: Sets the integer value in the property container.
setValue(PropertyPath.PropertyContainer, int[]) - Method in class adams.core.discovery.genetic.SegmentedSavitzkyGolayNumPoints: Sets the integer value in the property container.
setValue(String) - Method in class adams.flow.transformer.SetEvaluationMetaData: Sets the value to store.
setValue(String) - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.Property: Sets the value of the value property.
setValue(String) - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.Property: Sets the value of the value property.
setValue(String) - Method in class nz.ac.waikato.adams.webservice.spectral.get.Property: Sets the value of the value property.
setValue(String) - Method in class nz.ac.waikato.adams.webservice.spectral.put.Property: Sets the value of the value property.
setValue(String) - Method in class nz.ac.waikato.adams.webservice.spectral.transform.Property: Sets the value of the value property.
setVariableName(VariableName) - Method in class adams.flow.transformer.SpectrumFeatureGenerator: Sets the name of the variable to monitor.
setVariableName(VariableName) - Method in class adams.flow.transformer.ThreeWayDataFeatureGenerator: Sets the name of the variable to monitor.
setVariance(double) - Method in class adams.data.spectrumfilter.PCA: Sets the variance.
setVersion(String) - Method in class adams.data.conversion.WekaPredictionContainerToEvaluationContainer: Sets the version to use for the evaluation.
setVersion(String) - Method in class adams.flow.transformer.Evaluator: Sets the version to use.
setVisible(boolean) - Method in class adams.gui.visualization.spectrum.SpectrumContainer: Sets the spectrums visibility.
setVisible(int, boolean) - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: Sets the specified container's visibility.
setWaitPoll(int) - Method in class adams.flow.standalone.rats.WSMultiSpectrumReception: Sets the number of milli-seconds to wait before polling whether data has arrived.
setWaitPoll(int) - Method in class adams.flow.standalone.rats.WSSpectrumReception: Sets the number of milli-seconds to wait before polling whether data has arrived.
setWaveColumns(SpreadSheetColumnRange) - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Sets the columns containing the wave amplitudes.
setWaveNoInc(float) - Method in class adams.data.conversion.ArrayToSpectrum: Sets the increment to use between wave numbers.
setWaveNoStart(float) - Method in class adams.data.conversion.ArrayToSpectrum: Sets the first wave number to use.
setWaveNumber(float) - Method in class adams.data.spectrum.SpectrumPoint: Sets the wave number value.
setWaveNumber(float) - Method in class adams.flow.transformer.GetSpectrumAmplitude: Sets the wave number of the amplitude to retrieve.
setWaveNumber(float) - Method in class adams.flow.transformer.SetSpectrumAmplitude: Sets the wave number of the amplitude to set.
setWaveNumberAsSuffix(boolean) - Method in class adams.data.instances.SimpleInstanceGenerator: Sets whether the wave number is used as suffix instead of the index.
setWaveNumberAsSuffix(boolean) - Method in class adams.data.instances.SimpleSpectralInstanceGenerator: Sets whether the wave number is used as suffix instead of the index.
setWaveNumberColumn(SpreadSheetColumnIndex) - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Sets the column containing the wave numbers.
setWaveNumberPrefix(String) - Method in class adams.data.instances.AbstractSpectrumInstanceGenerator: Sets the prefix for the wave number attributes.
setWaveNumberRegExp(BaseRegExp) - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Sets the regular expression to identify the wave number (1st group is used).
setWaveNumberRegExp(BaseRegExp) - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Sets the regular expression to identify the wave number (1st group is used).
setWaveNumberRegExp(BaseRegExp) - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Sets the regular expression to identify the wave number (1st group is used).
setWaveNumbersInHeader(boolean) - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Sets whether the wave numbers are in the header.
setWaveNumbersInHeader(boolean) - Method in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: Sets whether to use the wave numbers in the header.
setWaveNumberStarts(BaseFloat[]) - Method in class adams.data.multifilter.Fusion: Sets the starting wave number for each sub-spectrum.
setWaveNumberStepSize(float) - Method in class adams.data.spectrumfilter.PadPower2: Sets the step size for the additional wave numbers.
setWaveNumberStepSizes(BaseFloat[]) - Method in class adams.data.multifilter.Fusion: Sets the wave number step sizes for each sub-spectrum.
setWaves(Waves) - Method in class nz.ac.waikato.adams.webservice.rats.multispectrum.Spectrum: Sets the value of the waves property.
setWaves(Waves) - Method in class nz.ac.waikato.adams.webservice.rats.spectrum.Spectrum: Sets the value of the waves property.
setWaves(Waves) - Method in class nz.ac.waikato.adams.webservice.spectral.get.Spectrum: Sets the value of the waves property.
setWaves(Waves) - Method in class nz.ac.waikato.adams.webservice.spectral.put.Spectrum: Sets the value of the waves property.
setWaves(Waves) - Method in class nz.ac.waikato.adams.webservice.spectral.transform.Spectrum: Sets the value of the waves property.
setWaveStep(float) - Method in class adams.data.spectrumfilter.Rebase: Sets the difference between two wave numbers when updating them.
setWaveStep(float) - Method in class adams.flow.transformer.InstanceToSpectrum: Sets the step size for the wave numbers, if lastWave is not defined.
setWebService(WebServiceProvider) - Method in class adams.flow.standalone.rats.WSMultiSpectrumReception: Sets the webservice provider to use.
setWebService(WebServiceProvider) - Method in class adams.flow.standalone.rats.WSSpectrumReception: Sets the webservice provider to use.
setWidth(int) - Method in class adams.data.spectrumimage.Intensity: Sets the width of the image.
setWidth(int) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlayWithDimensions: Sets the width of the overlay.
setWindowSize(int) - Method in class adams.data.sampledata.SignalToNoiseRatio: Sets the window size for determining the 'smoothed' abundances.
setWindowSize(int) - Method in class adams.data.spectrumoutlier.Oscillation: Sets the polynomial order.
setWindowSizeFirst(int) - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Sets the Savitzky-Golay window size for filter with first derivative.
setWindowSizeNone(int) - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Sets the Savitzky-Golay window size for filter with no derivative.
setWindowSizeSecond(int) - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Sets the Savitzky-Golay window size for filter with second derivative.
setWrap(boolean) - Method in class adams.data.postprocessor.instances.WekaFilter: Sets whether to wrap the filter in a SpectrumFilter.
setWriter(AbstractSpectrumWriter) - Method in class adams.data.io.output.FilteredSpectrumWriter: Sets the underlying writer.
setWriter(AbstractSpectrumWriter) - Method in class adams.flow.standalone.rats.SaveMultiSpectrumFileOutput: Sets the writer to use.
setWriter(AbstractSpectrumWriter) - Method in class adams.flow.standalone.rats.SaveSpectrumFileOutput: Sets the writer to use.
setWriter(SpreadSheetWriter) - Method in class adams.data.io.output.SpreadSheetSpectrumWriter: Sets the spreadsheet writer to use.
setX(double) - Method in class adams.data.io.input.SimpleEEMReader: Sets the value to use for the X axis.
setX(double) - Method in class adams.data.threeway.L1Point: Set the X.
setX(int) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlay: Sets the X position of the overlay.
setY(double) - Method in class adams.data.threeway.L1Point: Sets the Y.
setY(int) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlay: Sets the Y position of the overlay.
setZ(double) - Method in class adams.data.threeway.L2Point: Sets the Z.
setZoom(double) - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Sets the zoom level in percent (0-1600).
setZoom(double) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Sets the zoom factor (0-16).
setZoomOverview(boolean) - Method in class adams.flow.sink.SpectrumDisplay: Sets whether to display the zoom overview.
setZoomOverviewPanelVisible(boolean) - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Sets the zoom overview panel visible or not.
setZoomOverviewPanelVisible(boolean) - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Sets the zoom overview panel visible or hides it.
shallowCopy() - Method in class adams.data.cleaner.instance.AbstractCleaner: Returns a shallow copy of itself, i.e., based on the commandline options.
shallowCopy() - Method in class adams.data.cleaner.spectrum.AbstractCleaner: Returns a shallow copy of itself, i.e., based on the commandline options.
shallowCopy() - Method in class adams.data.evaluator.instance.AbstractEvaluator: Returns a shallow copy of itself, i.e., based on the commandline options.
shallowCopy() - Method in class adams.data.multifilter.AbstractMultiSpectrumFilter: Returns a shallow copy of itself, i.e., based on the commandline options.
shallowCopy() - Method in class adams.data.multireportfilter.AbstractMultiSpectrumReportFilter: Returns a shallow copy of itself, i.e., based on the commandline options.
shallowCopy() - Method in class adams.data.postprocessor.instances.AbstractPostProcessor: Returns a shallow copy of itself, i.e., based on the commandline options.
shallowCopy() - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Returns a shallow copy of itself, i.e., based on the commandline options.
shallowCopy() - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Returns a shallow copy of itself, i.e., based on the commandline options.
shallowCopy() - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Returns a shallow copy of itself, i.e., based on the commandline options.
shallowCopy(boolean) - Method in class adams.data.cleaner.instance.AbstractCleaner: Returns a shallow copy of itself, i.e., based on the commandline options.
shallowCopy(boolean) - Method in class adams.data.cleaner.spectrum.AbstractCleaner: Returns a shallow copy of itself, i.e., based on the commandline options.
shallowCopy(boolean) - Method in class adams.data.evaluator.instance.AbstractEvaluator: Returns a shallow copy of itself, i.e., based on the commandline options.
shallowCopy(boolean) - Method in class adams.data.multifilter.AbstractMultiSpectrumFilter: Returns a shallow copy of itself, i.e., based on the commandline options.
shallowCopy(boolean) - Method in class adams.data.multireportfilter.AbstractMultiSpectrumReportFilter: Returns a shallow copy of itself, i.e., based on the commandline options.
shallowCopy(boolean) - Method in class adams.data.postprocessor.instances.AbstractPostProcessor: Returns a shallow copy of itself, i.e., based on the commandline options.
shallowCopy(boolean) - Method in class adams.data.spectrum.AbstractSpectrumFeatureGenerator: Returns a shallow copy of itself, i.e., based on the commandline options.
shallowCopy(boolean) - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Returns a shallow copy of itself, i.e., based on the commandline options.
shallowCopy(boolean) - Method in class adams.data.threewayfeatures.AbstractThreeWayDataFeatureGenerator: Returns a shallow copy of itself, i.e., based on the commandline options.
sheet() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader.SingleSheetIterator: Reads the sheets if necessary and returns them.
SheetIterator(SpreadSheetReader, File) - Constructor for class adams.data.io.input.RowWiseSpreadSheetSpectrumReader.SheetIterator: Initializes the iterator.
sheets() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader.MultiSheetIterator: Reads the sheets if necessary and returns them.
Shift - Class in adams.data.threewayfilter
Shift() - Constructor for class adams.data.threewayfilter.Shift
showBytes(byte[]) - Static method in class adams.data.io.output.foss.FossOutputHelper: Output byte array in hex form.
showConditions() - Method in class adams.gui.tools.idprovider.DatabaseSearchPanel: Shows GOE dialog with the conditions.
showHistogram(List<SpectrumContainer>) - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Displays the histograms for the given spectrums.
showReport() - Method in class adams.gui.tools.UpdateSampleDataPanel: Loads the associated report and displays it.
showReportTableTipText() - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Returns the tip text for this property.
showSampleData(List<SpectrumContainer>) - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Displays a dialog with the given sample data.
showSidePanelTipText() - Method in class adams.flow.sink.SpectrumDisplay: Returns the tip text for this property.
showSpectralData(SpectrumContainer) - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Displays a dialog with the given spectral data.
showStatistics(List<InformativeStatistic>) - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Displays a dialog with the given statistics.
showStatus(String) - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Displays a message.
showStatus(String) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Displays a message.
SIC_4250 - adams.data.io.output.foss.FossOutputHelper.InstrumentHeader.InstrumentType
SIC_4500 - adams.data.io.output.foss.FossOutputHelper.InstrumentHeader.InstrumentType
SIC_5000 - adams.data.io.output.foss.FossOutputHelper.InstrumentHeader.InstrumentType
SIC_5500 - adams.data.io.output.foss.FossOutputHelper.InstrumentHeader.InstrumentType
SIC_6250 - adams.data.io.output.foss.FossOutputHelper.InstrumentHeader.InstrumentType
SIC_6250V - adams.data.io.output.foss.FossOutputHelper.InstrumentHeader.InstrumentType
SIC_6500 - adams.data.io.output.foss.FossOutputHelper.InstrumentHeader.InstrumentType
SignalToNoiseRatio - Class in adams.data.sampledata
SignalToNoiseRatio() - Constructor for class adams.data.sampledata.SignalToNoiseRatio
SimpleCSVSampleDataHandler - Class in adams.gui.tools.previewbrowser: Displays the following report types: csv

Valid options are:
SimpleCSVSampleDataHandler() - Constructor for class adams.gui.tools.previewbrowser.SimpleCSVSampleDataHandler
SimpleCSVSampleDataReader - Class in adams.data.io.input: Reads a report file in CSV file format.
SimpleCSVSampleDataReader() - Constructor for class adams.data.io.input.SimpleCSVSampleDataReader
SimpleCSVSampleDataWriter - Class in adams.data.io.output: Writes reports in CSV file format.
SimpleCSVSampleDataWriter() - Constructor for class adams.data.io.output.SimpleCSVSampleDataWriter
SimpleEEMReader - Class in adams.data.io.input: Reads EEM data in spreadsheet format (tab-separated columns).
SimpleEEMReader() - Constructor for class adams.data.io.input.SimpleEEMReader
SimpleEEMWriter - Class in adams.data.io.output: Writes 3-way data in spreadsheet format (tab-separated columns).
SimpleEEMWriter() - Constructor for class adams.data.io.output.SimpleEEMWriter
SimpleInstanceGenerator - Class in adams.data.instances: A simple scheme for turning spectra and fields of the associated sample data into weka.core.Instance objects.
SimpleInstanceGenerator() - Constructor for class adams.data.instances.SimpleInstanceGenerator
SimpleJsonSampleDataReader - Class in adams.data.io.input: Reads a report file in Json file format.
SimpleJsonSampleDataReader() - Constructor for class adams.data.io.input.SimpleJsonSampleDataReader
SimpleJsonSampleDataWriter - Class in adams.data.io.output: Writes reports in Json file format.
SimpleJsonSampleDataWriter() - Constructor for class adams.data.io.output.SimpleJsonSampleDataWriter
SimplePlotUpdater - Class in adams.flow.sink.spectrumdisplay: Updates the display after the specified number of tokens have been processed.
SimplePlotUpdater() - Constructor for class adams.flow.sink.spectrumdisplay.SimplePlotUpdater
SimpleRatsMultiSpectrumService - Class in adams.flow.webservice.multispectrum: Class that implements the RATS multispectrum web service.
SimpleRatsMultiSpectrumService() - Constructor for class adams.flow.webservice.multispectrum.SimpleRatsMultiSpectrumService: Default Constructor.
SimpleRatsSpectrumService - Class in adams.flow.webservice.spectrum: Class that implements the RATS spectrum web service.
SimpleRatsSpectrumService() - Constructor for class adams.flow.webservice.spectrum.SimpleRatsSpectrumService: Default Constructor.
SimpleRowGenerator - Class in adams.data.spreadsheetrowgenerator: Outputs spectral and sample data.
SimpleRowGenerator() - Constructor for class adams.data.spreadsheetrowgenerator.SimpleRowGenerator
SimpleSampleDataHandler - Class in adams.gui.tools.previewbrowser: Displays the following report types: props

Valid options are:
SimpleSampleDataHandler() - Constructor for class adams.gui.tools.previewbrowser.SimpleSampleDataHandler
SimpleSampleDataReader - Class in adams.data.io.input: Reads a report file in properties file format.
SimpleSampleDataReader() - Constructor for class adams.data.io.input.SimpleSampleDataReader
SimpleSampleDataWriter - Class in adams.data.io.output: Writes reports in properties file format.
SimpleSampleDataWriter() - Constructor for class adams.data.io.output.SimpleSampleDataWriter
SimpleSavitzkyGolay - Class in adams.data.spectrumfilter: A filter that applies a simplified Savitzky-Golay smoothing.

For more information on Savitzky-Golay see:

A.
SimpleSavitzkyGolay() - Constructor for class adams.data.spectrumfilter.SimpleSavitzkyGolay
SimpleSpectralGetService - Class in adams.flow.webservice: Class that implements the Spectral get web service.
SimpleSpectralGetService() - Constructor for class adams.flow.webservice.SimpleSpectralGetService: Default Constructor.
SimpleSpectralInstanceGenerator - Class in adams.data.instances: A simple scheme for turning spectra and fields of the associated sample data into weka.core.Instance objects (without class attribute).
SimpleSpectralInstanceGenerator() - Constructor for class adams.data.instances.SimpleSpectralInstanceGenerator
SimpleSpectralPutService - Class in adams.flow.webservice: Class that implements the Spectral put web service.
SimpleSpectralPutService() - Constructor for class adams.flow.webservice.SimpleSpectralPutService: Default Constructor.
SimpleSpectralTransformService - Class in adams.flow.webservice: Class that implements the Spectral web service.
SimpleSpectralTransformService() - Constructor for class adams.flow.webservice.SimpleSpectralTransformService: Default Constructor.
SimpleSpectrumHandler - Class in adams.gui.tools.previewbrowser: Displays the following spectrum types: spec

Valid options are:
SimpleSpectrumHandler() - Constructor for class adams.gui.tools.previewbrowser.SimpleSpectrumHandler
SimpleSpectrumPaintlet - Class in adams.gui.visualization.spectrum: Paintlet for painting the spectral graph, without any markers.
SimpleSpectrumPaintlet() - Constructor for class adams.gui.visualization.spectrum.SimpleSpectrumPaintlet
SimpleSpectrumReader - Class in adams.data.io.input: Reads spectrums in the internal CSV format.
SimpleSpectrumReader() - Constructor for class adams.data.io.input.SimpleSpectrumReader
SimpleSpectrumWriter - Class in adams.data.io.output: Writer that stores spectrums in the simple CSV format.
SimpleSpectrumWriter() - Constructor for class adams.data.io.output.SimpleSpectrumWriter
SimpleXYZReader - Class in adams.data.io.input: Reads 3-day data in CSV format with X, Y, Z and data columns.
SimpleXYZReader() - Constructor for class adams.data.io.input.SimpleXYZReader
SimpleXYZWriter - Class in adams.data.io.output: Writes 3-way data in CSV format (x/y/z/data columns).
SimpleXYZWriter() - Constructor for class adams.data.io.output.SimpleXYZWriter
SingleSheetIterator(SpreadSheetReader, File) - Constructor for class adams.data.io.input.RowWiseSpreadSheetSpectrumReader.SingleSheetIterator: Initializes the iterator.
size() - Method in class adams.data.io.input.opus.OpusBlockHelper.Block: Returns the size of the block.
size() - Method in class adams.data.io.input.opus.OpusBlockHelper.CommandlineData: Returns the number of values.
size() - Method in class adams.flow.control.InstanceCleaner: Returns the size of the group.
size() - Method in class adams.flow.control.SpectrumCleaner: Returns the size of the group.
skipFieldsRegExpTipText() - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Returns the tip text for this property.
skipFieldsTipText() - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Returns the tip text for this property.
SlidingWindow - Class in adams.data.spectrumsmoothing: Uses a sliding window for determining the median/average inside the window.
SlidingWindow() - Constructor for class adams.data.spectrumsmoothing.SlidingWindow
SNR_byParabolicRegression(Spectrum) - Method in class adams.data.sampledata.SignalToNoiseRatio: Return the SNR measured from quadratic approximation
SNR_bySmoothing(Spectrum) - Method in class adams.data.sampledata.SignalToNoiseRatio: Return the SNR measured from smoothed spectrum
SoilCaresScannerSpectrumReader - Class in adams.data.io.input: Reads spectra from ZIP files generated by the SoilCares Scanner app.
SoilCaresScannerSpectrumReader() - Constructor for class adams.data.io.input.SoilCaresScannerSpectrumReader
SoilCaresScannerSpectrumReader.AmplitudeType - Enum in adams.data.io.input: Determines the type of amplitudes to load.
SoilCaresScannerSpectrumReader.SpectrumType - Enum in adams.data.io.input: Determines the type of spectrum to load.
sortOnInsertTimestampTipText() - Method in class adams.db.AbstractSpectrumConditions: Returns the tip text for this property.
sortOnSampleIDTipText() - Method in class adams.db.AbstractSpectrumConditions: Returns the tip text for this property.
SOURCE - Static variable in class adams.data.sampledata.SampleData: field name for the source.
SOURCE - Static variable in class adams.data.threewayreport.ThreeWayReport: field name for the source.
sourceTipText() - Method in class adams.data.spectrumfilter.ReportFieldFromStringValue: Returns the tip text for this property.
sourceTipText() - Method in class adams.data.spectrumfilter.ReportFieldFromStringValueWithLookup: Returns the tip text for this property.
SPASpectrumHandler - Class in adams.gui.tools.previewbrowser: Displays the following spectrum types: spa

Valid options are:
SPASpectrumHandler() - Constructor for class adams.gui.tools.previewbrowser.SPASpectrumHandler
SPASpectrumReader - Class in adams.data.io.input: Loads spectral data files in Nicolet SPA format.
SPASpectrumReader() - Constructor for class adams.data.io.input.SPASpectrumReader
SPCSpectrumHandler - Class in adams.gui.tools.previewbrowser: Displays the following spectrum types: spc

Valid options are:
SPCSpectrumHandler() - Constructor for class adams.gui.tools.previewbrowser.SPCSpectrumHandler
SPCSpectrumReader - Class in adams.data.io.input: Reads spectra in SPC format (Galactic Universal Data Format) format.
See the specifications here:
http://serswiki.bme.gatech.edu/images/a/ae/SPC_Open_Specification.pdf
SPCSpectrumReader() - Constructor for class adams.data.io.input.SPCSpectrumReader
SPCSpectrumReader.AbstractParser - Class in adams.data.io.input: Parser class for SPC files.
SPCSpectrumReader.FileParser - Class in adams.data.io.input: Parser class for SPC files (header).
SPCSpectrumReader.SubFileParser - Class in adams.data.io.input: Parser class for SPC files (header).
SpecLibSampleDataReader - Class in adams.data.io.input: Reads USGS SpecLib HTML Description files.

http://speclab.cr.usgs.gov/spectral.lib06/
SpecLibSampleDataReader() - Constructor for class adams.data.io.input.SpecLibSampleDataReader
SpecLibSpectrumHandler - Class in adams.gui.tools.previewbrowser: Displays the following spectrum types: asc

Valid options are:
SpecLibSpectrumHandler() - Constructor for class adams.gui.tools.previewbrowser.SpecLibSpectrumHandler
SpecLibSpectrumReader - Class in adams.data.io.input: Reads spectra in USGS SpecLib ASCII format.

http://speclab.cr.usgs.gov/spectral.lib06/
SpecLibSpectrumReader() - Constructor for class adams.data.io.input.SpecLibSpectrumReader
spectra - Variable in class nz.ac.waikato.adams.webservice.rats.multispectrum.MultiSpectrum
SpectralAngleMapper - Class in adams.flow.transformer: Performs Spectral Angle Mapping on a set of spectra.
SpectralAngleMapper() - Constructor for class adams.flow.transformer.SpectralAngleMapper
SpectralCommandProcessor - Class in adams.gui.scripting: Command processor for the spectral module.
SpectralCommandProcessor() - Constructor for class adams.gui.scripting.SpectralCommandProcessor: Initializes the processor.
SpectralCommandProcessor(AbstractScriptingEngine) - Constructor for class adams.gui.scripting.SpectralCommandProcessor: Initializes the processor.
SpectralData - Class in adams.gui.visualization.spectrum.containerlistpopup: Displays the spectral data as table.
SpectralData() - Constructor for class adams.gui.visualization.spectrum.containerlistpopup.SpectralData
spectralDataAttributesTipText() - Method in class adams.flow.transformer.InstanceToSpectrum: Returns the tip text for this property.
SpectralDbBackend - Class in adams.db.autodetect: Auto-detect Spectral backend.
SpectralDbBackend - Class in adams.db.h2: H2 Spectral backend.
SpectralDbBackend - Class in adams.db.mirrored: MySQL Spectral backend.
SpectralDbBackend - Class in adams.db.mssql: MS SQL Server Spectral backend.
SpectralDbBackend - Class in adams.db.mysql: MySQL Spectral backend.
SpectralDbBackend - Class in adams.db.postgresql: PostgreSQL Spectral backend.
SpectralDbBackend - Class in adams.db.sqlite: SQLite Spectral backend.
SpectralDbBackend - Interface in adams.db: Interface for classes that return actual implementations of the processing database interfaces.
SpectralDbBackend() - Constructor for class adams.db.autodetect.SpectralDbBackend
SpectralDbBackend() - Constructor for class adams.db.h2.SpectralDbBackend
SpectralDbBackend() - Constructor for class adams.db.mirrored.SpectralDbBackend
SpectralDbBackend() - Constructor for class adams.db.mssql.SpectralDbBackend
SpectralDbBackend() - Constructor for class adams.db.mysql.SpectralDbBackend
SpectralDbBackend() - Constructor for class adams.db.postgresql.SpectralDbBackend
SpectralDbBackend() - Constructor for class adams.db.sqlite.SpectralDbBackend
SpectralDbBackendDefinition - Class in adams.env: Definition for the SpectralDbBackend props file.
SpectralDbBackendDefinition() - Constructor for class adams.env.SpectralDbBackendDefinition
SpectralGetService - Interface in nz.ac.waikato.adams.webservice.spectral.get: This class was generated by Apache CXF 3.6.6 2025-09-19T23:39:46.676+12:00 Generated source version: 3.6.6
SpectralGetServicePort - Static variable in class nz.ac.waikato.adams.webservice.spectral.get.SpectralGetServiceService
SpectralGetServiceService - Class in nz.ac.waikato.adams.webservice.spectral.get: This class was generated by Apache CXF 3.6.6 2025-09-19T23:39:46.711+12:00 Generated source version: 3.6.6
SpectralGetServiceService() - Constructor for class nz.ac.waikato.adams.webservice.spectral.get.SpectralGetServiceService
SpectralGetServiceService(URL) - Constructor for class nz.ac.waikato.adams.webservice.spectral.get.SpectralGetServiceService
SpectralGetServiceService(URL, QName) - Constructor for class nz.ac.waikato.adams.webservice.spectral.get.SpectralGetServiceService
SpectralGetServiceWS - Class in adams.flow.webservice: Webservice for Spectral.
SpectralGetServiceWS() - Constructor for class adams.flow.webservice.SpectralGetServiceWS
SpectralPutService - Interface in nz.ac.waikato.adams.webservice.spectral.put: This class was generated by Apache CXF 3.6.6 2025-09-19T23:39:49.139+12:00 Generated source version: 3.6.6
SpectralPutServicePort - Static variable in class nz.ac.waikato.adams.webservice.spectral.put.SpectralPutServiceService
SpectralPutServiceService - Class in nz.ac.waikato.adams.webservice.spectral.put: This class was generated by Apache CXF 3.6.6 2025-09-19T23:39:49.172+12:00 Generated source version: 3.6.6
SpectralPutServiceService() - Constructor for class nz.ac.waikato.adams.webservice.spectral.put.SpectralPutServiceService
SpectralPutServiceService(URL) - Constructor for class nz.ac.waikato.adams.webservice.spectral.put.SpectralPutServiceService
SpectralPutServiceService(URL, QName) - Constructor for class nz.ac.waikato.adams.webservice.spectral.put.SpectralPutServiceService
SpectralPutServiceWS - Class in adams.flow.webservice: Webservice for Spectral.
SpectralPutServiceWS() - Constructor for class adams.flow.webservice.SpectralPutServiceWS
SpectralScriptingEngine - Class in adams.gui.scripting: Scripting engine for spectral module.
SpectralScriptingEngine() - Constructor for class adams.gui.scripting.SpectralScriptingEngine
SpectralScriptingEngineDefinition - Class in adams.env: Definition for the ScriptingEngine props file.
SpectralScriptingEngineDefinition() - Constructor for class adams.env.SpectralScriptingEngineDefinition
SpectralTransformService - Interface in nz.ac.waikato.adams.webservice.spectral.transform: This class was generated by Apache CXF 3.6.6 2025-09-19T23:39:51.623+12:00 Generated source version: 3.6.6
SpectralTransformServicePort - Static variable in class nz.ac.waikato.adams.webservice.spectral.transform.SpectralTransformServiceService
SpectralTransformServiceService - Class in nz.ac.waikato.adams.webservice.spectral.transform: This class was generated by Apache CXF 3.6.6 2025-09-19T23:39:51.656+12:00 Generated source version: 3.6.6
SpectralTransformServiceService() - Constructor for class nz.ac.waikato.adams.webservice.spectral.transform.SpectralTransformServiceService
SpectralTransformServiceService(URL) - Constructor for class nz.ac.waikato.adams.webservice.spectral.transform.SpectralTransformServiceService
SpectralTransformServiceService(URL, QName) - Constructor for class nz.ac.waikato.adams.webservice.spectral.transform.SpectralTransformServiceService
SpectralTransformServiceWS - Class in adams.flow.webservice: Webservice for Spectral.
SpectralTransformServiceWS() - Constructor for class adams.flow.webservice.SpectralTransformServiceWS
SpectraToMultiSpectrum - Class in adams.data.conversion: Generates a adams.data.spectrum.MultiSpectrum from the incoming array of adams.data.spectrum.Spectrum.
If the first spectrum in the array is a report-only spectrum (ie no spectral data points), then this report is used as the 'global' report for the multi-spectrum.
SpectraToMultiSpectrum() - Constructor for class adams.data.conversion.SpectraToMultiSpectrum
Spectrogram - Class in adams.data.spectrumimage: Generates a spectrogram image of the spectrum.
Spectrogram() - Constructor for class adams.data.spectrumimage.Spectrogram
spectrum - Variable in class nz.ac.waikato.adams.webservice.rats.multispectrum.UploadRequest
spectrum - Variable in class nz.ac.waikato.adams.webservice.rats.spectrum.UploadRequest
spectrum - Variable in class nz.ac.waikato.adams.webservice.spectral.get.GetResponse
spectrum - Variable in class nz.ac.waikato.adams.webservice.spectral.put.PutRequest
spectrum - Variable in class nz.ac.waikato.adams.webservice.spectral.transform.TransformRequest
spectrum - Variable in class nz.ac.waikato.adams.webservice.spectral.transform.TransformResponse
Spectrum - Class in adams.data.spectrum: Abstract superclass for containers for sequence points.
Spectrum - Class in nz.ac.waikato.adams.webservice.rats.multispectrum: Java class for Spectrum complex type.
Spectrum - Class in nz.ac.waikato.adams.webservice.rats.spectrum: Java class for Spectrum complex type.
Spectrum - Class in nz.ac.waikato.adams.webservice.spectral.get: Java class for Spectrum complex type.
Spectrum - Class in nz.ac.waikato.adams.webservice.spectral.put: Java class for Spectrum complex type.
Spectrum - Class in nz.ac.waikato.adams.webservice.spectral.transform: Java class for Spectrum complex type.
Spectrum() - Constructor for class adams.data.spectrum.Spectrum: Initializes the container.
Spectrum() - Constructor for class nz.ac.waikato.adams.webservice.rats.multispectrum.Spectrum
Spectrum() - Constructor for class nz.ac.waikato.adams.webservice.rats.spectrum.Spectrum
Spectrum() - Constructor for class nz.ac.waikato.adams.webservice.spectral.get.Spectrum
Spectrum() - Constructor for class nz.ac.waikato.adams.webservice.spectral.put.Spectrum
Spectrum() - Constructor for class nz.ac.waikato.adams.webservice.spectral.transform.Spectrum
SPECTRUM - adams.data.io.input.ScioLabExportSpectrumReader.SpectrumType
SPECTRUM - adams.data.io.input.SoilCaresScannerSpectrumReader.AmplitudeType
SPECTRUM - Static variable in class adams.data.io.input.SoilCaresScannerSpectrumReader: the column name for the spectrum.
SpectrumAppend - Class in adams.flow.transformer: Appends the incoming spectrum to the one available from storage.
If none yet available from storage, then the current one simply put into storage.
If the spectrum already contains elements with the same wave number, then these will get replaced by the current ones.
SpectrumAppend() - Constructor for class adams.flow.transformer.SpectrumAppend
spectrumBlockTypeTipText() - Method in class adams.data.io.input.OpusSpectrumReaderExt: Returns the tip text for this property.
SpectrumClassifier - Class in weka.classifiers.meta: Automatically removes some IDs from the dataset before training the base classifier: id, db_id, sample_id.
SpectrumClassifier() - Constructor for class weka.classifiers.meta.SpectrumClassifier: Default constructor.
SpectrumCleaner - Class in adams.flow.control: 'Cleanses' the tokens being passed through.
SpectrumCleaner() - Constructor for class adams.flow.control.SpectrumCleaner
SpectrumClusterer - Class in weka.clusterers: Automatically removes some IDs from the dataset before training the base classifier: id, db_id, sample_id.
SpectrumClusterer() - Constructor for class weka.clusterers.SpectrumClusterer: Default constructor.
spectrumColumnsTipText() - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Returns the tip text for this property.
SpectrumComparator - Class in adams.data.spectrum: A comparator for Spectrum objects.
SpectrumComparator() - Constructor for class adams.data.spectrum.SpectrumComparator
SpectrumComparatorByReportValue - Class in adams.data.spectrum: Compares spectra based on the specified report field value.
SpectrumComparatorByReportValue() - Constructor for class adams.data.spectrum.SpectrumComparatorByReportValue
SpectrumConditionsMulti - Class in adams.db: Conditions for the retrieval of spectra.
Several fields can be specified.
SpectrumConditionsMulti() - Constructor for class adams.db.SpectrumConditionsMulti
SpectrumConditionsSingle - Class in adams.db: Conditions for the retrieval of spectra.
Only a single field can be specified.
SpectrumConditionsSingle() - Constructor for class adams.db.SpectrumConditionsSingle
SpectrumContainer - Class in adams.gui.visualization.spectrum: A container class for a spectrum and additional information.
SpectrumContainer(SpectrumContainerManager, Spectrum) - Constructor for class adams.gui.visualization.spectrum.SpectrumContainer: Initializes the container.
SpectrumContainerDisplayIDGenerator - Class in adams.gui.visualization.spectrum: Class for generating display IDs.
SpectrumContainerDisplayIDGenerator() - Constructor for class adams.gui.visualization.spectrum.SpectrumContainerDisplayIDGenerator
SpectrumContainerList - Class in adams.gui.visualization.spectrum: A class encapsulating containers tailored for spectrums.
SpectrumContainerList() - Constructor for class adams.gui.visualization.spectrum.SpectrumContainerList
SpectrumContainerManager - Class in adams.gui.visualization.spectrum: A handler for the spectrum containers.
SpectrumContainerManager(SpectrumPanel, AbstractDatabaseConnection) - Constructor for class adams.gui.visualization.spectrum.SpectrumContainerManager: Initializes the manager.
SpectrumContainerModel - Class in adams.gui.visualization.spectrum: A model for displaying the currently loaded spectrums.
SpectrumContainerModel(ContainerListManager<SpectrumContainerManager>) - Constructor for class adams.gui.visualization.spectrum.SpectrumContainerModel: Initializes the model.
SpectrumContainerModel(SpectrumContainerManager) - Constructor for class adams.gui.visualization.spectrum.SpectrumContainerModel: Initializes the model.
SpectrumContainerTable - Class in adams.gui.visualization.spectrum: Specialized container table for spectra.
SpectrumContainerTable() - Constructor for class adams.gui.visualization.spectrum.SpectrumContainerTable
SpectrumContainerTableColumnNameGenerator - Class in adams.gui.visualization.spectrum: Abstract class for generating the column names of a table.
SpectrumContainerTableColumnNameGenerator() - Constructor for class adams.gui.visualization.spectrum.SpectrumContainerTableColumnNameGenerator
SpectrumCorrelation - Class in adams.data.compare: Compares the spectral data of two spectra using correlation coefficient.
Does not use wave numbers to determine common data points, simply the index.
Outputs true if the minimum is achieved, otherwise false.
SpectrumCorrelation() - Constructor for class adams.data.compare.SpectrumCorrelation
SpectrumCosineSimilarity - Class in adams.data.compare: Compares the spectral data of two spectra using cosine similarity.
SpectrumCosineSimilarity() - Constructor for class adams.data.compare.SpectrumCosineSimilarity
SpectrumDatabaseReader - Interface in adams.flow.transformer: Indicator interface for database readers for spectra.
SpectrumDatabaseWriter - Interface in adams.flow.transformer: Indicator interface for database writers for spectra.
SpectrumDatasetExportDialog - Class in adams.gui.visualization.spectrum: Export dialog for spectra to a dataset.
SpectrumDatasetExportDialog(Dialog) - Constructor for class adams.gui.visualization.spectrum.SpectrumDatasetExportDialog: Creates a modeless dialog without a title with the specified Dialog as its owner.
SpectrumDatasetExportDialog(Dialog, Dialog.ModalityType) - Constructor for class adams.gui.visualization.spectrum.SpectrumDatasetExportDialog: Creates a dialog with the specified owner Dialog and modality.
SpectrumDatasetExportDialog(Frame) - Constructor for class adams.gui.visualization.spectrum.SpectrumDatasetExportDialog: Creates a modeless dialog without a title with the specified Frame as its owner.
SpectrumDatasetExportDialog(Frame, boolean) - Constructor for class adams.gui.visualization.spectrum.SpectrumDatasetExportDialog: Creates a dialog with the specified owner Frame, modality and an empty title.
SpectrumDbReader - Class in adams.flow.transformer: Loads a spectrum from the database and passes it on.
SpectrumDbReader() - Constructor for class adams.flow.transformer.SpectrumDbReader
SpectrumDbWriter - Class in adams.flow.transformer: Writes a spectrum to the database and passes its ID on.
SpectrumDbWriter() - Constructor for class adams.flow.transformer.SpectrumDbWriter
SpectrumDiff - Class in adams.flow.transformer: Computes the difference between two spectra (received as array) and outputs the difference as spectrum again: spectrum 1 - spectrum 2

Input/output:
- accepts:
knir.data.spectrum.Spectrum[]
- generates:
knir.data.spectrum.Spectrum
SpectrumDiff() - Constructor for class adams.flow.transformer.SpectrumDiff
SpectrumDisplay - Class in adams.flow.sink: Actor that displays spectra or multi-spectra.
SpectrumDisplay() - Constructor for class adams.flow.sink.SpectrumDisplay
SpectrumDisplay.DisplayPanel - Class in adams.flow.sink: Panel to be used in DisplayPanelManager sink.
SpectrumExplorer - Class in adams.gui.menu: Displays the Spectrum Explorer.
SpectrumExplorer - Class in adams.gui.visualization.spectrum: A panel for exploring Spectrums, manipulating them with filters, etc.
SpectrumExplorer() - Constructor for class adams.gui.menu.SpectrumExplorer: Initializes the menu item.
SpectrumExplorer() - Constructor for class adams.gui.visualization.spectrum.SpectrumExplorer: default constructor.
SpectrumExplorer(AbstractApplicationFrame) - Constructor for class adams.gui.menu.SpectrumExplorer: Initializes the menu item.
SpectrumExportDialog - Class in adams.gui.visualization.spectrum: Export dialog for spectra.
SpectrumExportDialog(Dialog) - Constructor for class adams.gui.visualization.spectrum.SpectrumExportDialog: Creates a modeless dialog without a title with the specified Dialog as its owner.
SpectrumExportDialog(Dialog, Dialog.ModalityType) - Constructor for class adams.gui.visualization.spectrum.SpectrumExportDialog: Creates a dialog with the specified owner Dialog and modality.
SpectrumExportDialog(Frame) - Constructor for class adams.gui.visualization.spectrum.SpectrumExportDialog: Creates a modeless dialog without a title with the specified Frame as its owner.
SpectrumExportDialog(Frame, boolean) - Constructor for class adams.gui.visualization.spectrum.SpectrumExportDialog: Creates a dialog with the specified owner Frame, modality and an empty title.
SpectrumExporter - Class in adams.gui.visualization.debug.objectexport: Exports Spectrum objects.
SpectrumExporter() - Constructor for class adams.gui.visualization.debug.objectexport.SpectrumExporter
SpectrumF - Class in adams.db: Facade for spectrum tables.
SpectrumF(AbstractDatabaseConnection, String) - Constructor for class adams.db.SpectrumF: Constructor.
SpectrumFeatureGenerator - Class in adams.flow.transformer: Applies a spectrum feature generator to the incoming spectrum and outputs the generated features.
SpectrumFeatureGenerator() - Constructor for class adams.flow.transformer.SpectrumFeatureGenerator
SpectrumFileChecker - Class in adams.flow.control: Only passes on files/directories containing spectra that could be loaded successfully.
SpectrumFileChecker() - Constructor for class adams.flow.control.SpectrumFileChecker
SpectrumFileChooser - Class in adams.gui.chooser: A specialized JFileChooser that lists all available file Readers and Writers for spectrums.
SpectrumFileChooser() - Constructor for class adams.gui.chooser.SpectrumFileChooser: Constructs a FileChooser pointing to the user's default directory.
SpectrumFileChooser(File) - Constructor for class adams.gui.chooser.SpectrumFileChooser: Constructs a FileChooser using the given File as the path.
SpectrumFileChooser(String) - Constructor for class adams.gui.chooser.SpectrumFileChooser: Constructs a FileChooser using the given path.
SpectrumFileReader - Class in adams.flow.transformer: Loads a file/directory containing spectrums from disk with a specified reader and passes them on.
SpectrumFileReader() - Constructor for class adams.flow.transformer.SpectrumFileReader
SpectrumFileWriter - Class in adams.flow.transformer: Saves a spectrum to disk with the specified writer and passes the absolute filename on.
As filename/directory name (depending on the writer) the database ID of the spectrum is used (below the specified output directory).
SpectrumFileWriter() - Constructor for class adams.flow.transformer.SpectrumFileWriter
SpectrumFilter - Class in adams.flow.transformer: Filters data using the specified filter.
SpectrumFilter - Class in weka.filters.unsupervised.attribute: A meta-filter that applies the base filter only to the spectral part of the dataset, i.e., attributes starting with 'amplitude-'.
SpectrumFilter() - Constructor for class adams.flow.transformer.SpectrumFilter
SpectrumFilter() - Constructor for class weka.filters.unsupervised.attribute.SpectrumFilter
SpectrumFilterContainer - Class in adams.flow.container: Container for spectrum filters.
SpectrumFilterContainer() - Constructor for class adams.flow.container.SpectrumFilterContainer: Initializes the container.
SpectrumFilterContainer(Object, Filter, Spectrum) - Constructor for class adams.flow.container.SpectrumFilterContainer: Initializes the container with the filter and the associated data.
spectrumFormatTipText() - Method in class adams.data.spectrumfilter.ChangeFormat: Returns the tip text for this property.
SpectrumIDConditions - Class in adams.db: Conditions for the retrieval of spectrum IDs.
SpectrumIDConditions() - Constructor for class adams.db.SpectrumIDConditions
SpectrumIdSource - Interface in adams.flow.source: Indicator interface for sources that supply spectrum IDs.
SpectrumIdSupplier - Class in adams.flow.source: Returns spectrum IDs from the database.
SpectrumIdSupplier() - Constructor for class adams.flow.source.SpectrumIdSupplier
SpectrumImageWriter - Class in adams.data.io.output: Writes spectra as images using the supplied generator.
SpectrumImageWriter - Class in adams.flow.sink: Actor that takes screenshots of spectra.
SpectrumImageWriter() - Constructor for class adams.data.io.output.SpectrumImageWriter
SpectrumImageWriter() - Constructor for class adams.flow.sink.SpectrumImageWriter
SpectrumInfo - Class in adams.flow.transformer: Outputs statistics of a spectrum.
SpectrumInfo() - Constructor for class adams.flow.transformer.SpectrumInfo
SpectrumInfo.InfoType - Enum in adams.flow.transformer: The type of information to generate.
SpectrumIntf - Interface in adams.db: Interface for spectrum tables.
SpectrumJsonUtils - Class in adams.data.spectrum: For converting spectra to JSON and vice versa.
SpectrumJsonUtils() - Constructor for class adams.data.spectrum.SpectrumJsonUtils
SpectrumMinMax - Class in adams.flow.transformer: Keeps track of min/max per wave number and outputs these min/max spectra at the specified interval of spectra processed.
SpectrumMinMax() - Constructor for class adams.flow.transformer.SpectrumMinMax
SpectrumPaintlet - Class in adams.gui.visualization.spectrum: Paintlet for painting the spectral graph.
SpectrumPaintlet() - Constructor for class adams.gui.visualization.spectrum.SpectrumPaintlet
SpectrumPaintlet.MarkerShape - Enum in adams.gui.visualization.spectrum: Enum for the marker shape to plot around the data points.
SpectrumPaintletNumericField - Class in adams.gui.visualization.spectrum: Paintlet for painting the spectral graph.
SpectrumPaintletNumericField() - Constructor for class adams.gui.visualization.spectrum.SpectrumPaintletNumericField
SpectrumPaintletStringField - Class in adams.gui.visualization.spectrum: Paintlet for painting the spectral graph.
SpectrumPaintletStringField() - Constructor for class adams.gui.visualization.spectrum.SpectrumPaintletStringField
SpectrumPanel - Class in adams.gui.visualization.spectrum: Special panel for displaying the spectral data.
SpectrumPanel() - Constructor for class adams.gui.visualization.spectrum.SpectrumPanel: Initializes the panel without title.
SpectrumPanel(String) - Constructor for class adams.gui.visualization.spectrum.SpectrumPanel: Initializes the panel with the given title.
SpectrumPanelWithSampleData - Class in adams.gui.visualization.spectrum: Spectrum panel that also shows the sample data next to it.
SpectrumPanelWithSampleData() - Constructor for class adams.gui.visualization.spectrum.SpectrumPanelWithSampleData
SpectrumPoint - Class in adams.data.spectrum: Abstract superclass for sequence points.
SpectrumPoint() - Constructor for class adams.data.spectrum.SpectrumPoint: Initializes the point with wave number and amplitude as -1.
SpectrumPoint(float, float) - Constructor for class adams.data.spectrum.SpectrumPoint: Initializes the point with no ID.
SpectrumPointComparator - Class in adams.data.spectrum: A comparator for SpectrumPoint points.
SpectrumPointComparator() - Constructor for class adams.data.spectrum.SpectrumPointComparator: The default constructor uses comparison by wave number in ascending manner.
SpectrumPointComparator(boolean, boolean) - Constructor for class adams.data.spectrum.SpectrumPointComparator: This constructor initializes the comparator either with comparison by wave number or by amplitude.
SpectrumPointHitDetector - Class in adams.gui.visualization.spectrum: Detects selections of spectrum points in the spectrum panel.
SpectrumPointHitDetector(SpectrumPanel) - Constructor for class adams.gui.visualization.spectrum.SpectrumPointHitDetector: Initializes the hit detector.
SpectrumReaderWithSampleIDExtraction - Interface in adams.data.io.input: Interface for spectrum readers that extract the sample ID from the filename.
SpectrumRenderer - Class in adams.gui.visualization.debug.objectrenderer: Renders Spectrum objects.
SpectrumRenderer() - Constructor for class adams.gui.visualization.debug.objectrenderer.SpectrumRenderer
SpectrumStatistic - Class in adams.data.statistics: Statistical information specific to a spectrum.
SpectrumStatistic() - Constructor for class adams.data.statistics.SpectrumStatistic: Initializes the statistic.
SpectrumStatistic(Spectrum) - Constructor for class adams.data.statistics.SpectrumStatistic: Initializes the statistic.
SpectrumT - Class in adams.db.generic: Manages Spectrum tables.
SpectrumT - Class in adams.db.h2: H2 implementation.
SpectrumT - Class in adams.db.mirrored: Allows mirroring to another database.
SpectrumT - Class in adams.db.mssql: H2 implementation.
SpectrumT - Class in adams.db.mysql: MySQL implementation.
SpectrumT - Class in adams.db.postgresql: PostgreSQL implementation.
SpectrumT - Class in adams.db.sqlite: SQLite implementation.
SpectrumT(AbstractDatabaseConnection) - Constructor for class adams.db.generic.SpectrumT: Constructor - initalise with database connection.
SpectrumT(AbstractDatabaseConnection) - Constructor for class adams.db.h2.SpectrumT: Constructor - initalise with database connection.
SpectrumT(AbstractDatabaseConnection) - Constructor for class adams.db.mssql.SpectrumT: Constructor - initalise with database connection.
SpectrumT(AbstractDatabaseConnection) - Constructor for class adams.db.mysql.SpectrumT: Constructor - initalise with database connection.
SpectrumT(AbstractDatabaseConnection) - Constructor for class adams.db.postgresql.SpectrumT: Constructor - initalise with database connection.
SpectrumT(AbstractDatabaseConnection) - Constructor for class adams.db.sqlite.SpectrumT: Constructor - initalise with database connection.
SpectrumT(AbstractDatabaseConnection, SpectrumIntf) - Constructor for class adams.db.mirrored.SpectrumT: Initializes the mirroring.
SpectrumTableModel - Class in adams.gui.visualization.spectrum: Table model for displaying a spectrum in a table.
SpectrumTableModel() - Constructor for class adams.gui.visualization.spectrum.SpectrumTableModel: Initializes the model with no spectrum.
SpectrumTableModel(Spectrum) - Constructor for class adams.gui.visualization.spectrum.SpectrumTableModel: Initializes the model with the specified spectrum.
SpectrumToArray - Class in adams.data.conversion: Turns either the wave numbers or amplitudes of the incoming spectrum into a float array.
SpectrumToArray() - Constructor for class adams.data.conversion.SpectrumToArray
SpectrumToArray.DataType - Enum in adams.data.conversion: The type of data to output.
SpectrumToBufferedImage - Class in adams.data.conversion: Converts a spectrum into an image by treating it like an audio signal, and producing a spectrogram for it.
SpectrumToBufferedImage() - Constructor for class adams.data.conversion.SpectrumToBufferedImage
spectrumToContainers(Object, SpectrumContainerManager, Logger) - Static method in class adams.flow.sink.SpectrumDisplay: Turns the object into spectrum containers.
SpectrumToJson - Class in adams.data.conversion: Turns a spectrum into a JSON string.
Output format:
- outputting the complete report:
{
"id": "someid",
"format": "NIR",
"waves": [1.0, 2.0],
"amplitudes": [1.1, 2.1],
"report": {
"Sample ID": "someid",
"GLV2": 1.123,
"valid": true
}
}

- outputting specific reference and meta-data values:
{
"id": "someid",
"format": "NIR",
"waves": [1.0, 2.0],
"amplitudes": [1.1, 2.1],
"reference": {
"GLV2": 1.123
},
"meta-data": {
"valid": true
}
}
SpectrumToJson() - Constructor for class adams.data.conversion.SpectrumToJson
SpectrumToSpreadSheet - Class in adams.data.conversion: Turns a spectrum into a spreadsheet.
SpectrumToSpreadSheet() - Constructor for class adams.data.conversion.SpectrumToSpreadSheet
SpectrumToWave - Class in adams.data.conversion: Turns a spectrum into a WAV.
SpectrumToWave() - Constructor for class adams.data.conversion.SpectrumToWave
spectrumTypeTipText() - Method in class adams.data.io.input.SoilCaresScannerSpectrumReader: Returns the tip text for this property.
SpectrumUtils - Class in adams.data.spectrum: Utility class for spectrums.
SpectrumUtils() - Constructor for class adams.data.spectrum.SpectrumUtils
SpectrumZoomOverviewPaintlet - Class in adams.gui.visualization.spectrum: Highlights the current zoom in the spectrum panel.
SpectrumZoomOverviewPaintlet() - Constructor for class adams.gui.visualization.spectrum.SpectrumZoomOverviewPaintlet
SpectrumZoomOverviewPanel - Class in adams.gui.visualization.spectrum: Panel that shows the zoom in the spectrum panel as overlay.
SpectrumZoomOverviewPanel() - Constructor for class adams.gui.visualization.spectrum.SpectrumZoomOverviewPanel
split(String) - Static method in class adams.data.io.input.OpusSpectrumReader: Attempts to split a string, using the specified delimiter character.
SPREADSHEET_COLUMN - Static variable in class adams.gui.tools.idprovider.SpreadSheetIDPanel
SPREADSHEET_FILE - Static variable in class adams.gui.tools.idprovider.SpreadSheetIDPanel
SPREADSHEET_FORMAT - Static variable in class adams.gui.tools.idprovider.SpreadSheetIDPanel
SPREADSHEET_READER - Static variable in class adams.gui.tools.idprovider.SpreadSheetIDPanel
SpreadSheetColumnsToSampleData - Class in adams.data.conversion: Turns spreadsheet columns into sample data.
SpreadSheetColumnsToSampleData() - Constructor for class adams.data.conversion.SpreadSheetColumnsToSampleData
SpreadSheetColumnsToSpectra - Class in adams.data.conversion: Turns spreadsheet columns into spectra.
SpreadSheetColumnsToSpectra() - Constructor for class adams.data.conversion.SpreadSheetColumnsToSpectra
SpreadSheetIDPanel - Class in adams.gui.tools.idprovider: Allows the user to load IDs from a spreadsheet.
SpreadSheetIDPanel(IDConsumer) - Constructor for class adams.gui.tools.idprovider.SpreadSheetIDPanel: Initializes the panel with the owner.
SpreadSheetRowGenerator - Class in adams.flow.transformer: Generates spreadsheet row objects from spectra or reports/sample data.
SpreadSheetRowGenerator() - Constructor for class adams.flow.transformer.SpreadSheetRowGenerator
SpreadSheetRowsToSampleData - Class in adams.data.conversion: Turns spreadsheet rows into sample data.
SpreadSheetRowsToSampleData() - Constructor for class adams.data.conversion.SpreadSheetRowsToSampleData
SpreadSheetRowsToSpectra - Class in adams.data.conversion: Turns spreadsheet rows into spectra.
SpreadSheetRowsToSpectra() - Constructor for class adams.data.conversion.SpreadSheetRowsToSpectra
SpreadSheetSpectrumWriter - Class in adams.data.io.output: Uses the supplied spreadsheet writer to write the spectra as spreadsheets.
SpreadSheetSpectrumWriter() - Constructor for class adams.data.io.output.SpreadSheetSpectrumWriter
SpreadSheetTo2DTensor - Class in adams.data.conversion: Converts a spreadsheet into a 2-D Tensor data structure (ie a matrix).
SpreadSheetTo2DTensor() - Constructor for class adams.data.conversion.SpreadSheetTo2DTensor
SpreadSheetTo3DTensor - Class in adams.data.conversion: Converts a spreadsheet into a 3-way Tensor data structure.
The sheet requires four columns: X, Y, Z and data.
SpreadSheetTo3DTensor() - Constructor for class adams.data.conversion.SpreadSheetTo3DTensor
SpreadSheetToSpectrum - Class in adams.data.conversion: Turns a spreadsheet into a spectrum.
SpreadSheetToSpectrum() - Constructor for class adams.data.conversion.SpreadSheetToSpectrum
SpreadSheetToThreeWayData - Class in adams.data.conversion: Converts a spreadsheet into a 3-way data structure.
The sheet requires four columns: X, Y, Z and data.
The Z column is optional, which, if not provided, is simply assumed to be 0.
SpreadSheetToThreeWayData() - Constructor for class adams.data.conversion.SpreadSheetToThreeWayData
SQLSpectrumIdSupplier - Class in adams.flow.source: Executes an SQL statement for generating the IDs.
SQLSpectrumIdSupplier() - Constructor for class adams.flow.source.SQLSpectrumIdSupplier
standardise(double[], FossStdise) - Static method in class adams.data.io.input.foss.FossStdise: standardise nir data according to coefficients and intercepts taken from .std file.
StandardiseByInterpolation - Class in adams.data.spectrumfilter: Standardises spectrum to start-end with given step.
StandardiseByInterpolation() - Constructor for class adams.data.spectrumfilter.StandardiseByInterpolation
standardizeTipText() - Method in class adams.data.multifilter.Average: Returns the tip text for this property.
startDateTipText() - Method in class adams.db.AbstractSpectrumConditions: Returns the tip text for this property.
startDateTipText() - Method in class adams.db.OrphanedSampleDataConditions: Returns the tip text for this property.
startPointsTipText() - Method in class adams.data.io.output.NIRSpectrumWriter: Returns the tip text for this property.
startRecording() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Starts the recording of commands.
startTipText() - Method in class adams.data.io.input.CALSpectrumReader: Returns the tip text for this property.
startTipText() - Method in class adams.data.io.input.OpusSpectrumReader: Returns the tip text for this property.
startTipText() - Method in class adams.data.spectrumfilter.Rebase: Returns the tip text for this property.
startTipText() - Method in class weka.filters.unsupervised.attribute.SavitzkyGolayRange: Returns the tip text for this property.
Statistics - Class in adams.gui.visualization.spectrum.plotpopup: Generates statistics from the visible containers.
Statistics - Class in adams.gui.visualization.threewaydata.heatmapviewer.multipageaction: Displays statistics for the 3-day data container.
Statistics() - Constructor for class adams.gui.visualization.spectrum.plotpopup.Statistics
Statistics() - Constructor for class adams.gui.visualization.threewaydata.heatmapviewer.multipageaction.Statistics
statisticTipText() - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Returns the tip text for this property.
statisticTipText() - Method in class adams.data.evaluator.instance.CrossValidatedPrediction: Returns the tip text for this property.
statisticTipText() - Method in class adams.flow.transformer.threewaydatamerge.CollapseX: Returns the tip text for this property.
StdDev - Class in adams.data.threewayfeatures: Determines the sample standard deviation of all the data values.
StdDev() - Constructor for class adams.data.threewayfeatures.StdDev
STDEV - adams.data.evaluator.instance.CrossValidatedPrediction.StatisticType
STDEV - adams.flow.transformer.threewaydatamerge.CollapseX.StatisticType
STDEV_AMPLITUDE - Static variable in class adams.data.statistics.SpectrumStatistic
STDEV_DELTA_WAVE_NUMBER - Static variable in class adams.data.statistics.SpectrumStatistic
STDEV_NORMALIZED - adams.data.evaluator.instance.CrossValidatedPrediction.StatisticType
stepTipText() - Method in class adams.data.spectrumfilter.AbstractStandardiseFilter: Returns the tip text for this property.
stopBulkAdd() - Method in class adams.db.generic.SpectrumT: Interrupts a currently running bulk store, if possible.
stopBulkAdd() - Method in class adams.db.mirrored.SpectrumT: Interrupts a currently running bulk store, if possible.
stopBulkAdd() - Method in class adams.db.SpectrumF: Interrupts a currently running bulk store, if possible.
stopBulkAdd() - Method in interface adams.db.SpectrumIntf: Interrupts a currently running bulk store, if possible.
stopBulkStore() - Method in class adams.db.generic.SampleDataT: Interrupts a currently running bulk store, if possible.
stopBulkStore() - Method in class adams.db.mirrored.SampleDataT: Interrupts a currently running bulk store, if possible.
stopBulkStore() - Method in class adams.db.SampleDataF: Interrupts a currently running bulk store, if possible.
stopExecution() - Method in class adams.data.cleaner.instance.RemoveOutliers: Stops the execution.
stopExecution() - Method in class adams.data.evaluator.instance.CrossValidatedNeighborHood: Stops the execution.
stopExecution() - Method in class adams.data.evaluator.instance.EnsembleEvaluator: Stops the execution.
stopExecution() - Method in class adams.data.evaluator.instance.MultiClassifierEvaluator: Stops the execution.
stopExecution() - Method in class adams.data.io.input.AbstractSpectrumReader: Stops the execution.
stopExecution() - Method in class adams.data.io.input.AbstractThreeWayDataReader: Stops the execution.
stopExecution() - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Stops the execution.
stopExecution() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Stops the execution.
stopExecution() - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Stops the execution.
stopExecution() - Method in class adams.flow.control.InstanceCleaner: Stops the execution.
stopExecution() - Method in class adams.flow.control.SpectrumCleaner: Stops the execution.
stopExecution() - Method in class adams.flow.standalone.rats.WSMultiSpectrumReception: Stops the execution.
stopExecution() - Method in class adams.flow.standalone.rats.WSSpectrumReception: Stops the execution.
stopExecution() - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Stops the execution.
stopExecution() - Method in class adams.flow.transformer.BulkSpectrumDbWriter: Stops the execution.
stopExecution() - Method in class adams.flow.transformer.Cleaner.CleanJob: Stops the execution.
stopExecution() - Method in class adams.flow.transformer.Cleaner: Stops the execution.
stopExecution() - Method in class adams.flow.transformer.Evaluator.EvaluateJob: Stops the execution.
stopExecution() - Method in class adams.flow.transformer.Evaluator: Stops the execution.
stopExecution() - Method in class adams.flow.transformer.PostProcessor: Stops the execution.
stopExecution() - Method in class adams.flow.transformer.ThreeWayDataTrain: Stops the execution.
stopRecording() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: Stops the recording of commands.
storageNameTipText() - Method in class adams.flow.transformer.MergeSampleDataFromMap: Returns the tip text for this property.
storageNameTipText() - Method in class adams.flow.transformer.MultiSpectrumAdd: Returns the tip text for this property.
storageNameTipText() - Method in class adams.flow.transformer.SpectrumAppend: Returns the tip text for this property.
store(String, SampleData) - Method in class adams.db.mirrored.SampleDataT: Stores the report.
store(String, SampleData) - Method in class adams.db.SampleDataF: Stores the report.
store(String, SampleData, boolean, boolean, Field[]) - Method in class adams.db.mirrored.SampleDataT: Stores the report.
store(String, SampleData, boolean, boolean, Field[]) - Method in class adams.db.SampleDataF: Stores the report.
storeColorInReport(int[], String) - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Stores the color of the container in the report of container's data object.
storeSetup(Instances, AbstractGeneticAlgorithm.GeneticAlgorithmJob) - Method in class adams.opt.genetic.RonWeasley: Generates a Properties file that stores information on the setup of the genetic algorithm.
storeValueInReport(int[], AbstractField, Object) - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Stores the value in the report of container's data object.
storeWaveNoTipText() - Method in class adams.flow.transformer.BulkSpectrumDbWriter: Returns the tip text for this property.
storeWaveNoTipText() - Method in class adams.flow.transformer.SpectrumDbWriter: Returns the tip text for this property.
STRICT - adams.data.io.input.JCampDX2SpectrumReader.ReaderMode
STRING - nz.ac.waikato.adams.webservice.rats.multispectrum.DataType
STRING - nz.ac.waikato.adams.webservice.rats.spectrum.DataType
STRING - nz.ac.waikato.adams.webservice.spectral.get.DataType
STRING - nz.ac.waikato.adams.webservice.spectral.put.DataType
STRING - nz.ac.waikato.adams.webservice.spectral.transform.DataType
StringMatcher - Class in adams.data.spectrumoutlier: Checks whether the specified string field is available in the report and the value matches the specified regular expression.
StringMatcher() - Constructor for class adams.data.spectrumoutlier.StringMatcher
SubFileParser(SPCSpectrumReader.AbstractParser, byte[], int, boolean) - Constructor for class adams.data.io.input.SPCSpectrumReader.SubFileParser: Initializes the parser.
subGeneratorsTipText() - Method in class adams.data.threewayfeatures.MultiThreeWayDataFeatureGenerator: Returns the tip text for this property.
SubRange - Class in adams.data.spectrumfilter: Returns a sub-range of wave numbers from a spectrum.
SubRange() - Constructor for class adams.data.spectrumfilter.SubRange
subtract(DataPoint, DataPoint) - Method in class adams.data.spectrumbaseline.LOWESSBased: Subtracts the baseline from the old data point and creates a new data point.
subtract(DataPoint, DataPoint) - Method in class adams.data.spectrumbaseline.SavitzkyGolayBased: Subtracts the baseline from the old data point and creates a new data point.
Subtract - Class in adams.data.multifilter: Subtracts the amplitudes of first spectrum with the amplitudes of the second.
Subtract() - Constructor for class adams.data.multifilter.Subtract
SubtractSpectrum - Class in adams.data.spectrumfilter
SubtractSpectrum() - Constructor for class adams.data.spectrumfilter.SubtractSpectrum
success - Variable in class nz.ac.waikato.adams.webservice.rats.multispectrum.UploadResponse
success - Variable in class nz.ac.waikato.adams.webservice.rats.spectrum.UploadResponse
success - Variable in class nz.ac.waikato.adams.webservice.spectral.get.GetResponse
success - Variable in class nz.ac.waikato.adams.webservice.spectral.put.PutResponse
success - Variable in class nz.ac.waikato.adams.webservice.spectral.transform.TransformResponse
successTipText() - Method in class adams.data.spectrumfilter.ConditionalReportField: Returns the tip text for this property.
SUFFIX_BACK - Static variable in class adams.data.io.input.SoilCaresScannerSpectrumReader: the suffix for 'back' files.
SUFFIX_CORR - Static variable in class adams.data.io.input.SoilCaresScannerSpectrumReader: the suffix for 'corr' files.
SUFFIX_DEVICE - Static variable in class adams.data.io.input.SoilCaresScannerSpectrumReader: the suffix for 'device' files.
SUFFIX_FAILURE - Static variable in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: the suffix for failed files.
SUFFIX_FAILURE - Static variable in class adams.flow.standalone.rats.LoadSpectrumFileOutput: the suffix for failed files.
SUFFIX_PASSED - Static variable in class adams.flow.transformer.predictioncheck.Range: the suffix for the passed flag.
SUFFIX_SC - Static variable in class adams.data.io.input.SoilCaresScannerSpectrumReader: the suffix for 'sc' files.
SUFFIX_SUCESS - Static variable in class adams.flow.standalone.rats.LoadMultiSpectrumFileOutput: the suffix for successful files.
SUFFIX_SUCESS - Static variable in class adams.flow.standalone.rats.LoadSpectrumFileOutput: the suffix for successful files.
SUM_AMPLITUDE - Static variable in class adams.data.statistics.SpectrumStatistic
sumBytes(int, int) - Method in class adams.data.io.input.SPCSpectrumReader.AbstractParser: Sums up the bytes.
supplyComponent() - Method in class adams.flow.sink.SpectrumDisplay.DisplayPanel
supportsClear() - Method in class adams.flow.sink.SpectrumDisplay: Whether "clear" is supported and shows up in the menu.
supportsClear() - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Whether "clear" is supported and shows up in the menu.
supportsStoreColorInReport() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Returns true if storing the color in the report of container's data object is supported.
supportsStoreValueInReport() - Method in class adams.gui.visualization.spectrum.SpectrumPanel: Returns true if storing a value in the report of container's data object is supported.
Swapped - Class in adams.data.spectrumoutlier: Smooths spectrum (using SavitzkyGolay) and then splits it into two halves.
Swapped() - Constructor for class adams.data.spectrumoutlier.Swapped

T

Table() - Constructor for class adams.gui.visualization.spectrum.SampleDataFactory.Table: Initializes the table.
Table(SampleData) - Constructor for class adams.gui.visualization.spectrum.SampleDataFactory.Table: Initializes the table.
Table(TableModel) - Constructor for class adams.gui.visualization.spectrum.SampleDataFactory.Table: Initializes the table.
TABLE_NAME - Static variable in interface adams.db.SampleDataIntf: this table name.
TABLE_NAME - Static variable in interface adams.db.SpectrumIntf: the table names.
TableModel - Class in adams.gui.tools.idprovider: Table model for displaying the database IDs, IDs, formats and selected state of spectra.
TableModel() - Constructor for class adams.gui.selection.SelectSpectrumPanel.TableModel: default constructor.
TableModel(SelectSpectrumPanel.TableModel, String) - Constructor for class adams.gui.tools.idprovider.TableModel: the constructor.
TableModel(String) - Constructor for class adams.gui.tools.idprovider.TableModel: default constructor.
TableModel(String[]) - Constructor for class adams.gui.selection.SelectSpectrumPanel.TableModel: the constructor.
TableModel(List<String>) - Constructor for class adams.gui.selection.SelectSpectrumPanel.TableModel: the constructor.
targetTipText() - Method in class adams.data.spectrumfilter.ConditionalReportField: Returns the tip text for this property.
targetTipText() - Method in class adams.data.spectrumfilter.ReportFieldFromStringValue: Returns the tip text for this property.
targetTipText() - Method in class adams.data.spectrumfilter.ReportFieldFromStringValueWithLookup: Returns the tip text for this property.
TensorContainer - Class in adams.data.container: Container for a Tensor.
TensorContainer() - Constructor for class adams.data.container.TensorContainer
TensorToSpreadSheet - Class in adams.data.conversion: Turns a Tensor data structure into a spreadsheet.
- 1D: single row
- 2D: matrix
- 3D: three index columns (X,Y,Z) and data column
TensorToSpreadSheet() - Constructor for class adams.data.conversion.TensorToSpreadSheet
TensorToThreeWayData - Class in adams.data.conversion: Turns a Tensor data structure into a ThreeWayData one.
TensorToThreeWayData() - Constructor for class adams.data.conversion.TensorToThreeWayData
TEXT_SEPARATOR - Static variable in class adams.data.io.input.opus.OpusBlockHelper: the text separator.
textColorTipText() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Returns the tip text for this property.
TextOverlay - Class in adams.gui.visualization.threewaydata.heatmapviewer.overlay: Displays text as overlay, either the fixed text, or if empty, a report value.
TextOverlay() - Constructor for class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay
textTipText() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Returns the tip text for this property.
ThreeWayData - Class in adams.data.threeway: Stores 3-way data and associated meta-data.
ThreeWayData() - Constructor for class adams.data.threeway.ThreeWayData: Initialise data.
ThreeWayData(String) - Constructor for class adams.data.threeway.ThreeWayData: Initialise data.
ThreeWayDataContainer - Class in adams.gui.visualization.threewaydata.heatmapviewer: Container for 3-way data.
ThreeWayDataContainer(ThreeWayDataContainerManager, ThreeWayData) - Constructor for class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataContainer: Initializes the container.
ThreeWayDataContainerManager - Class in adams.gui.visualization.threewaydata.heatmapviewer: Container manager for heatmaps.
ThreeWayDataContainerManager() - Constructor for class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataContainerManager
ThreeWayDataExporter - Class in adams.gui.visualization.debug.objectexport: Exports ThreeWayData objects.
ThreeWayDataExporter() - Constructor for class adams.gui.visualization.debug.objectexport.ThreeWayDataExporter
ThreeWayDataFeatureGenerator - Class in adams.flow.transformer: Applies a 3-way data feature generator to the incoming data and outputs the generated features.
ThreeWayDataFeatureGenerator() - Constructor for class adams.flow.transformer.ThreeWayDataFeatureGenerator
ThreeWayDataFileChooser - Class in adams.gui.chooser: A specialized JFileChooser that lists all available file Readers and Writers for 3-way data.
ThreeWayDataFileChooser() - Constructor for class adams.gui.chooser.ThreeWayDataFileChooser: Constructs a FileChooser pointing to the user's default directory.
ThreeWayDataFileChooser(File) - Constructor for class adams.gui.chooser.ThreeWayDataFileChooser: Constructs a FileChooser using the given File as the path.
ThreeWayDataFileChooser(String) - Constructor for class adams.gui.chooser.ThreeWayDataFileChooser: Constructs a FileChooser using the given path.
ThreeWayDataFileReader - Class in adams.flow.transformer
ThreeWayDataFileReader() - Constructor for class adams.flow.transformer.ThreeWayDataFileReader
ThreeWayDataFileWriter - Class in adams.flow.transformer
ThreeWayDataFileWriter() - Constructor for class adams.flow.transformer.ThreeWayDataFileWriter
ThreeWayDataFilter - Class in adams.flow.transformer: Filters data using the specified filter.
ThreeWayDataFilter() - Constructor for class adams.flow.transformer.ThreeWayDataFilter
ThreeWayDataFilterContainer - Class in adams.flow.container: Container for spectrum filters.
ThreeWayDataFilterContainer() - Constructor for class adams.flow.container.ThreeWayDataFilterContainer: Initializes the container.
ThreeWayDataFilterContainer(Object, Filter, ThreeWayData) - Constructor for class adams.flow.container.ThreeWayDataFilterContainer: Initializes the container with the filter and the associated data.
ThreeWayDataHeatmapDisplay - Class in adams.flow.sink: Actor that displays 3-way data as heatmaps.
ThreeWayDataHeatmapDisplay() - Constructor for class adams.flow.sink.ThreeWayDataHeatmapDisplay
ThreeWayDataHeatmapPanel - Class in adams.gui.visualization.threewaydata.heatmapviewer: Panel for displaying a single 3-way data structure.
ThreeWayDataHeatmapPanel(ThreeWayDataHeatmapViewerPanel) - Constructor for class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapPanel: Initializes the panel.
ThreeWayDataHeatmapRenderer - Class in adams.gui.visualization.debug.objectrenderer: Renders 3way data objects as heatmaps.
ThreeWayDataHeatmapRenderer() - Constructor for class adams.gui.visualization.debug.objectrenderer.ThreeWayDataHeatmapRenderer
ThreeWayDataHeatmapViewer - Class in adams.gui.menu: For displaying 3-day data as heatmaps.
ThreeWayDataHeatmapViewer() - Constructor for class adams.gui.menu.ThreeWayDataHeatmapViewer: Initializes the menu item with no owner.
ThreeWayDataHeatmapViewer(AbstractApplicationFrame) - Constructor for class adams.gui.menu.ThreeWayDataHeatmapViewer: Initializes the menu item.
ThreeWayDataHeatmapViewerMultiPagePane - Class in adams.gui.visualization.threewaydata.heatmapviewer: Specialized multi-page pane for the 3way data heatmap viewer.
ThreeWayDataHeatmapViewerMultiPagePane() - Constructor for class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerMultiPagePane
ThreeWayDataHeatmapViewerPanel - Class in adams.gui.visualization.threewaydata.heatmapviewer: Panel for viewing/processing 3-way data as data structures.
ThreeWayDataHeatmapViewerPanel() - Constructor for class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel
ThreeWayDataLoadingMatrix - Class in adams.flow.transformer
ThreeWayDataLoadingMatrix() - Constructor for class adams.flow.transformer.ThreeWayDataLoadingMatrix
ThreeWayDataMerge - Class in adams.flow.transformer: Merges the incoming 3-way data structures using the specified algorithm.
ThreeWayDataMerge() - Constructor for class adams.flow.transformer.ThreeWayDataMerge
ThreeWayDataModelContainer - Class in adams.flow.container: Container for spectrum filters.
ThreeWayDataModelContainer() - Constructor for class adams.flow.container.ThreeWayDataModelContainer: Initializes the container.
ThreeWayDataModelContainer(AbstractAlgorithm, TensorContainer) - Constructor for class adams.flow.container.ThreeWayDataModelContainer: Initializes the container with the model and the associated data.
ThreeWayDataModelContainer(AbstractAlgorithm, TensorContainer[]) - Constructor for class adams.flow.container.ThreeWayDataModelContainer: Initializes the container with the model and the associated data.
ThreeWayDataModelFilter - Class in adams.flow.transformer
ThreeWayDataModelFilter() - Constructor for class adams.flow.transformer.ThreeWayDataModelFilter
ThreeWayDataModelFilterLoader - Class in adams.flow.core: Model loader for AbstractAlgorithm objects.
ThreeWayDataModelFilterLoader() - Constructor for class adams.flow.core.ThreeWayDataModelFilterLoader
ThreeWayDataStatistic - Class in adams.data.statistics: Statistical information specific to a ThreeWayData.
ThreeWayDataStatistic() - Constructor for class adams.data.statistics.ThreeWayDataStatistic: Initializes the statistic.
ThreeWayDataStatistic(ThreeWayData) - Constructor for class adams.data.statistics.ThreeWayDataStatistic: Initializes the statistic.
ThreeWayDataToHeatmap - Class in adams.data.conversion: Turns a adams.data.threeway.ThreeWayData data structure into a heatmap.
Sums up the data values of the Z layers that fall into the specified min/max.
ThreeWayDataToHeatmap() - Constructor for class adams.data.conversion.ThreeWayDataToHeatmap
ThreeWayDataToSpreadSheet - Class in adams.data.conversion: Flattens 3-way data into a spreadsheet.
ThreeWayDataToSpreadSheet() - Constructor for class adams.data.conversion.ThreeWayDataToSpreadSheet
ThreeWayDataToTensor - Class in adams.data.conversion: Converts 3-way data into the Tensor data structure.
ThreeWayDataToTensor() - Constructor for class adams.data.conversion.ThreeWayDataToTensor
ThreeWayDataTrain - Class in adams.flow.transformer
ThreeWayDataTrain() - Constructor for class adams.flow.transformer.ThreeWayDataTrain
ThreeWayDataUtils - Class in adams.data.threeway: Utility class for ThreeWayData objects.
ThreeWayDataUtils() - Constructor for class adams.data.threeway.ThreeWayDataUtils
ThreeWayEEMHandler - Class in adams.gui.tools.previewbrowser: Handles 3-way data EEM fluorescence files.
ThreeWayEEMHandler() - Constructor for class adams.gui.tools.previewbrowser.ThreeWayEEMHandler
ThreeWayHeatmapReader - Class in adams.data.io.input: Uses the specified reader to load 3-way data and turns it into a heatmap.
ThreeWayHeatmapReader() - Constructor for class adams.data.io.input.ThreeWayHeatmapReader
ThreeWayReport - Class in adams.data.threewayreport: Read and store data from the Report for a ThreeWayData structure.
ThreeWayReport() - Constructor for class adams.data.threewayreport.ThreeWayReport
ThreeWayXYZHandler - Class in adams.gui.tools.previewbrowser: Handles 3-way data XYZ fluorescence files.
ThreeWayXYZHandler() - Constructor for class adams.gui.tools.previewbrowser.ThreeWayXYZHandler
thresholdTipText() - Method in class adams.data.multispectrumoperation.outlierremoval.CorrelationBasedThreshold: Returns the tip text for this property.
thresholdTipText() - Method in class adams.data.multispectrumoperation.outlierremoval.CosineSimilarityBasedThreshold: Returns the tip text for this property.
thresholdTipText() - Method in class adams.data.multispectrumoperation.outlierremoval.MeanSpectrumCosineSimilarityBasedThreshold: Returns the tip text for this property.
thresholdTipText() - Method in class adams.data.spectrumoutlier.Oscillation: Returns the tip text for this property.
timestampTipText() - Method in class adams.data.io.output.NIRSpectrumWriter: Returns the tip text for this property.
toArray(ThreeWayData) - Method in class adams.data.threewayfeatures.Histogram: Returns all the data values as array.
toCommandLine() - Method in class adams.data.spectrum.AbstractSpectrumComparator: Returns the commandline string.
toDataPoint(AbstractDerivative.Point) - Method in class adams.data.spectrumfilter.Derivative: Turns the intermediate format point back into a DataPoint.
toDoubleArray(Spectrum) - Static method in class adams.data.spectrum.SpectrumUtils: Returns the amplitudes as double array.
toDoubleArray(Spectrum) - Method in class adams.flow.transformer.SpectralAngleMapper: Converts a spectrum into a double array of its wave amplitudes.
toDoubleArray(L1Point) - Static method in class adams.data.threeway.L1PointUtils: Returns the abundance as double array.
toDoubleArray(List<SpectrumPoint>) - Static method in class adams.data.spectrum.SpectrumUtils: Returns the amplitudes as double array.
toDoubleArray(List<L2Point>) - Static method in class adams.data.threeway.L1PointUtils: Returns the abundance as double array.
toJson(Spectrum) - Static method in class adams.data.spectrum.SpectrumJsonUtils: Turns the spectrum into a json structure (spectral + report).
toJson(Spectrum, Field[], Field[]) - Static method in class adams.data.spectrum.SpectrumJsonUtils: Turns the spectrum into a json structure (spectral + ref + meta).
tokenToContainers(Token, SpectrumExplorer, AbstractPlotUpdater, Logger) - Static method in class adams.flow.sink.SpectrumDisplay: Displays the token.
tolerateHeaderChangesTipText() - Method in class adams.data.spreadsheetrowgenerator.AbstractSpreadSheetRowGenerator: Returns the tip text for this property.
toPoint(DataPoint) - Method in class adams.data.spectrumfilter.Derivative: Turns the DataPoint into the intermediate format.
toSpreadSheet() - Method in class adams.data.spectrum.Spectrum: Returns the content as spreadsheet.
toSpreadSheet() - Method in class adams.data.threeway.ThreeWayData: Returns the content as spreadsheet.
toStatistic() - Method in class adams.data.spectrum.Spectrum: Returns a statistic object of this spectrum.
toStatistic() - Method in class adams.data.threeway.L1Point: Returns a statistic object of this GC point.
toStatistic() - Method in class adams.data.threeway.ThreeWayData: Returns a statistic object of this data structure.
toString() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner.InterPercentileRange: Returns a string representation of the container.
toString() - Method in class adams.data.io.input.foss.FossHelper.FossFields: String representation of this.
toString() - Method in class adams.data.io.input.opus.OpusBlockHelper.Block: Returns a short description of the block.
toString() - Method in class adams.data.io.input.opus.OpusBlockHelper.BlockDefinition: String representation of the container.
toString() - Method in class adams.data.io.input.opus.OpusBlockHelper.CommandlineData: Returns the raw data.
toString() - Method in class adams.data.spectrum.AbstractSpectrumComparator: Returns a string representation of the options.
toString() - Method in class adams.data.spectrum.MultiSpectrum: Returns a string representation of the sequence.
toString() - Method in class adams.data.spectrum.Spectrum: Returns a string representation of the sequence.
toString() - Method in class adams.data.spectrum.SpectrumPoint: Returns a string representation of the point.
toString() - Method in class adams.data.threeway.L1Point: Returns a string representation of the GC points.
toString() - Method in class adams.data.threeway.L2Point: Returns a string representation of the GC points.
toString() - Method in class adams.data.threeway.ThreeWayData: Returns a short string representation of the chromatogram.
toString() - Method in class adams.flow.transformer.Cleaner.CleanJob: Returns a string representation of this job.
toString() - Method in class adams.flow.transformer.Evaluator.EvaluateJob: Returns a string representation of this job.
toString() - Method in class adams.gui.visualization.spectrum.SpectrumContainer: Returns a short string representation of the container.
toString() - Method in class weka.classifiers.meta.SpectrumClassifier: Output a representation of this classifier
toString() - Method in class weka.clusterers.SpectrumClusterer: Output a representation of this clusterer
trainDetector(Spectrum[]) - Method in class adams.data.spectrumoutlier.AmplitudeRange: Trains the detector with the specified data.
trainFilter(Spectrum[]) - Method in class adams.data.spectrumfilter.MultiplicativeScatterCorrection: Trains the filter with the specified data.
transferPrefixTipText() - Method in class adams.data.conversion.MultiSpectrumToSpectra: Returns the tip text for this property.
transferPrefixTipText() - Method in class adams.flow.transformer.MultiSpectrumFilter: Returns the tip text for this property.
transferRegExpTipText() - Method in class adams.data.conversion.MultiSpectrumToSpectra: Returns the tip text for this property.
transferRegExpTipText() - Method in class adams.flow.transformer.MultiSpectrumFilter: Returns the tip text for this property.
transferReportTipText() - Method in class adams.data.conversion.MultiSpectrumToSpectra: Returns the tip text for this property.
transferReportTipText() - Method in class adams.flow.transformer.MultiSpectrumFilter: Returns the tip text for this property.
transform(int, SpectrumPoint) - Method in class adams.data.spectrumfilter.amplitudetransform.AbstractAmplitudeTransformer: Transform the spectrum point and returns a new object.
transform(int, SpectrumPoint) - Method in class adams.data.spectrumfilter.amplitudetransform.ApplyMultiplicativeScatterCorrection: Transform the spectrum point and returns a new object.
transform(int, SpectrumPoint) - Method in class adams.data.spectrumfilter.amplitudetransform.PassThrough: Transform the spectrum point and returns a new object.
transform(int, SpectrumPoint) - Method in class adams.data.spectrumfilter.amplitudetransform.Triangle: Transform the spectrum point and returns a new object.
transform(Spectrum) - Method in class adams.data.spectrumfilter.amplitudetransform.AbstractAmplitudeTransformer: Transforms the spectrum.
transform(TransformRequest) - Method in class adams.flow.webservice.SimpleSpectralTransformService: Transforms a spectrum.
transform(TransformRequest) - Method in interface nz.ac.waikato.adams.webservice.spectral.transform.SpectralTransformService
Transform - Class in adams.flow.webservice: Transforms a spectrum.
Transform() - Constructor for class adams.flow.webservice.Transform
transformerTipText() - Method in class adams.data.spectrumfilter.AmplitudeTransform: Returns the tip text for this property.
transformInstance(Instances, Instance) - Method in class weka.filters.unsupervised.attribute.SpectrumFilter: Transforms the instance (filters spectral part and adds all other data again).
TransformRequest - Class in nz.ac.waikato.adams.webservice.spectral.transform: Java class for transformRequest complex type.
TransformRequest() - Constructor for class nz.ac.waikato.adams.webservice.spectral.transform.TransformRequest
TransformResponse - Class in nz.ac.waikato.adams.webservice.spectral.transform: Java class for transformResponse complex type.
TransformResponse() - Constructor for class nz.ac.waikato.adams.webservice.spectral.transform.TransformResponse
transformSpectrum(Instances) - Method in class weka.filters.unsupervised.attribute.SpectrumFilter: Transforms the spectral data.
TransformSpectrum - Class in adams.flow.rest: REST plugin for filtering spectra.
TransformSpectrum() - Constructor for class adams.flow.rest.TransformSpectrum
TransformSpectrumHelper - Class in adams.flow.core: Helper class for converting spectra.
TransformSpectrumHelper() - Constructor for class adams.flow.core.TransformSpectrumHelper
Triangle - Class in adams.data.spectrumfilter.amplitudetransform: Multiplies the amplitude by the value from a triangle function.
Triangle() - Constructor for class adams.data.spectrumfilter.amplitudetransform.Triangle
TRIANGLE - adams.gui.visualization.spectrum.SpectrumPaintlet.MarkerShape: a triangle.
TrinamixSpectrumJsonReader - Class in adams.data.io.input: Reader for the trinamiX (https://trinamixsensing.com/) JSON format.
TrinamixSpectrumJsonReader() - Constructor for class adams.data.io.input.TrinamixSpectrumJsonReader
TrinamixSpectrumReader - Class in adams.data.io.input: Reader for the trinamiX (https://trinamixsensing.com/) CSV format.
TrinamixSpectrumReader() - Constructor for class adams.data.io.input.TrinamixSpectrumReader
TrinamixSpectrumWriter - Class in adams.data.io.output: Writer for the trinamiX (https://trinamixsensing.com/) CSV format.
TrinamixSpectrumWriter() - Constructor for class adams.data.io.output.TrinamixSpectrumWriter
type - Variable in class adams.data.io.input.opus.OpusBlockHelper.BlockDefinition: the type of the block.
type - Variable in class nz.ac.waikato.adams.webservice.rats.multispectrum.Property
type - Variable in class nz.ac.waikato.adams.webservice.rats.spectrum.Property
type - Variable in class nz.ac.waikato.adams.webservice.spectral.get.Property
type - Variable in class nz.ac.waikato.adams.webservice.spectral.put.Property
type - Variable in class nz.ac.waikato.adams.webservice.spectral.transform.Property
typefieldTipText() - Method in class adams.data.io.input.CALSpectrumReader: Returns the tip text for this property.
typeTipText() - Method in class adams.data.conversion.SpectrumToArray: Returns the tip text for this property.
typeTipText() - Method in class adams.data.io.input.ScioLabExportSpectrumReader: Returns the tip text for this property.
typeTipText() - Method in class adams.flow.transformer.GetSpectrumAmplitude: Returns the tip text for this property.
typeTipText() - Method in class adams.flow.transformer.SetSpectrumAmplitude: Returns the tip text for this property.
typeTipText() - Method in class adams.flow.transformer.SpectrumInfo: Returns the tip text for this property.

U

undo() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: performs an undo if possible.
undoOccurred(UndoEvent) - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: An undo event occurred.
union(Spectrum, Spectrum) - Static method in class adams.data.spectrum.SpectrumUtils: Returns the union of the two spectrums "a" and "b".
UNKNOWN - nz.ac.waikato.adams.webservice.rats.multispectrum.DataType
UNKNOWN - nz.ac.waikato.adams.webservice.rats.spectrum.DataType
UNKNOWN - nz.ac.waikato.adams.webservice.spectral.get.DataType
UNKNOWN - nz.ac.waikato.adams.webservice.spectral.put.DataType
UNKNOWN - nz.ac.waikato.adams.webservice.spectral.transform.DataType
UnscramblerSpectrumReader - Class in adams.data.io.input
UnscramblerSpectrumReader() - Constructor for class adams.data.io.input.UnscramblerSpectrumReader
unsignedTipText() - Method in class adams.data.io.input.FitsLibsReader: Returns the tip text for this property.
unstandardise(double[], FossStdise) - Static method in class adams.data.io.input.foss.FossStdise: Unstandardise nir data according to coefficients and intercepts taken from .std file.
update() - Method in class adams.data.sampledata.SampleData: Updates certain dependant fields.
update() - Method in class adams.data.threewayreport.ThreeWayReport: Updates certain dependant fields.
update() - Method in class adams.db.AbstractSpectrumConditions: Automatically corrects values.
update() - Method in class adams.db.OrphanedSampleDataConditions: Automatically corrects values, but does not throw any exceptions.
update() - Method in class adams.db.SpectrumConditionsMulti: Automatically corrects values.
update() - Method in class adams.db.SpectrumConditionsSingle: Automatically corrects values.
update() - Method in class adams.db.SpectrumIDConditions: Automatically corrects values.
update(AbstractEnvironment) - Method in class adams.env.SpectralDbBackendDefinition: Updates the environment object with its definition for the props file (whether to add/replace/etc the values).
update(AbstractEnvironment) - Method in class adams.env.SpectralScriptingEngineDefinition: Updates the environment object with its definition for the props file (whether to add/replace/etc the values).
updateButtons() - Method in class adams.gui.tools.DeleteSampleDataPanel: Updates the state of the buttons.
updateButtons() - Method in class adams.gui.tools.DeleteSpectrumPanel: Updates the enabled state of the buttons.
updateButtons() - Method in class adams.gui.tools.idprovider.AbstractIDProviderPanel: Updates the state of the buttons.
updateButtons() - Method in class adams.gui.tools.idprovider.DatabaseSearchPanel: Updates the state of the buttons.
updateButtons() - Method in class adams.gui.tools.idprovider.ManualListPanel: Updates the state of the buttons.
updateButtons() - Method in class adams.gui.tools.idprovider.SpreadSheetIDPanel: Updates the state of the buttons.
updateButtons() - Method in class adams.gui.tools.ListSampleDataPanel: Updates the state of the buttons.
updateButtons() - Method in class adams.gui.tools.UpdateSampleDataPanel: Updates the state of the buttons.
updateContainerColorTipText() - Method in class adams.gui.visualization.spectrum.ReportColorSpectrumPaintlet: Returns the tip text for this property.
updateDatabaseConnection() - Method in class adams.data.cleaner.instance.AbstractDatabaseConnectionCleaner: Updates the database connection in dependent schemes.
updateDatabaseConnection() - Method in class adams.data.cleaner.spectrum.AbstractDatabaseConnectionCleaner: Updates the database connection in dependent schemes.
updateDatabaseConnection() - Method in class adams.data.spectrumfilter.Covariance: Updates the database connection in dependent schemes.
updateDatabaseConnection() - Method in class adams.data.spectrumfilter.LRCoeff: Updates the database connection in dependent schemes.
UpdateDatabaseID - Class in adams.flow.transformer.datacontainer: Attempts to update the database ID of the spectrum.
UpdateDatabaseID - Class in adams.flow.transformer.report: Attempts to update the database ID of the sample data.
UpdateDatabaseID() - Constructor for class adams.flow.transformer.datacontainer.UpdateDatabaseID
UpdateDatabaseID() - Constructor for class adams.flow.transformer.report.UpdateDatabaseID
updateIDPanel() - Method in class adams.gui.tools.DeleteSampleDataPanel: Updates the panel to be displayed for determining the IDs.
updateIDPanel() - Method in class adams.gui.tools.ListSampleDataPanel: Updates the panel to be displayed for determining the IDs.
updateIDPanel() - Method in class adams.gui.tools.UpdateSampleDataPanel: Updates the panel to be displayed for determining the IDs.
updateIntervalTipText() - Method in class adams.flow.sink.spectrumdisplay.SimplePlotUpdater: Returns the tip text for this property.
updateMenu() - Method in class adams.gui.tools.DeleteSpectrumPanel: updates the enabled state of the menu items.
updateMenu() - Method in class adams.gui.visualization.spectrum.MultiSpectrumPanel: updates the enabled state of the menu items.
updateMenu() - Method in class adams.gui.visualization.spectrum.SpectrumExplorer: updates the enabled state of the menu items.
updateMenu() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: updates the enabled state of the menu items.
updateName(SpectrumContainer, SpectrumContainer) - Method in class adams.gui.visualization.spectrum.SpectrumContainerManager: Updates the ID of the container, i.e., gives it a unique ID.
updateOptions() - Method in class adams.gui.selection.SelectSpectrumPanel: Updates the options object used internally and refreshes the display if necessary.
updatePlot() - Method in class adams.flow.sink.SpectrumDisplay: Updates the panel regardless, notifying the listeners.
updatePoint(DataPoint, double) - Method in class adams.data.spectrumsmoothing.SlidingWindow: Updates the X-value of the data point.
updateProperties() - Method in class adams.gui.tools.DeleteSampleDataPanel: Updates and stores the properties on disk.
updateProperties() - Method in interface adams.gui.tools.idprovider.IDConsumer: Updates and stores the session properties on disk.
updateProperties() - Method in class adams.gui.tools.ListSampleDataPanel: Updates and stores the properties on disk.
updateProperties() - Method in class adams.gui.tools.UpdateSampleDataPanel: Updates and stores the properties on disk.
UpdateSampleData - Class in adams.gui.menu: Displays the dialog for updating sample data.
UpdateSampleData() - Constructor for class adams.gui.menu.UpdateSampleData: Initializes the menu item.
UpdateSampleData(AbstractApplicationFrame) - Constructor for class adams.gui.menu.UpdateSampleData: Initializes the menu item.
UpdateSampleDataPanel - Class in adams.gui.tools: Allows the user to update/set values in selected spectra.
UpdateSampleDataPanel() - Constructor for class adams.gui.tools.UpdateSampleDataPanel
updateWaveNumbersTipText() - Method in class adams.data.spectrumfilter.Rebase: Returns the tip text for this property.
upload(UploadRequest) - Method in class adams.flow.webservice.multispectrum.SimpleRatsMultiSpectrumService: Downloads a spectrum.
upload(UploadRequest) - Method in interface nz.ac.waikato.adams.webservice.rats.multispectrum.RatsMultiSpectrumService
upload(UploadRequest) - Method in class adams.flow.webservice.spectrum.SimpleRatsSpectrumService: Downloads a spectrum.
upload(UploadRequest) - Method in interface nz.ac.waikato.adams.webservice.rats.spectrum.RatsSpectrumService
Upload - Class in adams.flow.webservice.spectrum: Uploads a spectrum.
Upload() - Constructor for class adams.flow.webservice.spectrum.Upload
UploadRequest - Class in nz.ac.waikato.adams.webservice.rats.multispectrum: Java class for uploadRequest complex type.
UploadRequest - Class in nz.ac.waikato.adams.webservice.rats.spectrum: Java class for uploadRequest complex type.
UploadRequest() - Constructor for class nz.ac.waikato.adams.webservice.rats.multispectrum.UploadRequest
UploadRequest() - Constructor for class nz.ac.waikato.adams.webservice.rats.spectrum.UploadRequest
UploadResponse - Class in nz.ac.waikato.adams.webservice.rats.multispectrum: Java class for uploadResponse complex type.
UploadResponse - Class in nz.ac.waikato.adams.webservice.rats.spectrum: Java class for uploadResponse complex type.
UploadResponse() - Constructor for class nz.ac.waikato.adams.webservice.rats.multispectrum.UploadResponse
UploadResponse() - Constructor for class nz.ac.waikato.adams.webservice.rats.spectrum.UploadResponse
upperPercentileTipText() - Method in class adams.data.cleaner.spectrum.InterPercentileRangeCleaner: Returns the tip text for this property.
useAbsoluteErrorTipText() - Method in class adams.data.postprocessor.instances.PredictionErrorIQR: Returns the tip text for this property.
useAbsoluteSourceTipText() - Method in class adams.data.io.input.AbstractSpectrumReader: Returns the tip text for this property.
useAbsoluteSourceTipText() - Method in class adams.data.io.input.AbstractThreeWayDataReader: Returns the tip text for this property.
useCompressionTipText() - Method in class adams.data.io.output.SimpleSpectrumWriter: Returns the tip text for this property.
useCompressionTipText() - Method in class adams.data.io.output.SimpleXYZWriter: Returns the tip text for this property.
useCustomComparatorTipText() - Method in class adams.data.conversion.SpectraToMultiSpectrum: Returns the tip text for this property.
useCustomComparatorTipText() - Method in class adams.flow.transformer.SpectrumFileReader: Returns the tip text for this property.
useEvaluatorResetVariableTipText() - Method in class adams.flow.transformer.Evaluator: Returns the tip text for this property.
useFilenameAsIDTipText() - Method in class adams.data.io.input.AbstractJCampSpectrumReader: Returns the tip text for this property.
useFilenameAsIDTipText() - Method in class adams.data.io.input.JCampDX2SpectrumReader: Returns the tip text for this property.
useFilenameAsSampleIDTipText() - Method in class adams.data.io.input.RelabSpectrumReader: Returns the tip text for this property.
useModelResetVariableTipText() - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Returns the tip text for this property.
useReferenceAndMetaDataTipText() - Method in class adams.data.conversion.SpectrumToJson: Returns the tip text for this property.
useReferenceAndMetaDataTipText() - Method in class adams.data.io.output.JsonSpectrumWriter: Returns the tip text for this property.
useStoreTableTipText() - Method in class adams.data.spectrumfilter.AbstractDatabaseFilter: Returns the tip text for this property.
useStoreTableTipText() - Method in class adams.data.spectrumfilter.ChangeFormat: Returns the tip text for this property.

V

validateMinMax() - Method in class adams.data.spectrum.Spectrum: Initializes the min/max amplitude/wavenumber points.
validateMinMax() - Method in class adams.data.threeway.L1Point: Initializes the min/max abundance/timestmap points.
validateMinMax() - Method in class adams.data.threeway.ThreeWayData: Initializes the min/max abundance/timestmap points.
validateTipText() - Method in class adams.data.io.input.JCampDX2SpectrumReader: Returns the tip text for this property.
VALIDATION_REPORT_FLAG - Static variable in class adams.gui.menu.ExportValidationSets
value - Variable in class nz.ac.waikato.adams.webservice.rats.multispectrum.Property
value - Variable in class nz.ac.waikato.adams.webservice.rats.spectrum.Property
value - Variable in class nz.ac.waikato.adams.webservice.spectral.get.Property
value - Variable in class nz.ac.waikato.adams.webservice.spectral.put.Property
value - Variable in class nz.ac.waikato.adams.webservice.spectral.transform.Property
value() - Method in enum nz.ac.waikato.adams.webservice.rats.multispectrum.DataType
value() - Method in enum nz.ac.waikato.adams.webservice.rats.spectrum.DataType
value() - Method in enum nz.ac.waikato.adams.webservice.spectral.get.DataType
value() - Method in enum nz.ac.waikato.adams.webservice.spectral.put.DataType
value() - Method in enum nz.ac.waikato.adams.webservice.spectral.transform.DataType
VALUE_ABSTENTION_CLASSIFICATION - Static variable in class adams.flow.container.EvaluationContainer: the identifier for the classification of an abstaining classifier.
VALUE_CHECKS - Static variable in class adams.flow.container.CleaningContainer: the identifier for the checks.
VALUE_CLASSIFICATION - Static variable in class adams.flow.container.EvaluationContainer: the identifier for the classification.
VALUE_CLEANER - Static variable in class adams.flow.container.CleaningContainer: the identifier for the cleaner.
VALUE_COMPONENT - Static variable in class adams.flow.container.EvaluationContainer: the identifier for the component.
VALUE_DISTRIBUTION - Static variable in class adams.flow.container.EvaluationContainer: the identifier for the class distribution.
VALUE_EVALUATIONS - Static variable in class adams.flow.container.EvaluationContainer: the identifier for the evaluations.
VALUE_EVALUATOR - Static variable in class adams.flow.container.EvaluationContainer: the identifier for the evaluatior.
VALUE_ID - Static variable in class adams.flow.container.EvaluationContainer: the identifier for the (optional) ID.
VALUE_INPUT_INSTANCE - Static variable in class adams.flow.container.PostProcessingContainer: the identifier for the input instance.
VALUE_INPUT_INSTANCES - Static variable in class adams.flow.container.PostProcessingContainer: the identifier for the input instances.
VALUE_INSTANCE - Static variable in class adams.flow.container.CleaningContainer: the identifier for the instance.
VALUE_INSTANCE - Static variable in class adams.flow.container.EvaluationContainer: the identifier for the instance.
VALUE_INSTANCES - Static variable in class adams.flow.container.CleaningContainer: the identifier for the instances.
VALUE_INSTANCES - Static variable in class adams.flow.container.EvaluationContainer: the identifier for the instances.
VALUE_MODEL - Static variable in class adams.flow.container.ThreeWayDataModelContainer: the model key.
VALUE_OUTPUT_INSTANCE - Static variable in class adams.flow.container.PostProcessingContainer: the identifier for the output instance.
VALUE_OUTPUT_INSTANCES - Static variable in class adams.flow.container.PostProcessingContainer: the identifier for the output instances.
VALUE_POSTPROCESSOR - Static variable in class adams.flow.container.PostProcessingContainer: the identifier for the post-processor.
VALUE_TRAIN - Static variable in class adams.flow.container.ThreeWayDataModelContainer: the training data key.
VALUE_VERSION - Static variable in class adams.flow.container.EvaluationContainer: the identifier for the version.
valueOf(String) - Static method in enum adams.data.conversion.SpectrumToArray.DataType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum adams.data.evaluator.instance.CrossValidatedPrediction.StatisticType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader.SampleIDLocation: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum adams.data.io.input.JCampDX2SpectrumReader.ReaderMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum adams.data.io.input.ScioLabExportSpectrumReader.SpectrumType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum adams.data.io.input.SoilCaresScannerSpectrumReader.AmplitudeType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum adams.data.io.input.SoilCaresScannerSpectrumReader.SpectrumType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum adams.data.io.output.foss.FossOutputHelper.InstrumentHeader.InstrumentType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum adams.data.spectrumimage.ImageType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum adams.flow.transformer.GetSpectrumAmplitude.RetrievalType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum adams.flow.transformer.MergeSampleDataFromMap.MergeType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum adams.flow.transformer.SetSpectrumAmplitude.UpdateType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum adams.flow.transformer.SpectrumInfo.InfoType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum adams.flow.transformer.threewaydatamerge.CollapseX.StatisticType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum adams.gui.visualization.spectrum.SpectrumPaintlet.MarkerShape: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum nz.ac.waikato.adams.webservice.rats.multispectrum.DataType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum nz.ac.waikato.adams.webservice.rats.spectrum.DataType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum nz.ac.waikato.adams.webservice.spectral.get.DataType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum nz.ac.waikato.adams.webservice.spectral.put.DataType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum nz.ac.waikato.adams.webservice.spectral.transform.DataType: Returns the enum constant of this type with the specified name.
ValueRange - Class in adams.data.threewayoutlier: Detects data containers where a least one value is too low or too high.
ValueRange() - Constructor for class adams.data.threewayoutlier.ValueRange
values() - Static method in enum adams.data.conversion.SpectrumToArray.DataType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum adams.data.evaluator.instance.CrossValidatedPrediction.StatisticType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader.SampleIDLocation: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum adams.data.io.input.JCampDX2SpectrumReader.ReaderMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum adams.data.io.input.ScioLabExportSpectrumReader.SpectrumType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum adams.data.io.input.SoilCaresScannerSpectrumReader.AmplitudeType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum adams.data.io.input.SoilCaresScannerSpectrumReader.SpectrumType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum adams.data.io.output.foss.FossOutputHelper.InstrumentHeader.InstrumentType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum adams.data.spectrumimage.ImageType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum adams.flow.transformer.GetSpectrumAmplitude.RetrievalType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum adams.flow.transformer.MergeSampleDataFromMap.MergeType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum adams.flow.transformer.SetSpectrumAmplitude.UpdateType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum adams.flow.transformer.SpectrumInfo.InfoType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum adams.flow.transformer.threewaydatamerge.CollapseX.StatisticType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum adams.gui.visualization.spectrum.SpectrumPaintlet.MarkerShape: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum nz.ac.waikato.adams.webservice.rats.multispectrum.DataType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum nz.ac.waikato.adams.webservice.rats.spectrum.DataType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum nz.ac.waikato.adams.webservice.spectral.get.DataType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum nz.ac.waikato.adams.webservice.spectral.put.DataType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum nz.ac.waikato.adams.webservice.spectral.transform.DataType: Returns an array containing the constants of this enum type, in the order they are declared.
valueTipText() - Method in class adams.flow.transformer.SetEvaluationMetaData: Returns the tip text for this property.
valueTipText() - Method in class adams.flow.transformer.SetSampleDataValue: Returns the tip text for this property.
variableChanged(VariableChangeEvent) - Method in class adams.flow.transformer.Evaluator: Gets triggered when a variable changed (added, modified, removed).
variableChanged(VariableChangeEvent) - Method in class adams.flow.transformer.SpectrumFeatureGenerator: Gets triggered when a variable changed (added, modified, removed).
variableChanged(VariableChangeEvent) - Method in class adams.flow.transformer.ThreeWayDataFeatureGenerator: Gets triggered when a variable changed (added, modified, removed).
variableChanged(VariableChangeEvent) - Method in class adams.flow.transformer.ThreeWayDataModelFilter: Gets triggered when a variable changed (added, modified, removed).
variableNameTipText() - Method in class adams.flow.transformer.SpectrumFeatureGenerator: Returns the tip text for this property.
variableNameTipText() - Method in class adams.flow.transformer.ThreeWayDataFeatureGenerator: Returns the tip text for this property.
varianceTipText() - Method in class adams.data.spectrumfilter.PCA: Returns the tip text for this property.
versionTipText() - Method in class adams.data.conversion.WekaPredictionContainerToEvaluationContainer: Returns the tip text for this property.
versionTipText() - Method in class adams.flow.transformer.Evaluator: Returns the tip text for this property.
ViewAsSpreadSheet - Class in adams.gui.visualization.threewaydata.heatmapviewer.multipageaction: Views the 3-way data in a spreadsheet table.
ViewAsSpreadSheet() - Constructor for class adams.gui.visualization.threewaydata.heatmapviewer.multipageaction.ViewAsSpreadSheet
Viewport - Class in adams.gui.visualization.spectrum.plotpopup: Allows the user to perform operations on the spectra visible in the current viewport.
Viewport() - Constructor for class adams.gui.visualization.spectrum.plotpopup.Viewport

W

wait(int) - Method in class adams.data.evaluator.instance.FakeEvaluator: Waits for a specified amount of time.
waitPollTipText() - Method in class adams.flow.standalone.rats.WSMultiSpectrumReception: Returns the tip text for this property.
waitPollTipText() - Method in class adams.flow.standalone.rats.WSSpectrumReception: Returns the tip text for this property.
wave - Variable in class nz.ac.waikato.adams.webservice.rats.multispectrum.Waves
wave - Variable in class nz.ac.waikato.adams.webservice.rats.spectrum.Waves
wave - Variable in class nz.ac.waikato.adams.webservice.spectral.get.Waves
wave - Variable in class nz.ac.waikato.adams.webservice.spectral.put.Waves
wave - Variable in class nz.ac.waikato.adams.webservice.spectral.transform.Waves
Wave - Class in nz.ac.waikato.adams.webservice.rats.multispectrum: Java class for Wave complex type.
Wave - Class in nz.ac.waikato.adams.webservice.rats.spectrum: Java class for Wave complex type.
Wave - Class in nz.ac.waikato.adams.webservice.spectral.get: Java class for Wave complex type.
Wave - Class in nz.ac.waikato.adams.webservice.spectral.put: Java class for Wave complex type.
Wave - Class in nz.ac.waikato.adams.webservice.spectral.transform: Java class for Wave complex type.
Wave() - Constructor for class nz.ac.waikato.adams.webservice.rats.multispectrum.Wave
Wave() - Constructor for class nz.ac.waikato.adams.webservice.rats.spectrum.Wave
Wave() - Constructor for class nz.ac.waikato.adams.webservice.spectral.get.Wave
Wave() - Constructor for class nz.ac.waikato.adams.webservice.spectral.put.Wave
Wave() - Constructor for class nz.ac.waikato.adams.webservice.spectral.transform.Wave
WAVE_NUMBER - adams.flow.transformer.GetSpectrumAmplitude.RetrievalType
WAVE_NUMBER - adams.flow.transformer.SetSpectrumAmplitude.UpdateType
WAVE_NUMBER_CLOSEST - adams.flow.transformer.GetSpectrumAmplitude.RetrievalType
WAVE_NUMBER_CLOSEST - adams.flow.transformer.SetSpectrumAmplitude.UpdateType
Wave_offset - Static variable in class adams.data.io.input.foss.FossHelper
waveColumnsTipText() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Returns the tip text for this property.
WAVELENGTH - Static variable in class adams.data.io.input.SoilCaresScannerSpectrumReader: the column name for the wavelengths.
waveNoIncTipText() - Method in class adams.data.conversion.ArrayToSpectrum: Returns the tip text for this property.
waveNoStartTipText() - Method in class adams.data.conversion.ArrayToSpectrum: Returns the tip text for this property.
WAVENUMBER - adams.data.conversion.SpectrumToArray.DataType
waveNumberAsSuffixTipText() - Method in class adams.data.instances.SimpleInstanceGenerator: Returns the tip text for this property.
waveNumberAsSuffixTipText() - Method in class adams.data.instances.SimpleSpectralInstanceGenerator: Returns the tip text for this property.
waveNumberColumnTipText() - Method in class adams.data.io.input.ColumnWiseSpreadSheetSpectrumReader: Returns the tip text for this property.
WaveNumberExpression - Class in adams.data.spectrumfilter: Applies the specified mathematical expression to each wave number.
The following symbols are available:
- A: the current amplitude
- W: the current wave number
- I: the 0-based index of the wave number/amplitude
- S: the number of wave numbers in the current spectrum

The following grammar is used for the expressions:

expr_list ::= '=' expr_list expr_part | expr_part ;
expr_part ::= expr ;

expr ::= ( expr )

# data types
| number
| string
| boolean
| date

# constants
| true
| false
| pi
| e
| now()
| today()

# negating numeric value
| -expr

# comparisons
| expr < expr
| expr <= expr
| expr > expr
| expr >= expr
| expr = expr
| expr !
WaveNumberExpression() - Constructor for class adams.data.spectrumfilter.WaveNumberExpression
WaveNumberHitDetector - Class in adams.gui.visualization.spectrum: Detects selections of wave numbers.
WaveNumberHitDetector(SpectrumPanel) - Constructor for class adams.gui.visualization.spectrum.WaveNumberHitDetector: Initializes the hit detector.
waveNumberPrefixTipText() - Method in class adams.data.instances.AbstractSpectrumInstanceGenerator: Returns the tip text for this property.
waveNumberRegExpTipText() - Method in class adams.data.conversion.SpreadSheetColumnsToSpectra: Returns the tip text for this property.
waveNumberRegExpTipText() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns the tip text for this property.
waveNumberRegExpTipText() - Method in class adams.data.io.input.RowWiseSpreadSheetSpectrumReader: Returns the tip text for this property.
waveNumbersInHeaderTipText() - Method in class adams.data.conversion.SpreadSheetRowsToSpectra: Returns the tip text for this property.
waveNumbersInHeaderTipText() - Method in class adams.data.spreadsheetrowgenerator.SimpleRowGenerator: Returns the tip text for this property.
waveNumberStartsTipText() - Method in class adams.data.multifilter.Fusion: Returns the tip text for this property.
waveNumberStepSizesTipText() - Method in class adams.data.multifilter.Fusion: Returns the tip text for this property.
waveNumberStepSizeTipText() - Method in class adams.data.spectrumfilter.PadPower2: Returns the tip text for this property.
waveNumberTipText() - Method in class adams.flow.transformer.GetSpectrumAmplitude: Returns the tip text for this property.
waveNumberTipText() - Method in class adams.flow.transformer.SetSpectrumAmplitude: Returns the tip text for this property.
waves - Variable in class nz.ac.waikato.adams.webservice.rats.multispectrum.Spectrum
waves - Variable in class nz.ac.waikato.adams.webservice.rats.spectrum.Spectrum
waves - Variable in class nz.ac.waikato.adams.webservice.spectral.get.Spectrum
waves - Variable in class nz.ac.waikato.adams.webservice.spectral.put.Spectrum
waves - Variable in class nz.ac.waikato.adams.webservice.spectral.transform.Spectrum
Waves - Class in nz.ac.waikato.adams.webservice.rats.multispectrum: Java class for Waves complex type.
Waves - Class in nz.ac.waikato.adams.webservice.rats.spectrum: Java class for Waves complex type.
Waves - Class in nz.ac.waikato.adams.webservice.spectral.get: Java class for Waves complex type.
Waves - Class in nz.ac.waikato.adams.webservice.spectral.put: Java class for Waves complex type.
Waves - Class in nz.ac.waikato.adams.webservice.spectral.transform: Java class for Waves complex type.
Waves() - Constructor for class nz.ac.waikato.adams.webservice.rats.multispectrum.Waves
Waves() - Constructor for class nz.ac.waikato.adams.webservice.rats.spectrum.Waves
Waves() - Constructor for class nz.ac.waikato.adams.webservice.spectral.get.Waves
Waves() - Constructor for class nz.ac.waikato.adams.webservice.spectral.put.Waves
Waves() - Constructor for class nz.ac.waikato.adams.webservice.spectral.transform.Waves
waveStepTipText() - Method in class adams.data.spectrumfilter.Rebase: Returns the tip text for this property.
waveStepTipText() - Method in class adams.flow.transformer.InstanceToSpectrum: Returns the tip text for this property.
WaveType_offset - Static variable in class adams.data.io.input.foss.FossHelper
webServiceTipText() - Method in class adams.flow.standalone.rats.WSMultiSpectrumReception: Returns the tip text for this property.
webServiceTipText() - Method in class adams.flow.standalone.rats.WSSpectrumReception: Returns the tip text for this property.
webserviceToKnir(MultiSpectrum) - Static method in class adams.flow.core.RatsMultiSpectrumHelper: Converts a Webservice spectrum into a KNIR one.
webserviceToKnir(Spectrum) - Static method in class adams.flow.core.RatsSpectrumHelper: Converts a Webservice spectrum into a KNIR one.
webserviceToKnir(Spectrum) - Static method in class adams.flow.core.GetSpectrumHelper: Converts a Webservice spectrum into a KNIR one.
webserviceToKnir(Spectrum) - Static method in class adams.flow.core.PutSpectrumHelper: Converts a Webservice spectrum into a KNIR one.
webserviceToKnir(Spectrum) - Static method in class adams.flow.core.TransformSpectrumHelper: Converts a Webservice spectrum into a KNIR one.
weka.classifiers.meta - package weka.classifiers.meta
weka.clusterers - package weka.clusterers
weka.core.converters - package weka.core.converters
weka.filters.unsupervised.attribute - package weka.filters.unsupervised.attribute
WekaClassifierBasedEvaluator - Interface in adams.data.evaluator.instance: Interface for evaluators that make use of classifiers.
WekaFilter - Class in adams.data.postprocessor.instances: Uses a WEKA filter for post-processing.
Automatically wraps a SpectrumFilter meta-filter around the actual filter.
WekaFilter() - Constructor for class adams.data.postprocessor.instances.WekaFilter
WekaFilterToReport - Class in adams.data.spectrumfilter: Generates a Weka Instance using the specified instance generator.
WekaFilterToReport() - Constructor for class adams.data.spectrumfilter.WekaFilterToReport
WekaPredictionContainerToEvaluationContainer - Class in adams.data.conversion: Turns a adams.flow.container.WekaPredictionContainer into a knir.flow.container.EvaluationContainer.
WekaPredictionContainerToEvaluationContainer() - Constructor for class adams.data.conversion.WekaPredictionContainerToEvaluationContainer
widthTipText() - Method in class adams.data.spectrumimage.Intensity: Returns the tip text for this property.
widthTipText() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlayWithDimensions: Returns the tip text for this property.
widthTipText() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.TextOverlay: Returns the tip text for this property.
windowSizeFirstTipText() - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Returns the tip text for this property.
windowSizeNoneTipText() - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Returns the tip text for this property.
windowSizeSecondTipText() - Method in class adams.data.evaluator.instance.SavitzkyGolayRange: Returns the tip text for this property.
windowSizeTipText() - Method in class adams.data.sampledata.SignalToNoiseRatio: Returns the tip text for this property.
windowSizeTipText() - Method in class adams.data.spectrumoutlier.Oscillation: Returns the tip text for this property.
WR_RAW - adams.data.io.input.ScioLabExportSpectrumReader.SpectrumType
wrapTipText() - Method in class adams.data.postprocessor.instances.WekaFilter: Returns the tip text for this property.
wrapUp() - Method in class adams.flow.sink.SpectrumDisplay: Cleans up after the execution has finished.
wrapUp() - Method in class adams.flow.transformer.BulkSampleDataDbWriter: Cleans up after the execution has finished.
wrapUp() - Method in class adams.flow.transformer.BulkSpectrumDbWriter: Cleans up after the execution has finished.
wrapUp() - Method in class adams.flow.transformer.Cleaner: Cleans up after the execution has finished.
wrapUp() - Method in class adams.flow.transformer.Evaluator: Cleans up after the execution has finished.
wrapUp() - Method in class adams.flow.transformer.InstanceGenerator: Cleans up after the execution has finished.
wrapUp() - Method in class adams.flow.transformer.PostProcessor: Cleans up after the execution has finished.
wrapUp() - Method in class adams.flow.transformer.SpectrumFeatureGenerator: Cleans up after the execution has finished.
wrapUp() - Method in class adams.flow.transformer.SpectrumInfo: Cleans up after the execution has finished.
wrapUp() - Method in class adams.flow.transformer.SpreadSheetRowGenerator: Cleans up after the execution has finished.
wrapUp() - Method in class adams.flow.transformer.ThreeWayDataFeatureGenerator: Cleans up after the execution has finished.
write(BufferedWriter) - Method in class adams.data.spectrum.Spectrum: Writes its content with the given writer.
write(BufferedWriter, boolean) - Method in class adams.data.spectrum.Spectrum: Writes its content with the given writer.
write(String) - Method in class adams.data.spectrum.Spectrum: Writes its content to the given file.
write(String, boolean) - Method in class adams.data.spectrum.Spectrum: Writes its content to the given file.
write(List<Spectrum>, BufferedWriter, boolean) - Method in class adams.data.io.output.ASCIIXYSpectrumWriter: Writes its content with the given writer.
write(List<Spectrum>, BufferedWriter, boolean) - Method in class adams.data.io.output.SimpleSpectrumWriter: Writes its content with the given writer.
write(List<Spectrum>, String, boolean) - Method in class adams.data.io.output.ASCIIXYSpectrumWriter: Writes its content to the given file.
write(List<Spectrum>, String, boolean) - Method in class adams.data.io.output.SimpleSpectrumWriter: Writes its content to the given file.
writeData(List<Spectrum>) - Method in class adams.data.io.output.ASCIIXYSpectrumWriter: Performs the actual writing.
writeData(List<Spectrum>) - Method in class adams.data.io.output.ASCSpectrumWriter: Performs the actual writing.
writeData(List<Spectrum>) - Method in class adams.data.io.output.DPTSpectrumWriter: Performs the actual writing.
writeData(List<Spectrum>) - Method in class adams.data.io.output.FilteredSpectrumWriter: Performs the actual writing.
writeData(List<Spectrum>) - Method in class adams.data.io.output.JCampDX2SpectrumWriter: Performs the actual writing.
writeData(List<Spectrum>) - Method in class adams.data.io.output.JsonSpectrumWriter: Performs the actual writing.
writeData(List<Spectrum>) - Method in class adams.data.io.output.NIRSpectrumWriter: Performs the actual writing.
writeData(List<Spectrum>) - Method in class adams.data.io.output.SimpleSpectrumWriter: Performs the actual writing.
writeData(List<Spectrum>) - Method in class adams.data.io.output.SpectrumImageWriter: Performs the actual writing.
writeData(List<Spectrum>) - Method in class adams.data.io.output.SpreadSheetSpectrumWriter: Performs the actual writing.
writeData(List<Spectrum>) - Method in class adams.data.io.output.TrinamixSpectrumWriter: Performs the actual writing.
writeData(List<ThreeWayData>) - Method in class adams.data.io.output.SimpleEEMWriter: Performs the actual writing.
writeData(List<ThreeWayData>) - Method in class adams.data.io.output.SimpleXYZWriter: Performs the actual writing.
writerTipText() - Method in class adams.data.io.output.FilteredSpectrumWriter: Returns the tip text for this property.
writerTipText() - Method in class adams.data.io.output.SpreadSheetSpectrumWriter: Returns the tip text for this property.
writerTipText() - Method in class adams.flow.standalone.rats.SaveMultiSpectrumFileOutput: Returns the tip text for this property.
writerTipText() - Method in class adams.flow.standalone.rats.SaveSpectrumFileOutput: Returns the tip text for this property.
WriteSpectrum - Class in adams.gui.scripting: Action parameters:
WriteSpectrum() - Constructor for class adams.gui.scripting.WriteSpectrum
WSDL_LOCATION - Static variable in class nz.ac.waikato.adams.webservice.rats.multispectrum.RatsMultiSpectrumServiceService
WSDL_LOCATION - Static variable in class nz.ac.waikato.adams.webservice.rats.spectrum.RatsSpectrumServiceService
WSDL_LOCATION - Static variable in class nz.ac.waikato.adams.webservice.spectral.get.SpectralGetServiceService
WSDL_LOCATION - Static variable in class nz.ac.waikato.adams.webservice.spectral.put.SpectralPutServiceService
WSDL_LOCATION - Static variable in class nz.ac.waikato.adams.webservice.spectral.transform.SpectralTransformServiceService
WSMultiSpectrumReception - Class in adams.flow.standalone.rats: Uses a webservice for retrieving spectra.
WSMultiSpectrumReception() - Constructor for class adams.flow.standalone.rats.WSMultiSpectrumReception
WSSpectrumReception - Class in adams.flow.standalone.rats: Uses a webservice for retrieving spectra.
WSSpectrumReception() - Constructor for class adams.flow.standalone.rats.WSSpectrumReception

X

xTipText() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlay: Returns the tip text for this property.
XTipText() - Method in class adams.data.io.input.SimpleEEMReader: Returns the tip text for this property.

Y

yTipText() - Method in class adams.gui.visualization.threewaydata.heatmapviewer.overlay.AbstractPositionableThreeWayDataOverlay: Returns the tip text for this property.

Z

ZeroCenterBurst - Class in adams.data.spectrumfilter: Locates the largest burst (negative or positive) and splits the spectrum into the following parts:
left, burst, right

These parts then get reassembled as:
right, left, burst
ZeroCenterBurst() - Constructor for class adams.data.spectrumfilter.ZeroCenterBurst
ZippedSpectrumReader - Class in adams.data.io.input: Reads spectra from the zip file using the specified base reader.
ZippedSpectrumReader() - Constructor for class adams.data.io.input.ZippedSpectrumReader
zoom(int) - Method in class adams.gui.visualization.threewaydata.heatmapviewer.ThreeWayDataHeatmapViewerPanel: Zooms in/out.
zoomOverviewTipText() - Method in class adams.flow.sink.SpectrumDisplay: Returns the tip text for this property.
zoomTipText() - Method in class adams.flow.sink.ThreeWayDataHeatmapDisplay: Returns the tip text for this property.

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