A B C D E F G H I L M N O P R S T U V W

A

AbstractDatabaseConnectionFeatureGenerator - Class in adams.data.featuregenerator

Ancestor for feature generators that require database access.

AbstractDatabaseConnectionFeatureGenerator() - Constructor for class adams.data.featuregenerator.AbstractDatabaseConnectionFeatureGenerator

AbstractFeatureGenerator - Class in adams.data.featuregenerator

Abstract base class for feature generators.

AbstractFeatureGenerator() - Constructor for class adams.data.featuregenerator.AbstractFeatureGenerator

AbstractFieldInstanceGenerator - Class in adams.data.instances

Abstract base class for schemes that turn heatmaps into weka.core.Instance objects.

AbstractFieldInstanceGenerator() - Constructor for class adams.data.instances.AbstractFieldInstanceGenerator

AbstractHeatmapOverlay - Class in adams.gui.visualization.heatmap

Ancestor for heatmap image overlays.

AbstractHeatmapOverlay() - Constructor for class adams.gui.visualization.heatmap.AbstractHeatmapOverlay

AbstractHeatmapReader - Class in adams.data.io.input

Ancestor for readers that read heatmaps.

AbstractHeatmapReader() - Constructor for class adams.data.io.input.AbstractHeatmapReader

AbstractHeatmapWriter - Class in adams.data.io.output

Ancestor for writers that output heatmaps.

AbstractHeatmapWriter() - Constructor for class adams.data.io.output.AbstractHeatmapWriter

accepts() - Method in class adams.data.conversion.BufferedImageToHeatmap

Returns the class that is accepted as input.

accepts() - Method in class adams.data.conversion.HeatmapToArray

Returns the class that is accepted as input.

accepts() - Method in class adams.data.conversion.HeatmapToBufferedImage

Returns the class that is accepted as input.

accepts() - Method in class adams.data.conversion.HeatmapToSpreadSheet

Returns the class that is accepted as input.

accepts() - Method in class adams.data.conversion.SpreadSheetToHeatmap

Returns the class that is accepted as input.

accepts() - Method in class adams.flow.sink.HeatmapDisplay

Returns the class that the consumer accepts.

accepts() - Method in class adams.flow.transformer.HeatmapInstanceGenerator

Returns the class that the consumer accepts.

adams.data.conversion - package adams.data.conversion

adams.data.featuregenerator - package adams.data.featuregenerator

adams.data.filter - package adams.data.filter

adams.data.heatmap - package adams.data.heatmap

adams.data.instances - package adams.data.instances

adams.data.io.input - package adams.data.io.input

adams.data.io.output - package adams.data.io.output

adams.flow.sink - package adams.flow.sink

adams.flow.transformer - package adams.flow.transformer

adams.gui.chooser - package adams.gui.chooser

adams.gui.menu - package adams.gui.menu

adams.gui.tools.previewbrowser - package adams.gui.tools.previewbrowser

adams.gui.visualization.heatmap - package adams.gui.visualization.heatmap

add(HeatmapValue) - Method in class adams.data.heatmap.Heatmap

Adds the value specified by this value object.

addAll(Collection<? extends HeatmapValue>) - Method in class adams.data.heatmap.Heatmap

Sets all the values stored in the collection in this heatmap.

addFeature(Heatmap, double) - Method in class adams.data.featuregenerator.AbstractFeatureGenerator

Adds the specified feature.

addFeature(Heatmap, String, double) - Method in class adams.data.featuregenerator.AbstractFeatureGenerator

Adds the specified feature.

addFields(Heatmap, double[]) - Method in class adams.data.instances.AbstractFieldInstanceGenerator

Adds the fields of the heatmap to the data array.

applyImageFilter(HeatmapPanel, AbstractImageFilter) - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Applies the image filter to the heatmap image.

applyImageJ(HeatmapPanel) - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Applies ImageJ to the heatmap images.

applyImageMagick(HeatmapPanel) - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Applies ImageMagick to the heatmap images.

applyJAI(HeatmapPanel) - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Applies JAI to the heatmap images.

assign(DataContainer<HeatmapValue>) - Method in class adams.data.heatmap.Heatmap

Obtains the stored variables from the other data point, but not the actual data points.

assign(DataPoint) - Method in class adams.data.heatmap.HeatmapValue

Obtains the stored variables from the other data point.

B

BufferedImageToHeatmap - Class in adams.data.conversion

Turns a class java.awt.image.BufferedImage into a heatmap.
Simply uses the RGB value as heatmap value.

BufferedImageToHeatmap() - Constructor for class adams.data.conversion.BufferedImageToHeatmap

C

calcCentroid() - Method in class adams.gui.visualization.heatmap.CentroidOverlay

Calculates the centroid.

calculate() - Method in class adams.data.heatmap.HeatmapStatistic

Generates the statistics.

canReload() - Method in class adams.gui.visualization.heatmap.HeatmapPanel

Checks whether this panel can be reloaded.

Centroid - Class in adams.data.filter

Computes the centroid of a heatmap and adds this to the heatmap's report.
It is possible to perform multiple iterations and each time with a shrunken heatmap.

Centroid() - Constructor for class adams.data.filter.Centroid

CENTROID_X - Static variable in class adams.data.filter.Centroid

the X of the centroid.

CENTROID_Y - Static variable in class adams.data.filter.Centroid

the Y of the centroid.

CentroidOverlay - Class in adams.gui.visualization.heatmap

Paints the centroid's location over the heatmap image.

CentroidOverlay() - Constructor for class adams.gui.visualization.heatmap.CentroidOverlay

centroidTipText() - Method in class adams.data.filter.CropToCentroid

Returns the tip text for this property.

checkData(Heatmap) - Method in class adams.data.featuregenerator.AbstractFeatureGenerator

The default implementation only checks whether there is any data set.

checkHeader(Heatmap) - Method in class adams.data.instances.AbstractFieldInstanceGenerator

Checks whether the number of waves are the same.

checkHeader(Heatmap) - Method in class adams.data.instances.HistogramInstanceGenerator

Checks whether the number of waves are the same.

checkHeader(Heatmap) - Method in class adams.data.instances.IntensityInstanceGenerator

Checks whether the number of waves are the same.

checkHeader(Heatmap) - Method in class adams.data.instances.RawInstanceGenerator

Checks whether the number of waves are the same.

cleanUp() - Method in class adams.data.featuregenerator.AbstractFeatureGenerator

Cleans up data structures, frees up memory.

clear() - Method in class adams.data.heatmap.Heatmap

Sets all values to 0.0.

clearPanel() - Method in class adams.flow.sink.HeatmapDisplay

Clears the content of the panel.

close() - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

closes the dialog/frame.

closeAll() - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Removes all the data.

closeCurrent() - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Removes the current tab.

colorGeneratorTipText() - Method in class adams.flow.sink.HeatmapDisplay

Returns the tip text for this property.

colorTipText() - Method in class adams.gui.visualization.heatmap.CentroidOverlay

Returns the tip text for this property.

columnTipText() - Method in class adams.data.filter.Submap

Returns the tip text for this property.

compareTo(Object) - Method in class adams.data.featuregenerator.AbstractFeatureGenerator

Compares this object with the specified object for order.

compareTo(Object) - Method in class adams.data.heatmap.Heatmap

Compares this object with the specified object for order.

compareTo(Object) - Method in class adams.data.heatmap.HeatmapValue

Compares this object with the specified object for order.

compareToHeader(Object) - Method in class adams.data.heatmap.Heatmap

Compares this object with the specified object for order.

contains(Object) - Method in class adams.data.heatmap.Heatmap

Checks whether the heatmap contains the specified object.

containsAll(Collection<?>) - Method in class adams.data.heatmap.Heatmap

Checks whether all of the items in the collection are stored in this heatmap.

COUNT_NONZEROES - Static variable in class adams.data.heatmap.HeatmapStatistic

the non-zeroes count.

COUNT_ZEROES - Static variable in class adams.data.heatmap.HeatmapStatistic

the zeroes count.

createAttribute(Field, StringBuilder) - Method in class adams.data.instances.AbstractFieldInstanceGenerator

Creates an attribute from the specified field.

createDisplayPanel(Token) - Method in class adams.flow.sink.HeatmapDisplay

Creates a new display panel for the token.

createEmptyReport() - Static method in class adams.data.heatmap.Heatmap

Returns an empty report.

createPreview(File) - Method in class adams.gui.tools.previewbrowser.HeatmapImageHandler

Creates the actual view.

createPreview(File) - Method in class adams.gui.tools.previewbrowser.HeatmapSpreadSheetHandler

Creates the actual view.

createTitle() - Method in class adams.flow.sink.HeatmapDisplay

Creates a title for the dialog.

crop(Heatmap, int, int, int, int) - Static method in class adams.data.filter.CropToCentroid

Crops the heatmap around the centroid stored in the heatmap's report.

CROP_BOTTOM - Static variable in class adams.data.filter.CropToCentroid

the bottom coordinate of the crop in the original heatmap.

CROP_LEFT - Static variable in class adams.data.filter.CropToCentroid

the left coordinate of the crop in the original heatmap.

CROP_RIGHT - Static variable in class adams.data.filter.CropToCentroid

the right coordinate of the crop in the original heatmap.

CROP_TOP - Static variable in class adams.data.filter.CropToCentroid

the right coordinate of the crop in the original heatmap.

CropToCentroid - Class in adams.data.filter

Generates a cropped heatmap centered around the centroid calculated on the pre-filtered data.

CropToCentroid() - Constructor for class adams.data.filter.CropToCentroid

D

defineOptions() - Method in class adams.data.conversion.HeatmapToBufferedImage

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.conversion.SpreadSheetToHeatmap

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.featuregenerator.AbstractFeatureGenerator

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.featuregenerator.FilteredFeatureGenerator

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.featuregenerator.MultiGenerator

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.filter.Centroid

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.filter.CropToCentroid

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.filter.FeatureGenerator

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.filter.NormalizeToField

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.filter.Rotate

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.filter.Submap

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.filter.SubtractField

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.filter.Threshold

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.HistogramInstanceGenerator

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.instances.IntensityInstanceGenerator

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.io.input.FloatMatrixHeatmapReader

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.io.input.SpreadSheetHeatmapReader

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.io.output.SpreadSheetHeatmapWriter

Adds options to the internal list of options.

defineOptions() - Method in class adams.flow.sink.HeatmapDisplay

Adds options to the internal list of options.

defineOptions() - Method in class adams.gui.visualization.heatmap.CentroidOverlay

Adds options to the internal list of options.

display(Token) - Method in class adams.flow.sink.HeatmapDisplay

Displays the token (the panel and dialog have already been created at this stage).

displayPanelRequiresScrollPane() - Method in class adams.flow.sink.HeatmapDisplay

Returns whether the created display panel requires a scroll pane or not.

doConvert() - Method in class adams.data.conversion.BufferedImageToHeatmap

Performs the actual conversion.

doConvert() - Method in class adams.data.conversion.HeatmapToArray

Performs the actual conversion.

doConvert() - Method in class adams.data.conversion.HeatmapToBufferedImage

Performs the actual conversion.

doConvert() - Method in class adams.data.conversion.HeatmapToSpreadSheet

Performs the actual conversion.

doConvert() - Method in class adams.data.conversion.SpreadSheetToHeatmap

Performs the actual conversion.

doInitializeFilters() - Method in class adams.gui.chooser.HeatmapFileChooser

Performs the actual initialization of the filters.

doPaintOverlay(ImagePanel.PaintPanel, Graphics) - Method in class adams.gui.visualization.heatmap.CentroidOverlay

Paints the overlay over the image.

E

equals(Object) - Method in class adams.data.featuregenerator.AbstractFeatureGenerator

Returns whether the two objects are the same.

equals(Object) - Method in class adams.data.heatmap.Heatmap

Checks whether the specified object has the same content as this one.

equalsHeader(Object) - Method in class adams.data.heatmap.Heatmap

Indicates whether some other chromatogram's header is "equal to" this ones.

F

FeatureGenerator - Class in adams.data.filter

A filter that modifies the quantitation reports of chromatograms being passed through.

FeatureGenerator() - Constructor for class adams.data.filter.FeatureGenerator

FIELD_FILENAME - Static variable in class adams.data.heatmap.Heatmap

the field for the "filename" meta-data entry.

FIELD_TIMESTAMP - Static variable in class adams.data.heatmap.Heatmap

the field for the "timestamp" meta-data entry.

FieldInstanceGenerator - Class in adams.data.instances

A generator for turning fields of a heatmap's report into weka.core.Instance objects.

FieldInstanceGenerator() - Constructor for class adams.data.instances.FieldInstanceGenerator

fieldsTipText() - Method in class adams.data.instances.AbstractFieldInstanceGenerator

Returns the tip text for this property.

fieldTipText() - Method in class adams.data.filter.NormalizeToField

Returns the tip text for this property.

fieldTipText() - Method in class adams.data.filter.SubtractField

Returns the tip text for this property.

filter() - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

pops up GOE dialog for filter.

filter(FilterEvent<Heatmap>) - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Filters the data.

FilteredFeatureGenerator - Class in adams.data.featuregenerator

This feature generator first pushes the data through the provided data filter before applying the actual feature generator.

FilteredFeatureGenerator() - Constructor for class adams.data.featuregenerator.FilteredFeatureGenerator

filterTipText() - Method in class adams.data.featuregenerator.FilteredFeatureGenerator

Returns the tip text for this property.

findCentroid(Heatmap) - Method in class adams.data.filter.Centroid

Finds the centroid.

FloatMatrixHeatmapReader - Class in adams.data.io.input

Reads heat map files (2-D array of single precision floating point numbers).

FloatMatrixHeatmapReader() - Constructor for class adams.data.io.input.FloatMatrixHeatmapReader

FloatMatrixHeatmapWriter - Class in adams.data.io.output

Writes heat map files (2-D array of single precision floating point numbers).

FloatMatrixHeatmapWriter() - Constructor for class adams.data.io.output.FloatMatrixHeatmapWriter

forCommandLine(String) - Static method in class adams.data.featuregenerator.AbstractFeatureGenerator

Instantiates the generator from the given commandline (i.e., classname and optional options).

forName(String, String[]) - Static method in class adams.data.featuregenerator.AbstractFeatureGenerator

Instantiates the generator with the given options.

fromIntensityString(int, int, String) - Static method in class adams.data.heatmap.Heatmap

Creates a heatmap from the intensity string using the specified dimensions.

G

generate(Heatmap) - Method in class adams.data.featuregenerator.AbstractFeatureGenerator

Generates the features and adds them to the report.

generateHeader(Heatmap) - Method in class adams.data.instances.FieldInstanceGenerator

Generates the header of the output data.

generateHeader(Heatmap) - Method in class adams.data.instances.HistogramInstanceGenerator

Generates the header of the output data.

generateHeader(Heatmap) - Method in class adams.data.instances.IntensityInstanceGenerator

Generates the header of the output data.

generateHeader(Heatmap) - Method in class adams.data.instances.RawInstanceGenerator

Generates the header of the output data.

generateOutput(Heatmap) - Method in class adams.data.instances.FieldInstanceGenerator

Generates the actual data.

generateOutput(Heatmap) - Method in class adams.data.instances.HistogramInstanceGenerator

Generates the actual data.

generateOutput(Heatmap) - Method in class adams.data.instances.IntensityInstanceGenerator

Generates the actual data.

generateOutput(Heatmap) - Method in class adams.data.instances.RawInstanceGenerator

Generates the actual data.

generates() - Method in class adams.data.conversion.BufferedImageToHeatmap

Returns the class that is generated as output.

generates() - Method in class adams.data.conversion.HeatmapToArray

Returns the class that is generated as output.

generates() - Method in class adams.data.conversion.HeatmapToBufferedImage

Returns the class that is generated as output.

generates() - Method in class adams.data.conversion.HeatmapToSpreadSheet

Returns the class that is generated as output.

generates() - Method in class adams.data.conversion.SpreadSheetToHeatmap

Returns the class that is generated as output.

generates() - Method in class adams.flow.transformer.HeatmapFileReader

Returns the class of objects that it generates.

generatorTipText() - Method in class adams.data.conversion.HeatmapToBufferedImage

Returns the tip text for this property.

generatorTipText() - Method in class adams.data.featuregenerator.FilteredFeatureGenerator

Returns the tip text for this property.

generatorTipText() - Method in class adams.data.filter.FeatureGenerator

Returns the tip text for this property.

generatorTipText() - Method in class adams.flow.transformer.HeatmapInstanceGenerator

Returns the tip text for this property.

get(int, int) - Method in class adams.data.heatmap.Heatmap

Returns the map value at the specified location.

get(int) - Method in class adams.data.heatmap.Heatmap

Returns the map value the specified position from the top left corner of the map, wlkaing through row-wise.

getCategory() - Method in class adams.gui.menu.HeatmapViewer

Returns the category of the menu item in which it should appear, i.e., the name of the menu.

getCentroid() - Method in class adams.data.filter.CropToCentroid

Returns the centroid filter.

getClone() - Method in class adams.data.heatmap.Heatmap

Returns a clone of the object.

getClone() - Method in class adams.data.heatmap.HeatmapValue

Returns a clone of itself.

getColor() - Method in class adams.gui.visualization.heatmap.CentroidOverlay

Returns the color for the overlay.

getColorGenerator() - Method in class adams.flow.sink.HeatmapDisplay

Returns the generator for the color gradient.

getColorGenerator() - Method in class adams.gui.visualization.heatmap.HeatmapPanel

Returns the generator for the color gradient.

getColumn() - Method in class adams.data.filter.Submap

Returns the column start the submap from.

getComparator() - Method in class adams.data.heatmap.Heatmap

Returns the comparator in use.

getCurrentPanel() - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Returns the currently selected heatmap panel.

getDatabaseConnection() - Method in class adams.data.featuregenerator.AbstractDatabaseConnectionFeatureGenerator

Returns the currently used database connection object, can be null.

getDatabaseConnection() - Method in class adams.flow.transformer.HeatmapFilter

Determines the database connection in the flow.

getDatabaseConnection() - Method in class adams.flow.transformer.HeatmapInstanceGenerator

Returns the database connection to use.

getDataContainerClass() - Method in class adams.flow.transformer.HeatmapFileWriter

Returns the data container class in use.

getDataContainerClass() - Method in class adams.flow.transformer.HeatmapFilter

Returns the data container class in use.

getDefaultDatabaseConnection() - Method in class adams.data.featuregenerator.AbstractDatabaseConnectionFeatureGenerator

Returns the default database connection.

getDefaultDatabaseConnection() - Method in class adams.data.featuregenerator.FilteredFeatureGenerator

Returns the default database connection.

getDefaultDatabaseConnection() - Method in class adams.data.featuregenerator.MultiGenerator

Returns the default database connection.

getDefaultDatabaseConnection() - Method in class adams.data.filter.FeatureGenerator

Returns the default database connection.

getDefaultDatabaseConnection() - Method in class adams.data.instances.AbstractFieldInstanceGenerator

Returns the default database connection.

getDefaultFilter() - Method in class adams.data.filter.CropToCentroid

Returns the default pre-filter to use.

getDefaultGenerator() - Method in class adams.flow.transformer.HeatmapInstanceGenerator

Returns the default generator.

getDefaultHeight() - Method in class adams.data.io.input.FloatMatrixHeatmapReader

Returns the default height of the heatmap.

getDefaultHeight() - Method in class adams.flow.sink.HeatmapDisplay

Returns the default height for the dialog.

getDefaultPrefix() - Method in class adams.data.featuregenerator.AbstractFeatureGenerator

Returns the default prefix for the generated features.

getDefaultReader() - Method in class adams.flow.transformer.HeatmapFileReader

Returns the default reader to use.

getDefaultReader() - Method in class adams.gui.chooser.HeatmapFileChooser

Returns the default reader.

getDefaultWidth() - Method in class adams.data.io.input.FloatMatrixHeatmapReader

Returns the default width of the heatmap.

getDefaultWidth() - Method in class adams.flow.sink.HeatmapDisplay

Returns the default width for the dialog.

getDefaultWriter() - Method in class adams.flow.transformer.HeatmapFileWriter

Returns the default writer to use.

getDefaultWriter() - Method in class adams.gui.chooser.HeatmapFileChooser

Returns the default writer.

getDisplayID() - Method in class adams.gui.visualization.heatmap.HeatmapContainer

Returns the displayed container's ID.

getExtensions() - Method in class adams.gui.tools.previewbrowser.HeatmapImageHandler

Returns the list of extensions (without dot) that this handler can take care of.

getExtensions() - Method in class adams.gui.tools.previewbrowser.HeatmapSpreadSheetHandler

Returns the list of extensions (without dot) that this handler can take care of.

getField() - Method in class adams.data.filter.NormalizeToField

Returns the field to normalize to.

getField() - Method in class adams.data.filter.SubtractField

Returns the field to normalize to.

getFields() - Method in class adams.data.instances.AbstractFieldInstanceGenerator

Returns the targets to add.

getFilter() - Method in class adams.data.featuregenerator.FilteredFeatureGenerator

Returns the filter.

getFormatDescription() - Method in class adams.data.io.input.FloatMatrixHeatmapReader

Returns a string describing the format (used in the file chooser).

getFormatDescription() - Method in class adams.data.io.input.SpreadSheetHeatmapReader

Returns a string describing the format (used in the file chooser).

getFormatDescription() - Method in class adams.data.io.output.FloatMatrixHeatmapWriter

Returns a string describing the format (used in the file chooser).

getFormatDescription() - Method in class adams.data.io.output.SpreadSheetHeatmapWriter

Returns a string describing the format (used in the file chooser).

getFormatExtensions() - Method in class adams.data.io.input.FloatMatrixHeatmapReader

Returns the extension(s) of the format.

getFormatExtensions() - Method in class adams.data.io.input.SpreadSheetHeatmapReader

Returns the extension(s) of the format.

getFormatExtensions() - Method in class adams.data.io.output.FloatMatrixHeatmapWriter

Returns the extension(s) of the format.

getFormatExtensions() - Method in class adams.data.io.output.SpreadSheetHeatmapWriter

Returns the extension(s) of the format.

getGenerator() - Method in class adams.data.conversion.HeatmapToBufferedImage

Returns the number of gradient colors to use.

getGenerator() - Method in class adams.data.featuregenerator.FilteredFeatureGenerator

Returns the generator.

getGenerator() - Method in class adams.data.filter.FeatureGenerator

Returns the current generator.

getGenerators() - Static method in class adams.data.featuregenerator.AbstractFeatureGenerator

Returns a list with classnames of generators.

getGradientColors() - Method in class adams.data.conversion.HeatmapToBufferedImage

Generates the gradient colors.

getHeader() - Method in class adams.data.heatmap.Heatmap

Returns an empty container with the same meta-data as this one.

getHeader(int, int) - Method in class adams.data.heatmap.Heatmap

Returns an empty container with the same meta-data as this one, but with different dimensions of the map.

getHeatmap() - Method in class adams.data.heatmap.HeatmapStatistic

Returns the underlying heatmap.

getHeatmap() - Method in class adams.gui.visualization.heatmap.HeatmapPanel

The current heatmap on display.

getHeatmapPanel() - Method in class adams.gui.visualization.heatmap.AbstractHeatmapOverlay

Returns the heatmap panel this overlay is for.

getHeight() - Method in class adams.data.filter.CropToCentroid

Returns the height start the submap from.

getHeight() - Method in class adams.data.filter.Submap

Returns the height start the submap from.

getHeight() - Method in class adams.data.heatmap.Heatmap

Returns the height of the map.

getHeight() - Method in class adams.data.io.input.FloatMatrixHeatmapReader

Returns the height of the heatmap.

getIconName() - Method in class adams.gui.menu.HeatmapViewer

Returns the file name of the icon.

getID() - Method in class adams.data.heatmap.Heatmap

Returns the ID.

getID() - Method in class adams.gui.visualization.heatmap.HeatmapContainer

Returns the container's ID.

getImagePanel() - Method in class adams.gui.visualization.heatmap.HeatmapPanel

Returns the underlying image panel

getIntensityName(int, int) - Static method in class adams.data.instances.HeatmapArffUtils

Generates the attribute name for an intensity value.

getMax() - Method in class adams.data.heatmap.Heatmap

Returns the largest value in the heatmap.

getMaxIntensity() - Method in class adams.data.instances.HistogramInstanceGenerator

Returns the maximum intensity to keep.

getMaxIntensity() - Method in class adams.data.instances.IntensityInstanceGenerator

Returns the maximum intensity to keep.

getMenuBar() - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Creates a menu bar (singleton per panel object).

getMin() - Method in class adams.data.heatmap.Heatmap

Returns the smallest value in the heatmap.

getMinIntensity() - Method in class adams.data.instances.HistogramInstanceGenerator

Returns the minimum intensity to keep.

getMinIntensity() - Method in class adams.data.instances.IntensityInstanceGenerator

Returns the minimum intensity to keep.

getMissingValue() - Method in class adams.data.conversion.SpreadSheetToHeatmap

Returns the value to use for missing values/celss.

getNotes() - Method in class adams.data.heatmap.Heatmap

Returns the currently stored notes.

getNumBins() - Method in class adams.data.instances.HistogramInstanceGenerator

Returns the number of bins to use.

getNumIterations() - Method in class adams.data.filter.Centroid

Returns the number of iterations for finding the centroid.

getOnlyIndicators() - Method in class adams.data.instances.HistogramInstanceGenerator

Returns whether only indicator attributes are output instead of counts.

getOverridePrefix() - Method in class adams.data.featuregenerator.MultiGenerator

Returns whether the prefix of the generators are overridden.

getOwner() - Method in class adams.gui.visualization.heatmap.HeatmapPanel

Returns the owner of this panel.

getPanelAt(int) - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Returns the specified heatmap panel.

getParent() - Method in class adams.data.heatmap.HeatmapValue

Returns the heatmap this point belongs to.

getPrefix() - Method in class adams.data.featuregenerator.AbstractFeatureGenerator

Returns the prefix in use for the generated features.

getProperties() - Method in class adams.gui.visualization.heatmap.HeatmapPanel

Returns the properties for this panel.

getProperties() - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Returns the properties for this panel.

getQuickInfo() - Method in class adams.flow.sink.HeatmapDisplay

Returns a quick info about the actor, which will be displayed in the GUI.

getReader() - Method in class adams.data.io.input.SpreadSheetHeatmapReader

Returns the spreadsheet reader in use.

getReader() - Method in class adams.gui.visualization.heatmap.HeatmapPanel

Returns the heatmap reader that was used for loading this heatmap.

getReaderForFile(File) - Method in class adams.gui.chooser.HeatmapFileChooser

Returns the reader for the specified file.

getReaders() - Static method in class adams.data.io.input.AbstractHeatmapReader

Returns a list with classnames of readers.

getRemoveFilter(Instances) - Static method in class adams.data.instances.HeatmapArffUtils

Initializes the Remove filter for removing all IDs from the dataset.

getReport() - Method in class adams.data.heatmap.Heatmap

Returns the report.

getRotation() - Method in class adams.data.filter.Rotate

Returns the type of rotation to perform.

getRow() - Method in class adams.data.filter.Submap

Returns the row start the submap from.

getSendToClasses() - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Returns the classes that the supporter generates.

getSendToItem(Class[]) - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Returns the object to send.

getShowCentroid() - Method in class adams.gui.visualization.heatmap.HeatmapPanel

Returns whether the centroid overlay is painted as well.

getShrinkFactor() - Method in class adams.data.filter.Centroid

Returns the factor to shrink the heatmap with after each iteration

getStatistic(String) - Method in class adams.data.heatmap.HeatmapStatistic

Returns the statistical value for the given statistic name.

getStatisticDescription() - Method in class adams.data.heatmap.HeatmapStatistic

Returns a description for this statistic.

getSubGenerators() - Method in class adams.data.featuregenerator.MultiGenerator

Returns the generators in use.

getTechnicalInformation() - Method in class adams.data.filter.Centroid

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.

getThreshold() - Method in class adams.data.filter.Threshold

Returns the threshold in use.

getTitle() - Method in class adams.gui.menu.HeatmapViewer

Returns the title of the window (and text of menuitem).

getTitle() - Method in class adams.gui.visualization.heatmap.HeatmapPanel

Returns the database ID or filename as title.

getType() - Method in class adams.data.filter.Threshold

Returns the type of threshold in use.

getUserMode() - Method in class adams.gui.menu.HeatmapViewer

Returns the user mode, which determines visibility as well.

getValue() - Method in class adams.data.heatmap.HeatmapValue

Returns the value in the heatmap.

getWidth() - Method in class adams.data.filter.CropToCentroid

Returns the width start the submap from.

getWidth() - Method in class adams.data.filter.Submap

Returns the width start the submap from.

getWidth() - Method in class adams.data.heatmap.Heatmap

Returns the width of the map.

getWidth() - Method in class adams.data.io.input.FloatMatrixHeatmapReader

Returns the width of the heatmap.

getWriter() - Method in class adams.data.io.output.SpreadSheetHeatmapWriter

Returns the spreadsheet writer in use.

getWriterForFile(File) - Method in class adams.gui.chooser.HeatmapFileChooser

Returns the writer for the specified file.

getWriters() - Static method in class adams.data.io.output.AbstractHeatmapWriter

Returns a list with classnames of writers.

getX(int) - Method in class adams.data.heatmap.Heatmap

Returns the X location from the position.

getX() - Method in class adams.data.heatmap.HeatmapValue

Returns the X position in the map.

getY(int) - Method in class adams.data.heatmap.Heatmap

Returns Y location from the position.

getY() - Method in class adams.data.heatmap.HeatmapValue

Returns the Y position in the map.

globalInfo() - Method in class adams.data.conversion.BufferedImageToHeatmap

Returns a string describing the object.

globalInfo() - Method in class adams.data.conversion.HeatmapToArray

Returns a string describing the object.

globalInfo() - Method in class adams.data.conversion.HeatmapToBufferedImage

Returns a string describing the object.

globalInfo() - Method in class adams.data.conversion.HeatmapToSpreadSheet

Returns a string describing the object.

globalInfo() - Method in class adams.data.conversion.SpreadSheetToHeatmap

Returns a string describing the object.

globalInfo() - Method in class adams.data.featuregenerator.FilteredFeatureGenerator

Returns a string describing the object.

globalInfo() - Method in class adams.data.featuregenerator.Max

Returns a string describing the object.

globalInfo() - Method in class adams.data.featuregenerator.Mean

Returns a string describing the object.

globalInfo() - Method in class adams.data.featuregenerator.Median

Returns a string describing the object.

globalInfo() - Method in class adams.data.featuregenerator.Min

Returns a string describing the object.

globalInfo() - Method in class adams.data.featuregenerator.MultiGenerator

Returns a string describing the object.

globalInfo() - Method in class adams.data.featuregenerator.PassThrough

Returns a string describing the object.

globalInfo() - Method in class adams.data.filter.Centroid

Returns a string describing the object.

globalInfo() - Method in class adams.data.filter.CropToCentroid

Returns a string describing the object.

globalInfo() - Method in class adams.data.filter.FeatureGenerator

Returns a string describing the object.

globalInfo() - Method in class adams.data.filter.Normalize

Returns a string describing the object.

globalInfo() - Method in class adams.data.filter.NormalizeToField

Returns a string describing the object.

globalInfo() - Method in class adams.data.filter.Rotate

Returns a string describing the object.

globalInfo() - Method in class adams.data.filter.Standardize

Returns a string describing the object.

globalInfo() - Method in class adams.data.filter.Submap

Returns a string describing the object.

globalInfo() - Method in class adams.data.filter.SubtractField

Returns a string describing the object.

globalInfo() - Method in class adams.data.filter.Threshold

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.HistogramInstanceGenerator

Returns a string describing the object.

globalInfo() - Method in class adams.data.instances.IntensityInstanceGenerator

Returns a string describing the object.

globalInfo() - Method in class adams.data.instances.RawInstanceGenerator

Returns a string describing the object.

globalInfo() - Method in class adams.data.io.input.FloatMatrixHeatmapReader

Returns a string describing the object.

globalInfo() - Method in class adams.data.io.input.SpreadSheetHeatmapReader

Returns a string describing the object.

globalInfo() - Method in class adams.data.io.output.FloatMatrixHeatmapWriter

Returns a string describing the object.

globalInfo() - Method in class adams.data.io.output.SpreadSheetHeatmapWriter

Returns a string describing the object.

globalInfo() - Method in class adams.flow.sink.HeatmapDisplay

Returns a string describing the object.

globalInfo() - Method in class adams.flow.transformer.HeatmapFileReader

Returns a string describing the object.

globalInfo() - Method in class adams.flow.transformer.HeatmapFileWriter

Returns a string describing the object.

globalInfo() - Method in class adams.flow.transformer.HeatmapInstanceGenerator

Returns a string describing the object.

globalInfo() - Method in class adams.gui.tools.previewbrowser.HeatmapImageHandler

Returns a string describing the object.

globalInfo() - Method in class adams.gui.tools.previewbrowser.HeatmapSpreadSheetHandler

Returns a string describing the object.

globalInfo() - Method in class adams.gui.visualization.heatmap.CentroidOverlay

Returns a string describing the object.

H

hasParent() - Method in class adams.data.heatmap.HeatmapValue

Returns whether the point belongs to a heatmap.

hasReport() - Method in class adams.data.heatmap.Heatmap

Checks whether a report is present.

hasSendToItem(Class[]) - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Checks whether something to send is available.

Heatmap - Class in adams.data.heatmap

Simple wrapper around a 2-D array representing a heatmap.

Heatmap(int, int) - Constructor for class adams.data.heatmap.Heatmap

Initializes an empty heatmap with a given size.

Heatmap(double[][]) - Constructor for class adams.data.heatmap.Heatmap

Initializes the heatmap with the 2-D data.

HeatmapArffUtils - Class in adams.data.instances

A helper class for turning heatmap data into ARFF files and vice versa.

HeatmapArffUtils() - Constructor for class adams.data.instances.HeatmapArffUtils

HeatmapContainer - Class in adams.gui.visualization.heatmap

Container for heatmaps.

HeatmapContainer(HeatmapContainerManager, Heatmap) - Constructor for class adams.gui.visualization.heatmap.HeatmapContainer

Initializes the container.

HeatmapContainerManager - Class in adams.gui.visualization.heatmap

Container manager for heatmaps.

HeatmapContainerManager() - Constructor for class adams.gui.visualization.heatmap.HeatmapContainerManager

HeatmapDisplay - Class in adams.flow.sink

Actor that displays heatmaps.

HeatmapDisplay() - Constructor for class adams.flow.sink.HeatmapDisplay

HeatmapFileChooser - Class in adams.gui.chooser

A specialized JFileChooser that lists all available file Readers and Writers for heatmaps.

HeatmapFileChooser() - Constructor for class adams.gui.chooser.HeatmapFileChooser

Constructs a FileChooser pointing to the user's default directory.

HeatmapFileChooser(File) - Constructor for class adams.gui.chooser.HeatmapFileChooser

Constructs a FileChooser using the given File as the path.

HeatmapFileChooser(String) - Constructor for class adams.gui.chooser.HeatmapFileChooser

Constructs a FileChooser using the given path.

HeatmapFileReader - Class in adams.flow.transformer

Reads heat map files.

HeatmapFileReader() - Constructor for class adams.flow.transformer.HeatmapFileReader

HeatmapFileWriter - Class in adams.flow.transformer

Reads heat map files.

HeatmapFileWriter() - Constructor for class adams.flow.transformer.HeatmapFileWriter

HeatmapFilter - Class in adams.flow.transformer

Filters data using the specified filter.

HeatmapFilter() - Constructor for class adams.flow.transformer.HeatmapFilter

HeatmapImageHandler - Class in adams.gui.tools.previewbrowser

Displays a heatmap as image.

HeatmapImageHandler() - Constructor for class adams.gui.tools.previewbrowser.HeatmapImageHandler

HeatmapInstanceGenerator - Class in adams.flow.transformer

Generates weka.core.Instance objects from heatmaps or reports/sample data.

HeatmapInstanceGenerator() - Constructor for class adams.flow.transformer.HeatmapInstanceGenerator

HeatmapPanel - Class in adams.gui.visualization.heatmap

Panel for displaying a single heatmap.

HeatmapPanel(HeatmapViewerPanel) - Constructor for class adams.gui.visualization.heatmap.HeatmapPanel

Initializes the panel.

HeatmapSpreadSheetHandler - Class in adams.gui.tools.previewbrowser

Displays a heatmap as a spreadsheet.

HeatmapSpreadSheetHandler() - Constructor for class adams.gui.tools.previewbrowser.HeatmapSpreadSheetHandler

HeatmapStatistic - Class in adams.data.heatmap

Generates some statistics for a heatmap.

HeatmapStatistic() - Constructor for class adams.data.heatmap.HeatmapStatistic

Initializes the statistics.

HeatmapStatistic(Heatmap) - Constructor for class adams.data.heatmap.HeatmapStatistic

Initializes the statistics with the specified heatmap.

HeatmapToArray - Class in adams.data.conversion

Turns a heatmap into a Double array.

HeatmapToArray() - Constructor for class adams.data.conversion.HeatmapToArray

HeatmapToBufferedImage - Class in adams.data.conversion

Turns a heatmap into a BufferedImage.

HeatmapToBufferedImage() - Constructor for class adams.data.conversion.HeatmapToBufferedImage

HeatmapToSpreadSheet - Class in adams.data.conversion

Turns a heatmap into a spreadsheet object.

HeatmapToSpreadSheet() - Constructor for class adams.data.conversion.HeatmapToSpreadSheet

HeatmapValue - Class in adams.data.heatmap

Wrapper class for a value in a heatmap.

HeatmapValue() - Constructor for class adams.data.heatmap.HeatmapValue

Initializes the heatmap value with 0.0 and coordinates of 0,0.

HeatmapValue(int, int, double) - Constructor for class adams.data.heatmap.HeatmapValue

Initializes the heatmap value.

HeatmapViewer - Class in adams.gui.menu

For displaying heatmaps.

HeatmapViewer() - Constructor for class adams.gui.menu.HeatmapViewer

Initializes the menu item with no owner.

HeatmapViewer(AbstractApplicationFrame) - Constructor for class adams.gui.menu.HeatmapViewer

Initializes the menu item.

HeatmapViewerPanel - Class in adams.gui.visualization.heatmap

Panel for viewing/processing heatmaps.

HeatmapViewerPanel() - Constructor for class adams.gui.visualization.heatmap.HeatmapViewerPanel

HEIGHT - Static variable in class adams.data.heatmap.HeatmapStatistic

the height.

heightTipText() - Method in class adams.data.filter.CropToCentroid

Returns the tip text for this property.

heightTipText() - Method in class adams.data.filter.Submap

Returns the tip text for this property.

heightTipText() - Method in class adams.data.io.input.FloatMatrixHeatmapReader

Returns the tip text for this property.

HistogramInstanceGenerator - Class in adams.data.instances

A generator for turning a heatmap and fields of its report into weka.core.Instance objects.
Zero values are omitted.

HistogramInstanceGenerator() - Constructor for class adams.data.instances.HistogramInstanceGenerator

I

indexOf(String) - Method in class adams.gui.visualization.heatmap.HeatmapContainerManager

Returns the index of the first ID or display ID that matches the specified one.

initGUI() - Method in class adams.gui.visualization.heatmap.HeatmapPanel

Initializes the widgets.

initGUI() - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Initializes the widgets.

initialize() - Method in class adams.data.featuregenerator.AbstractDatabaseConnectionFeatureGenerator

Initializes the members.

initialize() - Method in class adams.data.io.output.FloatMatrixHeatmapWriter

Initializes the members.

initialize() - Method in class adams.data.io.output.SpreadSheetHeatmapWriter

Initializes the members.

initialize() - Method in class adams.gui.visualization.heatmap.HeatmapPanel

Initializes the members.

initialize() - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Initializes the members.

IntensityInstanceGenerator - Class in adams.data.instances

A generator for turning a heatmap's intensities and fields of its report into weka.core.Instance objects.

IntensityInstanceGenerator() - Constructor for class adams.data.instances.IntensityInstanceGenerator

isEmpty() - Method in class adams.data.heatmap.Heatmap

Only false if all values are 0.0.

isSearchPanelVisible() - Method in class adams.gui.visualization.heatmap.HeatmapPanel

Returns whether the search panel is visible.

isSingleton() - Method in class adams.gui.menu.HeatmapViewer

Whether the panel can only be displayed once.

iterator() - Method in class adams.data.heatmap.Heatmap

Returns an iterator over the elements in this collection.

L

launch() - Method in class adams.gui.menu.HeatmapViewer

Launches the functionality of the menu item.

load(File[], AbstractHeatmapReader) - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Loads heatmaps from disk, popping up a file chooser dialog.

load(File) - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Loads the specified file from disk.

load() - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Loads heatmaps from disk, popping up a file chooser dialog.

M

m_Centroid - Variable in class adams.data.filter.CropToCentroid

the centroid filter.

m_Centroid - Variable in class adams.gui.visualization.heatmap.CentroidOverlay

the calculated centroid.

m_CentroidOverlay - Variable in class adams.gui.visualization.heatmap.HeatmapPanel

the centroid image overlay.

m_Color - Variable in class adams.gui.visualization.heatmap.CentroidOverlay

the color to paint the centroid in.

m_ColorGenerator - Variable in class adams.flow.sink.HeatmapDisplay

the generator for the color gradient.

m_ColorGenerator - Variable in class adams.gui.visualization.heatmap.HeatmapPanel

the color generator to use.

m_Column - Variable in class adams.data.filter.Submap

the column to start (top-left).

m_Comparator - Static variable in class adams.data.heatmap.Heatmap

the singleton comparator.

m_CurrentFilter - Variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

the current filter.

m_DatabaseConnection - Variable in class adams.data.featuregenerator.AbstractDatabaseConnectionFeatureGenerator

the database connection.

m_DialogFilter - Variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

the filter dialog.

m_Field - Variable in class adams.data.filter.NormalizeToField

the field containing the ambient temperature.

m_Field - Variable in class adams.data.filter.SubtractField

the field containing the numeric value.

m_Fields - Variable in class adams.data.instances.AbstractFieldInstanceGenerator

fields to add to the output data.

m_FileChooser - Variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

for loading heatmaps from disk.

m_Filter - Variable in class adams.data.featuregenerator.FilteredFeatureGenerator

the pre-filter for filtering the data.

m_FilterAll - Variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

indicates whether filter is applied to all heatmaps.

m_FilterOverlayOriginalData - Variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

indicates whether the filtered data was overlayed over the original.

m_Generator - Variable in class adams.data.conversion.HeatmapToBufferedImage

the generator to use.

m_Generator - Variable in class adams.data.featuregenerator.FilteredFeatureGenerator

the actual feature generator.

m_Generator - Variable in class adams.data.filter.FeatureGenerator

the report filter.

m_Generators - Variable in class adams.data.featuregenerator.MultiGenerator

the generators.

m_GradientColors - Variable in class adams.data.conversion.HeatmapToBufferedImage

the gradient colors.

m_Heatmap - Variable in class adams.data.heatmap.HeatmapStatistic

the heatmap to create the statistics for.

m_Heatmap - Variable in class adams.gui.visualization.heatmap.HeatmapPanel

the heatmap on display.

m_HeatmapImage - Variable in class adams.gui.visualization.heatmap.HeatmapPanel

the panel for displaying the heatmap as image.

m_HeatmapPanel - Variable in class adams.gui.visualization.heatmap.AbstractHeatmapOverlay

the heatmap panel.

m_HeatmapTable - Variable in class adams.gui.visualization.heatmap.HeatmapPanel

the table with the heatmap as spreadsheet.

m_Height - Variable in class adams.data.filter.CropToCentroid

the height of the crop region around the centroid.

m_Height - Variable in class adams.data.filter.Submap

the height of the submap.

m_Height - Variable in class adams.data.io.input.FloatMatrixHeatmapReader

the height of the heatmap.

m_ID - Variable in class adams.data.heatmap.Heatmap

the ID of the heatmap (basically the filename).

m_IsSample - Variable in class adams.data.filter.Standardize

whether the arrays are samples or populations.

m_Map - Variable in class adams.data.heatmap.Heatmap

the actual heat map.

m_Max - Variable in class adams.data.heatmap.Heatmap

the maximum intensity value.

m_MaxIntensity - Variable in class adams.data.instances.HistogramInstanceGenerator

the maximum intensity to keep.

m_MaxIntensity - Variable in class adams.data.instances.IntensityInstanceGenerator

the maximum m/z ratio to keep.

m_MenuBar - Variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

the menu bar.

m_MenuItemFileCloseAll - Variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

the "close all" menu item.

m_MenuItemFileCloseCurrent - Variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

the "close current" menu item.

m_MenuItemFileReloadAll - Variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

the "reload all" menu item.

m_MenuItemFileReloadCurrent - Variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

the "reload current" menu item.

m_MenuItemFileSaveAs - Variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

the "save as" menu item.

m_MenuItemProcessApplyImageJ - Variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

the ImageJ menu item.

m_MenuItemProcessApplyImageMagick - Variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

the ImageMagick menu item.

m_MenuItemProcessApplyJAI - Variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

the JAI menu item.

m_MenuItemProcessFilterAllHeatmaps - Variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

the filter all menu item.

m_MenuItemProcessFilterHeatmap - Variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

the filter menu item.

m_MenuItemViewShowCentroid - Variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

the show centroid menu item.

m_MenuItemViewShowNotes - Variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

the show notes menu item.

m_MenuItemViewShowSpreadsheet - Variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

the show spreadhseet menu item.

m_MenuItemViewShowStatistics - Variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

the show statistics menu item.

m_Min - Variable in class adams.data.heatmap.Heatmap

the minimum intensity value.

m_MinIntensity - Variable in class adams.data.instances.HistogramInstanceGenerator

the minimum intensity to keep.

m_MinIntensity - Variable in class adams.data.instances.IntensityInstanceGenerator

the minimum m/z ratio to keep.

m_MissingValue - Variable in class adams.data.conversion.SpreadSheetToHeatmap

the default value for missing values.

m_Notes - Variable in class adams.data.heatmap.Heatmap

the attached notes.

m_NumBins - Variable in class adams.data.instances.HistogramInstanceGenerator

the number of bins to generate.

m_NumIterations - Variable in class adams.data.filter.Centroid

the number of iterations to peform.

m_OnlyIndicators - Variable in class adams.data.instances.HistogramInstanceGenerator

whether to generate only indicator attributes.

m_OverridePrefix - Variable in class adams.data.featuregenerator.MultiGenerator

whether to override the sub-generators' prefix.

m_Owner - Variable in class adams.gui.visualization.heatmap.HeatmapPanel

the owner.

m_Parent - Variable in class adams.data.heatmap.HeatmapValue

the parent.

m_Prefix - Variable in class adams.data.featuregenerator.AbstractFeatureGenerator

the prefix for the feature fields.

m_Properties - Static variable in class adams.gui.visualization.heatmap.HeatmapPanel

the setup for the panel.

m_Properties - Static variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

the setup for the panel.

m_Reader - Variable in class adams.data.io.input.SpreadSheetHeatmapReader

the spreadsheet reader to use.

m_Reader - Variable in class adams.gui.visualization.heatmap.HeatmapPanel

the reader that was used for reading in the heatmap.

m_Report - Variable in class adams.data.heatmap.Heatmap

meta-information on the heatmap.

m_ReportTable - Variable in class adams.gui.visualization.heatmap.HeatmapPanel

the report of the heatmap.

m_Rotation - Variable in class adams.data.filter.Rotate

the type of rotation to perform.

m_Row - Variable in class adams.data.filter.Submap

the row to start (top-left).

m_SearchPanel - Variable in class adams.gui.visualization.heatmap.HeatmapPanel

the search panel for the heatmap report.

m_SearchPanel - Variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

the search panel for the heatmap report.

m_ShrinkFactor - Variable in class adams.data.filter.Centroid

the factor to shrink the heatmap after each iteration.

m_SplitPane - Variable in class adams.gui.visualization.heatmap.HeatmapPanel

the split pane for image/spreadsheet and report.

m_Statistics - Variable in class adams.data.heatmap.HeatmapStatistic

the statistics.

m_StatusBar - Variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

the status bar.

m_TabbedPane - Variable in class adams.gui.visualization.heatmap.HeatmapPanel

the tabbed pane for the image and spreadsheet view.

m_TabbedPane - Variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

the tabbed pane for the heatmaps.

m_Threshold - Variable in class adams.data.filter.Threshold

the threshold percentage.

m_Type - Variable in class adams.data.filter.Threshold

the type of threshold.

m_Value - Variable in class adams.data.heatmap.HeatmapValue

the heatmap value.

m_Width - Variable in class adams.data.filter.CropToCentroid

the width of the crop region around the centroid.

m_Width - Variable in class adams.data.filter.Submap

the width of the submap.

m_Width - Variable in class adams.data.io.input.FloatMatrixHeatmapReader

the width of the heatmap.

m_Writer - Variable in class adams.data.io.output.SpreadSheetHeatmapWriter

the spreadsheet writer to use.

m_X - Variable in class adams.data.heatmap.HeatmapValue

the X position in the heatmap.

m_Y - Variable in class adams.data.heatmap.HeatmapValue

the Y position in the heatmap.

Max - Class in adams.data.featuregenerator

Outputs the largest intensity value in the heatmap as feature.

Max() - Constructor for class adams.data.featuregenerator.Max

MAXIMUM - Static variable in class adams.data.heatmap.HeatmapStatistic

the maximum value.

maxIntensityTipText() - Method in class adams.data.instances.HistogramInstanceGenerator

Returns the tip text for this property.

maxIntensityTipText() - Method in class adams.data.instances.IntensityInstanceGenerator

Returns the tip text for this property.

Mean - Class in adams.data.featuregenerator

Outputs the mean of the intensity values in the heatmap as feature.

Mean() - Constructor for class adams.data.featuregenerator.Mean

Median - Class in adams.data.featuregenerator

Outputs the median of the intensity values in the heatmap as feature.

Median() - Constructor for class adams.data.featuregenerator.Median

mergeWith(DataContainer) - Method in class adams.data.heatmap.Heatmap

Merges its own data with the one provided by the specified object.

Min - Class in adams.data.featuregenerator

Outputs the smallest intensity value in the heatmap as feature.

Min() - Constructor for class adams.data.featuregenerator.Min

MINIMUM - Static variable in class adams.data.heatmap.HeatmapStatistic

the minimum value.

minIntensityTipText() - Method in class adams.data.instances.HistogramInstanceGenerator

Returns the tip text for this property.

minIntensityTipText() - Method in class adams.data.instances.IntensityInstanceGenerator

Returns the tip text for this property.

missingValueTipText() - Method in class adams.data.conversion.SpreadSheetToHeatmap

Returns the tip text for this property.

MultiGenerator - Class in adams.data.featuregenerator

A meta-generator that applies multiple feature generators to the data.

MultiGenerator() - Constructor for class adams.data.featuregenerator.MultiGenerator

N

newComparator() - Method in class adams.data.heatmap.Heatmap

Returns a new instance of the default comparator.

newPanel() - Method in class adams.flow.sink.HeatmapDisplay

Creates the panel to display in the dialog.

newPanel(Heatmap) - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Creates a new panel and configures it.

newPoint() - Method in class adams.data.heatmap.Heatmap

Returns a new instance of a DataContainer point.

Normalize - Class in adams.data.filter

Normalizes the values of a heatmap to have a range of 0 to 1.

Normalize() - Constructor for class adams.data.filter.Normalize

NormalizeToField - Class in adams.data.filter

Divides all the heatmap values by the value of the specified numeric field.
If the report field is not available or not numeric, then an error gets attached to the notes.

NormalizeToField() - Constructor for class adams.data.filter.NormalizeToField

numBinsTipText() - Method in class adams.data.instances.HistogramInstanceGenerator

Returns the tip text for this property.

numIterationsTipText() - Method in class adams.data.filter.Centroid

Returns the tip text for this property.

O

onlyIndicatorsTipText() - Method in class adams.data.instances.HistogramInstanceGenerator

Returns the tip text for this property.

overridePrefixTipText() - Method in class adams.data.featuregenerator.MultiGenerator

Returns the tip text for this property.

P

paintOverlay(ImagePanel.PaintPanel, Graphics) - Method in class adams.gui.visualization.heatmap.AbstractHeatmapOverlay

Paints the overlay over the image.

PassThrough - Class in adams.data.featuregenerator

A dummy generator that just passes the data through.

PassThrough() - Constructor for class adams.data.featuregenerator.PassThrough

PREFIX_BIN - Static variable in class adams.data.instances.HistogramInstanceGenerator

the prefix for the bins.

PREFIX_FEATURE - Static variable in class adams.data.featuregenerator.AbstractFeatureGenerator

the default prefix for the feature fields.

PREFIX_INTENSITY - Static variable in class adams.data.instances.HeatmapArffUtils

the prefix for intensity values.

prefixTipText() - Method in class adams.data.featuregenerator.AbstractFeatureGenerator

Returns the tip text for this property.

processData(Heatmap) - Method in class adams.data.featuregenerator.AbstractFeatureGenerator

Performs the actual feature generation.

processData(Heatmap) - Method in class adams.data.featuregenerator.FilteredFeatureGenerator

Processes the data/report.

processData(Heatmap) - Method in class adams.data.featuregenerator.Max

Performs the actual feature generation.

processData(Heatmap) - Method in class adams.data.featuregenerator.Mean

Performs the actual feature generation.

processData(Heatmap) - Method in class adams.data.featuregenerator.Median

Performs the actual feature generation.

processData(Heatmap) - Method in class adams.data.featuregenerator.Min

Performs the actual feature generation.

processData(Heatmap) - Method in class adams.data.featuregenerator.MultiGenerator

Performs the actual feature generation.

processData(Heatmap) - Method in class adams.data.featuregenerator.PassThrough

Does nothing with the report.

processData(Heatmap) - Method in class adams.data.filter.Centroid

Performs the actual filtering.

processData(Heatmap, Heatmap) - Method in class adams.data.filter.CropToCentroid

Performs the actual filtering, using the pre-filtered data to manipulate the original data.

processData(Heatmap) - Method in class adams.data.filter.FeatureGenerator

Performs the actual filtering.

processData(Heatmap) - Method in class adams.data.filter.Normalize

Performs the actual filtering.

processData(Heatmap) - Method in class adams.data.filter.NormalizeToField

Performs the actual filtering.

processData(Heatmap) - Method in class adams.data.filter.Rotate

Performs the actual filtering.

processData(Heatmap) - Method in class adams.data.filter.Standardize

Performs the actual filtering.

processData(Heatmap) - Method in class adams.data.filter.Submap

Performs the actual filtering.

processData(Heatmap) - Method in class adams.data.filter.SubtractField

Performs the actual filtering.

processData(Heatmap) - Method in class adams.data.filter.Threshold

Performs the actual filtering.

R

RawInstanceGenerator - Class in adams.data.instances

A generator for turning a heatmap and fields of its report into weka.core.Instance objects.
The intensities are output row-wise.

RawInstanceGenerator() - Constructor for class adams.data.instances.RawInstanceGenerator

readData() - Method in class adams.data.io.input.FloatMatrixHeatmapReader

Performs the actual reading.

readData() - Method in class adams.data.io.input.SpreadSheetHeatmapReader

Performs the actual reading.

readerTipText() - Method in class adams.data.io.input.SpreadSheetHeatmapReader

Returns the tip text for this property.

reload() - Method in class adams.gui.visualization.heatmap.HeatmapPanel

Reloads the data, if possible.

reloadAll() - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Reloads all heatmaps.

reloadCurrent() - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Reloads the current panel's heatmap.

remove(Object) - Method in class adams.data.heatmap.Heatmap

Sets the value at the location of the provided object to 0.0.

removeAll(Collection<?>) - Method in class adams.data.heatmap.Heatmap

Sets all values in this heatmap to 0.0 for locations stored in the collection provided.

reset() - Method in class adams.data.conversion.HeatmapToBufferedImage

Resets the object.

reset() - Method in class adams.data.featuregenerator.AbstractFeatureGenerator

Resets the generator.

reset() - Method in class adams.gui.visualization.heatmap.CentroidOverlay

Resets the overlay.

resetMinMax() - Method in class adams.data.heatmap.Heatmap

Resets the min/max values.

retainAll(Collection<?>) - Method in class adams.data.heatmap.Heatmap

Always throws UnsupportedOperationException.

Rotate - Class in adams.data.filter

Rotates a heatmap by a specified number of degrees clockwise.

Rotate() - Constructor for class adams.data.filter.Rotate

Rotate.Rotation - Enum in adams.data.filter

Defines the type of rotation to perform.

rotationTipText() - Method in class adams.data.filter.Rotate

Returns the tip text for this property.

rowTipText() - Method in class adams.data.filter.Submap

Returns the tip text for this property.

S

saveAs() - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Saves the current heatmap to disk.

search(String, boolean) - Method in class adams.gui.visualization.heatmap.HeatmapPanel

Performs a search.

search(String, boolean) - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Performs a search.

SESSION_FILE - Static variable in class adams.gui.visualization.heatmap.HeatmapViewerPanel

the file to store the recent files in.

set(int, int, double) - Method in class adams.data.heatmap.Heatmap

Sets the map value at the specified location.

set(int, double) - Method in class adams.data.heatmap.Heatmap

Sets the map value at the specified position from the top left corner of the map, walking through row-wise.

set(double[]) - Method in class adams.data.heatmap.Heatmap

Sets all the values, if the size of the array matches this heatmap.

set(Double[]) - Method in class adams.data.heatmap.Heatmap

Sets all the values, if the size of the array matches this heatmap.

setCentroid(Centroid) - Method in class adams.data.filter.CropToCentroid

Sets the centroid filter.

setColor(Color) - Method in class adams.gui.visualization.heatmap.CentroidOverlay

Sets the color for the overlay.

setColorGenerator(AbstractColorGradientGenerator) - Method in class adams.flow.sink.HeatmapDisplay

Sets the generator for the color gradient.

setColorGenerator(AbstractColorGradientGenerator) - Method in class adams.gui.visualization.heatmap.HeatmapPanel

Sets the generator for the color gradient.

setColumn(int) - Method in class adams.data.filter.Submap

Sets the column to start the submap from.

setDatabaseConnection(AbstractDatabaseConnection) - Method in class adams.data.featuregenerator.AbstractDatabaseConnectionFeatureGenerator

Sets the database connection object to use.

setField(Field) - Method in class adams.data.filter.NormalizeToField

Sets the field to normalize to.

setField(Field) - Method in class adams.data.filter.SubtractField

Sets the field to normalize to.

setFields(Field[]) - Method in class adams.data.instances.AbstractFieldInstanceGenerator

Sets the targets to add.

setFilter(AbstractFilter) - Method in class adams.data.featuregenerator.FilteredFeatureGenerator

Sets the filter.

setGenerator(AbstractColorGradientGenerator) - Method in class adams.data.conversion.HeatmapToBufferedImage

Sets the number of gradient colors to use.

setGenerator(AbstractFeatureGenerator) - Method in class adams.data.featuregenerator.FilteredFeatureGenerator

Sets the generator.

setGenerator(AbstractFeatureGenerator) - Method in class adams.data.filter.FeatureGenerator

Sets the generator to use.

setHeatmap(Heatmap) - Method in class adams.data.heatmap.HeatmapStatistic

Sets the heatmap to generate the statistics for.

setHeatmap(Heatmap) - Method in class adams.gui.visualization.heatmap.HeatmapPanel

Sets the heatmap to display.

setHeatmapPanel(HeatmapPanel) - Method in class adams.gui.visualization.heatmap.AbstractHeatmapOverlay

Sets the heatmap panel this overlay is for.

setHeight(int) - Method in class adams.data.filter.CropToCentroid

Sets the height of the submap.

setHeight(int) - Method in class adams.data.filter.Submap

Sets the height of the submap.

setHeight(int) - Method in class adams.data.io.input.FloatMatrixHeatmapReader

Sets the height of the heatmap.

setID(String) - Method in class adams.data.heatmap.Heatmap

Sets the ID.

setID(String) - Method in class adams.gui.visualization.heatmap.HeatmapContainer

Sets the container's ID.

setMaxIntensity(double) - Method in class adams.data.instances.HistogramInstanceGenerator

Sets the maximum intensity to keep.

setMaxIntensity(double) - Method in class adams.data.instances.IntensityInstanceGenerator

Sets the maximum intensity to keep.

setMinIntensity(double) - Method in class adams.data.instances.HistogramInstanceGenerator

Sets the minimum intensity to keep.

setMinIntensity(double) - Method in class adams.data.instances.IntensityInstanceGenerator

Sets the minimum intensity to keep.

setMissingValue(double) - Method in class adams.data.conversion.SpreadSheetToHeatmap

Sets the value to use for missing values/cells.

setNumBins(int) - Method in class adams.data.instances.HistogramInstanceGenerator

Sets the number of bins to use.

setNumIterations(int) - Method in class adams.data.filter.Centroid

Sets the number of iterations for finding the centroid.

setOnlyIndicators(boolean) - Method in class adams.data.instances.HistogramInstanceGenerator

Sets whether only indicator attributes are output instead of counts.

setOverridePrefix(boolean) - Method in class adams.data.featuregenerator.MultiGenerator

Sets whether to override the generators' prefix.

setParent(DataContainer) - Method in class adams.data.heatmap.HeatmapValue

Sets the heatmap this point belongs to.

setPrefix(String) - Method in class adams.data.featuregenerator.AbstractFeatureGenerator

Sets the prefix to use for the generated features.

setReader(SpreadSheetReader) - Method in class adams.data.io.input.SpreadSheetHeatmapReader

Sets the spreadsheet reader to use.

setReader(AbstractHeatmapReader) - Method in class adams.gui.visualization.heatmap.HeatmapPanel

Sets the heatmap reader that was used for loading this heatmap.

setReport(Report) - Method in class adams.data.heatmap.Heatmap

Sets a new report.

setRotation(Rotate.Rotation) - Method in class adams.data.filter.Rotate

Sets the type of rotation to perform.

setRow(int) - Method in class adams.data.filter.Submap

Sets the row to start the submap from.

setSearchPanelVisible(boolean) - Method in class adams.gui.visualization.heatmap.HeatmapPanel

Sets whether to display the search panel or not.

setShowCentroid(boolean) - Method in class adams.gui.visualization.heatmap.HeatmapPanel

Sets whether the centroid overlay is painted as well.

setShrinkFactor(double) - Method in class adams.data.filter.Centroid

Sets the factor to shrink the heatmap with after each iteration.

setSubGenerators(AbstractFeatureGenerator[]) - Method in class adams.data.featuregenerator.MultiGenerator

Sets the generators to use.

setThreshold(double) - Method in class adams.data.filter.Threshold

Sets the threshold to use.

setType(Threshold.Type) - Method in class adams.data.filter.Threshold

Sets the type of threshold to use.

setWidth(int) - Method in class adams.data.filter.CropToCentroid

Sets the width of the submap.

setWidth(int) - Method in class adams.data.filter.Submap

Sets the width of the submap.

setWidth(int) - Method in class adams.data.io.input.FloatMatrixHeatmapReader

Sets the width of the heatmap.

setWriter(SpreadSheetWriter) - Method in class adams.data.io.output.SpreadSheetHeatmapWriter

Sets the spreadsheet writer to use.

shallowCopy() - Method in class adams.data.featuregenerator.AbstractFeatureGenerator

Returns a shallow copy of itself, i.e., based on the commandline options.

shallowCopy(boolean) - Method in class adams.data.featuregenerator.AbstractFeatureGenerator

Returns a shallow copy of itself, i.e., based on the commandline options.

showNotes() - Method in class adams.gui.visualization.heatmap.HeatmapPanel

Displays the notes of the heatmap.

showSpreadsheet() - Method in class adams.gui.visualization.heatmap.HeatmapPanel

Displays the heatmap as spreadsheet.

showStatistics() - Method in class adams.gui.visualization.heatmap.HeatmapPanel

Displays somes stats on the heatmap.

showStatus(String) - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

Displays a message.

shrinkFactorTipText() - Method in class adams.data.filter.Centroid

Returns the tip text for this property.

size() - Method in class adams.data.heatmap.Heatmap

Returns the total amount of data points in the map.

SpreadSheetHeatmapReader - Class in adams.data.io.input

Turns spreadsheets into heatmaps.

SpreadSheetHeatmapReader() - Constructor for class adams.data.io.input.SpreadSheetHeatmapReader

SpreadSheetHeatmapWriter - Class in adams.data.io.output

Writes heat map files using a spreadsheet format.

SpreadSheetHeatmapWriter() - Constructor for class adams.data.io.output.SpreadSheetHeatmapWriter

SpreadSheetToHeatmap - Class in adams.data.conversion

Turns an all-numeric spreadsheet into a heatmap.
Missing values/cells are tolerated and replaced with the specified value for missing values.

SpreadSheetToHeatmap() - Constructor for class adams.data.conversion.SpreadSheetToHeatmap

Standardize - Class in adams.data.filter

Standardizes the values of a heatmap to have mean of 1 and stdev 1.
NB: normally, the mean is 0 when standardizing, but heatmaps only allow positive values.

Standardize() - Constructor for class adams.data.filter.Standardize

statisticNames() - Method in class adams.data.heatmap.HeatmapStatistic

Returns all the names of the available statistical values.

subGeneratorsTipText() - Method in class adams.data.featuregenerator.MultiGenerator

Returns the tip text for this property.

Submap - Class in adams.data.filter

Creates a submap, specified by the coordinates of the top-left corner (row and column), width and height.

Submap() - Constructor for class adams.data.filter.Submap

submap(int, int, int, int) - Method in class adams.data.heatmap.Heatmap

Returns the specified submap.

SubtractField - Class in adams.data.filter

Subtracts the value of the numeric field from all non-zero heatmap values.
Values that fall below zero are automatically set to zero (minimum value for a heatmap).

SubtractField() - Constructor for class adams.data.filter.SubtractField

T

Threshold - Class in adams.data.filter

Zeroes all intensity values that are either below or above a user-specified threshold, depending on the selected threshold type.

Threshold() - Constructor for class adams.data.filter.Threshold

Threshold.Type - Enum in adams.data.filter

The type of threshold.

thresholdTipText() - Method in class adams.data.filter.Threshold

Returns the tip text for this property.

toArray() - Method in class adams.data.heatmap.Heatmap

Turns the heatmap into an array (row wise).

toArray(HeatmapValue[]) - Method in class adams.data.heatmap.Heatmap

Returns the stored points as array.

toDoubleArray() - Method in class adams.data.heatmap.Heatmap

Turns the heatmap into a Double array (row wise).

toIntensityString() - Method in class adams.data.heatmap.Heatmap

Returns a comma-separated string of all the intensity values.

toList() - Method in class adams.data.heatmap.Heatmap

Returns a list with the points.

toList(DataPointComparator) - Method in class adams.data.heatmap.Heatmap

Returns a list with the points.

toString() - Method in class adams.data.heatmap.Heatmap

Returns a short string representation.

toString() - Method in class adams.data.heatmap.HeatmapStatistic

Returns a string representation of the statistic.

toString() - Method in class adams.data.heatmap.HeatmapValue

Returns a string representation of the value.

toTreeSet() - Method in class adams.data.heatmap.Heatmap

Returns a treeset with the points.

toTreeSet(DataPointComparator<HeatmapValue>) - Method in class adams.data.heatmap.Heatmap

Returns a treeset with the points, sorted according to the given comparator.

typeTipText() - Method in class adams.data.filter.Threshold

Returns the tip text for this property.

U

updateDatabaseConnection() - Method in class adams.data.featuregenerator.AbstractDatabaseConnectionFeatureGenerator

Updates the database connection in dependent schemes.

updateDatabaseConnection() - Method in class adams.data.featuregenerator.FilteredFeatureGenerator

Updates the database connection in dependent schemes.

updateDatabaseConnection() - Method in class adams.data.featuregenerator.MultiGenerator

Updates the database connection in the sub-generators.

updateDatabaseConnection() - Method in class adams.data.filter.FeatureGenerator

Updates the database connection in the filter.

updateMenu() - Method in class adams.gui.visualization.heatmap.HeatmapViewerPanel

updates the enabled state of the menu items.

updateMinMax(double) - Method in class adams.data.heatmap.Heatmap

Updates the min/max values.

V

valueOf(String) - Static method in enum adams.data.filter.Rotate.Rotation

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum adams.data.filter.Threshold.Type

Returns the enum constant of this type with the specified name.

values() - Static method in enum adams.data.filter.Rotate.Rotation

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum adams.data.filter.Threshold.Type

Returns an array containing the constants of this enum type, in the order they are declared.

W

WIDTH - Static variable in class adams.data.heatmap.HeatmapStatistic

the width.

widthTipText() - Method in class adams.data.filter.CropToCentroid

Returns the tip text for this property.

widthTipText() - Method in class adams.data.filter.Submap

Returns the tip text for this property.

widthTipText() - Method in class adams.data.io.input.FloatMatrixHeatmapReader

Returns the tip text for this property.

writeData(List<Heatmap>) - Method in class adams.data.io.output.FloatMatrixHeatmapWriter

Performs the actual writing.

writeData(List<Heatmap>) - Method in class adams.data.io.output.SpreadSheetHeatmapWriter

Performs the actual writing.

writerTipText() - Method in class adams.data.io.output.SpreadSheetHeatmapWriter

Returns the tip text for this property.

A B C D E F G H I L M N O P R S T U V W