Package adams.flow.transformer

Class SampleDataFileWriter

  • All Implemented Interfaces:
    adams.core.AdditionalInformationHandler, adams.core.CleanUpHandler, adams.core.Destroyable, adams.core.GlobalInfoSupporter, adams.core.logging.LoggingLevelHandler, adams.core.logging.LoggingSupporter, adams.core.option.OptionHandler, adams.core.QuickInfoSupporter, adams.core.ShallowCopySupporter<adams.flow.core.Actor>, adams.core.SizeOfHandler, adams.core.Stoppable, adams.core.StoppableWithFeedback, adams.core.VariablesInspectionHandler, adams.event.VariableChangeListener, adams.flow.core.Actor, adams.flow.core.ErrorHandler, adams.flow.core.InputConsumer, adams.flow.core.OutputProducer, Serializable, Comparable
    public class SampleDataFileWriter
extends adams.flow.transformer.AbstractReportFileWriter<SampleData>
    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).

    Input/output:
    - accepts:
       knir.data.sampledata.SampleData
    - generates:
       java.lang.String


    Valid options are: 

    -D (property: debug)
         If set to true, scheme may output additional info to the console.
 
    -name <java.lang.String> (property: name)
         The name of the actor.
         default: SampleDataFileWriter
 
    -annotation <adams.core.base.BaseText> (property: annotations)
         The annotations to attach to this actor.
         default:
 
    -skip (property: skip)
         If set to true, transformation is skipped and the input token is just forwarded
          as it is.
 
    -writer <adams.data.io.output.AbstractReportWriter [options]> (property: writer)
         The writer to use for saving the reports.
         default: knir.data.output.SimpleSampleDataWriter -output ${TMP}/out.chrom
 
    -dir <adams.core.io.PlaceholderFile> (property: outputDir)
         The output directory for the reports.
         default: .
    Default options for knir.data.output.SimpleSampleDataWriter (-writer/writer): 
    -D (property: debug)
         If set to true, scheme may output additional info to the console.
 
    -output <adams.core.io.PlaceholderFile> (property: output)
         The file to write the report to.
         default: ${TMP}/out.chrom
    Version:
    $Revision: 2242 $
    Author:
    fracpete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Summary

      • Fields inherited from class adams.flow.transformer.AbstractReportFileWriter

        m_Generator, m_OutputDir, m_Writer

      • Fields inherited from class adams.flow.transformer.AbstractTransformer

        BACKUP_INPUT, BACKUP_OUTPUT, m_InputToken, m_OutputToken

      • Fields inherited from class adams.flow.core.AbstractActor

        m_Annotations, m_BackupState, m_DetectedObjectVariables, m_DetectedVariables, m_ErrorHandler, m_Executed, m_Executing, m_ExecutionListeningSupporter, m_FullName, m_LoggingPrefix, m_Name, m_Parent, m_ScopeHandler, m_Self, m_Silent, m_Skip, m_StopFlowOnError, m_StopMessage, m_Stopped, m_StorageHandler, m_VariablesUpdated

      • Fields inherited from class adams.core.option.AbstractOptionHandler

        m_OptionManager

      • Fields inherited from class adams.core.logging.LoggingObject

        m_Logger, m_LoggingIsEnabled, m_LoggingLevel

      • Fields inherited from interface adams.flow.core.Actor

        FILE_EXTENSION, FILE_EXTENSION_GZ

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      Class[] accepts()
      Returns the class that the consumer accepts.
      protected adams.data.io.output.AbstractReportWriter<SampleData> getDefaultWriter()
      Returns the default writer.
      String globalInfo()
      Returns a string describing the object.

      • Methods inherited from class adams.flow.transformer.AbstractReportFileWriter

        defineOptions, doExecute, extractReport, extractReports, filenameGeneratorTipText, generates, getDefaultFilenameGenerator, getFilenameGenerator, getOutputDir, getQuickInfo, getWriter, outputDirTipText, setFilenameGenerator, setOutputDir, setWriter, writerTipText

      • Methods inherited from class adams.flow.transformer.AbstractTransformer

        backupState, currentInput, execute, hasInput, hasPendingOutput, input, output, postExecute, restoreState, wrapUp

      • Methods inherited from class adams.flow.core.AbstractActor

        annotationsTipText, canInspectOptions, canPerformSetUpCheck, cleanUp, compareTo, configureLogger, destroy, equals, finalUpdateVariables, findVariables, findVariables, forceVariables, forCommandLine, forName, forName, getAdditionalInformation, getAnnotations, getDefaultName, getDetectedVariables, getErrorHandler, getFlowActors, getFlowExecutionListeningSupporter, getFullName, getName, getNextSibling, getParent, getParentComponent, getPreviousSibling, getRoot, getScopeHandler, getSilent, getSkip, getStopFlowOnError, getStopMessage, getStorageHandler, getVariables, handleError, handleException, hasErrorHandler, hasStopMessage, index, initialize, isBackedUp, isExecuted, isExecuting, isFinished, isHeadless, isStopped, nameTipText, performSetUpChecks, performVariableChecks, preExecute, pruneBackup, pruneBackup, reset, setAnnotations, setErrorHandler, setName, setParent, setSilent, setSkip, setStopFlowOnError, setUp, setVariables, shallowCopy, shallowCopy, silentTipText, sizeOf, skipTipText, stopExecution, stopExecution, stopFlowOnErrorTipText, updateDetectedVariables, updatePrefix, updateVariables, variableChanged

      • Methods inherited from class adams.core.option.AbstractOptionHandler

        cleanUpOptions, finishInit, getDefaultLoggingLevel, getOptionManager, loggingLevelTipText, newOptionManager, setLoggingLevel, toCommandLine, toString

      • Methods inherited from class adams.core.logging.LoggingObject

        getLogger, getLoggingLevel, initializeLogging, isLoggingEnabled

      • Methods inherited from interface adams.flow.core.Actor

        cleanUp, compareTo, destroy, equals, findVariables, getAnnotations, getDefaultName, getDetectedVariables, getErrorHandler, getFlowExecutionListeningSupporter, getFullName, getName, getNextSibling, getParent, getParentComponent, getPreviousSibling, getRoot, getScopeHandler, getSilent, getSkip, getStopFlowOnError, getStopMessage, getStorageHandler, getVariables, handleError, hasErrorHandler, hasStopMessage, index, isExecuted, isFinished, isHeadless, isStopped, setAnnotations, setErrorHandler, setName, setParent, setSilent, setSkip, setStopFlowOnError, setUp, setVariables, shallowCopy, shallowCopy, sizeOf, stopExecution, stopExecution, toCommandLine, variableChanged

      • Methods inherited from interface adams.core.AdditionalInformationHandler

        getAdditionalInformation

      • Methods inherited from interface adams.core.logging.LoggingLevelHandler

        getLoggingLevel, setLoggingLevel

      • Methods inherited from interface adams.core.logging.LoggingSupporter

        getLogger, isLoggingEnabled

      • Methods inherited from interface adams.core.option.OptionHandler

        cleanUpOptions, getOptionManager

      • Methods inherited from interface adams.core.VariablesInspectionHandler

        canInspectOptions

    • Constructor Detail

      • SampleDataFileWriter

        public SampleDataFileWriter()

    • Method Detail

      • globalInfo

        public String globalInfo()
        Returns a string describing the object.
        Specified by:
        globalInfo in interface adams.core.GlobalInfoSupporter
        Specified by:
        globalInfo in class adams.core.option.AbstractOptionHandler
        Returns:
        a description suitable for displaying in the gui

      • getDefaultWriter

        protected adams.data.io.output.AbstractReportWriter<SampleData> getDefaultWriter()
        Returns the default writer.
        Specified by:
        getDefaultWriter in class adams.flow.transformer.AbstractReportFileWriter<SampleData>
        Returns:
        the writer

      • accepts

        public Class[] accepts()
        Returns the class that the consumer accepts.
        Specified by:
        accepts in interface adams.flow.core.InputConsumer
        Specified by:
        accepts in class adams.flow.transformer.AbstractReportFileWriter<SampleData>
        Returns:
        the type of report