Package adams.data.filter

Class HeatmapFeatureGenerator

  • Type Parameters:
    T - the type of data to filter
    All Implemented Interfaces:
    adams.core.CleanUpHandler, adams.core.Destroyable, adams.core.GlobalInfoSupporter, adams.core.logging.LoggingLevelHandler, adams.core.logging.LoggingSupporter, adams.core.option.OptionHandler, adams.core.ShallowCopySupporter<adams.data.filter.Filter>, adams.core.SizeOfHandler, adams.data.filter.Filter<Heatmap>, adams.db.DatabaseConnectionHandler, adams.db.DatabaseConnectionProvider, adams.db.DatabaseConnectionUser, Serializable, Comparable
    public class HeatmapFeatureGenerator
extends adams.data.filter.AbstractDatabaseConnectionFilter<Heatmap>
    A filter that modifies the quantitation reports of chromatograms being passed through. The supplied quantitation report filter updates/modifies the quantitation report.

    Valid options are: 

    -D (property: debug)
         If set to true, scheme may output additional info to the console.
 
    -debug-out <java.io.File> (property: debugOutputFilePrefix)
         If the file is not pointing to a directory, then the filtered data gets
         dumped to a file with a filename consisting of this prefix, the database
          ID and the extension 'chrom'.
         default: .
 
    -filter <gcms.data.quantitation.AbstractFeatureGenerator [options]> (property: filter)
         The filter to use for updating/modifying the quantitation report.
         default: gcms.data.quantitation.PassThrough -debug-out .
    Default options for gcms.data.quantitation.PassThrough (-filter/filter): 
    -D (property: debug)
         If set to true, scheme may output additional info to the console.
 
    -debug-out <java.io.File> (property: debugOutputFilePrefix)
         If the file is not pointing to a directory, then the filtered data gets
         dumped to a file with a filename consisting of this prefix, the database
          ID and the extension 'chrom'.
         default: .
    Version:
    $Revision$
    Author:
    fracpete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Nested Class Summary

      • Nested classes/interfaces inherited from class adams.data.filter.AbstractFilter

        adams.data.filter.AbstractFilter.FilterJob<T extends adams.data.container.DataContainer>

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected AbstractFeatureGenerator m_Generator
      the report filter.

      • Fields inherited from class adams.data.filter.AbstractDatabaseConnectionFilter

        m_DatabaseConnection

      • Fields inherited from class adams.data.filter.AbstractFilter

        m_DontUpdateID

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

        m_OptionManager

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

        m_Logger, m_LoggingIsEnabled, m_LoggingLevel

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void defineOptions()
      Adds options to the internal list of options.
      String generatorTipText()
      Returns the tip text for this property.
      protected adams.db.AbstractDatabaseConnection getDefaultDatabaseConnection()
      Returns the default database connection.
      AbstractFeatureGenerator getGenerator()
      Returns the current generator.
      String globalInfo()
      Returns a string describing the object.
      protected Heatmap processData​(Heatmap data)
      Performs the actual filtering.
      void setGenerator​(AbstractFeatureGenerator value)
      Sets the generator to use.
      protected void updateDatabaseConnection()
      Updates the database connection in the filter.

      • Methods inherited from class adams.data.filter.AbstractDatabaseConnectionFilter

        getDatabaseConnection, initialize, setDatabaseConnection

      • Methods inherited from class adams.data.filter.AbstractFilter

        checkData, cleanUp, compareTo, destroy, dontUpdateIDTipText, equals, filter, forCommandLine, getDontUpdateID, reset, setDontUpdateID, shallowCopy, shallowCopy

      • 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

        configureLogger, getLogger, getLoggingLevel, initializeLogging, isLoggingEnabled, sizeOf

      • 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, toCommandLine

    • Constructor Detail

      • HeatmapFeatureGenerator

        public HeatmapFeatureGenerator()

    • 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

      • defineOptions

        public void defineOptions()
        Adds options to the internal list of options.
        Specified by:
        defineOptions in interface adams.core.option.OptionHandler
        Overrides:
        defineOptions in class adams.data.filter.AbstractFilter<Heatmap>

      • getDefaultDatabaseConnection

        protected adams.db.AbstractDatabaseConnection getDefaultDatabaseConnection()
        Returns the default database connection.
        Specified by:
        getDefaultDatabaseConnection in class adams.data.filter.AbstractDatabaseConnectionFilter<Heatmap>
        Returns:
        the default database connection

      • setGenerator

        public void setGenerator​(AbstractFeatureGenerator value)
        Sets the generator to use.
        Parameters:
        value - the generator

      • generatorTipText

        public String generatorTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the gui

      • updateDatabaseConnection

        protected void updateDatabaseConnection()
        Updates the database connection in the filter.
        Overrides:
        updateDatabaseConnection in class adams.data.filter.AbstractDatabaseConnectionFilter<Heatmap>

      • processData

        protected Heatmap processData​(Heatmap data)
        Performs the actual filtering.
        Specified by:
        processData in class adams.data.filter.AbstractFilter<Heatmap>
        Parameters:
        data - the data to filter
        Returns:
        the filtered data