Package adams.data.io.output

Class SpreadSheetHeatmapWriter

  • All Implemented Interfaces:
    adams.core.AdditionalInformationHandler, adams.core.CleanUpHandler, adams.core.Destroyable, adams.core.GlobalInfoSupporter, adams.core.io.FileFormatHandler, adams.core.logging.LoggingLevelHandler, adams.core.logging.LoggingSupporter, adams.core.option.OptionHandler, adams.core.ShallowCopySupporter<adams.data.io.output.DataContainerWriter>, adams.core.SizeOfHandler, adams.data.io.output.DataContainerWriter<Heatmap>, Serializable, Comparable
    public class SpreadSheetHeatmapWriter
extends AbstractHeatmapWriter
    Writes heat map files using a spreadsheet format.

    Valid options are: 

    -D <int> (property: debugLevel)
    The greater the number the more additional info the scheme may output to 
    the console (0 = off).
    default: 0
    minimum: 0
 
    -output <adams.core.io.PlaceholderFile> (property: output)
    The file to write the container to.
    default: ${TMP}/out.tmp
 
    -writer <adams.data.io.output.AbstractSpreadSheetWriter> (property: writer)
    The spreadsheet writer to use for writing the heatmap data.
    default: adams.data.io.output.CsvSpreadSheetWriter
    Version:
    $Revision$
    Author:
    fracpete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected adams.data.io.output.SpreadSheetWriter m_Writer
      the spreadsheet writer to use.

      • Fields inherited from class adams.data.io.output.AbstractDataContainerWriter

        m_Output, m_OutputIsFile

      • 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 getFormatDescription()
      Returns a string describing the format (used in the file chooser).
      String[] getFormatExtensions()
      Returns the extension(s) of the format.
      adams.data.io.output.SpreadSheetWriter getWriter()
      Returns the spreadsheet writer in use.
      String globalInfo()
      Returns a string describing the object.
      protected void initialize()
      Initializes the members.
      void setWriter​(adams.data.io.output.SpreadSheetWriter value)
      Sets the spreadsheet writer to use.
      protected boolean writeData​(List<Heatmap> data)
      Performs the actual writing.
      String writerTipText()
      Returns the tip text for this property.

      • Methods inherited from class adams.data.io.output.AbstractDataContainerWriter

        cleanUp, compareTo, destroy, equals, forCommandLine, forName, getAdditionalInformation, getDefaultFormatExtension, getOutput, isOutputFile, outputTipText, reset, setOutput, shallowCopy, shallowCopy, write, write

      • 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

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

        cleanUpOptions, getOptionManager, toCommandLine

    • Field Detail

      • m_Writer

        protected adams.data.io.output.SpreadSheetWriter m_Writer
        the spreadsheet writer to use.

    • Constructor Detail

      • SpreadSheetHeatmapWriter

        public SpreadSheetHeatmapWriter()

    • 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

      • initialize

        protected void initialize()
        Initializes the members.
        Overrides:
        initialize in class adams.core.option.AbstractOptionHandler

      • 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.io.output.AbstractDataContainerWriter<Heatmap>

      • setWriter

        public void setWriter​(adams.data.io.output.SpreadSheetWriter value)
        Sets the spreadsheet writer to use.
        Parameters:
        value - the writer

      • getWriter

        public adams.data.io.output.SpreadSheetWriter getWriter()
        Returns the spreadsheet writer in use.
        Returns:
        the writer

      • writerTipText

        public String writerTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • getFormatDescription

        public String getFormatDescription()
        Returns a string describing the format (used in the file chooser).
        Specified by:
        getFormatDescription in interface adams.core.io.FileFormatHandler
        Specified by:
        getFormatDescription in class adams.data.io.output.AbstractDataContainerWriter<Heatmap>
        Returns:
        a description suitable for displaying in the file chooser

      • getFormatExtensions

        public String[] getFormatExtensions()
        Returns the extension(s) of the format.
        Specified by:
        getFormatExtensions in interface adams.core.io.FileFormatHandler
        Specified by:
        getFormatExtensions in class adams.data.io.output.AbstractDataContainerWriter<Heatmap>
        Returns:
        the extension(s) (without the dot!)

      • writeData

        protected boolean writeData​(List<Heatmap> data)
        Performs the actual writing.
        Specified by:
        writeData in class adams.data.io.output.AbstractDataContainerWriter<Heatmap>
        Parameters:
        data - the data to write
        Returns:
        true if successfully written