Package adams.data.io.input

Class FloatMatrixHeatmapReader

  • 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.input.DataContainerReader>, adams.core.SizeOfHandler, adams.data.io.input.DataContainerReader<Heatmap>, Serializable, Comparable
    public class FloatMatrixHeatmapReader
extends AbstractHeatmapReader
    Reads heat map files (2-D array of single precision floating point numbers).

    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
 
    -input <adams.core.io.PlaceholderFile> (property: input)
    The file to read and turn into a container.
    default: ${CWD}
 
    -create-dummy-report (property: createDummyReport)
    If true, then a dummy report is created if none present.
 
    -height <int> (property: height)
    The height of the heatmap.
    default: 240
    minimum: 1
 
    -width <int> (property: width)
    The width of the heatmap.
    default: 320
    minimum: 1
    Version:
    $Revision$
    Author:
    fracpete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected int m_Height
      the height of the heatmap.
      protected int m_Width
      the width of the heatmap.

      • Fields inherited from class adams.data.io.input.AbstractDataContainerReader

        m_CreateDummyReport, m_Input, m_InputIsFile, m_Processed, m_ReadData

      • 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.
      protected int getDefaultHeight()
      Returns the default height of the heatmap.
      protected int getDefaultWidth()
      Returns the default width of the heatmap.
      String getFormatDescription()
      Returns a string describing the format (used in the file chooser).
      String[] getFormatExtensions()
      Returns the extension(s) of the format.
      int getHeight()
      Returns the height of the heatmap.
      int getWidth()
      Returns the width of the heatmap.
      String globalInfo()
      Returns a string describing the object.
      String heightTipText()
      Returns the tip text for this property.
      protected void readData()
      Performs the actual reading.
      void setHeight​(int value)
      Sets the height of the heatmap.
      void setWidth​(int value)
      Sets the width of the heatmap.
      String widthTipText()
      Returns the tip text for this property.

      • Methods inherited from class adams.data.io.input.AbstractDataContainerReader

        checkData, cleanUp, compareTo, createDummyReport, createDummyReportTipText, destroy, doRead, equals, getAdditionalInformation, getCreateDummyReport, getDefaultFormatExtension, getInput, initialize, inputTipText, isInputFile, read, reset, setCreateDummyReport, setInput, 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

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

        cleanUpOptions, getOptionManager, toCommandLine

    • Field Detail

      • m_Height

        protected int m_Height
        the height of the heatmap.

      • m_Width

        protected int m_Width
        the width of the heatmap.

    • Constructor Detail

      • FloatMatrixHeatmapReader

        public FloatMatrixHeatmapReader()

    • 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 AbstractHeatmapReader

      • getDefaultHeight

        protected int getDefaultHeight()
        Returns the default height of the heatmap.
        Returns:
        the default height

      • setHeight

        public void setHeight​(int value)
        Sets the height of the heatmap.
        Parameters:
        value - the height

      • getHeight

        public int getHeight()
        Returns the height of the heatmap.
        Returns:
        the height

      • heightTipText

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

      • getDefaultWidth

        protected int getDefaultWidth()
        Returns the default width of the heatmap.
        Returns:
        the default width

      • setWidth

        public void setWidth​(int value)
        Sets the width of the heatmap.
        Parameters:
        value - the width

      • getWidth

        public int getWidth()
        Returns the width of the heatmap.
        Returns:
        the width

      • widthTipText

        public String widthTipText()
        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.input.AbstractDataContainerReader<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.input.AbstractDataContainerReader<Heatmap>
        Returns:
        the extension(s) (without the dot!)

      • readData

        protected void readData()
        Performs the actual reading.
        Specified by:
        readData in class adams.data.io.input.AbstractDataContainerReader<Heatmap>