Package adams.data.io.output

Class SimpleHeatmapWriter

  • 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.AbstractDataContainerWriter>, adams.core.SizeOfHandler, adams.data.CompressionSupporter, Serializable, Comparable
    public class SimpleHeatmapWriter
extends AbstractHeatmapWriter
implements adams.data.CompressionSupporter
    Writer that stores heatmaps in a simple CSV-like format. 

    -logging-level <OFF|SEVERE|WARNING|INFO|CONFIG|FINE|FINER|FINEST> (property: loggingLevel)
    The logging level for outputting errors and debugging output.
    default: WARNING
 
    -output <adams.core.io.PlaceholderFile> (property: output)
    The file to write the container to.
    default: ${TMP}/out.tmp
 
    -num-decimals <int> (property: numDecimals)
    The number of decimals to output after the decimal point (at most).
    default: 6
    minimum: 0
    maximum: 16
 
    -output-meta-data <boolean> (property: outputMetaData)
    If set to true, the meta data gets stored in the file as well (as comment
    ).
    default: true
 
    -use-compression <boolean> (property: useCompression)
    If enabled, the heatmap is compressed using GZIP and appending '.gz' to 
    the filename.
    default: false
    Version:
    $Revision: 2018 $
    Author:
    fracpete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected int m_NumDecimals
      the number of decimals to use.
      protected boolean m_OutputMetaData
      whether to output the meta data as well.
      protected boolean m_UseCompression
      whether to use compression.

      • 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.
      int getNumDecimals()
      Returns the number of decimals to output after the decimal point.
      boolean getOutputMetaData()
      Returns whether to output the meta data as well.
      boolean getUseCompression()
      Returns whether compression is in use.
      String globalInfo()
      Returns a string describing the object.
      protected void initialize()
      Initializes the members.
      String numDecimalsTipText()
      Returns the tip text for this property.
      String outputMetaDataTipText()
      Returns the tip text for this property.
      void setNumDecimals​(int value)
      Sets the number of decimals to output after the decimal point.
      void setOutputMetaData​(boolean value)
      Sets whether to output the meta data as well.
      void setUseCompression​(boolean value)
      Sets whether to use compression.
      String useCompressionTipText()
      Returns the tip text for this property.
      protected boolean write​(List<Heatmap> data, BufferedWriter writer, boolean report)
      Writes its content with the given writer.
      protected boolean write​(List<Heatmap> data, String filename, boolean report)
      Writes its content to the given file.
      protected boolean writeData​(List<Heatmap> data)
      Performs the actual writing.

      • 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.Destroyable

        destroy

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

        getLoggingLevel

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

        cleanUpOptions, getOptionManager, toCommandLine

    • Field Detail

      • m_NumDecimals

        protected int m_NumDecimals
        the number of decimals to use.

      • m_OutputMetaData

        protected boolean m_OutputMetaData
        whether to output the meta data as well.

      • m_UseCompression

        protected boolean m_UseCompression
        whether to use compression.

    • Constructor Detail

      • SimpleHeatmapWriter

        public SimpleHeatmapWriter()

    • 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.io.output.AbstractDataContainerWriter<Heatmap>

      • 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!)

      • setNumDecimals

        public void setNumDecimals​(int value)
        Sets the number of decimals to output after the decimal point.
        Parameters:
        value - the number of decimals

      • getNumDecimals

        public int getNumDecimals()
        Returns the number of decimals to output after the decimal point.
        Returns:
        the number of decimals

      • numDecimalsTipText

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

      • setOutputMetaData

        public void setOutputMetaData​(boolean value)
        Sets whether to output the meta data as well.
        Parameters:
        value - if true then the meta data gets output as well

      • getOutputMetaData

        public boolean getOutputMetaData()
        Returns whether to output the meta data as well.
        Returns:
        true if the meta data is output as well

      • outputMetaDataTipText

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

      • setUseCompression

        public void setUseCompression​(boolean value)
        Sets whether to use compression.
        Specified by:
        setUseCompression in interface adams.data.CompressionSupporter
        Parameters:
        value - true if to use compression

      • getUseCompression

        public boolean getUseCompression()
        Returns whether compression is in use.
        Specified by:
        getUseCompression in interface adams.data.CompressionSupporter
        Returns:
        true if compression is used

      • useCompressionTipText

        public String useCompressionTipText()
        Returns the tip text for this property.
        Specified by:
        useCompressionTipText in interface adams.data.CompressionSupporter
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • initialize

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

      • write

        protected boolean write​(List<Heatmap> data,
                        BufferedWriter writer,
                        boolean report)
        Writes its content with the given writer.
        Parameters:
        data - the spectra to write
        writer - the writer to use
        report - whether to output the report as well
        Returns:
        true if successfully written

      • write

        protected boolean write​(List<Heatmap> data,
                        String filename,
                        boolean report)
        Writes its content to the given file.
        Parameters:
        data - the spectra to write
        filename - the file to write to
        report - whether to output the report as well
        Returns:
        true if successfully written

      • 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