Package adams.data.io.output

Class JCampDX2SpectrumWriter

  • 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, Serializable, Comparable
    public class JCampDX2SpectrumWriter
extends AbstractSpectrumWriter
    Writer that stores spectrums in the simple CSV format.

    Valid options are: 

    -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
 
    -output-sample-data <boolean> (property: outputSampleData)
    If set to true, the sample data gets stored in the file as well (as comment
    ).
    default: false
    Version:
    $Revision: 2242 $
    Author:
    fracpete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static String COMMENT
      the comments.
      protected boolean m_OutputSampleData
      whether to output the sample data as well.

      • 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
      protected void checkData​(List<Spectrum> data)
      Writer can only write single chromatograms.
      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.
      boolean getOutputSampleData()
      Returns whether to output eh sample data as well.
      String globalInfo()
      Returns a string describing the object.
      protected void initialize()
      Initializes the members.
      String outputSampleDataTipText()
      Returns the tip text for this property.
      void setOutputSampleData​(boolean value)
      Sets whether to output the sample data as well.
      protected boolean writeData​(List<Spectrum> 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.logging.LoggingLevelHandler

        getLoggingLevel

    • Field Detail

      • m_OutputSampleData

        protected boolean m_OutputSampleData
        whether to output the sample data as well.

    • Constructor Detail

      • JCampDX2SpectrumWriter

        public JCampDX2SpectrumWriter()

    • 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<Spectrum>

      • 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<Spectrum>
        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<Spectrum>
        Returns:
        the extension(s) (without the dot!)

      • initialize

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

      • setOutputSampleData

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

      • getOutputSampleData

        public boolean getOutputSampleData()
        Returns whether to output eh sample data as well.
        Returns:
        true if the sample data is output as well

      • outputSampleDataTipText

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

      • checkData

        protected void checkData​(List<Spectrum> data)
        Writer can only write single chromatograms.
        Overrides:
        checkData in class adams.data.io.output.AbstractDataContainerWriter<Spectrum>
        Parameters:
        data - the data to write

      • writeData

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