Package adams.data.io.input

Class JCampDX2SpectrumReader

  • 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.core.Stoppable, adams.data.io.input.DataContainerReader<Spectrum>, adams.data.io.input.StreamableDataContainerReader<Spectrum>, adams.data.io.input.StreamableTextBasedDataContainerReader<Spectrum>, Serializable, Comparable
    public class JCampDX2SpectrumReader
extends AbstractTextBasedSpectrumReader
implements adams.data.io.input.StreamableTextBasedDataContainerReader<Spectrum>
    Reads spectra in JCamp-DX format.

    For more information see:
    http://www.jcamp-dx.org/ 

    -logging-level <OFF|SEVERE|WARNING|INFO|CONFIG|FINE|FINER|FINEST> (property: loggingLevel)
    The logging level for outputting errors and debugging output.
    default: WARNING
 
    -input <adams.core.io.PlaceholderFile> (property: input)
    The file to read and turn into a container.
    default: ${CWD}
 
    -create-dummy-report <boolean> (property: createDummyReport)
    If true, then a dummy report is created if none present.
    default: false
 
    -instrument <java.lang.String> (property: instrument)
    The name of the instrument that generated the spectra (if not already present 
    in data).
    default: unknown
 
    -format <java.lang.String> (property: format)
    The data format string.
    default: NIR
 
    -keep-format <boolean> (property: keepFormat)
    If enabled the format obtained from the file is not replaced by the format 
    defined here.
    default: false
 
    -use-absolute-source <boolean> (property: useAbsoluteSource)
    If enabled the source report field stores the absolute file name rather 
    than just the name.
    default: false
 
    -mode <STRICT|RELAXED> (property: mode)
    The reader mode.
    default: STRICT
 
    -validate <boolean> (property: validate)
    If enabled, the parser is validating the input.
    default: false
 
    -add-raw-metadata <boolean> (property: addRawMetaData)
    If enabled, the raw meta-data in the file is added to the report as well.
    default: false
    Author:
    fracpete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Detail

      • m_AddRawMetaData

        protected boolean m_AddRawMetaData
        whether to add the raw meta-data.

      • m_Validate

        protected boolean m_Validate
        whether the reader validates.

      • m_UseFilenameAsID

        protected boolean m_UseFilenameAsID
        whether to use the filename as ID.

    • Constructor Detail

      • JCampDX2SpectrumReader

        public JCampDX2SpectrumReader()

    • 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 AbstractSpectrumReader

      • modeTipText

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

      • setValidate

        public void setValidate​(boolean value)
        Sets whether to use a validating parser.
        Parameters:
        value - true if to validate

      • getValidate

        public boolean getValidate()
        Returns whether to use a validating parser.
        Returns:
        true if to validate

      • validateTipText

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

      • setAddRawMetaData

        public void setAddRawMetaData​(boolean value)
        Sets whether to add the raw meta-data to the report.
        Parameters:
        value - true if to add

      • getAddRawMetaData

        public boolean getAddRawMetaData()
        Returns whether to add the raw meta-data to the report.
        Returns:
        true if added

      • addRawMetaDataTipText

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

      • setUseFilenameAsID

        public void setUseFilenameAsID​(boolean value)
        Sets whether to use the filename as ID.
        Parameters:
        value - true if to use filename

      • getUseFilenameAsID

        public boolean getUseFilenameAsID()
        Returns whether to use the filename as ID.
        Returns:
        true if to use filename

      • useFilenameAsIDTipText

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

      • main

        public static void main​(String[] args)
        Runs the reader from the command-line. If the option AbstractSpectrumReader.OPTION_OUTPUTDIR is specified then the read spectra get output as .spec files in that directory.
        Parameters:
        args - the command-line options to use