Package adams.data.io.input

Class CALSpectrumReader

  • 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.StreamableBinaryDataContainerReader<Spectrum>, adams.data.io.input.StreamableDataContainerReader<Spectrum>, Serializable, Comparable
    Direct Known Subclasses:
    NIRSpectrumReader
    public class CALSpectrumReader
extends AbstractByteBasedSpectrumReader
    Reads spectra in BLGG ASC format.

    Valid options are: 

    -D (property: debug)
         If set to true, scheme may output additional info to the console.
 
    -input <java.io.File> (property: input)
         The file to read and turn into a spectrum.
         default: .
    Author:
    fracpete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Detail

      • sample_type

        protected String sample_type
        where to get sample type from. see param defs

      • sample_id

        protected String sample_id
        where to get sample id from. see param defs

      • m_start

        protected int m_start
        starting spectrum.

      • m_max

        protected int m_max
        maximum to load.

    • Constructor Detail

      • CALSpectrumReader

        public CALSpectrumReader()

    • 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

      • 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!)

      • 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

      • setMax

        public void setMax​(int value)
        Sets the nth point setting.
        Parameters:
        value - the nth point to use

      • getMax

        public int getMax()
        Returns the nth point setting.
        Returns:
        the nth point

      • maxTipText

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

      • setStart

        public void setStart​(int value)
        Sets the start point setting.
        Parameters:
        value - the nth point to use

      • getStart

        public int getStart()
        Returns the start point setting.
        Returns:
        the nth point

      • startTipText

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

      • getIdfield

        public String getIdfield()
        Get id field.
        Returns:
        id field

      • setIdfield

        public void setIdfield​(String tf)
        Set id field.
        Parameters:
        tf -

      • idfieldTipText

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

      • getTypefield

        public String getTypefield()
        Get type field.
        Returns:
        type field

      • setTypefield

        public void setTypefield​(String tf)
        Set type field.
        Parameters:
        tf -

      • typefieldTipText

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

      • getID

        protected String getID​(FossHelper.FossFields ff)
        Get SampleID.
        Parameters:
        ff - fields loaded from cal file
        Returns:
        sampleid

      • getSampleType

        protected String getSampleType​(FossHelper.FossFields ff)
        Get Sampletype.
        Parameters:
        ff - fields loaded from cal file
        Returns:
        sampletype

      • 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