Package adams.data.io.input

Class AniMLSpectrumReader

java.lang.Object

adams.core.logging.LoggingObject

adams.core.logging.CustomLoggingLevelObject

adams.core.option.AbstractOptionHandler

adams.data.io.input.AbstractDataContainerReader<Spectrum>

adams.data.io.input.AbstractSpectrumReader

adams.data.io.input.AbstractJCampSpectrumReader

adams.data.io.input.AniMLSpectrumReader

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.AbstractDataContainerReader>, adams.core.SizeOfHandler, adams.core.Stoppable, Serializable, Comparable

public class AniMLSpectrumReader
extends AbstractJCampSpectrumReader

Reads spectra in AniML (Analytical Information Markup Language) format.

For more information see:
http://animl.sourceforge.net/

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: .
 

-create-dummy-report (property: createDummyReport)
    If true, then a dummy report is created if none present.
 

-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
 

Author:

fracpete (fracpete at waikato dot ac dot nz)

See Also:

Serialized Form

Field Summary

Fields inherited from class adams.data.io.input.AbstractJCampSpectrumReader

FIELD_ABSORBANCE, FIELD_CONTINUOUS, FIELD_DATACLASS, FIELD_DATATYPE, FIELD_DATE, FIELD_HZTOPPM, FIELD_INCREASING, FIELD_JCAMPDX, FIELD_OBSERVEDFREQ, FIELD_ORIGIN, FIELD_OWNER, FIELD_PATHLENGTH, FIELD_TIME, FIELD_TITLE, FIELD_TRANSMITTANCE, FIELD_XFACTOR, FIELD_XUNITS, FIELD_YFACTOR, FIELD_YUNITS, m_UseFilenameAsID

Fields inherited from class adams.data.io.input.AbstractSpectrumReader

m_Format, m_Instrument, m_KeepFormat, m_Stopped, m_UseAbsoluteSource, OPTION_OUTPUTDIR

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

Constructor Summary

Constructors

Constructor	Description
AniMLSpectrumReader()

Method Summary

Modifier and Type	Method	Description
String	getFormatDescription()	Returns a string describing the format (used in the file chooser).
String[]	getFormatExtensions()	Returns the extension(s) of the format.
String	globalInfo()	Returns a string describing the object.
static void	main(String[] args)	Runs the reader from the command-line.

Methods inherited from class adams.data.io.input.AbstractJCampSpectrumReader

defineOptions, getUseFilenameAsID, initSampleData, readData, setUseFilenameAsID, useFilenameAsIDTipText

Methods inherited from class adams.data.io.input.AbstractSpectrumReader

checkData, createDummyReport, formatTipText, getDefaultFormat, getDefaultInstrument, getDefaultKeepFormat, getDefaultUseAbsoluteSource, getFormat, getInstrument, getKeepFormat, getReaders, getUseAbsoluteSource, instrumentTipText, keepFormatTipText, postProcessData, runReader, setFormat, setInstrument, setKeepFormat, setUseAbsoluteSource, stopExecution, useAbsoluteSourceTipText

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

cleanUp, compareTo, 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 class java.lang.Object

clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface adams.core.logging.LoggingLevelHandler

getLoggingLevel

Constructor Detail

AniMLSpectrumReader

public AniMLSpectrumReader()

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!)

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