Package adams.data.io.input

Class AbstractJCampSpectrumReader

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

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>, Serializable, Comparable

Direct Known Subclasses:

AniMLSpectrumReader, CMLSpectrumReader, JCampDXSpectrumReader

public abstract class AbstractJCampSpectrumReader
extends AbstractSpectrumReader

Ancestor for JCamp spectrum formats.

Version:

$Revision: 1905 $

Author:

fracpete (fracpete at waikato dot ac dot nz)

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static String	FIELD_ABSORBANCE	JCamp field: Absorbance.
static String	FIELD_CONTINUOUS	JCamp field: Continuous.
static String	FIELD_DATACLASS	JCamp field: DataClass.
static String	FIELD_DATATYPE	JCamp field: DataType.
static String	FIELD_DATE	JCamp field: Date.
static String	FIELD_HZTOPPM	JCamp field: HZtoPPM.
static String	FIELD_INCREASING	JCamp field: Increasing.
static String	FIELD_JCAMPDX	JCamp field: Jcampdx.
static String	FIELD_OBSERVEDFREQ	JCamp field: ObservedFreq.
static String	FIELD_ORIGIN	JCamp field: Origin.
static String	FIELD_OWNER	JCamp field: Owner.
static String	FIELD_PATHLENGTH	JCamp field: Pathlength.
static String	FIELD_TIME	JCamp field: Time.
static String	FIELD_TITLE	JCamp field: Title.
static String	FIELD_TRANSMITTANCE	JCamp field: Transmittance.
static String	FIELD_XFACTOR	JCamp field: XFactor.
static String	FIELD_XUNITS	JCamp field: XUnits.
static String	FIELD_YFACTOR	JCamp field: YFactor.
static String	FIELD_YUNITS	JCamp field: YUnits.
protected boolean	m_UseFilenameAsID	whether to use the filename as ID.

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
AbstractJCampSpectrumReader()

Method Summary

Modifier and Type	Method	Description
void	defineOptions()	Adds options to the internal list of options.
boolean	getUseFilenameAsID()	Returns whether to use the filename as ID.
protected void	initSampleData(Map<String,String> header, SampleData report)	Initializes the sample data.
protected void	readData()	Performs the actual reading.
void	setUseFilenameAsID(boolean value)	Sets whether to use the filename as ID.
String	useFilenameAsIDTipText()	Returns the tip text for this property.

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, getFormatDescription, getFormatExtensions, getInput, initialize, inputTipText, isInputFile, read, reset, setCreateDummyReport, setInput, shallowCopy, shallowCopy

Methods inherited from class adams.core.option.AbstractOptionHandler

cleanUpOptions, finishInit, getDefaultLoggingLevel, getOptionManager, globalInfo, 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

Methods inherited from interface adams.core.option.OptionHandler

cleanUpOptions, getOptionManager, toCommandLine

Field Detail

FIELD_CONTINUOUS

public static final String FIELD_CONTINUOUS

JCamp field: Continuous.

See Also:

Constant Field Values

FIELD_DATACLASS

public static final String FIELD_DATACLASS

JCamp field: DataClass.

See Also:

Constant Field Values

FIELD_DATATYPE

public static final String FIELD_DATATYPE

JCamp field: DataType.

See Also:

Constant Field Values

FIELD_HZTOPPM

public static final String FIELD_HZTOPPM

JCamp field: HZtoPPM.

See Also:

Constant Field Values

FIELD_INCREASING

public static final String FIELD_INCREASING

JCamp field: Increasing.

See Also:

Constant Field Values

FIELD_JCAMPDX

public static final String FIELD_JCAMPDX

JCamp field: Jcampdx.

See Also:

Constant Field Values

FIELD_OBSERVEDFREQ

public static final String FIELD_OBSERVEDFREQ

JCamp field: ObservedFreq.

See Also:

Constant Field Values

FIELD_ORIGIN

public static final String FIELD_ORIGIN

JCamp field: Origin.

See Also:

Constant Field Values

FIELD_OWNER

public static final String FIELD_OWNER

JCamp field: Owner.

See Also:

Constant Field Values

FIELD_TITLE

public static final String FIELD_TITLE

JCamp field: Title.

See Also:

Constant Field Values

FIELD_XFACTOR

public static final String FIELD_XFACTOR

JCamp field: XFactor.

See Also:

Constant Field Values

FIELD_XUNITS

public static final String FIELD_XUNITS

JCamp field: XUnits.

See Also:

Constant Field Values

FIELD_YFACTOR

public static final String FIELD_YFACTOR

JCamp field: YFactor.

See Also:

Constant Field Values

FIELD_YUNITS

public static final String FIELD_YUNITS

JCamp field: YUnits.

See Also:

Constant Field Values

FIELD_PATHLENGTH

public static final String FIELD_PATHLENGTH

JCamp field: Pathlength.

See Also:

Constant Field Values

FIELD_TRANSMITTANCE

public static final String FIELD_TRANSMITTANCE

JCamp field: Transmittance.

See Also:

Constant Field Values

FIELD_ABSORBANCE

public static final String FIELD_ABSORBANCE

JCamp field: Absorbance.

See Also:

Constant Field Values

FIELD_DATE

public static final String FIELD_DATE

JCamp field: Date.

See Also:

Constant Field Values

FIELD_TIME

public static final String FIELD_TIME

JCamp field: Time.

See Also:

Constant Field Values

m_UseFilenameAsID

protected boolean m_UseFilenameAsID

whether to use the filename as ID.

Constructor Detail

AbstractJCampSpectrumReader

public AbstractJCampSpectrumReader()

Method Detail

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

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.

initSampleData

protected void initSampleData(Map<String,String> header,
                              SampleData report)

Initializes the sample data.

Parameters:

header - the header table to use

report - the sample data to initialize

readData

protected void readData()

Performs the actual reading.

Specified by:

readData in class adams.data.io.input.AbstractDataContainerReader<Spectrum>