org.expasy.mzjava.core.io.ms.spectrum

Class MgfReader

java.lang.Object

org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader<A,S>

org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader<PeakAnnotation,MsnSpectrum>

org.expasy.mzjava.core.io.ms.spectrum.MgfReader

All Implemented Interfaces:

IterativeReader<MsnSpectrum>

public class MgfReader
extends AbstractMgfReader<PeakAnnotation,MsnSpectrum>

Author:

fnikitin, Oliver Horlacher

Nested Class Summary

Nested classes/interfaces inherited from class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader

AbstractMsReader.ParseContext

Field Summary

Fields inherited from class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader

acceptUnsortedSpectra, precision

Fields inherited from interface org.expasy.mzjava.core.io.IterativeReader

EMPTY_READER

Constructor Summary

Constructors

Constructor and Description
MgfReader(File file, PeakList.Precision precision)
MgfReader(File file, PeakList.Precision precision, PeakProcessorChain<PeakAnnotation> processorChain)
MgfReader(Reader reader, URI spectraSource, PeakList.Precision precision)

Method Summary

Methods

Modifier and Type	Method and Description
void	addTitleParser(TitleParser parser)
protected MsnSpectrum	newSpectrum(AbstractMsReader.ParseContext context, PeakList.Precision precision) Create a new spectrum.
MsnSpectrum	next() Overridden so that the compiler knows that MsnSpectra are returned by next().
protected boolean	parseTitleTag(String value, MsnSpectrum spectrum) Parse the line that starts with a TITLE tag.
protected void	setRetentionTimes(MsnSpectrum spectrum, RetentionTimeList retentionTimeList) Add the retention times contained in the retentionTimeList to the spectrum.
protected void	setScanNumbers(MsnSpectrum spectrum, ScanNumberList scanNumbers) Add the scan numbers contained in the scanNumbers to the spectrum.

Methods inherited from class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader

getExtension, handleBeginIonLine, handleComment, handleEndIonLine, handleIntermediaryLine, handlePeakLine, handleTagLine, handleUnknownLine, parseChargeTag, parseHeader, parseNextEntry, parseNextMs1Entry, parseNextMs2Entry, parsePepMassTag, parseRetentionTimeTag, parseScanTag, parseUnknownTag, skipIntermediaryLine

Methods inherited from class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader

acceptUnsortedSpectra, addPeaksToSpectrum, addPeakToSpectrum, close, getContext, getHeader, hasNext, init

Methods inherited from class java.lang.Object

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

Constructor Detail

MgfReader

public MgfReader(File file,
         PeakList.Precision precision)
          throws IOException

Throws:

IOException

MgfReader

public MgfReader(File file,
         PeakList.Precision precision,
         PeakProcessorChain<PeakAnnotation> processorChain)
          throws IOException

Throws:

IOException

MgfReader

public MgfReader(Reader reader,
         URI spectraSource,
         PeakList.Precision precision)
          throws IOException

Throws:

IOException

Method Detail

addTitleParser

public void addTitleParser(TitleParser parser)

newSpectrum

protected MsnSpectrum newSpectrum(AbstractMsReader.ParseContext context,
                      PeakList.Precision precision)

Description copied from class: AbstractMgfReader

Create a new spectrum. This method allows subclasses to specify what type of spectra is read.

Specified by:

newSpectrum in class AbstractMgfReader<PeakAnnotation,MsnSpectrum>

Parameters:

context - the parse context

precision - the precision for the new spectrum

Returns:

the newly created spectrum

setRetentionTimes

protected void setRetentionTimes(MsnSpectrum spectrum,
                     RetentionTimeList retentionTimeList)

Description copied from class: AbstractMgfReader

Add the retention times contained in the retentionTimeList to the spectrum.

Specified by:

setRetentionTimes in class AbstractMgfReader<PeakAnnotation,MsnSpectrum>

Parameters:

spectrum - the spectrum that is currently being read

retentionTimeList - the retention times that were read

setScanNumbers

protected void setScanNumbers(MsnSpectrum spectrum,
                  ScanNumberList scanNumbers)

Description copied from class: AbstractMgfReader

Add the scan numbers contained in the scanNumbers to the spectrum.

Specified by:

setScanNumbers in class AbstractMgfReader<PeakAnnotation,MsnSpectrum>

Parameters:

spectrum - the spectrum that is currently being read

scanNumbers - the scan numbers that were read

parseTitleTag

protected boolean parseTitleTag(String value,
                    MsnSpectrum spectrum)

Description copied from class: AbstractMgfReader

Parse the line that starts with a TITLE tag. This uses the list of title parsers to find a parser that can parse the title. Note that the title parsed value is assign to the spectrum metadata comment by default.

Specified by:

parseTitleTag in class AbstractMgfReader<PeakAnnotation,MsnSpectrum>

Parameters:

value - the title value

spectrum - the spectrum being parsed

Returns:

true if any of the registered title parses extracted information from the title

next

public MsnSpectrum next()
                 throws IOException

Overridden so that the compiler knows that MsnSpectra are returned by next(). If this method is missing the compiler thinks Spectrum are returned

Specified by:

next in interface IterativeReader<MsnSpectrum>

Overrides:

next in class AbstractMsReader<PeakAnnotation,MsnSpectrum>

Returns:

the next element in the iteration

Throws:

IOException - if there is an io exception