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

Class MgfWriter

java.lang.Object

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

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

public class MgfWriter
extends AbstractMgfWriter<PeakAnnotation,MsnSpectrum,MgfParameters>

MGF Writer

Version:

1.0

Author:

nikitin, Oliver Horlacher

Nested Class Summary

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

AbstractMgfWriter.Parameters

Constructor Summary

Constructors

Constructor and Description
MgfWriter(File file, MgfParameters parameters)
MgfWriter(File file, PeakList.Precision precision)
MgfWriter(Writer writer, MgfParameters parameters)
MgfWriter(Writer writer, PeakList.Precision precision)

Method Summary

Methods

Modifier and Type	Method and Description
protected int[]	extractChargeList(PeakList peakList, MsnSpectrum metaData)
protected List<RetentionTime>	extractRetentionTime(MsnSpectrum spectrum)
protected List<ScanNumber>	extractScanNumbers(MsnSpectrum spectrum)
protected String	extractTitle(MsnSpectrum spectrum)
void	write(MsnSpectrum peakList)
protected void	writeMs1Header(MgfParameters parameters, Writer writer)

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

close, writeCharge, writeComment, writeMs2, writeMs2Header, writePeakAnnotations, writePeaks, writePepmass, writeRtInSeconds, writeScans, writeTitle

Methods inherited from class java.lang.Object

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

Constructor Detail

MgfWriter

public MgfWriter(Writer writer,
         PeakList.Precision precision)
          throws IOException

Throws:

IOException

MgfWriter

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

Throws:

IOException

MgfWriter

public MgfWriter(Writer writer,
         MgfParameters parameters)
          throws IOException

Throws:

IOException

MgfWriter

public MgfWriter(File file,
         MgfParameters parameters)
          throws IOException

Throws:

IOException

Method Detail

write

public void write(MsnSpectrum peakList)
           throws IOException

Throws:

IOException

writeMs1Header

protected void writeMs1Header(MgfParameters parameters,
                  Writer writer)
                       throws IOException

Overrides:

writeMs1Header in class AbstractMgfWriter<PeakAnnotation,MsnSpectrum,MgfParameters>

Throws:

IOException

extractTitle

protected String extractTitle(MsnSpectrum spectrum)

Specified by:

extractTitle in class AbstractMgfWriter<PeakAnnotation,MsnSpectrum,MgfParameters>

extractScanNumbers

protected List<ScanNumber> extractScanNumbers(MsnSpectrum spectrum)

Specified by:

extractScanNumbers in class AbstractMgfWriter<PeakAnnotation,MsnSpectrum,MgfParameters>

extractRetentionTime

protected List<RetentionTime> extractRetentionTime(MsnSpectrum spectrum)

Specified by:

extractRetentionTime in class AbstractMgfWriter<PeakAnnotation,MsnSpectrum,MgfParameters>

extractChargeList

protected int[] extractChargeList(PeakList peakList,
                      MsnSpectrum metaData)

Specified by:

extractChargeList in class AbstractMgfWriter<PeakAnnotation,MsnSpectrum,MgfParameters>