org.expasy.mzjava.proteomics.io.ms.spectrum

Class SptxtWriter

java.lang.Object

org.expasy.mzjava.proteomics.io.ms.spectrum.AbstractSptxtWriter

org.expasy.mzjava.proteomics.io.ms.spectrum.SptxtWriter

public class SptxtWriter
extends AbstractSptxtWriter

Write PeptideSpectrums in sptxt format.

Author:

nikitin

Constructor Summary

Constructors

Constructor and Description
SptxtWriter(File file, boolean append, PeakList.Precision precision)
SptxtWriter(Writer writer, PeakList.Precision precision)

Method Summary

Methods

Modifier and Type	Method and Description
protected String	formatAnnotations(int peakIndex, PeakList<? extends PeakAnnotation> peakList)
void	setMaxAnnotationToWrite(int maxAnnotations)
void	write(PeptideConsensusSpectrum spectrum)
void	write(PeptideSpectrum spectrum)
protected void	writeLibId(PeakList peakList, Peptide peptide, Writer writer)

Methods inherited from class org.expasy.mzjava.proteomics.io.ms.spectrum.AbstractSptxtWriter

close, formatIntensity, formatMz, setIntensityFormat, setMzFormat, write, writeComment, writeName, writePeaks

Methods inherited from class java.lang.Object

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

Constructor Detail

SptxtWriter

public SptxtWriter(Writer writer,
           PeakList.Precision precision)

SptxtWriter

public SptxtWriter(File file,
           boolean append,
           PeakList.Precision precision)
            throws IOException

Throws:

IOException

Method Detail

write

public void write(PeptideSpectrum spectrum)
           throws IOException

Throws:

IOException

write

public void write(PeptideConsensusSpectrum spectrum)
           throws IOException

Throws:

IOException

formatAnnotations

protected String formatAnnotations(int peakIndex,
                       PeakList<? extends PeakAnnotation> peakList)
                            throws IOException

Specified by:

formatAnnotations in class AbstractSptxtWriter

Throws:

IOException

writeLibId

protected void writeLibId(PeakList peakList,
              Peptide peptide,
              Writer writer)
                   throws IOException

Specified by:

writeLibId in class AbstractSptxtWriter

Throws:

IOException

setMaxAnnotationToWrite

public void setMaxAnnotationToWrite(int maxAnnotations)