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

Class AbstractSptxtWriter

java.lang.Object

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

Direct Known Subclasses:

SptxtWriter

public abstract class AbstractSptxtWriter
extends Object

Version:

sqrt -1

Author:

Oliver Horlacher

Constructor Summary

Constructors

Constructor and Description
AbstractSptxtWriter(Writer writer, PeakList.Precision precision)

Method Summary

Methods

Modifier and Type	Method and Description
void	close()
protected abstract String	formatAnnotations(int peakIndex, PeakList<? extends PeakAnnotation> peakList)
protected String	formatIntensity(double intensity)
protected String	formatMz(double mz)
void	setIntensityFormat(NumberFormat intensityFormat)
void	setMzFormat(NumberFormat mzFormat)
void	write(PeakList<? extends PeakAnnotation> peakList, Peptide peptide, Collection<String> proteinAccessionNumbers)
protected void	writeComment(PeakList peakList, Peptide peptide, Writer writer, Collection<String> proteinAccessionNumbers)
protected abstract void	writeLibId(PeakList peakList, Peptide peptide, Writer writer)
protected void	writeName(PeakList peakList, Peptide peptide, Writer writer)
protected void	writePeaks(PeakList<? extends PeakAnnotation> peakList, Writer writer)

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractSptxtWriter

public AbstractSptxtWriter(Writer writer,
                   PeakList.Precision precision)

Method Detail

setMzFormat

public void setMzFormat(NumberFormat mzFormat)

setIntensityFormat

public void setIntensityFormat(NumberFormat intensityFormat)

write

public void write(PeakList<? extends PeakAnnotation> peakList,
         Peptide peptide,
         Collection<String> proteinAccessionNumbers)
           throws IOException

Throws:

IOException

writePeaks

protected void writePeaks(PeakList<? extends PeakAnnotation> peakList,
              Writer writer)
                   throws IOException

Throws:

IOException

formatAnnotations

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

Throws:

IOException

writeComment

protected void writeComment(PeakList peakList,
                Peptide peptide,
                Writer writer,
                Collection<String> proteinAccessionNumbers)
                     throws IOException

Throws:

IOException

writeLibId

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

Throws:

IOException

writeName

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

Throws:

IOException

formatMz

protected String formatMz(double mz)

formatIntensity

protected String formatIntensity(double intensity)

close

public void close()
           throws IOException

Throws:

IOException