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

Class AbstractMgfWriter<A extends PeakAnnotation,M,P extends AbstractMgfWriter.Parameters>

java.lang.Object

org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfWriter<A,M,P>

Type Parameters:

A - the annotations of the peaks in the peak list

M - the object that holds the meta data, can be the same object as the peak list

P - the object that holds the parameters for initialising this mgf writer

Direct Known Subclasses:

MgfWriter

public abstract class AbstractMgfWriter<A extends PeakAnnotation,M,P extends AbstractMgfWriter.Parameters>
extends Object

Abstract implementation of an MGF writer. This class takes care of writing the standard structure of an MGF file. For each spectrum the following tags are written BEGIN IONS TITLE= PEPMASS= CHARGE= RTINSECONDS= peak mz\tpeak intensity END IONS Subclasses have to implement methods to extract the charge list, retention time, scan number and title to fill in the values for the tags. By default this class does not write any ms1 header data, however subclasses can generate a ms1 header by using a Parameters implementation that contains data for the header and overriding writeMs1Header(P, Writer) method which is called by the constructor. To write a PeakList and associated meta data subclasses have to call writeMs2(PeakList peakList, M metaData).

Version:

sqrt -1

Author:

Oliver Horlacher, nikitin

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	AbstractMgfWriter.Parameters

Constructor Summary

Constructors

Constructor and Description
AbstractMgfWriter(Writer writer, P parameters)

Method Summary

Methods

Modifier and Type	Method and Description
void	close()
protected abstract int[]	extractChargeList(PeakList peakList, M metaData)
protected abstract List<RetentionTime>	extractRetentionTime(M metaData)
protected abstract List<ScanNumber>	extractScanNumbers(M metaData)
protected abstract String	extractTitle(M metaData)
protected void	writeCharge(PeakList peakList, M metaData, Writer writer)
void	writeComment(String comment)
protected void	writeMs1Header(P parameters, Writer writer)
protected void	writeMs2(PeakList<? extends A> peakList, M metaData)
protected void	writeMs2Header(PeakList peakList, M metaData, Writer writer)
protected void	writePeakAnnotations(List<? extends A> annotations, Writer writer) Subclasses that want to add annotation information to a peak can override this method.
protected void	writePeaks(PeakList<? extends A> peakList, Writer writer)
protected void	writePepmass(PeakList peakList, Writer writer)
protected void	writeRtInSeconds(M metaData, Writer writer)
protected void	writeScans(M metaData, Writer writer)
protected void	writeTitle(M metaData, Writer writer)

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractMgfWriter

public AbstractMgfWriter(Writer writer,
                 P parameters)
                  throws IOException

Throws:

IOException

Method Detail

writeMs1Header

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

Throws:

IOException

writeComment

public void writeComment(String comment)
                  throws IOException

Throws:

IOException

writeMs2

protected void writeMs2(PeakList<? extends A> peakList,
            M metaData)
                 throws IOException

Throws:

IOException

writeMs2Header

protected void writeMs2Header(PeakList peakList,
                  M metaData,
                  Writer writer)
                       throws IOException

Throws:

IOException

writeTitle

protected void writeTitle(M metaData,
              Writer writer)
                   throws IOException

Throws:

IOException

extractTitle

protected abstract String extractTitle(M metaData)

writePepmass

protected void writePepmass(PeakList peakList,
                Writer writer)
                     throws IOException

Throws:

IOException

writeScans

protected void writeScans(M metaData,
              Writer writer)
                   throws IOException

Throws:

IOException

extractScanNumbers

protected abstract List<ScanNumber> extractScanNumbers(M metaData)

writeRtInSeconds

protected void writeRtInSeconds(M metaData,
                    Writer writer)
                         throws IOException

Throws:

IOException

extractRetentionTime

protected abstract List<RetentionTime> extractRetentionTime(M metaData)

writePeaks

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

Throws:

IOException

writePeakAnnotations

protected void writePeakAnnotations(List<? extends A> annotations,
                        Writer writer)

Subclasses that want to add annotation information to a peak can override this method. Before this method is called the peak mz and intensity were written. Writing \n is taken care of in the method that calls this.

Parameters:

annotations - the annotations for the peak being written

writer - the writer

writeCharge

protected void writeCharge(PeakList peakList,
               M metaData,
               Writer writer)
                    throws IOException

Throws:

IOException

extractChargeList

protected abstract int[] extractChargeList(PeakList peakList,
                      M metaData)

close

public void close()
           throws IOException

Throws:

IOException