org.expasy.mzjava.proteomics.ms.consensus

Class PeptideConsensusPeakSink

java.lang.Object

org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusPeakSink

All Implemented Interfaces:

PeakSink<PepLibPeakAnnotation>

public class PeptideConsensusPeakSink
extends Object
implements PeakSink<PepLibPeakAnnotation>

Peak filter that retains peaks that are within tolerance of a peak in the theoretical spectrum or peaks that have a mergedPeakCount that is >= absoluteMinPeakCount && >= peakFraction*consensusSize.

Version:

sqrt -1

Author:

Markus Muller

Constructor Summary

Constructors

Constructor and Description
PeptideConsensusPeakSink(PeptideConsensusSpectrum consensus, double peakFraction, int minPeakCount)

Method Summary

Methods

Modifier and Type	Method and Description
void	end() Called after a PeakList is processed
void	processPeak(double mz, double intensity, List<PepLibPeakAnnotation> annotations) Process the peak
void	start(int size) Called before a new PeakList is processed.

Methods inherited from class java.lang.Object

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

Constructor Detail

PeptideConsensusPeakSink

public PeptideConsensusPeakSink(PeptideConsensusSpectrum consensus,
                        double peakFraction,
                        int minPeakCount)

Method Detail

start

public void start(int size)

Description copied from interface: PeakSink

Called before a new PeakList is processed. The size parameter is used to give an indication of the number of peaks that will be passed to this PeakSinks. The size does not have to be correct.

Specified by:

start in interface PeakSink<PepLibPeakAnnotation>

Parameters:

size - the number of peaks that will be processed.

processPeak

public void processPeak(double mz,
               double intensity,
               List<PepLibPeakAnnotation> annotations)

Description copied from interface: PeakSink

Process the peak

Specified by:

processPeak in interface PeakSink<PepLibPeakAnnotation>

Parameters:

mz - the peak's m/z

intensity - the peak's intensity

annotations - the peak's annotations

end

public void end()

Description copied from interface: PeakSink

Called after a PeakList is processed

Specified by:

end in interface PeakSink<PepLibPeakAnnotation>