org.expasy.mzjava.proteomics.ms.fragment

Class PeptideFragmenter

java.lang.Object

org.expasy.mzjava.proteomics.ms.fragment.PeptideFragmenter

public class PeptideFragmenter
extends Object

Version:

1.0

Author:

Oliver Horlacher

Constructor Summary

Constructors

Constructor and Description
PeptideFragmenter(List<PeptidePeakGenerator<PepFragAnnotation>> peakGeneratorList, PeakList.Precision precision) Constructs a CID peptide fragmenter that generates peaks using the supplied peak generators
PeptideFragmenter(Set<IonType> ionTypes, PeakList.Precision precision) Construct a CID peptide fragmenter that generates peaks for the supplied ion types.

Method Summary

Methods

Modifier and Type	Method and Description
PeptideSpectrum	fragment(Peptide peptide, int precursorCharge)
PeptideSpectrum	fragment(Peptide peptide, int precursorCharge, int[] fragmentCharges)
PeptideSpectrum	fragment(Peptide peptide, int precursorCharge, List<PeptideFragment> fragmentList, int[] fragmentCharges)
protected void	generateForward(Peptide peptide, List<PeptideFragment> fragments)
protected void	generateImmonium(Peptide peptide, List<PeptideFragment> fragments)
protected void	generateReverse(Peptide peptide, List<PeptideFragment> fragments)

Methods inherited from class java.lang.Object

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

Constructor Detail

PeptideFragmenter

public PeptideFragmenter(Set<IonType> ionTypes,
                 PeakList.Precision precision)

Construct a CID peptide fragmenter that generates peaks for the supplied ion types.

Parameters:

ionTypes - the ion types to generate peaks for

precision - the precision of the generated PeptideSpectrum

PeptideFragmenter

public PeptideFragmenter(List<PeptidePeakGenerator<PepFragAnnotation>> peakGeneratorList,
                 PeakList.Precision precision)

Constructs a CID peptide fragmenter that generates peaks using the supplied peak generators

Parameters:

peakGeneratorList - the list of peak generators to use for generating peaks

precision - the precision of the generated PeptideSpectrum

Method Detail

fragment

public PeptideSpectrum fragment(Peptide peptide,
                       int precursorCharge)

fragment

public PeptideSpectrum fragment(Peptide peptide,
                       int precursorCharge,
                       int[] fragmentCharges)

fragment

public PeptideSpectrum fragment(Peptide peptide,
                       int precursorCharge,
                       List<PeptideFragment> fragmentList,
                       int[] fragmentCharges)

generateForward

protected void generateForward(Peptide peptide,
                   List<PeptideFragment> fragments)

generateReverse

protected void generateReverse(Peptide peptide,
                   List<PeptideFragment> fragments)

generateImmonium

protected void generateImmonium(Peptide peptide,
                    List<PeptideFragment> fragments)