org.expasy.mzjava.proteomics.ms.fragment

Class BackbonePeakGenerator

java.lang.Object

org.expasy.mzjava.proteomics.ms.fragment.BackbonePeakGenerator

All Implemented Interfaces:

PeptidePeakGenerator<PepFragAnnotation>

public class BackbonePeakGenerator
extends Object
implements PeptidePeakGenerator<PepFragAnnotation>

Version:

1.0

Author:

Oliver Horlacher

Constructor Summary

Constructors

Constructor and Description
BackbonePeakGenerator(Set<IonType> ionTypes, double peakIntensity)

Method Summary

Methods

Modifier and Type	Method and Description
List<AnnotatedPeak<PepFragAnnotation>>	generatePeaks(Peptide precursor, PeptideFragment fragment, int[] charges, List<AnnotatedPeak<PepFragAnnotation>> peaks) Generate peaks that are observed for the fragment at the supplied charge states.
Set<FragmentType>	getFragmentTypes()

Methods inherited from class java.lang.Object

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

Constructor Detail

BackbonePeakGenerator

public BackbonePeakGenerator(Set<IonType> ionTypes,
                     double peakIntensity)

Method Detail

generatePeaks

public List<AnnotatedPeak<PepFragAnnotation>> generatePeaks(Peptide precursor,
                                                   PeptideFragment fragment,
                                                   int[] charges,
                                                   List<AnnotatedPeak<PepFragAnnotation>> peaks)

Description copied from interface: PeptidePeakGenerator

Generate peaks that are observed for the fragment at the supplied charge states. The generated peaks are to be added to peaks

Specified by:

generatePeaks in interface PeptidePeakGenerator<PepFragAnnotation>

Parameters:

precursor - the peptide that this fragment was derived from

fragment - the fragment

charges - the charges for which to generate peaks

peaks - the list of peaks

Returns:

the peaks list that was passed in

getFragmentTypes

public Set<FragmentType> getFragmentTypes()

Specified by:

getFragmentTypes in interface PeptidePeakGenerator<PepFragAnnotation>