org.expasy.mzjava.glycomics.ms.fragment

Class GlycanFragmentPeakGenerator

java.lang.Object

org.expasy.mzjava.glycomics.ms.fragment.GlycanFragmentPeakGenerator

All Implemented Interfaces:

GlycanPeakGenerator<GlycanFragAnnotation>

public class GlycanFragmentPeakGenerator
extends Object
implements GlycanPeakGenerator<GlycanFragAnnotation>

Version:

sqrt -1.

Author:

Davide Alocci

Constructor Summary

Constructors

Constructor and Description
GlycanFragmentPeakGenerator(Set<FragmentType> fragmentTypes, Set<IonType> ionTypes, int peakIntensity)

Method Summary

Methods

Modifier and Type	Method and Description
List<AnnotatedPeak<GlycanFragAnnotation>>	generatePeaks(Glycan precursor, GlycanFragment fragment, int[] charges, List<AnnotatedPeak<GlycanFragAnnotation>> annotatedPeaks) Generate peaks that are observed for the fragment at the supplied charge states.
Set<FragmentType>	getFragmentTypes() Return the set of fragment type used in the peak generator.

Methods inherited from class java.lang.Object

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

Constructor Detail

GlycanFragmentPeakGenerator

public GlycanFragmentPeakGenerator(Set<FragmentType> fragmentTypes,
                           Set<IonType> ionTypes,
                           int peakIntensity)

Method Detail

generatePeaks

public List<AnnotatedPeak<GlycanFragAnnotation>> generatePeaks(Glycan precursor,
                                                      GlycanFragment fragment,
                                                      int[] charges,
                                                      List<AnnotatedPeak<GlycanFragAnnotation>> annotatedPeaks)

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

Specified by:

generatePeaks in interface GlycanPeakGenerator<GlycanFragAnnotation>

Parameters:

fragment - the glycan fragment taken into account.

charges - an array of charges used for generate different peaks with different charges.

annotatedPeaks - the peaklist where you want to add the new generated peaks.

precursor - the glycan that this fragment was derived from.

Returns:

the annotatedPeaks with the new generated peaks

getFragmentTypes

public Set<FragmentType> getFragmentTypes()

Return the set of fragment type used in the peak generator.

Specified by:

getFragmentTypes in interface GlycanPeakGenerator<GlycanFragAnnotation>

Returns:

the fragment type used in the peak generator.