org.expasy.mzjava.glycomics.ms.fragment

Class GlycanFragmenter

java.lang.Object

org.expasy.mzjava.glycomics.ms.fragment.GlycanFragmenter

public class GlycanFragmenter
extends Object

Version:

sqrt -1.

Author:

Davide Alocci

Constructor Summary

Constructors

Constructor and Description
GlycanFragmenter(List<GlycanPeakGenerator<GlycanFragAnnotation>> peakGeneratorList, PeakList.Precision precision, int maxGlycosidicCuts, int maxCrossringCuts) Constructs a glycan fragmenter that generates peaks using the supplied peak generators.
GlycanFragmenter(Set<IonType> ionTypes, boolean intact, boolean internal, PeakList.Precision precision, int maxGlycosidicCuts, int maxCrossringCuts) Construct a glycan fragmenter that generates peaks for the supplied ion types.

Method Summary

Methods

Modifier and Type	Method and Description
GlycanSpectrum	fragment(Glycan glycan, int precursorCharge) Generate a GlycanSpectrum from the fragment in input.
GlycanSpectrum	fragment(Glycan glycan, int precursorCharge, CrossRingCutType crossRingCutType) Generate a GlycanSpectrum from the fragment in input.
GlycanSpectrum	fragment(Glycan glycan, int precursorCharge, int[] fragmentCharges, CrossRingCutType crossRingCutType) Generate a GlycanSpectrum from the fragment in input.
GlycanSpectrum	fragment(Glycan glycan, int precursorCharge, List<GlycanFragment> fragmentList, int[] fragmentCharges) Generate a GlycanSpectrum from the fragment in input.

Methods inherited from class java.lang.Object

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

Constructor Detail

GlycanFragmenter

public GlycanFragmenter(List<GlycanPeakGenerator<GlycanFragAnnotation>> peakGeneratorList,
                PeakList.Precision precision,
                int maxGlycosidicCuts,
                int maxCrossringCuts)

Constructs a glycan 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 GlycanSpectrum

maxCrossringCuts - maximum of crossring cuts

maxGlycosidicCuts - maximum of glycosidic cuts

GlycanFragmenter

public GlycanFragmenter(Set<IonType> ionTypes,
                boolean intact,
                boolean internal,
                PeakList.Precision precision,
                int maxGlycosidicCuts,
                int maxCrossringCuts)

Construct a glycan fragmenter that generates peaks for the supplied ion types. It uses only the default GlycanFragmentPeakGenerator as a peakgenerator. Both glycosidic and crossring fragment are generated depending on the ion type. The intensity of the fragment is set to 1 by default.

Parameters:

ionTypes - the ion types to generate peaks for

precision - the precision of the generated GlycanSpectrum

intact - allowed the generation of the intact fragment

internal - allowed the generation of internal fragments

maxCrossringCuts - maximum of crossring cuts

maxGlycosidicCuts - maximum of glycosidic cuts

Method Detail

fragment

public GlycanSpectrum fragment(Glycan glycan,
                      int precursorCharge)

Generate a GlycanSpectrum from the fragment in input. It uses all the peak generator in the list to create peaks for each fragment. This method will use all the possible charge from 0 to the charge of the precursor. It creates all the possible fragment (crossring and glycosidic) for the glycan precursor.

Parameters:

glycan - the glycan precursor.

precursorCharge - the charge of the precursor.

Returns:

a GlycanSpectrum

fragment

public GlycanSpectrum fragment(Glycan glycan,
                      int precursorCharge,
                      CrossRingCutType crossRingCutType)

Generate a GlycanSpectrum from the fragment in input. It uses all the peak generator in the list to create peaks for each fragment. This method will use all the possible charge from 0 to the charge of the precursor. It creates all the possible fragment (crossring and glycosidic) for the glycan precursor. The user can define the crossring type of cleavage to take into account using the interface CrossRingCutType.

Parameters:

glycan - the glycan precursor.

precursorCharge - the charge of the precursor.

crossRingCutType - the type of crossring fragments to generate.

Returns:

a GlycanSpectrum.

fragment

public GlycanSpectrum fragment(Glycan glycan,
                      int precursorCharge,
                      int[] fragmentCharges,
                      CrossRingCutType crossRingCutType)

Generate a GlycanSpectrum from the fragment in input. It uses all the peak generator in the list to create peaks for each fragment. The charges in the fragmentCharges array are use to calculate the m/z of the peaks. It creates all the possible fragment (crossring and glycosidic) for the glycan precursor. The user can define the crossring type of cleavage to take into account using the interface CrossRingCutType.

Parameters:

glycan - the glycan precursor.

precursorCharge - the charge of the precursor.

fragmentCharges - an array of charge.

crossRingCutType - the type of crossring fragments to generate.

Returns:

GlycanSpectrum.

fragment

public GlycanSpectrum fragment(Glycan glycan,
                      int precursorCharge,
                      List<GlycanFragment> fragmentList,
                      int[] fragmentCharges)

Generate a GlycanSpectrum from the fragment in input. It uses all the peak generator in the list to create peaks for each fragment. The charges in the fragmentCharges array are use to calculate the m/z of the peaks.

Parameters:

glycan - the glycan precursor.

precursorCharge - the charge of the precursor.

fragmentList - the list of fragment

fragmentCharges - an array of charge.

Returns:

a GlycanSpectrum.