org.expasy.mzjava.proteomics.ms.fragment

Class PeptideFragmentAnnotator

java.lang.Object

org.expasy.mzjava.proteomics.ms.fragment.PeptideFragmentAnnotator

public class PeptideFragmentAnnotator
extends Object

This facade highly simplifies and hides the complexity of annotated a peakList given a peptide as this process implies peptide fragmentation, aligning peaks and reporting annotations.

Author:

fnikitin Date: 5/31/13

Constructor Summary

Constructors

Constructor and Description
PeptideFragmentAnnotator(PeptideFragmenter fragmenter, PeakListAligner<PepFragAnnotation,PepFragAnnotation> aligner)
PeptideFragmentAnnotator(PeptideFragmenter fragmenter, Tolerance tolerance)

Method Summary

Methods

Modifier and Type	Method and Description
<S extends PeakList<PepFragAnnotation>> S	annotate(S peaklist, Peptide peptide) Annotate peaklist from peptide at precursor charge
<S extends PeakList<PepFragAnnotation>> S	annotate(S peaklist, Peptide peptide, int precursorCharge) Annotate peaklist from peptide at specific charge
<S extends PeakList<PepFragAnnotation>> S	annotate(S peaklist, Peptide peptide, int precursorCharge, int... fragmentCharges) Annotate peaklist from peptide at specific charge
protected PeptideSpectrum	fragment(Peptide peptidePrecursor, int precursorCharge)
protected PeptideSpectrum	fragment(Peptide peptidePrecursor, int precursorCharge, int... fragmentCharges)
protected void	reportAnnotations(PeakList<PepFragAnnotation> peakList, int index, List<PepFragAnnotation> fragAnnotations)

Methods inherited from class java.lang.Object

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

Constructor Detail

PeptideFragmentAnnotator

public PeptideFragmentAnnotator(PeptideFragmenter fragmenter,
                        Tolerance tolerance)

PeptideFragmentAnnotator

public PeptideFragmentAnnotator(PeptideFragmenter fragmenter,
                        PeakListAligner<PepFragAnnotation,PepFragAnnotation> aligner)

Method Detail

annotate

public <S extends PeakList<PepFragAnnotation>> S annotate(S peaklist,
                                                 Peptide peptide)

Annotate peaklist from peptide at precursor charge

Parameters:

peaklist - the peaklist to annotate

peptide - the peptide to fragment and to annotate peaklist with

annotate

public <S extends PeakList<PepFragAnnotation>> S annotate(S peaklist,
                                                 Peptide peptide,
                                                 int precursorCharge)

Annotate peaklist from peptide at specific charge

Parameters:

peaklist - the peaklist to annotate

peptide - the peptide to fragment and to annotate peaklist with

precursorCharge - the precursor charge (all fragments will be generated from +1 to precursorCharge)

annotate

public <S extends PeakList<PepFragAnnotation>> S annotate(S peaklist,
                                                 Peptide peptide,
                                                 int precursorCharge,
                                                 int... fragmentCharges)

Annotate peaklist from peptide at specific charge

Parameters:

peaklist - the peaklist to annotate

peptide - the peptide to fragment and to annotate peaklist with

precursorCharge - the precursor charge

fragmentCharges - the fragment charges

fragment

protected PeptideSpectrum fragment(Peptide peptidePrecursor,
                       int precursorCharge)

fragment

protected PeptideSpectrum fragment(Peptide peptidePrecursor,
                       int precursorCharge,
                       int... fragmentCharges)

reportAnnotations

protected void reportAnnotations(PeakList<PepFragAnnotation> peakList,
                     int index,
                     List<PepFragAnnotation> fragAnnotations)