Class SimplePeptideAnnotator
java.lang.Object
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.SimplePeptideAnnotator
public class SimplePeptideAnnotator extends Object
A simple annotator for peptides.
- Author:
- Marc Vaudel
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
SimplePeptideAnnotator.IonSeries
The type of ion series to annotate. -
Constructor Summary
Constructors Constructor Description SimplePeptideAnnotator()
Empty default constructorSimplePeptideAnnotator(Peptide peptide, String[] fixedModifications, int charge, boolean a, boolean b, boolean c, boolean x, boolean y, boolean z, boolean precursor, boolean immonium, boolean related, boolean reporter, boolean neutralLosses, boolean neutralLossesSequenceDependent, ReporterIon[] reporterIons)
Constructor.SimplePeptideAnnotator(Peptide peptide, String[] fixedModifications, int charge, AnnotationParameters annotationSettings)
Constructor. -
Method Summary
Modifier and Type Method Description ArrayList<IonMatch>
getIonMatches(SpectrumIndex spectrumIndex, int peptideCharge, int precursorIsotopeMax)
Returns the ion matches for the given spectrum.
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Constructor Details
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SimplePeptideAnnotator
public SimplePeptideAnnotator(Peptide peptide, String[] fixedModifications, int charge, AnnotationParameters annotationSettings)Constructor. Fixed modifications must be indexed as provided by the peptide class.- Parameters:
peptide
- the peptide to annotatefixedModifications
- the fixed modifications of the peptidecharge
- the charge of the peptideannotationSettings
- the annotation preferences
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SimplePeptideAnnotator
public SimplePeptideAnnotator()Empty default constructor -
SimplePeptideAnnotator
public SimplePeptideAnnotator(Peptide peptide, String[] fixedModifications, int charge, boolean a, boolean b, boolean c, boolean x, boolean y, boolean z, boolean precursor, boolean immonium, boolean related, boolean reporter, boolean neutralLosses, boolean neutralLossesSequenceDependent, ReporterIon[] reporterIons)Constructor. Fixed modifications must be indexed as provided by the peptide class.- Parameters:
peptide
- the peptide to annotatefixedModifications
- the fixed modifications of the peptidecharge
- the charge of the peptidea
- boolean indicating whether a ions should be annotatedb
- boolean indicating whether b ions should be annotatedc
- boolean indicating whether c ions should be annotatedx
- boolean indicating whether x ions should be annotatedy
- boolean indicating whether y ions should be annotatedz
- boolean indicating whether z ions should be annotatedprecursor
- boolean indicating whether precursor ions should be annotatedimmonium
- boolean indicating whether immonium ions should be annotatedrelated
- boolean indicating whether related ions should be annotatedreporter
- boolean indicating whether reporter ions should be annotatedneutralLosses
- boolean indicating whether fragment ions with neutral losses should be annotatedneutralLossesSequenceDependent
- boolean indicating whether the neutral losses should be selected depending on the sequencereporterIons
- the reporter ions to annotate
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Method Details
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getIonMatches
public ArrayList<IonMatch> getIonMatches(SpectrumIndex spectrumIndex, int peptideCharge, int precursorIsotopeMax)Returns the ion matches for the given spectrum.- Parameters:
spectrumIndex
- the spectrum indexpeptideCharge
- the peptide chargeprecursorIsotopeMax
- the number of isotopes to test for the precursor ion- Returns:
- the ion matches in a list
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