public class SimplePeptideAnnotator extends Object
Modifier and Type | Class and Description |
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static class |
SimplePeptideAnnotator.IonSeries
The type of ion series to annotate.
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Constructor and Description |
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SimplePeptideAnnotator()
Empty default constructor
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SimplePeptideAnnotator(Peptide peptide,
String[] fixedModifications,
int charge,
AnnotationParameters annotationSettings)
Constructor.
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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.
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Modifier and Type | Method and Description |
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ArrayList<IonMatch> |
getIonMatches(SpectrumIndex spectrumIndex,
int peptideCharge,
int precursorIsotopeMax)
Returns the ion matches for the given spectrum.
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public SimplePeptideAnnotator(Peptide peptide, String[] fixedModifications, int charge, AnnotationParameters annotationSettings)
peptide
- the peptide to annotatefixedModifications
- the fixed modifications of the peptidecharge
- the charge of the peptideannotationSettings
- the annotation preferencespublic 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)
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 annotatepublic ArrayList<IonMatch> getIonMatches(SpectrumIndex spectrumIndex, int peptideCharge, int precursorIsotopeMax)
spectrumIndex
- the spectrum indexpeptideCharge
- the peptide chargeprecursorIsotopeMax
- the number of isotopes to test for the
precursor ionCopyright © 2021. All rights reserved.