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(Peptide peptide,
int charge,
AnnotationSettings annotationSettings)
Constructor.
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SimplePeptideAnnotator(Peptide peptide,
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, int charge, AnnotationSettings annotationSettings) throws InterruptedException
peptide
- the peptide to annotatecharge
- the charge of the peptideannotationSettings
- the annotation preferencesInterruptedException
- exception thrown if a thread is
interruptedpublic SimplePeptideAnnotator(Peptide peptide, 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) throws InterruptedException
peptide
- the peptide to annotatecharge
- 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 annotateInterruptedException
- exception thrown if a thread is
interruptedpublic 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 © 2019. All rights reserved.