public class FragmentAnnotator extends Object
Constructor and Description |
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FragmentAnnotator()
Empty default constructor
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FragmentAnnotator(Peptide peptide,
String[] fixedModifications,
SimplePeptideAnnotator.IonSeries ionSeries)
Constructor.
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FragmentAnnotator(Peptide peptide,
String[] fixedModifications,
SimplePeptideAnnotator.IonSeries ionSeries,
boolean forward,
boolean complementary)
Constructor.
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Modifier and Type | Method and Description |
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ArrayList<IonMatch> |
getIonMatches(SpectrumIndex spectrumIndex,
int peptideCharge)
Returns the ions matched in the given spectrum at the given charge.
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public FragmentAnnotator()
public FragmentAnnotator(Peptide peptide, String[] fixedModifications, SimplePeptideAnnotator.IonSeries ionSeries)
peptide
- the peptidefixedModifications
- the fixed modifications on the peptideionSeries
- the ion series to annotatepublic FragmentAnnotator(Peptide peptide, String[] fixedModifications, SimplePeptideAnnotator.IonSeries ionSeries, boolean forward, boolean complementary)
peptide
- the peptidefixedModifications
- the fixed modifications on the peptideionSeries
- the ion series to annotateforward
- boolean indicating whether forward ions should be
annotatedcomplementary
- boolean indicating whether complementary ions should
be annotatedpublic ArrayList<IonMatch> getIonMatches(SpectrumIndex spectrumIndex, int peptideCharge)
spectrumIndex
- the index of the spectrumpeptideCharge
- the charge of the peptideCopyright © 2021. All rights reserved.