public class FragmentAnnotatorNL extends Object
Constructor and Description |
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FragmentAnnotatorNL()
Empty default constructor
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FragmentAnnotatorNL(Peptide peptide,
String[] fixedModifications,
SimplePeptideAnnotator.IonSeries ionSeries,
boolean sequenceDependent)
Constructor.
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FragmentAnnotatorNL(Peptide peptide,
String[] fixedModifications,
SimplePeptideAnnotator.IonSeries ionSeries,
boolean sequenceDependent,
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 FragmentAnnotatorNL()
public FragmentAnnotatorNL(Peptide peptide, String[] fixedModifications, SimplePeptideAnnotator.IonSeries ionSeries, boolean sequenceDependent)
peptide
- the peptidefixedModifications
- the fixed modifications of the peptideionSeries
- the ion series to annotatesequenceDependent
- boolean indicating whether the H2O and NH3
losses should be adapted to the sequencepublic FragmentAnnotatorNL(Peptide peptide, String[] fixedModifications, SimplePeptideAnnotator.IonSeries ionSeries, boolean sequenceDependent, boolean forward, boolean complementary)
peptide
- the peptidefixedModifications
- the fixed modificationsionSeries
- the ion series to annotatesequenceDependent
- boolean indicating whether the H2O and NH3
losses should be adapted to the sequenceforward
- 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.