Class FragmentAnnotatorNL
java.lang.Object
com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.FragmentAnnotatorNL
public class FragmentAnnotatorNL extends Object
A fragment annotator for peptide fragment ions with neutral losses.
- Author:
- Marc Vaudel
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Constructor Summary
Constructors Constructor Description FragmentAnnotatorNL()
Empty default constructorFragmentAnnotatorNL(Peptide peptide, String[] fixedModifications, SimplePeptideAnnotator.IonSeries ionSeries, boolean sequenceDependent)
Constructor.FragmentAnnotatorNL(Peptide peptide, String[] fixedModifications, SimplePeptideAnnotator.IonSeries ionSeries, boolean sequenceDependent, boolean forward, boolean complementary)
Constructor. -
Method Summary
Modifier and Type Method Description ArrayList<IonMatch>
getIonMatches(SpectrumIndex spectrumIndex, int peptideCharge)
Returns the ions matched in the given spectrum at the given charge.
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Constructor Details
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FragmentAnnotatorNL
public FragmentAnnotatorNL()Empty default constructor -
FragmentAnnotatorNL
public FragmentAnnotatorNL(Peptide peptide, String[] fixedModifications, SimplePeptideAnnotator.IonSeries ionSeries, boolean sequenceDependent)Constructor. Fixed modifications must be indexed as provided by the peptide class.- Parameters:
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 sequence
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FragmentAnnotatorNL
public FragmentAnnotatorNL(Peptide peptide, String[] fixedModifications, SimplePeptideAnnotator.IonSeries ionSeries, boolean sequenceDependent, boolean forward, boolean complementary)Constructor. Fixed modifications must be indexed as provided by the peptide class.- Parameters:
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 annotated
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Method Details
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getIonMatches
Returns the ions matched in the given spectrum at the given charge.- Parameters:
spectrumIndex
- the index of the spectrumpeptideCharge
- the charge of the peptide- Returns:
- the ions matched in the given spectrum at the given charge
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