Class ImmoniumIonAnnotator
java.lang.Object
com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.ImmoniumIonAnnotator
public class ImmoniumIonAnnotator extends Object
Annotator for immonium and related ions.
- Author:
- Marc Vaudel
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Constructor Summary
Constructors Constructor Description ImmoniumIonAnnotator()
Empty default constructorImmoniumIonAnnotator(char[] peptideSequence)
Constructor.ImmoniumIonAnnotator(char[] peptideSequence, boolean immonium, boolean related)
Constructor. -
Method Summary
Modifier and Type Method Description ArrayList<IonMatch>
getIonMatches(SpectrumIndex spectrumIndex)
Returns the ions matched in the given spectrum.
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Constructor Details
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ImmoniumIonAnnotator
public ImmoniumIonAnnotator()Empty default constructor -
ImmoniumIonAnnotator
public ImmoniumIonAnnotator(char[] peptideSequence)Constructor. Warning: there is no check for amino acid uniticy, if duplicates are present, they will be reported multiple times.- Parameters:
peptideSequence
- the peptide sequence
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ImmoniumIonAnnotator
public ImmoniumIonAnnotator(char[] peptideSequence, boolean immonium, boolean related)Constructor. Warning: there is no check for amino acid uniticy, if duplicates are present, they will be reported multiple times.- Parameters:
peptideSequence
- the peptide sequenceimmonium
- boolean indicating whether immonium ions should be annotatedrelated
- boolean indicating whether related ions should be annotated
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Method Details
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getIonMatches
Returns the ions matched in the given spectrum.- Parameters:
spectrumIndex
- the index of the spectrum- Returns:
- the ions matched in the given spectrum
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