Class FragmentAnnotator
java.lang.Object
com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.FragmentAnnotator
public class FragmentAnnotator extends Object
Annotator for b and y ions without neutral losses.
- Author:
- Marc Vaudel
-
Constructor Summary
Constructors Constructor Description FragmentAnnotator()
Empty default constructorFragmentAnnotator(Peptide peptide, String[] fixedModifications, SimplePeptideAnnotator.IonSeries ionSeries)
Constructor.FragmentAnnotator(Peptide peptide, String[] fixedModifications, SimplePeptideAnnotator.IonSeries ionSeries, 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.
-
Constructor Details
-
FragmentAnnotator
public FragmentAnnotator()Empty default constructor -
FragmentAnnotator
public FragmentAnnotator(Peptide peptide, String[] fixedModifications, SimplePeptideAnnotator.IonSeries ionSeries)Constructor. Fixed modifications must be indexed as provided by the peptide class.- Parameters:
peptide
- the peptidefixedModifications
- the fixed modifications on the peptideionSeries
- the ion series to annotate
-
FragmentAnnotator
public FragmentAnnotator(Peptide peptide, String[] fixedModifications, SimplePeptideAnnotator.IonSeries ionSeries, boolean forward, boolean complementary)Constructor. Fixed modifications must be indexed as provided by the peptide class.- Parameters:
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 annotated
-
-
Method Details
-
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
-