Uses of Class
com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex

Packages that use SpectrumIndex

Package	Description
com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators	This package contains implementations of the SimpleAnnotator allowing the annotation of specific sets of ions.
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators	This package contains implementations of the SpectrumAnnotator allowing the annotation of all ions.

Uses of SpectrumIndex in com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators

Methods in com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators with parameters of type SpectrumIndex

Modifier and Type	Method	Description
ArrayList<IonMatch>	FragmentAnnotator.getIonMatches(SpectrumIndex spectrumIndex, int peptideCharge)	Returns the ions matched in the given spectrum at the given charge.
ArrayList<IonMatch>	FragmentAnnotatorNL.getIonMatches(SpectrumIndex spectrumIndex, int peptideCharge)	Returns the ions matched in the given spectrum at the given charge.
ArrayList<IonMatch>	ImmoniumIonAnnotator.getIonMatches(SpectrumIndex spectrumIndex)	Returns the ions matched in the given spectrum.
ArrayList<IonMatch>	PrecursorAnnotator.getIonMatches(SpectrumIndex spectrumIndex, int peptideCharge, int isotopeMax)	Returns the ions matched in the given spectrum at the given charge.
ArrayList<IonMatch>	ReporterIonAnnotator.getIonMatches(SpectrumIndex spectrumIndex)	Returns the ions matched in the given spectrum.

Uses of SpectrumIndex in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators

Methods in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators with parameters of type SpectrumIndex

Modifier and Type	Method	Description
ArrayList<IonMatch>	SimplePeptideAnnotator.getIonMatches(SpectrumIndex spectrumIndex, int peptideCharge, int precursorIsotopeMax)	Returns the ion matches for the given spectrum.