Uses of Class
com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap

Packages that use NeutralLossesMap

Package	Description
com.compomics.util.experiment.identification.spectrum_annotation	Classes used for ms2 spectrum annotation.
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators	This package contains implementations of the SpectrumAnnotator allowing the annotation of all ions.
com.compomics.util.gui.spectrum	Spectrum and Chromatogram visualization GUI classes.

Uses of NeutralLossesMap in com.compomics.util.experiment.identification.spectrum_annotation

Methods in com.compomics.util.experiment.identification.spectrum_annotation that return NeutralLossesMap

Modifier and Type	Method	Description
NeutralLossesMap	NeutralLossesMap.clone()
static NeutralLossesMap	SpectrumAnnotator.getDefaultLosses(SpectrumIdentificationAssumption spectrumIdentificationAssumption, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the possible neutral losses expected by default for a given peptide.
NeutralLossesMap	SpecificAnnotationParameters.getNeutralLossesMap()	Returns the map of neutral losses to annotate.

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

Modifier and Type	Method	Description
boolean	SpectrumAnnotator.isAccounted(NeutralLossesMap neutralLosses, NeutralLoss neutralLoss, Ion ion)	Returns a boolean indicating whether the neutral loss should be accounted for.
boolean	SpectrumAnnotator.lossesValidated(NeutralLossesMap neutralLosses, Ion theoreticIon)	Returns a boolean indicating whether the neutral losses of the given fragment ion fit the requirement of the given neutral losses map.
void	SpecificAnnotationParameters.setNeutralLossesMap(NeutralLossesMap neutralLossesMap)	Sets the map of neutral losses to annotate.

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

Methods in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators that return NeutralLossesMap

Modifier and Type	Method	Description
static NeutralLossesMap	PeptideSpectrumAnnotator.getDefaultLosses(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the possible neutral losses expected by default for a given peptide.
static NeutralLossesMap	TagSpectrumAnnotator.getDefaultLosses(Tag tag, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the possible neutral losses expected by default for a given tag.

Uses of NeutralLossesMap in com.compomics.util.gui.spectrum

Constructors in com.compomics.util.gui.spectrum with parameters of type NeutralLossesMap

Modifier	Constructor	Description
	FragmentIonTable(Peptide currentPeptide, ArrayList<IonMatch[]> allAnnotations, ArrayList<Spectrum> allSpectra, HashSet<Integer> currentFragmentIonTypes, NeutralLossesMap neutralLosses, boolean singleCharge, boolean twoCharges, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Creates a novel fragment ion table displaying bar charts with the intensity of each fragment ion type.
	FragmentIonTable(Peptide currentPeptide, ArrayList<IonMatch[]> allAnnotations, HashSet<Integer> currentFragmentIonTypes, NeutralLossesMap neutralLosses, boolean singleCharge, boolean twoCharges, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Creates a traditional fragment ion table with the theoretical mz values and the detected fragment ions highlighted.