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