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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Modifier and Type | Method and Description |
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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.
|
Modifier and Type | Method and Description |
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boolean |
SpectrumAnnotator.isAccounted(NeutralLossesMap neutralLosses,
NeutralLoss neutralLoss,
Ion ion)
Returns a boolean indicating whether the neutral loss should be accounted
for.
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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.
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Modifier and Type | Method and Description |
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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.
|
Constructor and Description |
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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.
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