public class ModificationLocalizationScorer
extends com.compomics.util.experiment.personalization.ExperimentObject
| Constructor and Description |
|---|
ModificationLocalizationScorer()
Constructor.
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| Modifier and Type | Method and Description |
|---|---|
void |
attachDeltaScore(com.compomics.util.experiment.identification.Identification identification,
com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch,
com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters,
com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider)
Scores the modification locations using the delta score.
|
void |
modificationSiteInference(com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch,
com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider,
com.compomics.util.parameters.identification.IdentificationParameters identificationParameters)
Infers the modification site of the best peptide assumption of the given
spectrum match.
|
void |
scorePeptidePtms(com.compomics.util.experiment.identification.Identification identification,
com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider,
com.compomics.util.waiting.WaitingHandler waitingHandler,
com.compomics.util.parameters.identification.IdentificationParameters identificationParameters)
Scores the PTMs of all peptide matches contained in an identification
object.
|
void |
scorePTMs(com.compomics.util.experiment.identification.Identification identification,
com.compomics.util.experiment.identification.matches.PeptideMatch peptideMatch,
com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider,
com.compomics.util.waiting.WaitingHandler waitingHandler)
Scores the PTMs for a peptide match.
|
void |
scorePTMs(com.compomics.util.experiment.identification.Identification identification,
com.compomics.util.experiment.identification.matches.ProteinMatch proteinMatch,
com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
boolean scorePeptides,
com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider,
com.compomics.util.waiting.WaitingHandler waitingHandler)
Scores PTMs in a protein match.
|
void |
scorePTMs(com.compomics.util.experiment.identification.Identification identification,
com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch,
com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider,
com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
com.compomics.util.waiting.WaitingHandler waitingHandler,
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator peptideSpectrumAnnotator)
Scores PTM locations for a desired spectrum match.
|
public ModificationLocalizationScorer()
public void attachDeltaScore(com.compomics.util.experiment.identification.Identification identification,
com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch,
com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters,
com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider)
identification - Identification object containing the matches.spectrumMatch - The spectrum match of interest.sequenceMatchingParameters - The sequence matching preferences.modificationProvider - The modification provider to use.public void scorePTMs(com.compomics.util.experiment.identification.Identification identification,
com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch,
com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider,
com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
com.compomics.util.waiting.WaitingHandler waitingHandler,
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator peptideSpectrumAnnotator)
identification - Identification object containing the matches.spectrumMatch - The spectrum match to score.sequenceProvider - The protein sequence provider to use.spectrumProvider - The spectrum provider to use.modificationProvider - The modification provider to use.identificationParameters - The parameters used for identification.waitingHandler - The waiting handler to use to display progress and
allow canceling.peptideSpectrumAnnotator - The spectrum annotator to use.public void scorePTMs(com.compomics.util.experiment.identification.Identification identification,
com.compomics.util.experiment.identification.matches.PeptideMatch peptideMatch,
com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider,
com.compomics.util.waiting.WaitingHandler waitingHandler)
identification - identification object containing the identification
matchespeptideMatch - The peptide match to score.identificationParameters - The identification parameters.modificationProvider - The modification provider to use.waitingHandler - The waiting handler to use, ignored if null.public void scorePTMs(com.compomics.util.experiment.identification.Identification identification,
com.compomics.util.experiment.identification.matches.ProteinMatch proteinMatch,
com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
boolean scorePeptides,
com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider,
com.compomics.util.waiting.WaitingHandler waitingHandler)
identification - The identification object containing the matches.proteinMatch - The protein match.identificationParameters - The identification parameters.scorePeptides - If true, peptides will be scored as well.modificationProvider - The modification provider to use.waitingHandler - The waiting handler to sue, ignored if null.public void scorePeptidePtms(com.compomics.util.experiment.identification.Identification identification,
com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider,
com.compomics.util.waiting.WaitingHandler waitingHandler,
com.compomics.util.parameters.identification.IdentificationParameters identificationParameters)
identification - identification object containing the identification
matchesmodificationProvider - The modification provider to use.waitingHandler - the handler displaying feedback to the useridentificationParameters - the identification parameterspublic void modificationSiteInference(com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch,
com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider,
com.compomics.util.parameters.identification.IdentificationParameters identificationParameters)
spectrumMatch - The spectrum match.sequenceProvider - The sequence provider to use.modificationProvider - The modification provider to use.identificationParameters - The identification parameters.Copyright © 2021. All rights reserved.