eu.isas.peptideshaker.ptm

Class ModificationLocalizationScorer

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

eu.isas.peptideshaker.ptm.ModificationLocalizationScorer

All Implemented Interfaces:

Serializable

public class ModificationLocalizationScorer
extends com.compomics.util.experiment.personalization.ExperimentObject

This class scores the PSM PTMs using the scores implemented in compomics utilities.

Author:

Marc Vaudel, Harald Barsnes

See Also:

Serialized Form

Field Summary

Fields inherited from class com.compomics.util.experiment.personalization.ExperimentObject

NO_KEY

Constructor Summary

Constructors

Constructor and Description
ModificationLocalizationScorer() Constructor.

Method Summary

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.

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ModificationLocalizationScorer

public ModificationLocalizationScorer()

Constructor.

Method Detail

attachDeltaScore

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)

Scores the modification locations using the delta score.

Parameters:

identification - Identification object containing the matches.

spectrumMatch - The spectrum match of interest.

sequenceMatchingParameters - The sequence matching preferences.

modificationProvider - The modification provider to use.

scorePTMs

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)

Scores PTM locations for a desired spectrum match.

Parameters:

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.

scorePTMs

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)

Scores the PTMs for a peptide match.

Parameters:

identification - identification object containing the identification matches

peptideMatch - The peptide match to score.

identificationParameters - The identification parameters.

modificationProvider - The modification provider to use.

waitingHandler - The waiting handler to use, ignored if null.

scorePTMs

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)

Scores PTMs in a protein match.

Parameters:

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.

scorePeptidePtms

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)

Scores the PTMs of all peptide matches contained in an identification object.

Parameters:

identification - identification object containing the identification matches

modificationProvider - The modification provider to use.

waitingHandler - the handler displaying feedback to the user

identificationParameters - the identification parameters

modificationSiteInference

public 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.

Parameters:

spectrumMatch - The spectrum match.

sequenceProvider - The sequence provider to use.

modificationProvider - The modification provider to use.

identificationParameters - The identification parameters.