Package 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:

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    final int
    CONFIDENT_OFFSET
    Localization score offset for modification that are confidently localized.
    final int
    INFERRED_OFFSET
    Localization score offset for modification that are inferred.

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

    NO_KEY

  • Constructor Summary

    Constructors
    Constructor
    Description
    ModificationLocalizationScorer()
    Constructor.

  • Method Summary

    Modifier and Type
    Method
    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.experiment.io.biology.protein.SequenceProvider sequenceProvider, 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.experiment.io.biology.protein.SequenceProvider sequenceProvider, 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.experiment.io.biology.protein.SequenceProvider sequenceProvider, 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

  • Field Details

    • CONFIDENT_OFFSET

      public final int CONFIDENT_OFFSET
      Localization score offset for modification that are confidently localized.
      See Also:

    • INFERRED_OFFSET

      public final int INFERRED_OFFSET
      Localization score offset for modification that are inferred.
      See Also:

  • Constructor Details

    • ModificationLocalizationScorer

      public ModificationLocalizationScorer()
      Constructor.

  • Method Details

    • 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.experiment.io.biology.protein.SequenceProvider sequenceProvider, 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.
      sequenceProvider - The sequence matching parameters.
      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.experiment.io.biology.protein.SequenceProvider sequenceProvider, 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.
      sequenceProvider - The sequence 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.experiment.io.biology.protein.SequenceProvider sequenceProvider, 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.
      sequenceProvider - The sequence 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.