Package eu.isas.peptideshaker.protein_inference

Class ProteinInference

java.lang.Object
eu.isas.peptideshaker.protein_inference.ProteinInference
public class ProteinInference
extends Object
This class groups the methods for protein inference.
Author:
Marc Vaudel, Harald Barsnes

  • Nested Class Summary

    Nested Classes 
    Modifier and Type Class Description
    static class  ProteinInference.GroupSimplificationOption  

  • Field Summary

    Fields 
    Modifier and Type Field Description
    static String[] KEYWORDS_UNCHARACTERIZED
    Key words used to flag uncharacterized proteins.

  • Constructor Summary

    Constructors 
    Constructor Description
    ProteinInference()  

  • Method Summary

    Modifier and Type Method Description
    void distributeSharedPeptides​(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Distribute the shared peptides among the protein groups.
    void inferPiStatus​(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, TargetDecoyMap proteinMap, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Selects the leading protein of protein groups and infers PI status of peptide and proteins.
    void inferPiStatus​(com.compomics.util.experiment.identification.matches.ProteinMatch proteinMatch, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, TargetDecoyMap proteinMap, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Selects the leading protein of protein groups and infers PI status of peptide and proteins.

    Methods inherited from class java.lang.Object

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

  • Field Details

  • Constructor Details

  • Method Details

    • inferPiStatus

      public void inferPiStatus​(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, TargetDecoyMap proteinMap, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)
      Selects the leading protein of protein groups and infers PI status of peptide and proteins.
      Parameters:
      identification - the identification class containing all identification matches
      metrics - if provided protein metrics will be loaded while iterating the groups
      proteinMap - the protein matches scoring map
      identificationParameters - the identification parameters
      sequenceProvider - the sequence provider
      proteinDetailsProvider - the protein details provider
      waitingHandler - the handler displaying feedback to the user

    • inferPiStatus

      public void inferPiStatus​(com.compomics.util.experiment.identification.matches.ProteinMatch proteinMatch, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, TargetDecoyMap proteinMap, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)
      Selects the leading protein of protein groups and infers PI status of peptide and proteins.
      Parameters:
      proteinMatch - the protein match
      identification - the identification class containing all identification matches
      metrics - if provided protein metrics will be loaded while iterating the groups
      proteinMap - the protein matches scoring map
      identificationParameters - the identification parameters
      sequenceProvider - the sequence provider
      proteinDetailsProvider - the protein details provider
      waitingHandler - the handler displaying feedback to the user

    • distributeSharedPeptides

      public void distributeSharedPeptides​(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.waiting.WaitingHandler waitingHandler)
      Distribute the shared peptides among the protein groups.
      Parameters:
      identification - the identification class containing all identification matches
      waitingHandler - the handler displaying feedback to the user