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 enum 
    ProteinInference.GroupSimplificationOption
     

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final 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

    • KEYWORDS_UNCHARACTERIZED

      public static final String[] KEYWORDS_UNCHARACTERIZED
      Key words used to flag uncharacterized proteins.

  • Constructor Details

    • ProteinInference

      public ProteinInference()

  • 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