Package eu.isas.peptideshaker.protein_inference

Class PeptideChecker

java.lang.Object
eu.isas.peptideshaker.protein_inference.PeptideChecker
public class PeptideChecker extends Object
This class checks that the peptide to protein mapping is compatible with the modification status of the peptide.
Author:
Marc Vaudel

  • Constructor Summary

    Constructors
    Constructor
    Description
    PeptideChecker()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static void
    checkPeptide(com.compomics.util.experiment.biology.proteins.Peptide peptide, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters modificationMatchingParameters)
    Checks that only one variable modification is assigned per site and corrects the protein mapping based on the confident or inferred variable modifications when located at the protein termini or targeting amino acid patterns.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • PeptideChecker

      public PeptideChecker()

  • Method Details

    • checkPeptide

      public static void checkPeptide(com.compomics.util.experiment.biology.proteins.Peptide peptide, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters modificationMatchingParameters)
      Checks that only one variable modification is assigned per site and corrects the protein mapping based on the confident or inferred variable modifications when located at the protein termini or targeting amino acid patterns.
      Parameters:
      peptide - the peptide to check
      sequenceProvider - a protein sequence provider
      modificationMatchingParameters - the modification sequence matching parameters