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)
    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

  • 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)
      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