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 and Description
PeptideChecker()

Method Summary

Modifier and Type

Method and 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 Detail

PeptideChecker

public PeptideChecker()

Method Detail

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