Class ModificationLocalizationMapper

java.lang.Object
com.compomics.util.experiment.identification.modification.mapping.ModificationLocalizationMapper

public class ModificationLocalizationMapper
extends Object
Function attempting to map modification localization based on their type.
Author:
Marc Vaudel, Harald Barsnes
  • Field Details

    • MASS_PER_AA

      public static final double MASS_PER_AA
      The mass added per amino acid as part of the reference mass when converting Dalton tolerances to ppm.
      See Also:
      Constant Field Values
  • Constructor Details

  • Method Details

    • modificationLocalization

      public static void modificationLocalization​(Peptide peptide, HashMap<Integer,​ArrayList<String>> expectedNames, HashMap<ModificationMatch,​ArrayList<String>> modNames, IdentificationParameters identificationParameters, IdfileReader idfileReader, ModificationProvider modificationProvider)
      Makes an initial modification mapping based on the search engine results and the compatibility to the searched modifications.
      Parameters:
      peptide - The peptide where the modification was found.
      expectedNames - The expected modifications at each site.
      modNames - The possible names for every modification match.
      identificationParameters - The identification parameters.
      idfileReader - The identification file reader.
      modificationProvider - The modification provider to use.