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

public class ModificationMassMapper
extends Object
Function inferring the mass of a modification based on the search engine used.
Author:
Marc Vaudel, Harald Barsnes
  • Constructor Details

  • Method Details

    • getMass

      public static double getMass​(String searchEngineModificationName, IdfileReader idfileReader, SearchParameters searchParameters, ModificationProvider modificationProvider)
      Returns the mass indicated by the identification algorithm for the given modification.
      Parameters:
      searchEngineModificationName - The name according to the identification file reader.
      idfileReader - The identification file reader.
      searchParameters - The search parameters.
      modificationProvider - The modification provider to use.
      Returns:
      The mass of the modification.
    • getMassByMass

      public static double getMassByMass​(String searchEngineModificationName)
      Returns the mass indicated by the identification algorithm for the given modification.
      Parameters:
      searchEngineModificationName - The name according to the identification file reader.
      Returns:
      The mass of the modification.
    • getMassByName

      public static double getMassByName​(String searchEngineModificationName, ModificationProvider modificationProvider)
      Returns the mass indicated by the identification algorithm for the given modification.
      Parameters:
      searchEngineModificationName - The name according to the identification file reader.
      modificationProvider - The modification provider to use.
      Returns:
      The mass of the modification.
    • getMassOmssa

      public static double getMassOmssa​(String searchEngineModificationName, ModificationProvider modificationProvider, SearchParameters searchParameters)
      Returns the mass indicated by the OMSSA for the given modification.
      Parameters:
      searchEngineModificationName - The name according to the identification file reader.
      modificationProvider - The modification provider to use.
      searchParameters - The search parameters.
      Returns:
      The mass of the modification.
    • getMassAndromeda

      public static double getMassAndromeda​(String searchEngineModificationName, ModificationProvider modificationProvider, SearchParameters searchParameters)
      Returns the mass indicated by the Andromeda for the given modification.
      Parameters:
      searchEngineModificationName - The name according to the identification file reader.
      modificationProvider - The modification provider to use.
      searchParameters - The search parameters.
      Returns:
      The mass of the modification.