Class PtmToPrideMap

All Implemented Interfaces:
Serializable

public class PtmToPrideMap
extends ExperimentObject
Map linking user modification names to Unimod CV terms.
Author:
Marc Vaudel, Harald Barsnes
See Also:
Serialized Form
  • Field Details

  • Constructor Details

  • Method Details

    • getCVTerm

      public CvTerm getCVTerm​(String ptmName)
      Returns the CV term corresponding to the given PTM name. Null if not found.
      Parameters:
      ptmName - the PTM name
      Returns:
      the corresponding CV term
    • putCVTerm

      public void putCVTerm​(String modName, CvTerm cvTerm)
      Puts a new mapping in the map. If the modification name is already loaded it will be silently overwritten.
      Parameters:
      modName - the modification name
      cvTerm - the corresponding cvTerm
    • getDefaultCVTerm

      public static CvTerm getDefaultCVTerm​(String ptmName)
      Deprecated.
      use the getCvTerm method for the PTM instead
      Returns the default cvTerm of a modification when it exists.
      Parameters:
      ptmName - the PTM name according to the XML file, null if no mapping is found
      Returns:
      a default CV term
    • loadPtmToPrideMap

      public static PtmToPrideMap loadPtmToPrideMap​(SearchParameters searchParameters) throws FileNotFoundException, IOException, ClassNotFoundException
      Deprecated.
      the CV term is now part of the PTM object
      Loads the PRIDE to PTM map from the user folder or creates a new one if the file is not present. Loads a default mapping if a PTM is not mapped.
      Parameters:
      searchParameters - the search parameters
      Returns:
      the PRIDE to PTM map
      Throws:
      FileNotFoundException - if a FileNotFoundException occurs
      IOException - if an IOException occurs
      ClassNotFoundException - if a ClassNotFoundException occurs