Class ModificationFactory

java.lang.Object
com.compomics.util.protein.ModificationFactory

public class ModificationFactory
extends Object
This class can be used to generate a Modification instance from a code or title.
Modification information is loaded from files or database, as specified in the two available constructors for this Factory.
Author:
Lennart Martens
  • Method Details

    • getModification

      public static Modification getModification​(String aTitle, int aLocation)
      This method will return a Modification instance from a title.
      Parameters:
      aTitle - String with the title for a modification.
      aLocation - int with the location for the modification.
      Returns:
      Modification with the corresponding modification, or 'null' when the modification was not found.
    • getModification

      public static Modification getModification​(String aCode, String aResidue, int aLocation)
      This method takes a code and a residue (the residue for the N-terminus is NTERMINUS and for the C-terminus CTERMINUS!) and converts this into a Modification instance if possible.
      Parameters:
      aCode - String with the code for the modification
      aResidue - String with the residue carrying the modification (the residue for the N-terminus is defined in the constant NTERMINUS and for the C-terminus in the constant CTERMINUS!).
      aLocation - int with the location for the modification.
      Returns:
      Modification with the corresponding modification, or 'null' when the modification was not found.
    • modificationsToString

      public static String modificationsToString()
      Returns a String representation of the modifications.
      Returns:
      String with a String representation of the modification.
    • modificationConversionToString

      public static String modificationConversionToString()
      Returns a String representation of the modification title to code mappings.
      Returns:
      String with a String representation of the code tot title mappings.
    • reLoadAllData

      public static void reLoadAllData()
      This method can be used to refresh all data from the data store indicated in the ModificationFactory.properties file.
    • getAllModificationTitles

      public static String[] getAllModificationTitles()
      This method returns all modification titles known to the Factory.
      Returns:
      String[] with all the modification titles.