Interface Modification

All Superinterfaces:
Comparable
All Known Implementing Classes:
ModificationImplementation

public interface Modification
extends Comparable
This interface describes the behaviour for a modification on a peptide or aminoacid sequence.
Author:
Lennart Martens
  • Field Summary

    Fields 
    Modifier and Type Field Description
    static int AVERAGE
    Constant to indicate the position of the average mass in the mass array.
    static String CTERMINUS
    The residue code for the C-terminus.
    static int MONOISOTOPIC
    Constant to indicate the position of the monoisotopic mass in the mass array.
    static String NTERMINUS
    The residue code for the N-terminus.
  • Method Summary

    Modifier and Type Method Description
    double getAverageMassDelta​(String aResidue)
    This method returns a double with the average mass difference conferred on the sequence by this modification for the specified residue.
    String getCode()
    This method returns the short code for the modification, eg.
    int getLocation()
    This method returns the location of the modification in the sequence.
    double getMonoisotopicMassDelta​(String aResidue)
    This method returns a double with the monoisotopic mass difference conferred on the sequence by this modification for the specified residue.
    Collection getResidues()
    This method reports on all the residues that can be modified by this Modification.
    String getTitle()
    This method returns the title of the modification, eg.
    boolean isArtifact()
    This method indicates whether this modification is considered an artifact.
    void setLocation​(int aLocation)
    This method allows the setting of the location for this modification.
    String toString()
    This method returns a String representation of the Modification.

    Methods inherited from interface java.lang.Comparable

    compareTo
  • Field Details

  • Method Details

    • getLocation

      int getLocation()
      This method returns the location of the modification in the sequence. Note that the N-terminus is 0, and the C-terminus is (sequence_length)+1.
      Returns:
      int with the location for the modification.
    • isArtifact

      boolean isArtifact()
      This method indicates whether this modification is considered an artifact.
      Returns:
      boolean that indicates whether this modification is an artifact.
    • getCode

      String getCode()
      This method returns the short code for the modification, eg. 'Mox'.
      Returns:
      String with the short code for the modification. Can be used to annotate a sequence.
    • getTitle

      String getTitle()
      This method returns the title of the modification, eg. 'Oxidation Met'.
      Returns:
      String with the title for the modification.
    • getMonoisotopicMassDelta

      double getMonoisotopicMassDelta​(String aResidue)
      This method returns a double with the monoisotopic mass difference conferred on the sequence by this modification for the specified residue. This mass delta can be negative!
      Parameters:
      aResidue - String with the residue for which the mass delta needs to be calculated.
      Returns:
      double with the monoisotopic mass difference.
    • getAverageMassDelta

      double getAverageMassDelta​(String aResidue)
      This method returns a double with the average mass difference conferred on the sequence by this modification for the specified residue. This mass delta can be negative!
      Parameters:
      aResidue - String with the residue for which the mass delta needs to be calculated.
      Returns:
      double with the average mass difference.
    • setLocation

      void setLocation​(int aLocation)
      This method allows the setting of the location for this modification. The specified integer should be calculated from the start of the parent sequence, where the N-terminus is 0, and the C-terminus is (sequence_length)+1.
      Parameters:
      aLocation - int with the location for this modification within the parent sequence.
    • getResidues

      Collection getResidues()
      This method reports on all the residues that can be modified by this Modification.
      Returns:
      Collection with the residues that can be modified by this modification.
    • toString

      String toString()
      This method returns a String representation of the Modification.
      Overrides:
      toString in class Object
      Returns:
      String with a String Representation of the Modification.