Package com.compomics.util.interfaces

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 final int
    AVERAGE
    Constant to indicate the position of the average mass in the mass array.
    static final String
    CTERMINUS
    The residue code for the C-terminus.
    static final int
    MONOISOTOPIC
    Constant to indicate the position of the monoisotopic mass in the mass array.
    static final 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

    • MONOISOTOPIC

      static final int MONOISOTOPIC
      Constant to indicate the position of the monoisotopic mass in the mass array.
      See Also:

    • AVERAGE

      static final int AVERAGE
      Constant to indicate the position of the average mass in the mass array.
      See Also:

    • NTERMINUS

      static final String NTERMINUS
      The residue code for the N-terminus.
      See Also:

    • CTERMINUS

      static final String CTERMINUS
      The residue code for the C-terminus.
      See Also:

  • 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.