Package com.compomics.util.protein

Class ModificationImplementation

java.lang.Object
com.compomics.util.protein.ModificationImplementation
All Implemented Interfaces:
Modification, Cloneable, Comparable
public class ModificationImplementation extends Object implements Modification, Cloneable
This class implements a specific Modification.
Author:
Lennart Martens

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    protected int
    iLocation
    The location for the modification in the parent sequence.
    protected ModificationTemplate
    iTemplate
    The ModificationTemplate which holds all the shared information for a modification.

    Fields inherited from interface com.compomics.util.interfaces.Modification

    AVERAGE, CTERMINUS, MONOISOTOPIC, NTERMINUS

  • Constructor Summary

    Constructors
    Constructor
    Description
    ModificationImplementation()
    Empty default constructor
    ModificationImplementation(ModificationTemplate aTemplate, int aLocation)
    This constructor allows initialization of all the properties for the modification.
    ModificationImplementation(String aTitle, String aCode, HashMap aMassDeltas, boolean aArtifact, int aLocation)
    This constructor allows initialization of all the properties for the modification.
    ModificationImplementation(String aTitle, String aCode, HashMap aMassDeltas, int aLocation)
    This constructor allows initialization of all the properties for the modification.

  • Method Summary

    Modifier and Type
    Method
    Description
    Object
    clone()
    Override of the clone method.
    int
    compareTo(Object o)
    Compares this object with the specified object for order.
    boolean
    equals(Object obj)
    Indicates whether some other object is "equal to" this one.
    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.
    protected double
    getMassDelta(String aResidue, int aMonoOrAvg)
    This method returns the mass delta for the specified residue, measured either monoisotopically or averaged.
    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.
    int
    hashCode()
    Returns a hash code value for the object.
    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 class java.lang.Object

    finalize, getClass, notify, notifyAll, wait, wait, wait

  • Field Details

    • iTemplate

      protected ModificationTemplate iTemplate
      The ModificationTemplate which holds all the shared information for a modification. It is to be considered a singleton and it is immutable.

    • iLocation

      protected int iLocation
      The location for the modification in the parent sequence.

  • Constructor Details

    • ModificationImplementation

      public ModificationImplementation()
      Empty default constructor

    • ModificationImplementation

      public ModificationImplementation(ModificationTemplate aTemplate, int aLocation)
      This constructor allows initialization of all the properties for the modification.
      Parameters:
      aTemplate - ModificationTemplate with the shared information for this modification
      aLocation - int with the location of this modification in the parent sequence.

    • ModificationImplementation

      public ModificationImplementation(String aTitle, String aCode, HashMap aMassDeltas, int aLocation)
      This constructor allows initialization of all the properties for the modification.
      Parameters:
      aTitle - String with the title for the modification (eg., Oxidation Met).
      aCode - String with the code for the modification (eg., Mox). The code can be used when annotating a sequence String (eg., NH2-MGTEFSM<Mox>R-COOH).
      aMassDeltas - HashMap with the following 'key-value' mappings: (key > value)
      (residue > double[]{MONOISOTOPIC_DELTA, AVERAGE_DELTA}
      Note that the residues for the N-terminus and C-terminus are represented by the NTERMINUS and CTERMINUS constants, respectively.
      aLocation - int with the location for this modification.

    • ModificationImplementation

      public ModificationImplementation(String aTitle, String aCode, HashMap aMassDeltas, boolean aArtifact, int aLocation)
      This constructor allows initialization of all the properties for the modification.
      Parameters:
      aTitle - String with the title for the modification (eg., Oxidation Met).
      aCode - String with the code for the modification (eg., Mox). The code can be used when annotating a sequence String (eg., NH2-MGTEFSM<Mox>R-COOH).
      aMassDeltas - HashMap with the following 'key-value' mappings: (key > value)
      (residue > double[]{MONOISOTOPIC_DELTA, AVERAGE_DELTA}
      Note that the residues for the N-terminus and C-terminus are represented by the NTERMINUS and CTERMINUS constants, respectively.
      aArtifact - boolean to indicate whether this modification is an artifact.
      aLocation - int with the location for this modification.

  • Method Details

    • getAverageMassDelta

      public 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! When a residue was specified that is not affected by this modification, '0.0' is returned.
      Specified by:
      getAverageMassDelta in interface Modification
      Parameters:
      aResidue - String with the residue for which the mass delta needs to be calculated.
      Returns:
      double with the average mass difference.

    • getCode

      public String getCode()
      This method returns the short code for the modification, eg. 'Mox'.
      Specified by:
      getCode in interface Modification
      Returns:
      String with the short code for the modification. Can be used to annotate a sequence.

    • getTitle

      public String getTitle()
      This method returns the title of the modification, eg. 'Oxidation Met'.
      Specified by:
      getTitle in interface Modification
      Returns:
      String with the title for the modification.

    • getLocation

      public 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.
      Specified by:
      getLocation in interface Modification
      Returns:
      int with the location for the modification.

    • getResidues

      public Collection getResidues()
      This method reports on all the residues that can be modified by this Modification.
      Specified by:
      getResidues in interface Modification
      Returns:
      Collection with the residues that can be modified by this modification.

    • getMonoisotopicMassDelta

      public 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! When a residue was specified that is not affected by this modification, '0.0' is returned.
      Specified by:
      getMonoisotopicMassDelta in interface Modification
      Parameters:
      aResidue - String with the residue for which the mass delta needs to be calculated.
      Returns:
      double with the monoisotopic mass difference.

    • setLocation

      public 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.
      Specified by:
      setLocation in interface Modification
      Parameters:
      aLocation - int with the location for this modification within the parent sequence.

    • isArtifact

      public boolean isArtifact()
      This method indicates whether this modification is considered an artifact.
      Specified by:
      isArtifact in interface Modification
      Returns:
      boolean that indicates whether this modification is an artifact.

    • equals

      public boolean equals(Object obj)
      Indicates whether some other object is "equal to" this one. For this class comparison is based on:
      • class identity
      • title equality
      • location equality
      Overrides:
      equals in class Object
      Parameters:
      obj - the reference object with which to compare.
      Returns:
      true if this object is the same as the obj argument; false otherwise.
      See Also:

    • hashCode

      public int hashCode()
      Returns a hash code value for the object. This method is supported for the benefit of hashtables such as those provided by java.util.Hashtable.

      The general contract of hashCode is:

      • Whenever it is invoked on the same object more than once during an execution of a Java application, the hashCode method must consistently return the same integer, provided no information used in equals comparisons on the object is modified. This integer need not remain consistent from one execution of an application to another execution of the same application.
      • If two objects are equal according to the equals(Object) method, then calling the hashCode method on each of the two objects must produce the same integer result.
      • It is not required that if two objects are unequal according to the Object.equals(Object) method, then calling the hashCode method on each of the two objects must produce distinct integer results. However, the programmer should be aware that producing distinct integer results for unequal objects may improve the performance of hashtables.

      As much as is reasonably practical, the hashCode method defined by class Object does return distinct integers for distinct objects. (This is typically implemented by converting the internal address of the object into an integer, but this implementation technique is not required by the Java programming language.)

      Overrides:
      hashCode in class Object
      Returns:
      a hash code value for this object.
      See Also:

    • toString

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

    • clone

      public Object clone()
      Override of the clone method. It doesn't do anything except making the method public and catching the 'CloneNotSupportedException'. The method now returns a 'null' when cloning was not possible.
      Overrides:
      clone in class Object
      Returns:
      Object with a clone of this class, or 'null' when the CloneNotSupportedException was thrown.

    • compareTo

      public int compareTo(Object o)
      Compares this object with the specified object for order. Returns a negative integer, zero, or a positive integer as this object is less than, equal to, or greater than the specified object.

      In this implementation, ordering is first done on location, and only if this is identical, the title is compared. Therefore, since equals uses title and location as well, two equals instances will compare to '0'.

      Specified by:
      compareTo in interface Comparable
      Parameters:
      o - the Object to be compared.
      Returns:
      a negative integer, zero, or a positive integer as this object is less than, equal to, or greater than the specified object.
      Throws:
      ClassCastException - if the specified object's type prevents it from being compared to this Object.

    • getMassDelta

      protected double getMassDelta(String aResidue, int aMonoOrAvg)
      This method returns the mass delta for the specified residue, measured either monoisotopically or averaged.
      Parameters:
      aResidue - String with the residue for which the modification applies (value for the N-terminus is the NTERMINUS constant and for the C-terminus the CTERMINUS constant).
      aMonoOrAvg - int which should be either MONOISOTOPIC or AVERAGE
      Returns:
      double with the mass delta (can be negative, of course!) or '0.0' if this modification does not apply to the specified residue.