Class ModificationTemplate

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

public class ModificationTemplate
extends Object
This class holds a template for a Modification, meaning that it contains all shared characteristics of a Modification, but not the instance-specific one. As such, instances can be treated as singletons and are obviously immutable by nature.
Author:
Lennart Martens
  • Field Summary

    Fields 
    Modifier and Type Field Description
    protected boolean iArtifact
    Boolean to indicate whether this modification is an artifact.
    protected String iCode
    The code for this modification (eg., Mox).
    protected HashMap iMassDeltas
    This HashMap will contain the following 'key-value' mappings: (key > value)
    (residue > double[]{MONOISOTOPIC_DELTA, AVERAGE_DELTA})
    protected String iTitle
    The title for this modification (eg., Oxidation Met).
  • Constructor Summary

    Constructors 
    Constructor Description
    ModificationTemplate()
    Empty default constructor
    ModificationTemplate​(String aTitle, String aCode, HashMap aMassDeltas)
    This constructor allows initialization of all the properties for the modification template.
    ModificationTemplate​(String aTitle, String aCode, HashMap aMassDeltas, boolean aArtifact)
    This constructor allows initialization of all the properties for the modification template.
  • 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.
    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.
    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

    • iMassDeltas

      protected HashMap iMassDeltas
      This HashMap will contain the following 'key-value' mappings: (key > value)
      (residue > double[]{MONOISOTOPIC_DELTA, AVERAGE_DELTA})
    • iCode

      protected String iCode
      The code for this modification (eg., Mox).
    • iTitle

      protected String iTitle
      The title for this modification (eg., Oxidation Met).
    • iArtifact

      protected boolean iArtifact
      Boolean to indicate whether this modification is an artifact.
  • Constructor Details

    • ModificationTemplate

      public ModificationTemplate()
      Empty default constructor
    • ModificationTemplate

      public ModificationTemplate​(String aTitle, String aCode, HashMap aMassDeltas)
      This constructor allows initialization of all the properties for the modification template.
      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.
    • ModificationTemplate

      public ModificationTemplate​(String aTitle, String aCode, HashMap aMassDeltas, boolean aArtifact)
      This constructor allows initialization of all the properties for the modification template.
      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 class is an artifact.
  • 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.
      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'.
      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'.
      Returns:
      String with the title for the modification.
    • getResidues

      public Collection getResidues()
      This method reports on all the residues that can be modified by this Modification.
      The Collection is a keySet of a HashMap.
      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.
      Parameters:
      aResidue - String with the residue for which the mass delta needs to be calculated.
      Returns:
      double with the monoisotopic mass difference.
    • isArtifact

      public boolean isArtifact()
      This method indicates whether this modification is considered an artifact.
      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(), Hashtable
    • 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:
      Object.equals(Object), Hashtable
    • toString

      public 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.
    • 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'.

      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.