com.compomics.util.interfaces
Interface Modification

All Superinterfaces:
java.lang.Comparable
All Known Implementing Classes:
ModificationImplementation

public interface Modification
extends java.lang.Comparable

This interface describes the behaviour for a modification on a peptide or aminoacid sequence.

Author:
Lennart Martens

Field Summary
static int AVERAGE
          Constant to indicate the position of the average mass in the mass array.
static java.lang.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 java.lang.String NTERMINUS
          The residue code for the N-terminus.
 
Method Summary
 double getAverageMassDelta(java.lang.String aResidue)
          This method returns a double with the average mass difference conferred on the sequence by this modification for the specified residue.
 java.lang.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(java.lang.String aResidue)
          This method returns a double with the monoisotopic mass difference conferred on the sequence by this modification for the specified residue.
 java.util.Collection getResidues()
          This method reports on all the residues that can be modified by this Modification.
 java.lang.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.
 java.lang.String toString()
          This method returns a String representation of the Modification.
 
Methods inherited from interface java.lang.Comparable
compareTo
 

Field Detail

MONOISOTOPIC

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

See Also:
Constant Field Values

AVERAGE

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

See Also:
Constant Field Values

NTERMINUS

static final java.lang.String NTERMINUS
The residue code for the N-terminus.

See Also:
Constant Field Values

CTERMINUS

static final java.lang.String CTERMINUS
The residue code for the C-terminus.

See Also:
Constant Field Values
Method Detail

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

java.lang.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

java.lang.String getTitle()
This method returns the title of the modification, eg. 'Oxidation Met'.

Returns:
String with the title for the modification.

getMonoisotopicMassDelta

double getMonoisotopicMassDelta(java.lang.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(java.lang.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

java.util.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

java.lang.String toString()
This method returns a String representation of the Modification.

Overrides:
toString in class java.lang.Object
Returns:
String with a String Representation of the Modification.


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