org.expasy.mzjava.proteomics.ms.ident

Class ModificationMatch

java.lang.Object

org.expasy.mzjava.proteomics.ms.ident.ModificationMatch

public class ModificationMatch
extends Object

Class to hold information on modifications that were found for a PSM. Each modification match has the measured mass shift and a list of 0 or more candidate Modifications.

Version:

sqrt -1

Author:

Oliver Horlacher

Constructor Summary

Constructors

Constructor and Description
ModificationMatch(double massShift, AminoAcid residue, Integer position, ModAttachment modAttachment) Create a ModificationMatch given a mass shift
ModificationMatch(Modification modification, AminoAcid residue, int position, ModAttachment modAttachment) Create a ModificationMatch given a modification.

Method Summary

Methods

Modifier and Type	Method and Description
void	addPotentialModification(Modification modification) Add a modification to the list of potential modifications
boolean	equals(Object o)
int	getCandidateCount() Returns the number of modification candidates
double	getMassShift() Returns the mass shift
ModAttachment	getModAttachment()
Modification	getModificationCandidate(int index)
int	getPosition()
AminoAcid	getResidue()
int	hashCode()
boolean	isWithinTolerance(Tolerance tolerance) Checks whether all modification candidates are within tolerance of the massShift.
String	toString()
String	toString(NumberFormat numberFormat)

Methods inherited from class java.lang.Object

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

Constructor Detail

ModificationMatch

public ModificationMatch(double massShift,
                 AminoAcid residue,
                 Integer position,
                 ModAttachment modAttachment)

Create a ModificationMatch given a mass shift

Parameters:

massShift - the modifications mass (negative if loss)

ModificationMatch

public ModificationMatch(Modification modification,
                 AminoAcid residue,
                 int position,
                 ModAttachment modAttachment)

Create a ModificationMatch given a modification. The massShift is set from the modifications mass.

Parameters:

modification - the modification

Method Detail

addPotentialModification

public void addPotentialModification(Modification modification)

Add a modification to the list of potential modifications

Parameters:

modification - the modification to add

getMassShift

public double getMassShift()

Returns the mass shift

Returns:

the mass shift

isWithinTolerance

public boolean isWithinTolerance(Tolerance tolerance)

Checks whether all modification candidates are within tolerance of the massShift.

Parameters:

tolerance - the tolerance

Returns:

true if all modification candidates are within tolerance, false otherwise

getResidue

public AminoAcid getResidue()

getPosition

public int getPosition()

getModAttachment

public ModAttachment getModAttachment()

toString

public String toString()

Overrides:

toString in class Object

toString

public String toString(NumberFormat numberFormat)

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

getCandidateCount

public int getCandidateCount()

Returns the number of modification candidates

Returns:

the number of modification candidates

getModificationCandidate

public Modification getModificationCandidate(int index)