com.compomics.util.experiment.identification.matches

Class ModificationMatch

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.identification.matches.ModificationMatch

All Implemented Interfaces:

Serializable, Cloneable

public class ModificationMatch
extends ExperimentObject

This class models the match between theoretic PTM and identification results.

Author:

Marc Vaudel

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
ModificationMatch(String theoreticPtm, boolean variable, int modifiedSite) Constructor for a modification match.

Method Summary

Modifier and Type	Method and Description
ModificationMatch	clone() Clones the modification match into a new match with the same attributes.
int	getModificationSite() Getter for the modification site, 1 is the first amino acid.
String	getTheoreticPtm() Getter for the theoretic PTM name.
boolean	isConfident() Returns a boolean indicating whether the modification is confidently localized on the sequence.
boolean	isInferred() Returns a boolean indicating whether the modification is inferred from another peptide.
boolean	isSameAs(ModificationMatch anotherModificationMatch) Indicates whether this modification match is the same of another one.
boolean	isVariable() Returns a boolean indicating if the modification is variable.
void	setConfident(boolean confident) Sets whether the modification is confidently localized on the sequence.
void	setInferred(boolean inferred) Sets whether the modification is inferred from another peptide.
void	setModificationSite(int site) Setter for the modification site, 1 is the first amino acid.
void	setTheoreticPtm(String ptm) Sets the theoretic PTM.

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

addUrParam, getParameterKey, getUrParam

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ModificationMatch

public ModificationMatch(String theoreticPtm,
                         boolean variable,
                         int modifiedSite)

Constructor for a modification match.

Parameters:

theoreticPtm - the theoretic PTM

variable - true for variable modifications, false otherwise

modifiedSite - the position of the modification in the sequence, 1 is the first residue

Method Detail

isVariable

public boolean isVariable()

Returns a boolean indicating if the modification is variable.

Returns:

a boolean indicating if the modification is variable

getTheoreticPtm

public String getTheoreticPtm()

Getter for the theoretic PTM name.

Returns:

the theoretic PTM name

setTheoreticPtm

public void setTheoreticPtm(String ptm)

Sets the theoretic PTM.

Parameters:

ptm - the theoretic PTM name

getModificationSite

public int getModificationSite()

Getter for the modification site, 1 is the first amino acid.

Returns:

the index of the modification in the sequence

setModificationSite

public void setModificationSite(int site)

Setter for the modification site, 1 is the first amino acid.

Parameters:

site - the index of the modification in the sequence

isConfident

public boolean isConfident()

Returns a boolean indicating whether the modification is confidently localized on the sequence.

Returns:

a boolean indicating whether the modification is confidently localized on the sequence

setConfident

public void setConfident(boolean confident)

Sets whether the modification is confidently localized on the sequence.

Parameters:

confident - a boolean indicating whether the modification is confidently localized on the sequence

isInferred

public boolean isInferred()

Returns a boolean indicating whether the modification is inferred from another peptide.

Returns:

a boolean indicating whether the modification is inferred from another peptide

setInferred

public void setInferred(boolean inferred)

Sets whether the modification is inferred from another peptide.

Parameters:

inferred - a boolean indicating whether the modification is inferred from another peptide

isSameAs

public boolean isSameAs(ModificationMatch anotherModificationMatch)

Indicates whether this modification match is the same of another one. The match is only compared based on the theoretic PTM and the variability. The localization and its confidence is not taken into account.

Parameters:

anotherModificationMatch - another modification match

Returns:

a boolean indicating whether both modification matches are the same.

clone

public ModificationMatch clone()

Clones the modification match into a new match with the same attributes.

Overrides:

clone in class Object

Returns:

a new modification match with the same attributes