com.compomics.util.experiment.identification.matches

Class PeptideMatch

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.identification.IdentificationMatch

com.compomics.util.experiment.identification.matches.PeptideMatch

All Implemented Interfaces:

Serializable, Cloneable

public class PeptideMatch
extends IdentificationMatch

This class models a peptide match.

Author:

Marc Vaudel

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class com.compomics.util.experiment.identification.IdentificationMatch

IdentificationMatch.MatchType

Constructor Summary

Constructors

Constructor and Description
PeptideMatch() Constructor for the peptide match.
PeptideMatch(Peptide peptide, String matchKey) Constructor for the peptide match.

Method Summary

Modifier and Type	Method and Description
void	addSpectrumMatchKey(String spectrumMatchKey) Add a spectrum match key.
String	getKey() Returns the key of a match.
int	getSpectrumCount() Returns the number of spectra matched.
ArrayList<String>	getSpectrumMatchesKeys() Returns the keys of all spectra matched.
Peptide	getTheoreticPeptide() Getter for the theoretic peptide.
IdentificationMatch.MatchType	getType() Returns the type of match.
void	setKey(String newKey) Sets a new key for the match.
void	setTheoreticPeptide(Peptide theoreticPeptide) Setter for the theoretic peptide.

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

addUrParam, getParameterKey, getUrParam

Methods inherited from class java.lang.Object

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

Constructor Detail

PeptideMatch

public PeptideMatch()

Constructor for the peptide match.

PeptideMatch

public PeptideMatch(Peptide peptide,
                    String matchKey)

Constructor for the peptide match.

Parameters:

peptide - the matching peptide

matchKey - the key of the match as referenced in the identification.

Method Detail

getKey

public String getKey()

Description copied from class: IdentificationMatch

Returns the key of a match.

Specified by:

getKey in class IdentificationMatch

Returns:

the key of a match

setKey

public void setKey(String newKey)

Sets a new key for the match.

Parameters:

newKey - a new key for the match

getTheoreticPeptide

public Peptide getTheoreticPeptide()

Getter for the theoretic peptide.

Returns:

the theoretic peptide

setTheoreticPeptide

public void setTheoreticPeptide(Peptide theoreticPeptide)

Setter for the theoretic peptide.

Parameters:

theoreticPeptide - a theoretic peptide

getSpectrumMatchesKeys

public ArrayList<String> getSpectrumMatchesKeys()

Returns the keys of all spectra matched.

Returns:

the keys of all spectrum matches

addSpectrumMatchKey

public void addSpectrumMatchKey(String spectrumMatchKey)

Add a spectrum match key.

Parameters:

spectrumMatchKey - the key of a spectrum match

getSpectrumCount

public int getSpectrumCount()

Returns the number of spectra matched.

Returns:

spectrum count

getType

public IdentificationMatch.MatchType getType()

Description copied from class: IdentificationMatch

Returns the type of match.

Specified by:

getType in class IdentificationMatch

Returns:

the type of match