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

Method Summary

Methods

Modifier and Type	Method and Description
void	addSpectrumMatch(String spectrumMatchKey) Add a spectrum match.
String	getKey() Returns the key of a match.
String	getMainMatchKey() Returns the key of the main match.
int	getSpectrumCount() Returns the number of spectra matched.
ArrayList<String>	getSpectrumMatches() Returns all spectra matched.
Peptide	getTheoreticPeptide() Getter for the theoretic peptide.
IdentificationMatch.MatchType	getType() Returns the type of match.
void	setMainMatch(String spectrumMatchKey) Sets the main 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.

PeptideMatch

public PeptideMatch(Peptide peptide,
            String spectrumMatchKey,
            String matchKey)

Constructor for the peptide match.

Parameters:

peptide - The matching peptide

spectrumMatchKey - The key of the main spectrum match

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

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

getMainMatchKey

public String getMainMatchKey()

Returns the key of the main match.

Returns:

the main match key

setMainMatch

public void setMainMatch(String spectrumMatchKey)

Sets the main match.

Parameters:

spectrumMatchKey - the key of the main match

getSpectrumMatches

public ArrayList<String> getSpectrumMatches()

Returns all spectra matched.

Returns:

all spectrum matches

addSpectrumMatch

public void addSpectrumMatch(String spectrumMatchKey)

Add a spectrum match.

Parameters:

spectrumMatchKey - 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