Package 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

public class PeptideMatch
extends IdentificationMatch

This class models a peptide match.

Author:

Marc Vaudel, Dominik Kopczynski

See Also:

• Serialized Form

Nested Class Summary

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

IdentificationMatch.MatchType

Field Summary

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

NO_KEY

Constructor Summary

Constructors

Constructor	Description
PeptideMatch()	Default Constructor for the peptide match.
PeptideMatch(Peptide peptide, long matchKey, long spectrumMatchKey)	Constructor for the peptide match.

Method Summary

Modifier and Type	Method	Description
void	addSpectrumMatchKey(long spectrumMatchKey)	Add a spectrum match key.
long	getKey()	Returns the key of a match.
Peptide	getPeptide()	Getter for the peptide.
int	getSpectrumCount()	Returns the number of spectra matched.
long[]	getSpectrumMatchesKeys()	Returns the keys of all spectra matched.
IdentificationMatch.MatchType	getType()	Returns the type of match.
void	setKey(long newKey)	Sets a new key for the match.
void	setPeptide(Peptide peptide)	Setter for the peptide.
void	setSpectrumMatchesKeys(long[] spectrumMatchesKeys)	Sets the spectrum matches keys.

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

addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams

Methods inherited from class java.lang.Object

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

Constructor Details

PeptideMatch

public PeptideMatch()

Default Constructor for the peptide match.

PeptideMatch

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

Constructor for the peptide match.

Parameters:

peptide - the matching peptide

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

spectrumMatchKey - the key of a spectrum match linked to this peptide

Method Details

getKey

public long 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(long newKey)

Sets a new key for the match.

Parameters:

newKey - a new key for the match

getPeptide

public Peptide getPeptide()

Getter for the peptide.

Returns:

the peptide

setPeptide

public void setPeptide(Peptide peptide)

Setter for the peptide.

Parameters:

peptide - a peptide

getSpectrumMatchesKeys

public long[] getSpectrumMatchesKeys()

Returns the keys of all spectra matched.

Returns:

the keys of all spectrum matches

setSpectrumMatchesKeys

public void setSpectrumMatchesKeys(long[] spectrumMatchesKeys)

Sets the spectrum matches keys.

Parameters:

spectrumMatchesKeys - the keys

addSpectrumMatchKey

public void addSpectrumMatchKey(long 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