Package eu.isas.reporter.calculation

Class QuantificationFeaturesCache

java.lang.Object

eu.isas.reporter.calculation.QuantificationFeaturesCache

public class QuantificationFeaturesCache
extends Object

The quantification features cache stores quantification features.

Author:

Marc Vaudel, Harald Barsnes

Constructor Summary

Constructors

Constructor	Description
QuantificationFeaturesCache()	Constructor.

Method Summary

Modifier and Type	Method	Description
void	addPeptideMatchQuantificationDetails(int nPeptides, Long matchKey, PeptideQuantificationDetails matchQuantificationDetails)	Adds peptide quantification details ratio to the cache.
void	addProteinMatchQuantificationDetails(int nPeptides, long matchKey, ProteinQuantificationDetails matchQuantificationDetails)	Adds protein quantification details to the cache.
void	addPSMQuantificationDetails(String spectrumFile, String spectrumTitle, PsmQuantificationDetails matchQuantificationDetails)	Adds PSM quantification details ratio to the cache.
void	addPtmQuantificationDetails(String ptmName, long matchKey, int site, ProteinPtmQuantificationDetails matchQuantificationDetails)	Adds protein level PTM quantification details to the cache.
void	addSpectrumQuantificationDetails(String spectrumFile, String spectrumTitle, SpectrumQuantificationDetails matchQuantificationDetails)	Adds spectrum quantification details ratio to the cache.
PeptideQuantificationDetails	getPeptideMatchQuantificationDetails(int nPsms, Long matchKey)	Returns peptide quantification details, null if not in cache.
ProteinQuantificationDetails	getProteinMatchQuantificationDetails(int nPeptides, long matchKey)	Returns protein quantification details, null if not in cache.
PsmQuantificationDetails	getPSMQuantificationDetails(String spectrumFile, String spectrumTitle)	Returns PSM quantification details, null if not in cache.
ProteinPtmQuantificationDetails	getPtmQuantificationDetails(String ptmName, long matchKey, int site)	Returns protein level PTM quantification details, null if not in cache.
SpectrumQuantificationDetails	getSpectrumQuantificationDetails(String spectrumFile, String spectrumTitle)	Returns spectrum quantification details, null if not in cache.
boolean	isEmpty()	Indicates whether the cache is empty
boolean	memoryCheck()	Indicates whether the memory used by the application is lower than a given share of the heap size.

Methods inherited from class java.lang.Object

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

Constructor Details

QuantificationFeaturesCache

public QuantificationFeaturesCache()

Constructor.

Method Details

isEmpty

public boolean isEmpty()

Indicates whether the cache is empty

Returns:

true if the cache is empty

memoryCheck

public boolean memoryCheck()

Indicates whether the memory used by the application is lower than a given share of the heap size. The share is set by memoryShare.

Returns:

a boolean indicating whether the memory used by the application is lower than 99% of the heap

addProteinMatchQuantificationDetails

public void addProteinMatchQuantificationDetails(int nPeptides,
 long matchKey,
 ProteinQuantificationDetails matchQuantificationDetails)

Adds protein quantification details to the cache.

Parameters:

nPeptides - the number of peptides of this protein match

matchKey - the key of the protein match

matchQuantificationDetails - the protein quantification details

getProteinMatchQuantificationDetails

public ProteinQuantificationDetails getProteinMatchQuantificationDetails(int nPeptides,
 long matchKey)

Returns protein quantification details, null if not in cache.

Parameters:

nPeptides - the number of peptides of this protein match

matchKey - the key of the protein match

Returns:

the protein quantification details

addPtmQuantificationDetails

public void addPtmQuantificationDetails(String ptmName,
 long matchKey,
 int site,
 ProteinPtmQuantificationDetails matchQuantificationDetails)

Adds protein level PTM quantification details to the cache.

Parameters:

ptmName - the name of the PTM

matchKey - the key of the protein match

site - the site of the PTM on the protein sequence

matchQuantificationDetails - the protein quantification details

getPtmQuantificationDetails

public ProteinPtmQuantificationDetails getPtmQuantificationDetails(String ptmName,
 long matchKey,
 int site)

Returns protein level PTM quantification details, null if not in cache.

Parameters:

ptmName - the name of the PTM

matchKey - the key of the protein match

site - the site of the PTM on the protein sequence

Returns:

The protein quantification details

addPeptideMatchQuantificationDetails

public void addPeptideMatchQuantificationDetails(int nPeptides,
 Long matchKey,
 PeptideQuantificationDetails matchQuantificationDetails)

Adds peptide quantification details ratio to the cache.

Parameters:

nPeptides - the number of peptides of this protein match

matchKey - the key of the protein match

matchQuantificationDetails - The protein quantification details

getPeptideMatchQuantificationDetails

public PeptideQuantificationDetails getPeptideMatchQuantificationDetails(int nPsms,
 Long matchKey)

Returns peptide quantification details, null if not in cache.

Parameters:

nPsms - the number of PSMs of this peptide match

matchKey - the key of the peptide match

Returns:

the peptide quantification details

addPSMQuantificationDetails

public void addPSMQuantificationDetails(String spectrumFile,
 String spectrumTitle,
 PsmQuantificationDetails matchQuantificationDetails)

Adds PSM quantification details ratio to the cache.

Parameters:

spectrumFile - the spectrum file

spectrumTitle - the spectrum title

matchQuantificationDetails - the protein quantification details

getPSMQuantificationDetails

public PsmQuantificationDetails getPSMQuantificationDetails(String spectrumFile,
 String spectrumTitle)

Returns PSM quantification details, null if not in cache.

Parameters:

spectrumFile - the spectrum file

spectrumTitle - the spectrum title

Returns:

the PSM quantification details

addSpectrumQuantificationDetails

public void addSpectrumQuantificationDetails(String spectrumFile,
 String spectrumTitle,
 SpectrumQuantificationDetails matchQuantificationDetails)

Adds spectrum quantification details ratio to the cache.

Parameters:

spectrumFile - the spectrum file

spectrumTitle - the spectrum title

matchQuantificationDetails - the spectrum quantification details

getSpectrumQuantificationDetails

public SpectrumQuantificationDetails getSpectrumQuantificationDetails(String spectrumFile,
 String spectrumTitle)

Returns spectrum quantification details, null if not in cache.

Parameters:

spectrumFile - the spectrum file

spectrumTitle - the spectrum title

Returns:

the spectrum quantification details