eu.isas.peptideshaker.utils

Class StarHider

java.lang.Object

eu.isas.peptideshaker.utils.StarHider

public class StarHider
extends Object

This class provides information whether a hit should be hidden or starred.

Author:

Marc Vaudel, Harald Barsnes

Constructor Summary

Constructors

Constructor and Description

StarHider(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.gui.filtering.FilterParameters filterParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog, int nThreads, com.compomics.util.exceptions.ExceptionHandler exceptionHandler) Constructor.

Method Summary

Modifier and Type	Method and Description
void	hidePeptide(long matchKey) Hides a peptide match.
void	hideProtein(long matchKey) Hides a protein match.
void	hidePsm(long matchKey) Hides a PSM match.
boolean	isPeptideHidden(long matchKey) Tests whether a peptide match should be hidden according to the implemented filters.
boolean	isPeptideStarred(long matchKey) Tests whether a peptide match should be starred according to the implemented filters.
boolean	isProteinHidden(long matchKey) Tests whether a protein match should be hidden according to the implemented filters.
boolean	isProteinStarred(long matchKey) Tests whether a protein match should be starred according to the implemented filters.
boolean	isPsmHidden(long matchKey) Tests whether a PSM match should be hidden according to the implemented filters.
boolean	isPsmStarred(long matchKey) Tests whether a PSM match should be starred according to the implemented filters.
void	starHide() Updates the star/hide status of all identification items.
void	starPeptide(long matchKey) Stars a peptide match.
void	starProtein(long matchKey) Stars a protein match.
void	starPsm(long matchKey) Stars a PSM match.
void	unHidePeptide(long matchKey) Unhides a peptide match.
void	unHideProtein(long matchKey) Unhides a protein match.
void	unHidePsm(long matchKey) Unhides a psm match.
void	unStarPeptide(long matchKey) Unstars a peptide match.
void	unStarProtein(long matchKey) Unstars a protein match.
void	unStarPsm(long matchKey) Unstars a PSM match.

Methods inherited from class java.lang.Object

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

Constructor Detail

StarHider

public StarHider(com.compomics.util.experiment.identification.Identification identification,
                 com.compomics.util.gui.filtering.FilterParameters filterParameters,
                 com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                 com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider,
                 com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                 com.compomics.util.experiment.biology.genes.GeneMaps geneMaps,
                 com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator,
                 com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                 com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics,
                 com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog,
                 int nThreads,
                 com.compomics.util.exceptions.ExceptionHandler exceptionHandler)

Constructor.

Parameters:

identification - The identification.

filterParameters - The filter parameters.

sequenceProvider - The sequence provider.

proteinDetailsProvider - The protein details provider.

spectrumProvider - The spectrum provider.

geneMaps - The gene maps.

identificationFeaturesGenerator - The identification features generator.

identificationParameters - The identification parameters.

metrics - The metrics.

progressDialog - The progress dialog.

nThreads - The number of threads.

exceptionHandler - The exception handler.

Method Detail

starHide

public void starHide()

Updates the star/hide status of all identification items.

starProtein

public void starProtein(long matchKey)

Stars a protein match.

Parameters:

matchKey - the key of the match

unStarProtein

public void unStarProtein(long matchKey)

Unstars a protein match.

Parameters:

matchKey - the key of the match

hideProtein

public void hideProtein(long matchKey)

Hides a protein match.

Parameters:

matchKey - the key of the match

unHideProtein

public void unHideProtein(long matchKey)

Unhides a protein match.

Parameters:

matchKey - the key of the match

starPeptide

public void starPeptide(long matchKey)

Stars a peptide match.

Parameters:

matchKey - the key of the match

unStarPeptide

public void unStarPeptide(long matchKey)

Unstars a peptide match.

Parameters:

matchKey - the key of the match

hidePeptide

public void hidePeptide(long matchKey)

Hides a peptide match.

Parameters:

matchKey - the key of the match

unHidePeptide

public void unHidePeptide(long matchKey)

Unhides a peptide match.

Parameters:

matchKey - the key of the match

starPsm

public void starPsm(long matchKey)

Stars a PSM match.

Parameters:

matchKey - the key of the match

unStarPsm

public void unStarPsm(long matchKey)

Unstars a PSM match.

Parameters:

matchKey - the key of the match

hidePsm

public void hidePsm(long matchKey)

Hides a PSM match.

Parameters:

matchKey - the key of the match

unHidePsm

public void unHidePsm(long matchKey)

Unhides a psm match.

Parameters:

matchKey - the key of the match

isProteinHidden

public boolean isProteinHidden(long matchKey)

Tests whether a protein match should be hidden according to the implemented filters.

Parameters:

matchKey - the key of the match

Returns:

a boolean indicating whether a protein match should be hidden according to the implemented filters

isPeptideHidden

public boolean isPeptideHidden(long matchKey)

Tests whether a peptide match should be hidden according to the implemented filters.

Parameters:

matchKey - the key of the match

Returns:

a boolean indicating whether a protein match should be hidden according to the implemented filters

isPsmHidden

public boolean isPsmHidden(long matchKey)

Tests whether a PSM match should be hidden according to the implemented filters.

Parameters:

matchKey - the key of the match

Returns:

a boolean indicating whether a protein match should be hidden according to the implemented filters

isProteinStarred

public boolean isProteinStarred(long matchKey)

Tests whether a protein match should be starred according to the implemented filters.

Parameters:

matchKey - the key of the match

Returns:

a boolean indicating whether a protein match should be hidden according to the implemented filters

isPeptideStarred

public boolean isPeptideStarred(long matchKey)

Tests whether a peptide match should be starred according to the implemented filters.

Parameters:

matchKey - the key of the match

Returns:

a boolean indicating whether a protein match should be hidden according to the implemented filters

isPsmStarred

public boolean isPsmStarred(long matchKey)

Tests whether a PSM match should be starred according to the implemented filters.

Parameters:

matchKey - the key of the match

Returns:

a boolean indicating whether a protein match should be hidden according to the implemented filters