eu.isas.peptideshaker.parameters

Class PeptideShakerParameters

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

eu.isas.peptideshaker.parameters.PeptideShakerParameters

All Implemented Interfaces:

com.compomics.util.experiment.personalization.UrParameter, Serializable

public class PeptideShakerParameters
extends com.compomics.util.experiment.personalization.ExperimentObject
implements com.compomics.util.experiment.personalization.UrParameter

This class stores parameters for a PeptideShaker project.

Author:

Marc Vaudel, Harald Barsnes

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static long	KEY The key of the object when stored in settings table of a psdb file.

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

NO_KEY

Constructor Summary

Constructors

Constructor and Description
PeptideShakerParameters() Empty default constructor.
PeptideShakerParameters(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences, ProjectDetails projectDetails, com.compomics.util.gui.filtering.FilterParameters filterPreferences, DisplayParameters displayPreferences, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.parameters.peptide_shaker.ProjectType projectType, com.compomics.util.experiment.identification.features.IdentificationFeaturesCache identificationFeaturesCache) Constructor for a PeptideShaker Settings class.

Method Summary

Modifier and Type	Method and Description
void	cleanProviders() Cleans the SequenceProvider and ProteinDetailsProvider, please use only temporary or if you know what you do
DisplayParameters	getDisplayParameters() Returns the GUI display parameters.
com.compomics.util.gui.filtering.FilterParameters	getFilterParameters() Returns the GUI display parameters.
com.compomics.util.experiment.biology.genes.GeneMaps	getGeneMaps() Returns the gene maps.
com.compomics.util.experiment.identification.features.IdentificationFeaturesCache	getIdentificationFeaturesCache() Returns the identification features cache used by the identification features generator before saving the file.
com.compomics.util.parameters.identification.IdentificationParameters	getIdentificationParameters() Returns the identification parameters.
com.compomics.util.experiment.identification.peptide_shaker.Metrics	getMetrics() Returns the metrics saved when loading the files.
long	getParameterKey()
ProjectDetails	getProjectDetails() Returns the project details.
com.compomics.util.parameters.peptide_shaker.ProjectType	getProjectType() Returns the project type.
com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider	getProteinDetailsProvider() Returns the protein details provider.
com.compomics.util.experiment.io.biology.protein.SequenceProvider	getSequenceProvider() Returns the sequence provider saved when loading the files.
com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters	getSpectrumCountingPreferences() Returns the spectrum counting preferences of the project.
void	setProteinDetailsProvider(com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider) Setter for the protein details provider
void	setSequenceProvider(com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider) Setter for the sequence provider

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

Field Detail

KEY

public static final long KEY

The key of the object when stored in settings table of a psdb file.

Constructor Detail

PeptideShakerParameters

public PeptideShakerParameters()

Empty default constructor.

PeptideShakerParameters

public PeptideShakerParameters(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                               com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences,
                               ProjectDetails projectDetails,
                               com.compomics.util.gui.filtering.FilterParameters filterPreferences,
                               DisplayParameters displayPreferences,
                               com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics,
                               com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                               com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider,
                               com.compomics.util.experiment.biology.genes.GeneMaps geneMaps,
                               com.compomics.util.parameters.peptide_shaker.ProjectType projectType,
                               com.compomics.util.experiment.identification.features.IdentificationFeaturesCache identificationFeaturesCache)

Constructor for a PeptideShaker Settings class.

Parameters:

identificationParameters - the parameters used for identification

spectrumCountingPreferences - the spectrum counting preferences

projectDetails - the project details

filterPreferences - the filter preferences

displayPreferences - the display preferences

metrics - the metrics saved when loading the files

sequenceProvider - the sequence provider

proteinDetailsProvider - the protein details provider

geneMaps - the gene maps

projectType - the project type

identificationFeaturesCache - the identification features cache

Method Detail

getIdentificationParameters

public com.compomics.util.parameters.identification.IdentificationParameters getIdentificationParameters()

Returns the identification parameters.

Returns:

the identification parameters

getSpectrumCountingPreferences

public com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters getSpectrumCountingPreferences()

Returns the spectrum counting preferences of the project.

Returns:

the spectrum counting preferences of the project

getProjectDetails

public ProjectDetails getProjectDetails()

Returns the project details.

Returns:

the project details

getFilterParameters

public com.compomics.util.gui.filtering.FilterParameters getFilterParameters()

Returns the GUI display parameters.

Returns:

the GUI display parameters

getDisplayParameters

public DisplayParameters getDisplayParameters()

Returns the GUI display parameters.

Returns:

the GUI display parameters

getMetrics

public com.compomics.util.experiment.identification.peptide_shaker.Metrics getMetrics()

Returns the metrics saved when loading the files.

Returns:

the metrics saved when loading the files

getSequenceProvider

public com.compomics.util.experiment.io.biology.protein.SequenceProvider getSequenceProvider()

Returns the sequence provider saved when loading the files.

Returns:

the sequence provider saved when loading the files

getProteinDetailsProvider

public com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider getProteinDetailsProvider()

Returns the protein details provider.

Returns:

the protein details provider

getGeneMaps

public com.compomics.util.experiment.biology.genes.GeneMaps getGeneMaps()

Returns the gene maps.

Returns:

the gene maps

getIdentificationFeaturesCache

public com.compomics.util.experiment.identification.features.IdentificationFeaturesCache getIdentificationFeaturesCache()

Returns the identification features cache used by the identification features generator before saving the file.

Returns:

the identification features cache

getParameterKey

public long getParameterKey()

Specified by:

getParameterKey in interface com.compomics.util.experiment.personalization.UrParameter

getProjectType

public com.compomics.util.parameters.peptide_shaker.ProjectType getProjectType()

Returns the project type.

Returns:

the project type

cleanProviders

public void cleanProviders()

Cleans the SequenceProvider and ProteinDetailsProvider, please use only temporary or if you know what you do

setSequenceProvider

public void setSequenceProvider(com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider)

Setter for the sequence provider

Parameters:

sequenceProvider - the sequence provider instance

setProteinDetailsProvider

public void setProteinDetailsProvider(com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider)

Setter for the protein details provider

Parameters:

proteinDetailsProvider - the protein details provider instance