eu.isas.peptideshaker.utils

Class PsdbParent

java.lang.Object

eu.isas.peptideshaker.preferences.UserPreferencesParent

eu.isas.peptideshaker.utils.PsdbParent

All Implemented Interfaces:

AutoCloseable

Direct Known Subclasses:

FollowUpCLI, MzidCLI, PeptideShakerCLI, ReportCLI

public class PsdbParent
extends UserPreferencesParent
implements AutoCloseable

Implementing this abstract class allows interacting with a psdb files.

Author:

Marc Vaudel, Harald Barsnes

Field Summary

Fields

Modifier and Type	Field and Description
protected File	dbFolder The folder where the database is stored.
protected DisplayParameters	displayParameters The display parameters.
protected com.compomics.util.gui.filtering.FilterParameters	filterParameters The filter parameters.
protected com.compomics.util.experiment.biology.genes.GeneMaps	geneMaps The gene maps.
protected com.compomics.util.experiment.identification.Identification	identification The identification.
protected com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator	identificationFeaturesGenerator The identification features generator.
protected com.compomics.util.parameters.identification.IdentificationParameters	identificationParameters The identification parameters.
protected com.compomics.util.experiment.identification.peptide_shaker.Metrics	metrics The metrics stored during processing.
protected com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler	msFileHandler The mass spectrometry file handler.
protected ProjectDetails	projectDetails The project details.
com.compomics.util.experiment.ProjectParameters	projectParameters All parameters of a project.
protected com.compomics.util.parameters.peptide_shaker.ProjectType	projectType The project type.
protected com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider	proteinDetailsProvider The protein details provider.
protected File	psdbFile The currently loaded psdb file.
protected com.compomics.util.experiment.io.biology.protein.SequenceProvider	sequenceProvider The sequence provider.
protected com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters	spectrumCountingParameters The spectrum counting preferences.

Fields inherited from class eu.isas.peptideshaker.preferences.UserPreferencesParent

userPreferences

Constructor Summary

Constructors

Constructor and Description
PsdbParent() Empty constructor for instantiation purposes.
PsdbParent(File dbFolder) Constructor.

Method Summary

Modifier and Type	Method and Description
void	close()
File	getDbFolder() Returns the folder where the database is stored.
DisplayParameters	getDisplayParameters() Returns the display preferences.
String	getExtendedProjectReport(String waitingHandlerReport) Returns an extended HTML project report.
com.compomics.util.gui.filtering.FilterParameters	getFilterParameters() Returns the filter preferences.
com.compomics.util.experiment.biology.genes.GeneMaps	getGeneMaps() Returns the gene maps.
com.compomics.util.experiment.identification.Identification	getIdentification() Returns the identification object.
com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator	getIdentificationFeaturesGenerator() Returns the identification features generator object.
com.compomics.util.parameters.identification.IdentificationParameters	getIdentificationParameters() Returns the identification parameters.
com.compomics.util.experiment.identification.peptide_shaker.Metrics	getMetrics() Returns the metrics object.
ProjectDetails	getProjectDetails() Returns the project details.
com.compomics.util.experiment.ProjectParameters	getProjectParameters() Returns the project parameters.
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.
File	getPsdbFile() Returns the psdb file.
boolean	getPsdbImportFromZip() Returns the psdb import from zip.
com.compomics.util.experiment.io.biology.protein.SequenceProvider	getSequenceProvider() Returns the sequence provider.
com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters	getSpectrumCountingParameters() Returns the spectrum counting preferences.
com.compomics.util.experiment.mass_spectrometry.SpectrumProvider	getSpectrumProvider() Returns the spectrum provider.
UserParameters	getUserParameters() Returns the user preferences.
com.compomics.util.experiment.io.biology.protein.FastaSummary	loadFastaFile(com.compomics.util.waiting.WaitingHandler waitingHandler) Loads the FASTA file.
void	loadPsdbFile(File dbFolder, com.compomics.util.waiting.WaitingHandler waitingHandler, boolean openFromZip) Loads the information from a psdb file.
void	loadPsdbFromZipFile(File zipFile, File dbFolder, com.compomics.util.waiting.WaitingHandler waitingHandler) Loads the information from a psdb file.
void	loadSpectrumFile(File spectrumFile, com.compomics.util.waiting.WaitingHandler waitingHandler) Adds a spectrum file to the spectrum provider.
boolean	loadSpectrumFile(String spectrumFileName, ArrayList<File> spectrumFiles, com.compomics.util.waiting.WaitingHandler waitingHandler) Loads the spectrum file.
boolean	loadSpectrumFiles(File folder, com.compomics.util.waiting.WaitingHandler waitingHandler) Loads the spectrum files.
boolean	loadSpectrumFiles(com.compomics.util.waiting.WaitingHandler waitingHandler) Loads the spectra in the spectrum factory.
void	resetIdentificationFeaturesGenerator() Resets the feature generator.
void	saveProject(com.compomics.util.waiting.WaitingHandler waitingHandler, boolean emptyCache) Saves the project in the psdb file.
void	setDbFolder(File dbFolder) Sets the folder where the database is stored.
void	setDefaultParameters() Sets the default preferences.
void	setDisplayParameters(DisplayParameters displayPreferences) Sets the display preferences.
void	setFilterParameters(com.compomics.util.gui.filtering.FilterParameters filterPreferences) Sets the filter preferences.
void	setGeneMaps(com.compomics.util.experiment.biology.genes.GeneMaps geneMaps) Sets the gene maps.
void	setIdentification(com.compomics.util.experiment.identification.Identification identification) Sets the identification object.
void	setIdentificationFeaturesGenerator(com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator) Sets the identification feature generator.
void	setIdentificationParameters(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters) Sets new identification parameters.
void	setMetrics(com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics) Sets the metrics.
void	setMsFileHandler(com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler msFileHandler) Sets the mass spectrometry file handler.
void	setProject(com.compomics.util.experiment.ProjectParameters projectParameters) Sets the project parameters.
void	setProjectDetails(ProjectDetails projectDetails) Sets the project details.
void	setProjectType(com.compomics.util.parameters.peptide_shaker.ProjectType projectType) Sets the project type.
void	setProteinDetailsProvider(com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider) Sets the protein details provider.
void	setPsdbFile(File psdbFile) Sets the psdb file.
void	setPsdbImportFromZip(boolean importFromZip) Sets that the psdb file is imported from a zip file.
void	setSequenceProvider(com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider) Sets the sequence provider.
void	setSpectrumCountingParameters(com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences) Sets the spectrum counting preferences.

Methods inherited from class eu.isas.peptideshaker.preferences.UserPreferencesParent

loadUserParameters, saveUserParameters

Methods inherited from class java.lang.Object

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

Field Detail

identification

protected com.compomics.util.experiment.identification.Identification identification

The identification.

identificationFeaturesGenerator

protected com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator

The identification features generator.

identificationParameters

protected com.compomics.util.parameters.identification.IdentificationParameters identificationParameters

The identification parameters.

spectrumCountingParameters

protected com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingParameters

The spectrum counting preferences.

projectDetails

protected ProjectDetails projectDetails

The project details.

metrics

protected com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics

The metrics stored during processing.

sequenceProvider

protected com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider

The sequence provider.

proteinDetailsProvider

protected com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider

The protein details provider.

msFileHandler

protected com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler msFileHandler

The mass spectrometry file handler.

geneMaps

protected com.compomics.util.experiment.biology.genes.GeneMaps geneMaps

The gene maps.

filterParameters

protected com.compomics.util.gui.filtering.FilterParameters filterParameters

The filter parameters.

displayParameters

protected DisplayParameters displayParameters

The display parameters.

dbFolder

protected File dbFolder

The folder where the database is stored.

psdbFile

protected File psdbFile

The currently loaded psdb file.

projectParameters

public com.compomics.util.experiment.ProjectParameters projectParameters

All parameters of a project.

projectType

protected com.compomics.util.parameters.peptide_shaker.ProjectType projectType

The project type.

Constructor Detail

PsdbParent

public PsdbParent()

Empty constructor for instantiation purposes.

PsdbParent

public PsdbParent(File dbFolder)

Constructor.

Parameters:

dbFolder - the folder where the database is stored.

Method Detail

loadPsdbFromZipFile

public void loadPsdbFromZipFile(File zipFile,
                                File dbFolder,
                                com.compomics.util.waiting.WaitingHandler waitingHandler)
                         throws IOException

Loads the information from a psdb file.

Parameters:

zipFile - the zip file containing the psdb file

dbFolder - the folder where to extract the project

waitingHandler - a waiting handler displaying feedback to the user. Ignored if null

Throws:

IOException - thrown if an error occurred while reading the file

loadPsdbFile

public void loadPsdbFile(File dbFolder,
                         com.compomics.util.waiting.WaitingHandler waitingHandler,
                         boolean openFromZip)
                  throws IOException

Loads the information from a psdb file.

Parameters:

dbFolder - the folder where to untar the project

waitingHandler - a waiting handler displaying feedback to the user. Ignored if null

openFromZip - flag determining if pdsb file was opened from a zip file

Throws:

IOException - thrown of IOException occurs exception thrown whenever an error occurred while reading or writing a file

saveProject

public void saveProject(com.compomics.util.waiting.WaitingHandler waitingHandler,
                        boolean emptyCache)
                 throws IOException

Saves the project in the psdb file.

Parameters:

waitingHandler - waiting handler displaying feedback to the user. can be null.

emptyCache - if true the cache will be emptied

Throws:

IOException - thrown of IOException occurs exception thrown whenever an error occurred while writing the file

loadSpectrumFiles

public boolean loadSpectrumFiles(com.compomics.util.waiting.WaitingHandler waitingHandler)
                          throws IOException

Loads the spectra in the spectrum factory.

Parameters:

waitingHandler - a waiting handler displaying progress to the user. Can be null.

Returns:

a boolean indicating whether the loading was successful

Throws:

IOException - thrown of IOException occurs exception thrown whenever an error occurred loading the spectrum files

loadSpectrumFiles

public boolean loadSpectrumFiles(File folder,
                                 com.compomics.util.waiting.WaitingHandler waitingHandler)
                          throws IOException

Loads the spectrum files.

Parameters:

folder - The folder to look into. Can be null.

waitingHandler - The waiting handler displaying progress to the user. Can be null.

Returns:

a boolean indicating whether the loading was successful

Throws:

IOException - Exception thrown whenever an error occurred while reading or writing a file.

loadSpectrumFile

public boolean loadSpectrumFile(String spectrumFileName,
                                ArrayList<File> spectrumFiles,
                                com.compomics.util.waiting.WaitingHandler waitingHandler)
                         throws IOException

Loads the spectrum file.

Parameters:

spectrumFileName - The name of the spectrum file.

spectrumFiles - The list to add the detected spectrum files to.

waitingHandler - The waiting handler displaying progress to the user. Can be null.

Returns:

A boolean indicating whether the loading was successful.

Throws:

IOException - Exception thrown whenever an error occurred while reading or writing a file

loadSpectrumFile

public void loadSpectrumFile(File spectrumFile,
                             com.compomics.util.waiting.WaitingHandler waitingHandler)
                      throws IOException

Adds a spectrum file to the spectrum provider.

Parameters:

spectrumFile - The spectrum file to add.

waitingHandler - The waiting handler.

Throws:

IOException - Exception thrown whenever an error occurred while reading or writing a file

loadFastaFile

public com.compomics.util.experiment.io.biology.protein.FastaSummary loadFastaFile(com.compomics.util.waiting.WaitingHandler waitingHandler)
                                                                            throws IOException

Loads the FASTA file.

Parameters:

waitingHandler - a waiting handler displaying progress to the user. Can be null

Returns:

the FASTA summary

Throws:

IOException - exception thrown if an error occurred while reading or writing the file

getIdentification

public com.compomics.util.experiment.identification.Identification getIdentification()

Returns the identification object.

Returns:

the identification object

getIdentificationFeaturesGenerator

public com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator getIdentificationFeaturesGenerator()

Returns the identification features generator object.

Returns:

the identification features generator object

getSpectrumCountingParameters

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

Returns the spectrum counting preferences.

Returns:

the spectrum counting preferences

getProjectDetails

public ProjectDetails getProjectDetails()

Returns the project details.

Returns:

the project details

getMetrics

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

Returns the metrics object.

Returns:

the metrics object

getGeneMaps

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

Returns the gene maps.

Returns:

the gene maps

getFilterParameters

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

Returns the filter preferences.

Returns:

the filter preferences

getDisplayParameters

public DisplayParameters getDisplayParameters()

Returns the display preferences.

Returns:

the display preferences

getPsdbFile

public File getPsdbFile()

Returns the psdb file.

Returns:

the psdb file

getPsdbImportFromZip

public boolean getPsdbImportFromZip()

Returns the psdb import from zip.

Returns:

the psdb import from zip

setIdentificationFeaturesGenerator

public void setIdentificationFeaturesGenerator(com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator)

Sets the identification feature generator.

Parameters:

identificationFeaturesGenerator - the identification feature generator

setSpectrumCountingParameters

public void setSpectrumCountingParameters(com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences)

Sets the spectrum counting preferences.

Parameters:

spectrumCountingPreferences - the spectrum counting preferences

setProjectDetails

public void setProjectDetails(ProjectDetails projectDetails)

Sets the project details.

Parameters:

projectDetails - the project details

setMetrics

public void setMetrics(com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics)

Sets the metrics.

Parameters:

metrics - the metrics

setGeneMaps

public void setGeneMaps(com.compomics.util.experiment.biology.genes.GeneMaps geneMaps)

Sets the gene maps.

Parameters:

geneMaps - the gene maps

getProjectParameters

public com.compomics.util.experiment.ProjectParameters getProjectParameters()

Returns the project parameters.

Returns:

the project parameters

setProject

public void setProject(com.compomics.util.experiment.ProjectParameters projectParameters)

Sets the project parameters.

Parameters:

projectParameters - the project parameters

setFilterParameters

public void setFilterParameters(com.compomics.util.gui.filtering.FilterParameters filterPreferences)

Sets the filter preferences.

Parameters:

filterPreferences - the filter preferences

setDisplayParameters

public void setDisplayParameters(DisplayParameters displayPreferences)

Sets the display preferences.

Parameters:

displayPreferences - the display preferences

setPsdbFile

public void setPsdbFile(File psdbFile)

Sets the psdb file.

Parameters:

psdbFile - the psdb file

setPsdbImportFromZip

public void setPsdbImportFromZip(boolean importFromZip)

Sets that the psdb file is imported from a zip file.

Parameters:

importFromZip - if the psdb was extracted from a zip file

getUserParameters

public UserParameters getUserParameters()

Returns the user preferences.

Returns:

the user preferences

setIdentification

public void setIdentification(com.compomics.util.experiment.identification.Identification identification)

Sets the identification object.

Parameters:

identification - the identification object

setDefaultParameters

public void setDefaultParameters()

Sets the default preferences.

resetIdentificationFeaturesGenerator

public void resetIdentificationFeaturesGenerator()

Resets the feature generator.

getIdentificationParameters

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

Returns the identification parameters.

Returns:

the identification parameters

setIdentificationParameters

public void setIdentificationParameters(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters)

Sets new identification parameters.

Parameters:

identificationParameters - the new identification parameters

getDbFolder

public File getDbFolder()

Returns the folder where the database is stored.

Returns:

the folder where the database is stored

setDbFolder

public void setDbFolder(File dbFolder)

Sets the folder where the database is stored.

Parameters:

dbFolder - the folder where the database is stored

getSequenceProvider

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

Returns the sequence provider.

Returns:

the sequence provider

getSpectrumProvider

public com.compomics.util.experiment.mass_spectrometry.SpectrumProvider getSpectrumProvider()

Returns the spectrum provider.

Returns:

the spectrum provider

setMsFileHandler

public void setMsFileHandler(com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler msFileHandler)

Sets the mass spectrometry file handler.

Parameters:

msFileHandler - The mass spectrometry file handler.

setSequenceProvider

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

Sets the sequence provider.

Parameters:

sequenceProvider - the sequence provider

getProteinDetailsProvider

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

Returns the protein details provider.

Returns:

the protein details provider

setProteinDetailsProvider

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

Sets the protein details provider.

Parameters:

proteinDetailsProvider - the protein details provider

getProjectType

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

Returns the project type.

Returns:

the project type

setProjectType

public void setProjectType(com.compomics.util.parameters.peptide_shaker.ProjectType projectType)

Sets the project type.

Parameters:

projectType - the project type

getExtendedProjectReport

public String getExtendedProjectReport(String waitingHandlerReport)

Returns an extended HTML project report.

Parameters:

waitingHandlerReport - the progress report, if null the report from the project details will be used

Returns:

an extended HTML project report

close

public void close()

Specified by:

close in interface AutoCloseable