Package eu.isas.peptideshaker

Class PeptideShaker

java.lang.Object

eu.isas.peptideshaker.PeptideShaker

public class PeptideShaker
extends Object

This class will be responsible for the identification import and the associated calculations.

Author:

Marc Vaudel, Harald Barsnes

Field Summary

Fields

Modifier and Type	Field	Description
static String	DATA_DIRECTORY	Folder where the data files are stored by default.
static final String	PEPTIDESHAKER_CONFIGURATION_FILE	Default PeptideShaker modifications.
static final int	TIMEOUT_DAYS	Default time out in days.

Constructor Summary

Constructors

Constructor	Description
PeptideShaker(com.compomics.util.experiment.ProjectParameters projectParameters)	Constructor without mass specification.

Method Summary

Modifier and Type	Method	Description
void	createProject(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.parameters.tools.ProcessingParameters processingParameters, com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingParameters, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, ProjectDetails projectDetails, com.compomics.util.parameters.peptide_shaker.ProjectType projectType, com.compomics.util.waiting.WaitingHandler waitingHandler, boolean setWaitingHandlerFinshedWhenDone, com.compomics.util.exceptions.ExceptionHandler exceptionHandler)	Creates a PeptideShaker project.
static File	getConfigFolder()	Returns the folder where the configuration files are stored.
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 used when loading the files.
static String	getJarFilePath()	Retrieves the path to the jar file.
static String	getMatchesDirectoryParent()	Returns the matches directory parent.
static File	getMatchesDirectoryParentFile()	Returns the matches directory parent.
static String	getMatchesDirectorySubPath()	Returns the directory used to store the identification matches.
static File	getMatchesFolder()	Returns the path to the matches folder according to the user path settings.
com.compomics.util.experiment.identification.peptide_shaker.Metrics	getMetrics()	Returns the metrics picked-up while loading the files.
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.
static String	getUserPreferencesFile()	Returns the file used for user preferences storage.
static String	getUserPreferencesFolder()	Returns the folder used for user preferences storage.
static String	getVersion()	Retrieves the version number set in the pom file.
int	importFiles(com.compomics.util.waiting.WaitingHandler waitingHandler, ArrayList<File> idFiles, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, ProjectDetails projectDetails, com.compomics.util.parameters.tools.ProcessingParameters processingParameters, com.compomics.util.exceptions.ExceptionHandler exceptionHandler)	Imports identification results from result files.
static void	instantiateFacories(com.compomics.util.parameters.UtilitiesUserParameters utilitiesUserPreferences)	Instantiates the spectrum, sequence, and PTM factories with caches adapted to the memory available as set in the user preferences.
static String	loadModifications(com.compomics.util.parameters.identification.search.SearchParameters searchParameters)	Verifies that the modifications backed-up in the search parameters are loaded and returns an error message if one was already loaded, null otherwise.
void	peptideMapChanged(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider)	Processes the identifications if a change occurred in the peptide map.
void	proteinMapChanged(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider)	Processes the identifications if a change occurred in the protein map.
static void	setConfigFolder(File aConfigFolder)	Set the config folder.
void	setGeneMaps(com.compomics.util.experiment.biology.genes.GeneMaps geneMaps)	Sets the gene maps.
static void	setMatchesDirectoryParent(String matchesDirectoryParent)	Sets the matches directory parent.
static void	setUserPreferencesFolder(String userPreferencesFolder)	Sets the file used for user preferences storage.
void	spectrumMapChanged(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.parameters.tools.ProcessingParameters processingPreferences, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.peptide_shaker.ProjectType projectType)	Processes the identifications if a change occurred in the PSM map.

Methods inherited from class java.lang.Object

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

Field Details

TIMEOUT_DAYS

public static final int TIMEOUT_DAYS

Default time out in days.

See Also:

• Constant Field Values

PEPTIDESHAKER_CONFIGURATION_FILE

public static final String PEPTIDESHAKER_CONFIGURATION_FILE

Default PeptideShaker modifications.

See Also:

• Constant Field Values

DATA_DIRECTORY

public static String DATA_DIRECTORY

Folder where the data files are stored by default. Should be the same as in SearchGUI.

Constructor Details

PeptideShaker

public PeptideShaker(com.compomics.util.experiment.ProjectParameters projectParameters)

Constructor without mass specification. Calculation will be done on new maps which will be retrieved as compomics utilities parameters.

Parameters:

projectParameters - the experiment conducted

Method Details

importFiles

public int importFiles(com.compomics.util.waiting.WaitingHandler waitingHandler,
 ArrayList<File> idFiles,
 com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
 com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
 ProjectDetails projectDetails,
 com.compomics.util.parameters.tools.ProcessingParameters processingParameters,
 com.compomics.util.exceptions.ExceptionHandler exceptionHandler)

Imports identification results from result files.

Parameters:

waitingHandler - the handler displaying feedback to the user

idFiles - the files to import

spectrumProvider - the spectrum provider

identificationParameters - identification parameters

projectDetails - the project details

processingParameters - the initial processing preferences

exceptionHandler - the exception handler

Returns:

0 if the import went fine, 1 otherwise

createProject

public void createProject(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
 com.compomics.util.parameters.tools.ProcessingParameters processingParameters,
 com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingParameters,
 com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
 ProjectDetails projectDetails,
 com.compomics.util.parameters.peptide_shaker.ProjectType projectType,
 com.compomics.util.waiting.WaitingHandler waitingHandler,
 boolean setWaitingHandlerFinshedWhenDone,
 com.compomics.util.exceptions.ExceptionHandler exceptionHandler)
                   throws InterruptedException,
TimeoutException,
IOException

Creates a PeptideShaker project.

Parameters:

identificationParameters - the identification parameters

processingParameters - the processing parameters

spectrumCountingParameters - the spectrum counting parameters

spectrumProvider - the spectrum provider

projectDetails - the project details

projectType - the project type

waitingHandler - the handler displaying feedback to the user

setWaitingHandlerFinshedWhenDone - if true, the waiting handler is set to finished when the project is created

exceptionHandler - handler for exceptions

Throws:

InterruptedException - exception thrown if a thread gets interrupted

TimeoutException - exception thrown if a process times out

IOException - if an exception occurs when parsing files

spectrumMapChanged

public void spectrumMapChanged(com.compomics.util.experiment.identification.Identification identification,
 com.compomics.util.waiting.WaitingHandler waitingHandler,
 com.compomics.util.parameters.tools.ProcessingParameters processingPreferences,
 com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
 com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
 com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
 com.compomics.util.parameters.peptide_shaker.ProjectType projectType)

Processes the identifications if a change occurred in the PSM map.

Parameters:

identification - the identification object containing the identification matches

waitingHandler - the waiting handler

processingPreferences - the processing preferences

identificationParameters - the identification parameters

sequenceProvider - a protein sequence provider

spectrumProvider - the spectrum provider

projectType - the project type

peptideMapChanged

public void peptideMapChanged(com.compomics.util.experiment.identification.Identification identification,
 com.compomics.util.waiting.WaitingHandler waitingHandler,
 com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
 com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
 com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider)

Processes the identifications if a change occurred in the peptide map.

Parameters:

identification - the identification object containing the identification matches

waitingHandler - the waiting handler

identificationParameters - the identification parameters

sequenceProvider - a protein sequence provider

spectrumProvider - the spectrum provider

proteinMapChanged

public void proteinMapChanged(com.compomics.util.experiment.identification.Identification identification,
 com.compomics.util.waiting.WaitingHandler waitingHandler,
 com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
 com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider)

Processes the identifications if a change occurred in the protein map.

Parameters:

identification - the identification object containing the identification matches

waitingHandler - the waiting handler

identificationParameters - the identification parameters

sequenceProvider - a protein sequence provider

getMetrics

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

Returns the metrics picked-up while loading the files.

Returns:

the metrics picked-up while loading the files

getGeneMaps

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

Returns the gene maps.

Returns:

the gene maps

getIdentification

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

Returns the identification object.

Returns:

the identification object

getSequenceProvider

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

Returns the sequence provider.

Returns:

the sequence provider

getProteinDetailsProvider

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

Returns the protein details provider.

Returns:

the protein details provider

setGeneMaps

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

Sets the gene maps.

Parameters:

geneMaps - the new gene maps

getIdentificationFeaturesGenerator

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

Returns the identification features generator used when loading the files.

Returns:

the identification features generator used when loading the files

loadModifications

public static String loadModifications(com.compomics.util.parameters.identification.search.SearchParameters searchParameters)

Verifies that the modifications backed-up in the search parameters are loaded and returns an error message if one was already loaded, null otherwise.

Parameters:

searchParameters - the search parameters to load

Returns:

an error message if one was already loaded, null otherwise

getUserPreferencesFile

public static String getUserPreferencesFile()

Returns the file used for user preferences storage.

Returns:

the file used for user preferences storage

getUserPreferencesFolder

public static String getUserPreferencesFolder()

Returns the folder used for user preferences storage.

Returns:

the folder used for user preferences storage

setUserPreferencesFolder

public static void setUserPreferencesFolder(String userPreferencesFolder)

Sets the file used for user preferences storage.

Parameters:

userPreferencesFolder - the folder used for user preferences storage

getMatchesDirectorySubPath

public static String getMatchesDirectorySubPath()

Returns the directory used to store the identification matches.

Returns:

the directory used to store the identification matches

getMatchesDirectoryParent

public static String getMatchesDirectoryParent()

Returns the matches directory parent. An empty string if not set. Can be a relative path.

Returns:

the matches directory parent

getMatchesDirectoryParentFile

public static File getMatchesDirectoryParentFile()

Returns the matches directory parent. An empty string if not set.

Returns:

the matches directory parent

setMatchesDirectoryParent

public static void setMatchesDirectoryParent(String matchesDirectoryParent)
                                      throws IOException

Sets the matches directory parent.

Parameters:

matchesDirectoryParent - the matches directory parent

Throws:

IOException - thrown of an exception occurs

getMatchesFolder

public static File getMatchesFolder()

Returns the path to the matches folder according to the user path settings.

Returns:

the path to the match folder according to the user path settings

instantiateFacories

public static void instantiateFacories(com.compomics.util.parameters.UtilitiesUserParameters utilitiesUserPreferences)

Instantiates the spectrum, sequence, and PTM factories with caches adapted to the memory available as set in the user preferences.

Parameters:

utilitiesUserPreferences - the user preferences

getVersion

public static String getVersion()

Retrieves the version number set in the pom file.

Returns:

the version number of PeptideShaker

getJarFilePath

public static String getJarFilePath()

Retrieves the path to the jar file.

Returns:

the path to the jar file

getConfigFolder

public static File getConfigFolder()

Returns the folder where the configuration files are stored.

Returns:

the folder where the configuration files are stored

setConfigFolder

public static void setConfigFolder(File aConfigFolder)

Set the config folder.

Parameters:

aConfigFolder - the config folder