uk.ac.ebi.pride.utilities.pia.modeller

Class PIAModeller

java.lang.Object

uk.ac.ebi.pride.utilities.pia.modeller.PIAModeller

public class PIAModeller
extends Object

This modeller handles all PIA data, started by the import of identifications, intermediate structure creation and displaying of PSMs, peptides and proteins.

Author:

julian

Constructor Summary

Constructors

Constructor and Description
PIAModeller() Creates a modeller for the new creation of a intermediate structure using as many threads as processors are available.
PIAModeller(int nrThreads, boolean oboLookup) Creates a modeller for the new creation of a intermediate structure using only the specified number of threads
PIAModeller(String pathname) Creates a modeller which loads the intermediate structure from a file using as many threads as processors are available.
PIAModeller(String pathname, int nrThreads, boolean oboLookup) Creates a modeller which loads the intermediate structure from a file using only the specified number of threads

Method Summary

Methods

Modifier and Type	Method and Description
Integer	addFile(String pathname) Adds a file to the input files.
Integer	addFileAndImportSpectra(String pathname, List<AbstractFilter> filters) Adds a file to the input files and adds the filtered PSMs to the structure creator.
Integer	addFileAndImportSpectra(String pathname, List<AbstractFilter> filters, String cacheScoreAccession) Adds a file to the input files and adds the filtered PSMs to the structure creator.
Integer	addPrideControllerAsInput(uk.ac.ebi.pride.utilities.data.controller.DataAccessController controller) Adds a DataAccessController as source for import.
IntermediateStructure	buildIntermediateStructure() This method builds the intermediate structure with the data of the input files.
void	close() As some controllers should be closed, do this here.
DataImportController	getImportController(Integer fileID) Returns the DataImportController of the given file.
Set<Integer>	getImportControllerIds() Returns the IDs of the input controllers
IntermediateStructure	getIntermediateStructure() Returns the IntermediateStructure created or loaded by this modeller.
ProteinModeller	getProteinModeller() Returns the associated ProteinModeller
PSMModeller	getPSMModeller() Returns the associated PSMModeller
void	importAllDataFromFile(Integer fileID) Imports all spectrum identifications from the file to the structure creator.
void	importAllDataFromFile(Integer fileID, String cacheScoreAccession) Imports all spectrum identifications from the file to the structure creator.
void	importDataFromFile(Integer fileID, List<AbstractFilter> filters) Imports the filtered PSMs and adds them to the structure creator.
void	importDataFromFile(Integer fileID, List<AbstractFilter> filters, String cacheScoreAccession) Imports the filtered PSMs and adds them to the structure creator.

Methods inherited from class java.lang.Object

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

Constructor Detail

PIAModeller

public PIAModeller()

Creates a modeller for the new creation of a intermediate structure using as many threads as processors are available.

PIAModeller

public PIAModeller(int nrThreads,
           boolean oboLookup)

Creates a modeller for the new creation of a intermediate structure using only the specified number of threads

PIAModeller

public PIAModeller(String pathname)

Creates a modeller which loads the intermediate structure from a file using as many threads as processors are available.

PIAModeller

public PIAModeller(String pathname,
           int nrThreads,
           boolean oboLookup)

Creates a modeller which loads the intermediate structure from a file using only the specified number of threads

Method Detail

close

public void close()

As some controllers should be closed, do this here.

addFile

public Integer addFile(String pathname)

Adds a file to the input files.

This must be called before the intermediate structure is created.

Parameters:

pathname -

Returns:

the ID of the file

addPrideControllerAsInput

public Integer addPrideControllerAsInput(uk.ac.ebi.pride.utilities.data.controller.DataAccessController controller)

Adds a DataAccessController as source for import. Does the same as addFile(String) for other files.

Parameters:

controller -

Returns:

addFileAndImportSpectra

public Integer addFileAndImportSpectra(String pathname,
                              List<AbstractFilter> filters)

Adds a file to the input files and adds the filtered PSMs to the structure creator. Filtering is ok, if the used inference methods are not interfered by it.

This must be called before the intermediate structure is created.

Parameters:

pathname -

Returns:

the ID of the file

addFileAndImportSpectra

public Integer addFileAndImportSpectra(String pathname,
                              List<AbstractFilter> filters,
                              String cacheScoreAccession)

Adds a file to the input files and adds the filtered PSMs to the structure creator. Filtering is ok, if the used inference methods are not interfered by it.

Additionally, for the given score accession the scores will be cached for fast access, if the controller supports it.

This must be called before the intermediate structure is created.

Parameters:

pathname -

Returns:

the ID of the file

importAllDataFromFile

public void importAllDataFromFile(Integer fileID)

Imports all spectrum identifications from the file to the structure creator.

Parameters:

fileID -

importAllDataFromFile

public void importAllDataFromFile(Integer fileID,
                         String cacheScoreAccession)

Imports all spectrum identifications from the file to the structure creator. If score caching is supported, cache the given score name.

Parameters:

fileID -

importDataFromFile

public void importDataFromFile(Integer fileID,
                      List<AbstractFilter> filters)

Imports the filtered PSMs and adds them to the structure creator.

Parameters:

fileID -

importDataFromFile

public void importDataFromFile(Integer fileID,
                      List<AbstractFilter> filters,
                      String cacheScoreAccession)

Imports the filtered PSMs and adds them to the structure creator. If score caching is supported, cache the given score name.

Parameters:

fileID -

buildIntermediateStructure

public IntermediateStructure buildIntermediateStructure()

This method builds the intermediate structure with the data of the input files. The function can be called only once for a PIAModeller(), after all files are added.

Returns:

getImportController

public DataImportController getImportController(Integer fileID)

Returns the DataImportController of the given file.

Parameters:

fileID -

Returns:

getImportControllerIds

public Set<Integer> getImportControllerIds()

Returns the IDs of the input controllers

Returns:

getIntermediateStructure

public IntermediateStructure getIntermediateStructure()

Returns the IntermediateStructure created or loaded by this modeller.

Returns:

getPSMModeller

public PSMModeller getPSMModeller()

Returns the associated PSMModeller

Is initialized after the intermediate structure is created or loaded

Returns:

getProteinModeller

public ProteinModeller getProteinModeller()

Returns the associated ProteinModeller

Is initialized after the intermediate structure is created or loaded

Returns: