uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl

Class PrideImportController

java.lang.Object

uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl.PrideImportController

All Implemented Interfaces:

DataImportController

public class PrideImportController
extends Object
implements DataImportController

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PrideImportController.InputFileType Defines the input file type

Constructor Summary

Constructors

Constructor and Description
PrideImportController(uk.ac.ebi.pride.utilities.data.controller.DataAccessController controller, IntermediateStructureCreator structCreator) Creates an import controller for the given DataAccessController
PrideImportController(File inputFile, IntermediateStructureCreator structCreator) Creates an import controller guessing the file type
PrideImportController(File inputFile, PrideImportController.InputFileType fileType, IntermediateStructureCreator structCreator) Creates an import controller for the given file type.

Method Summary

Methods

Modifier and Type	Method and Description
String	addProteinsSpectrumIdentificationsToStructCreator(Comparable proteinId, List<AbstractFilter> filters, String cacheScoreAccession) Adds the spectrum identifications of a single protein to the structure creator.
void	addSpectrumIdentificationsToStructCreator(List<AbstractFilter> filters) Adds the filtered PSMs to the IntermediateStructureCreator.
void	addSpectrumIdentificationsToStructCreator(List<AbstractFilter> filters, String cacheScoreAccession) Adds the filtered PSMs to the IntermediateStructureCreator.
void	close() Some controllers should be closed after usage.
uk.ac.ebi.pride.utilities.data.controller.DataAccessController	getController() Returns the actual controller.
String	getID() Returns the ID of the controller.
String	getInputFileName() Returns the file name which is handled by this controller

Methods inherited from class java.lang.Object

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

Constructor Detail

PrideImportController

public PrideImportController(File inputFile,
                     PrideImportController.InputFileType fileType,
                     IntermediateStructureCreator structCreator)

Creates an import controller for the given file type.

Parameters:

inputFile -

fileType -

PrideImportController

public PrideImportController(File inputFile,
                     IntermediateStructureCreator structCreator)

Creates an import controller guessing the file type

Parameters:

inputFile -

fileType -

PrideImportController

public PrideImportController(uk.ac.ebi.pride.utilities.data.controller.DataAccessController controller,
                     IntermediateStructureCreator structCreator)

Creates an import controller for the given DataAccessController

Parameters:

inputFile -

fileType -

Method Detail

getID

public String getID()

Description copied from interface: DataImportController

Returns the ID of the controller.

Specified by:

getID in interface DataImportController

Returns:

getInputFileName

public String getInputFileName()

Description copied from interface: DataImportController

Returns the file name which is handled by this controller

Specified by:

getInputFileName in interface DataImportController

Returns:

getController

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

Returns the actual controller.

Returns:

close

public void close()

Description copied from interface: DataImportController

Some controllers should be closed after usage.

Specified by:

close in interface DataImportController

addSpectrumIdentificationsToStructCreator

public void addSpectrumIdentificationsToStructCreator(List<AbstractFilter> filters)

Description copied from interface: DataImportController

Adds the filtered PSMs to the IntermediateStructureCreator. Filtering is ok, if the used inference methods are not interfered by it.

Specified by:

addSpectrumIdentificationsToStructCreator in interface DataImportController

addSpectrumIdentificationsToStructCreator

public void addSpectrumIdentificationsToStructCreator(List<AbstractFilter> filters,
                                             String cacheScoreAccession)

Description copied from interface: DataImportController

Adds the filtered PSMs to the IntermediateStructureCreator. Filtering is ok, if the used inference methods are not interfered by it.

If the controller supports caching of scores, the score with the given accession will be cached for fast access, which might require slightly more memory.

Specified by:

addSpectrumIdentificationsToStructCreator in interface DataImportController

addProteinsSpectrumIdentificationsToStructCreator

public String addProteinsSpectrumIdentificationsToStructCreator(Comparable proteinId,
                                                       List<AbstractFilter> filters,
                                                       String cacheScoreAccession)

Adds the spectrum identifications of a single protein to the structure creator.

Parameters:

proteinId -

structCreator -

Returns:

the protein accession of the inserted protein