com.compomics.util.preferences

Class GenePreferences

java.lang.Object

com.compomics.util.preferences.GenePreferences

All Implemented Interfaces:

Serializable

public class GenePreferences
extends Object
implements Serializable

Contains methods for downloading gene and GO mappings.

Author:

Harald Barsnes

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	GENE_MAPPING_FILE_SUFFIX The suffix to use for files containing gene mappings.
static String	GO_MAPPING_FILE_SUFFIX The suffix to use for files containing GO mappings.

Constructor Summary

Constructors

Constructor and Description
GenePreferences() Create a new GenePreferences object.
GenePreferences(GenePreferences genePreferences) Creates new gene preferences based on a GenePreferences object.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	clearOldMappings(String currentEnsemblSpeciesType, String selectedSpecies, boolean commandLine) Clears the gene and GO mappings for the currently selected species.
void	createDefaultGeneMappingFiles(File aEnsemblVersionsFile, File aGoDomainsFile, File aSpeciesFile, File aDefaultSpeciesGoMappingsFile, File aDefaultSpeciesGeneMappingFile) Insert the default gene mappings files.
void	downloadGeneMappings(String ensemblType, String ensemblSchemaName, String selectedSpecies, String ensemblVersion, WaitingHandler waitingHandler) Download the gene mappings.
boolean	downloadGoMappings(String ensemblType, String ensemblSchemaName, String selectedSpecies, boolean swissProtMapping, WaitingHandler waitingHandler) Download the GO mappings.
boolean	downloadMappings(WaitingHandler waitingHandler, String currentEnsemblSpeciesType, String selectedSpecies, boolean commandLine) Try to download the gene and GO mappings for the currently selected species.
HashMap<String,ArrayList<String>>	getAllSpecies() Return the species lists.
HashMap<String,HashMap<String,String>>	getAllSpeciesMap() Returns the species map.
String	getCurrentSpecies() Returns the current species.
String	getCurrentSpeciesType() Returns the current species type.
String	getEnsemblDatabaseName(String speciesName) Deprecated. use the one with the Ensembl type parameter instead
String	getEnsemblDatabaseName(String ensemblType, String speciesName) Returns the Ensembl database name corresponding to a species name according to the speciesMap.
String	getEnsemblSpeciesVersion(String speciesName) Deprecated. use getEnsemblSpeciesVersion(String ensemblType, String speciesName) instead
String	getEnsemblSpeciesVersion(String ensemblType, String speciesName) Returns the Ensembl version for the given species name.
String	getEnsemblVersion(String ensemblDatabase) Returns the Ensembl version corresponding to the given Ensembl database according to the ensemblVersionsMap.
HashMap<String,String>	getEnsemblVersionsMap() Returns the Ensembl versions map.
static File	getGeneMappingFolder() Returns the path to the folder containing the gene mapping files.
HashMap<String,String>	getGoDomainMap() Returns the GO domain map, e.g., key: GO term: GO:0007568, element: biological_process.
static String	getProteinEvidencAsString(Integer type) Return the protein evidence type as text.
ArrayList<String>	getSpecies() Deprecated. use getAllSpecies instead
HashMap<String,String>	getSpeciesMap() Deprecated. use getAllSpeciesMap instead
void	loadEnsemblSpeciesVersions(File ensemblVersionsFile) Loads the given Ensembl species file.
boolean	loadGeneMappings(String jarFilePath, WaitingHandler waitingHandler) Imports the gene mappings.
void	loadSpeciesAndGoDomains() Load the mapping files.
void	setCurrentSpecies(String currentSpecies) Set the current species.
void	setCurrentSpeciesType(String currentSpeciesType) Set the current species type.
static void	setGeneMappingFolder(String geneMappingFolder) Sets the folder where gene mappings are saved.
void	updateEnsemblVersion(String selectedSpecies, String ensemblVersion) Update the Ensembl version for the given species.

Methods inherited from class java.lang.Object

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

Field Detail

GENE_MAPPING_FILE_SUFFIX

public static final String GENE_MAPPING_FILE_SUFFIX

The suffix to use for files containing gene mappings.

See Also:

Constant Field Values

GO_MAPPING_FILE_SUFFIX

public static final String GO_MAPPING_FILE_SUFFIX

The suffix to use for files containing GO mappings.

See Also:

Constant Field Values

Constructor Detail

GenePreferences

public GenePreferences()

Create a new GenePreferences object.

GenePreferences

public GenePreferences(GenePreferences genePreferences)

Creates new gene preferences based on a GenePreferences object.

Parameters:

genePreferences -

Method Detail

getProteinEvidencAsString

public static String getProteinEvidencAsString(Integer type)

Return the protein evidence type as text.

Parameters:

type - the type of evidence

Returns:

the protein evidence type as text

downloadGoMappings

public boolean downloadGoMappings(String ensemblType,
                         String ensemblSchemaName,
                         String selectedSpecies,
                         boolean swissProtMapping,
                         WaitingHandler waitingHandler)
                           throws MalformedURLException,
                                  IOException

Download the GO mappings.

Parameters:

ensemblType - the Ensembl type, e.g., default or plants

ensemblSchemaName - the Ensembl schema name, e.g., default or plants_mart_18

selectedSpecies -

swissProtMapping - if true, use the uniprot_swissprot_accession parameter, if false use the uniprot_sptrembl parameter

waitingHandler -

Returns:

true of the downloading was OK

Throws:

MalformedURLException

IOException

downloadGeneMappings

public void downloadGeneMappings(String ensemblType,
                        String ensemblSchemaName,
                        String selectedSpecies,
                        String ensemblVersion,
                        WaitingHandler waitingHandler)
                          throws MalformedURLException,
                                 IOException,
                                 IllegalArgumentException

Download the gene mappings.

Parameters:

ensemblType - the Ensembl type, e.g., default or plants

ensemblSchemaName - the Ensembl schema name, e.g., default or plants_mart_18

selectedSpecies -

ensemblVersion -

waitingHandler -

Throws:

MalformedURLException

IOException

IllegalArgumentException

getGeneMappingFolder

public static File getGeneMappingFolder()

Returns the path to the folder containing the gene mapping files.

Returns:

the gene mapping folder

setGeneMappingFolder

public static void setGeneMappingFolder(String geneMappingFolder)

Sets the folder where gene mappings are saved.

Parameters:

geneMappingFolder - the folder where gene mappings are saved

getCurrentSpecies

public String getCurrentSpecies()

Returns the current species.

Returns:

the currentSpecies

setCurrentSpecies

public void setCurrentSpecies(String currentSpecies)

Set the current species.

Parameters:

currentSpecies - the currentSpecies to set

getCurrentSpeciesType

public String getCurrentSpeciesType()

Returns the current species type.

Returns:

the currentSpeciesType

setCurrentSpeciesType

public void setCurrentSpeciesType(String currentSpeciesType)

Set the current species type.

Parameters:

currentSpeciesType - the currentSpeciesType to set

createDefaultGeneMappingFiles

public void createDefaultGeneMappingFiles(File aEnsemblVersionsFile,
                                 File aGoDomainsFile,
                                 File aSpeciesFile,
                                 File aDefaultSpeciesGoMappingsFile,
                                 File aDefaultSpeciesGeneMappingFile)

Insert the default gene mappings files. If newer versions of the mapping exists they will not be overwritten.

Parameters:

aEnsemblVersionsFile -

aGoDomainsFile -

aSpeciesFile -

aDefaultSpeciesGoMappingsFile -

aDefaultSpeciesGeneMappingFile -

loadSpeciesAndGoDomains

public void loadSpeciesAndGoDomains()
                             throws IOException,
                                    IllegalArgumentException

Load the mapping files.

Throws:

IOException

IllegalArgumentException

getGoDomainMap

public HashMap<String,String> getGoDomainMap()

Returns the GO domain map, e.g., key: GO term: GO:0007568, element: biological_process.

Returns:

the goDomainMap

getSpeciesMap

public HashMap<String,String> getSpeciesMap()

Deprecated. use getAllSpeciesMap instead

Returns the species map. Key: latin name, element: Ensembl database name, e.g., key: Homo sapiens, element: hsapiens.

Returns:

the speciesMap

getAllSpeciesMap

public HashMap<String,HashMap<String,String>> getAllSpeciesMap()

Returns the species map. Main key: Ensembl type, e.g., Vertebrates or Plants. Next level: key: latin name, element: ensembl database name, e.g., key: Homo sapiens, element: hsapiens_gene_ensembl.

Returns:

the speciesMap

getEnsemblDatabaseName

public String getEnsemblDatabaseName(String speciesName)

Deprecated. use the one with the Ensembl type parameter instead

Returns the Ensembl database name corresponding to a species name according to the speciesMap. Null if not found.

Parameters:

speciesName - the species name as available in the species list

Returns:

the Ensembl database name

getEnsemblDatabaseName

public String getEnsemblDatabaseName(String ensemblType,
                            String speciesName)

Returns the Ensembl database name corresponding to a species name according to the speciesMap. Null if not found.

Parameters:

ensemblType - the Ensembl type, e.g., Vertebrates or Plants

speciesName - the species name as available in the species list

Returns:

the Ensembl database name

getEnsemblVersionsMap

public HashMap<String,String> getEnsemblVersionsMap()

Returns the Ensembl versions map.

Returns:

the ensemblVersionsMap

getEnsemblVersion

public String getEnsemblVersion(String ensemblDatabase)

Returns the Ensembl version corresponding to the given Ensembl database according to the ensemblVersionsMap. Null if not found.

Parameters:

ensemblDatabase - the Ensembl database

Returns:

the Ensembl version

getEnsemblSpeciesVersion

public String getEnsemblSpeciesVersion(String speciesName)

Deprecated. use getEnsemblSpeciesVersion(String ensemblType, String speciesName) instead

Returns the Ensembl version for the given species name. Null if not found.

Parameters:

speciesName - the species name as available in the species list

Returns:

the Ensembl version

getEnsemblSpeciesVersion

public String getEnsemblSpeciesVersion(String ensemblType,
                              String speciesName)

Returns the Ensembl version for the given species name. Null if not found.

Parameters:

ensemblType - the Ensembl type, e.g., Vertebrates or Plants

speciesName - the species name as available in the species list

Returns:

the Ensembl version

getSpecies

public ArrayList<String> getSpecies()

Deprecated. use getAllSpecies instead

Return the species list. NB: also contains species separators.

Returns:

the species

getAllSpecies

public HashMap<String,ArrayList<String>> getAllSpecies()

Return the species lists.

Returns:

the species

updateEnsemblVersion

public void updateEnsemblVersion(String selectedSpecies,
                        String ensemblVersion)
                          throws IOException

Update the Ensembl version for the given species.

Parameters:

selectedSpecies - the database name of the species to update, e.g., hsapiens_gene_ensembl

ensemblVersion - the new Ensembl version

Throws:

IOException

loadEnsemblSpeciesVersions

public void loadEnsemblSpeciesVersions(File ensemblVersionsFile)
                                throws FileNotFoundException,
                                       IOException

Loads the given Ensembl species file.

Parameters:

ensemblVersionsFile - the Ensembl species file to load

Throws:

FileNotFoundException

IOException

loadGeneMappings

public boolean loadGeneMappings(String jarFilePath,
                       WaitingHandler waitingHandler)

Imports the gene mappings.

Parameters:

jarFilePath - the jar file path

waitingHandler - the waiting handler

Returns:

a boolean indicating whether the loading was successful

clearOldMappings

public boolean clearOldMappings(String currentEnsemblSpeciesType,
                       String selectedSpecies,
                       boolean commandLine)

Clears the gene and GO mappings for the currently selected species.

Parameters:

currentEnsemblSpeciesType - the species type

selectedSpecies - the species

commandLine - if command line of not

Returns:

true if no errors

downloadMappings

public boolean downloadMappings(WaitingHandler waitingHandler,
                       String currentEnsemblSpeciesType,
                       String selectedSpecies,
                       boolean commandLine)

Try to download the gene and GO mappings for the currently selected species.

Parameters:

waitingHandler - the waiting handler

currentEnsemblSpeciesType - the species type

selectedSpecies - the species

commandLine - command line or GUI?

Returns:

true if no errors