public class GenePreferences
extends java.lang.Object
implements java.io.Serializable
Modifier and Type | Field and Description |
---|---|
static java.lang.String |
GENE_MAPPING_FILE_SUFFIX
The suffix to use for files containing gene mappings.
|
static java.lang.String |
GENE_MAPPING_FOLDER
The folder where gene mapping related info is stored.
|
static java.lang.String |
GO_MAPPING_FILE_SUFFIX
The suffix to use for files containing GO mappings.
|
Constructor and Description |
---|
GenePreferences()
Create a new GenePreferences object.
|
GenePreferences(GenePreferences genePreferences)
Creates new gene preferences based on a GenePreferences object.
|
Modifier and Type | Method and Description |
---|---|
void |
createDefaultGeneMappingFiles(java.io.File aEnsemblVersionsFile,
java.io.File aGoDomainsFile,
java.io.File aSpeciesFile,
java.io.File aDefaultSpeciesGoMappingsFile,
java.io.File aDefaultSpeciesGeneMappingFile)
Insert the default gene mappings files.
|
void |
downloadGeneMappings(java.lang.String ensemblType,
java.lang.String ensemblSchemaName,
java.lang.String selectedSpecies,
java.lang.String ensemblVersion,
WaitingHandler waitingHandler)
Download the gene mappings.
|
boolean |
downloadGoMappings(java.lang.String ensemblType,
java.lang.String ensemblSchemaName,
java.lang.String selectedSpecies,
WaitingHandler waitingHandler)
Download the GO mappings.
|
java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.String>> |
getAllSpecies()
Return the species lists.
|
java.util.HashMap<java.lang.String,java.util.HashMap<java.lang.String,java.lang.String>> |
getAllSpeciesMap()
Returns the species map.
|
java.lang.String |
getCurrentSpecies()
Returns the current species.
|
java.lang.String |
getCurrentSpeciesType()
Returns the current species type.
|
java.lang.String |
getEnsemblDatabaseName(java.lang.String speciesName)
Deprecated.
use the one with the Ensembl type parameter instead
|
java.lang.String |
getEnsemblDatabaseName(java.lang.String ensemblType,
java.lang.String speciesName)
Returns the Ensembl database name corresponding to a species name
according to the speciesMap.
|
java.lang.String |
getEnsemblSpeciesVersion(java.lang.String speciesName)
Deprecated.
use getEnsemblSpeciesVersion(String ensemblType, String
speciesName) instead
|
java.lang.String |
getEnsemblSpeciesVersion(java.lang.String ensemblType,
java.lang.String speciesName)
Returns the Ensembl version for the given species name.
|
java.lang.String |
getEnsemblVersion(java.lang.String ensemblDatabase)
Returns the Ensembl version corresponding to the given Ensembl database
according to the ensemblVersionsMap.
|
java.util.HashMap<java.lang.String,java.lang.String> |
getEnsemblVersionsMap()
Returns the Ensembl versions map.
|
java.io.File |
getGeneMappingFolder()
Returns the path to the folder containing the gene mapping files.
|
java.util.HashMap<java.lang.String,java.lang.String> |
getGoDomainMap()
Returns the GO domain map, e.g., key: GO term: GO:0007568, element:
biological_process.
|
static java.lang.String |
getProteinEvidencAsString(java.lang.Integer type)
Return the protein evidence type as text.
|
java.util.ArrayList<java.lang.String> |
getSpecies()
Deprecated.
use getAllSpecies instead
|
java.util.HashMap<java.lang.String,java.lang.String> |
getSpeciesMap()
Deprecated.
use getAllSpeciesMap instead
|
void |
loadEnsemblSpeciesVersions(java.io.File ensemblVersionsFile)
Loads the given Ensembl species file.
|
boolean |
loadGeneMappings(java.lang.String jarFilePath,
WaitingHandler waitingHandler)
Imports the gene mappings.
|
void |
loadSpeciesAndGoDomains()
Load the mapping files.
|
void |
setCurrentSpecies(java.lang.String currentSpecies)
Set the current species.
|
void |
setCurrentSpeciesType(java.lang.String currentSpeciesType)
Set the current species type.
|
void |
updateEnsemblVersion(java.lang.String selectedSpecies,
java.lang.String ensemblVersion)
Update the Ensembl version for the given species.
|
public static final java.lang.String GENE_MAPPING_FOLDER
public static final java.lang.String GENE_MAPPING_FILE_SUFFIX
public static final java.lang.String GO_MAPPING_FILE_SUFFIX
public GenePreferences()
public GenePreferences(GenePreferences genePreferences)
genePreferences
- public static java.lang.String getProteinEvidencAsString(java.lang.Integer type)
type
- the type of evidencepublic boolean downloadGoMappings(java.lang.String ensemblType, java.lang.String ensemblSchemaName, java.lang.String selectedSpecies, WaitingHandler waitingHandler) throws java.net.MalformedURLException, java.io.IOException
ensemblType
- the Ensembl type, e.g., default or plantsensemblSchemaName
- the Ensembl schema name, e.g., default or
plants_mart_18selectedSpecies
- waitingHandler
- java.net.MalformedURLException
java.io.IOException
public void downloadGeneMappings(java.lang.String ensemblType, java.lang.String ensemblSchemaName, java.lang.String selectedSpecies, java.lang.String ensemblVersion, WaitingHandler waitingHandler) throws java.net.MalformedURLException, java.io.IOException, java.lang.IllegalArgumentException
ensemblType
- the Ensembl type, e.g., default or plantsensemblSchemaName
- the Ensembl schema name, e.g., default or
plants_mart_18selectedSpecies
- ensemblVersion
- waitingHandler
- java.net.MalformedURLException
java.io.IOException
java.lang.IllegalArgumentException
public java.io.File getGeneMappingFolder()
public java.lang.String getCurrentSpecies()
public void setCurrentSpecies(java.lang.String currentSpecies)
currentSpecies
- the currentSpecies to setpublic java.lang.String getCurrentSpeciesType()
public void setCurrentSpeciesType(java.lang.String currentSpeciesType)
currentSpeciesType
- the currentSpeciesType to setpublic void createDefaultGeneMappingFiles(java.io.File aEnsemblVersionsFile, java.io.File aGoDomainsFile, java.io.File aSpeciesFile, java.io.File aDefaultSpeciesGoMappingsFile, java.io.File aDefaultSpeciesGeneMappingFile)
aEnsemblVersionsFile
- aGoDomainsFile
- aSpeciesFile
- aDefaultSpeciesGoMappingsFile
- aDefaultSpeciesGeneMappingFile
- public void loadSpeciesAndGoDomains() throws java.io.IOException, java.lang.IllegalArgumentException
java.io.IOException
java.lang.IllegalArgumentException
public java.util.HashMap<java.lang.String,java.lang.String> getGoDomainMap()
public java.util.HashMap<java.lang.String,java.lang.String> getSpeciesMap()
public java.util.HashMap<java.lang.String,java.util.HashMap<java.lang.String,java.lang.String>> getAllSpeciesMap()
public java.lang.String getEnsemblDatabaseName(java.lang.String speciesName)
speciesName
- the species name as available in the species listpublic java.lang.String getEnsemblDatabaseName(java.lang.String ensemblType, java.lang.String speciesName)
ensemblType
- the Ensembl type, e.g., Vertebrates or PlantsspeciesName
- the species name as available in the species listpublic java.util.HashMap<java.lang.String,java.lang.String> getEnsemblVersionsMap()
public java.lang.String getEnsemblVersion(java.lang.String ensemblDatabase)
ensemblDatabase
- the Ensembl databasepublic java.lang.String getEnsemblSpeciesVersion(java.lang.String speciesName)
speciesName
- the species name as available in the species listpublic java.lang.String getEnsemblSpeciesVersion(java.lang.String ensemblType, java.lang.String speciesName)
ensemblType
- the Ensembl type, e.g., Vertebrates or PlantsspeciesName
- the species name as available in the species listpublic java.util.ArrayList<java.lang.String> getSpecies()
public java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.String>> getAllSpecies()
public void updateEnsemblVersion(java.lang.String selectedSpecies, java.lang.String ensemblVersion) throws java.io.IOException
selectedSpecies
- the database name of the species to update, e.g.,
hsapiens_gene_ensemblensemblVersion
- the new Ensembl versionjava.io.IOException
public void loadEnsemblSpeciesVersions(java.io.File ensemblVersionsFile) throws java.io.FileNotFoundException, java.io.IOException
ensemblVersionsFile
- the Ensembl species file to loadjava.io.FileNotFoundException
java.io.IOException
public boolean loadGeneMappings(java.lang.String jarFilePath, WaitingHandler waitingHandler)
jarFilePath
- the jar file pathwaitingHandler
- the waiting handlerCopyright © 2013. All Rights Reserved.