public class GenePreferences
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
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.
|
java.lang.String |
GO_MAPPING_FILE_SUFFIX
The suffix to use for files containing GO mappings.
|
java.lang.String |
SPECIES_SEPARATOR
The species separator used in the species comboboxes.
|
Constructor and Description |
---|
GenePreferences()
Create a new 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.
|
boolean |
downloadGeneMappings(java.lang.String selectedSpecies,
WaitingHandler waitingHandler)
Download the gene mappings.
|
boolean |
downloadGoMappings(java.lang.String selectedSpecies,
java.lang.String ensemblVersion,
WaitingHandler waitingHandler)
Download the GO mappings.
|
java.lang.String |
getCurrentSpecies()
Returns the current species.
|
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.
|
java.util.Vector<java.lang.String> |
getSpecies()
Return the species list.
|
java.util.HashMap<java.lang.String,java.lang.String> |
getSpeciesMap()
Returns the species map.
|
void |
loadSpeciesAndGoDomains()
Load the mapping files.
|
void |
setCurrentSpecies(java.lang.String currentSpecies)
Set the current species.
|
public static final java.lang.String GENE_MAPPING_FOLDER
public final java.lang.String SPECIES_SEPARATOR
public final java.lang.String GENE_MAPPING_FILE_SUFFIX
public final java.lang.String GO_MAPPING_FILE_SUFFIX
public boolean downloadGoMappings(java.lang.String selectedSpecies, java.lang.String ensemblVersion, WaitingHandler waitingHandler) throws java.net.MalformedURLException, java.io.IOException
selectedSpecies
- ensemblVersion
- waitingHandler
- java.net.MalformedURLException
java.io.IOException
public boolean downloadGeneMappings(java.lang.String selectedSpecies, WaitingHandler waitingHandler) throws java.net.MalformedURLException, java.io.IOException, java.lang.IllegalArgumentException
selectedSpecies
- 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 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.lang.String> getEnsemblVersionsMap()
public java.util.Vector<java.lang.String> getSpecies()
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