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java.lang.Objectcom.compomics.util.preferences.GenePreferences
public class GenePreferences
Contains methods for downloading gene and GO mappings.
Field Summary | |
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String |
GENE_MAPPING_FILE_SUFFIX
The suffix to use for files containing gene mappings. |
static String |
GENE_MAPPING_FOLDER
The folder where gene mapping related info is stored. |
String |
GO_MAPPING_FILE_SUFFIX
The suffix to use for files containing GO mappings. |
String |
NO_SPECIES_TAG
The text to use for no species selected. |
String |
SELECT_SPECIES_TAG
The text to use to tell the user to please select a species in the list. |
String |
SPECIES_SEPARATOR
The species separator used in the species comboboxes. |
Constructor Summary | |
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GenePreferences()
Create a new GenePreferences object. |
Method Summary | |
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void |
createDefaultGeneMappingFiles(File aEnsemblVersionsFile,
File aGoDomainsFile,
File aSpeciesFile,
File aDefaultSpeciesGoMappingsFile,
File aDefaultSpeciesGeneMappingFile)
Insert the default gene mappings files. |
boolean |
downloadGeneMappings(String selectedSpecies,
WaitingHandler waitingHandler)
Download the gene mappings. |
boolean |
downloadGoMappings(String selectedSpecies,
String ensemblVersion,
WaitingHandler waitingHandler)
Download the GO mappings. |
String |
getCurrentSpecies()
Returns the current species. |
HashMap<String,String> |
getEnsemblVersionsMap()
Returns the Ensembl versions map. |
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. |
Vector<String> |
getSpecies()
Return the species list. |
HashMap<String,String> |
getSpeciesMap()
Returns the species map. |
void |
loadSpeciesAndGoDomains()
Load the mapping files. |
void |
setCurrentSpecies(String currentSpecies)
Set the current species. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final String GENE_MAPPING_FOLDER
public final String SPECIES_SEPARATOR
public final String SELECT_SPECIES_TAG
public final String NO_SPECIES_TAG
public final String GENE_MAPPING_FILE_SUFFIX
public final String GO_MAPPING_FILE_SUFFIX
Constructor Detail |
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public GenePreferences()
Method Detail |
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public boolean downloadGoMappings(String selectedSpecies, String ensemblVersion, WaitingHandler waitingHandler) throws MalformedURLException, IOException
selectedSpecies
- ensemblVersion
- waitingHandler
-
MalformedURLException
IOException
public boolean downloadGeneMappings(String selectedSpecies, WaitingHandler waitingHandler) throws MalformedURLException, IOException, IllegalArgumentException
selectedSpecies
- waitingHandler
-
MalformedURLException
IOException
IllegalArgumentException
public File getGeneMappingFolder()
public String getCurrentSpecies()
public void setCurrentSpecies(String currentSpecies)
currentSpecies
- the currentSpecies to setpublic void createDefaultGeneMappingFiles(File aEnsemblVersionsFile, File aGoDomainsFile, File aSpeciesFile, File aDefaultSpeciesGoMappingsFile, File aDefaultSpeciesGeneMappingFile)
aEnsemblVersionsFile
- aGoDomainsFile
- aSpeciesFile
- aDefaultSpeciesGoMappingsFile
- aDefaultSpeciesGeneMappingFile
- public void loadSpeciesAndGoDomains() throws IOException, IllegalArgumentException
IOException
IllegalArgumentException
public HashMap<String,String> getGoDomainMap()
public HashMap<String,String> getSpeciesMap()
public HashMap<String,String> getEnsemblVersionsMap()
public Vector<String> getSpecies()
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