Package | Description |
---|---|
org.biojava.bio.program.das |
Development client for the Distributed Annotation System.
|
org.biojava.bio.seq.db.biofetch |
Client for the OBDA BioFetch protocol.
|
org.biojava.bio.seq.db.biosql |
General purpose Sequence storage in a relational database.
|
org.biojava.bio.seq.db.flat |
Support for OBDA flatfile databases.
|
org.biojava.directory |
Open Bio Sequence Database Access (OBDA) registry support.
|
Modifier and Type | Method and Description |
---|---|
SequenceDBLite |
DASSequenceDBProvider.getSequenceDB(java.util.Map config) |
Modifier and Type | Method and Description |
---|---|
SequenceDBLite |
BioFetchSequenceDBProvider.getSequenceDB(java.util.Map config) |
Modifier and Type | Method and Description |
---|---|
SequenceDBLite |
BioSQLSequenceDBProvider.getSequenceDB(java.util.Map config)
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
SequenceDBLite |
FlatSequenceDBProvider.getSequenceDB(java.util.Map config) |
Modifier and Type | Class and Description |
---|---|
class |
ProviderNotFoundException
ProviderNotFoundException is thrown when a sequence
database provider can not be located. |
Modifier and Type | Method and Description |
---|---|
void |
RegistryConfiguration.Composite.addBottomConfig(RegistryConfiguration newConfig)
Add a configuration as the most default place to look.
|
void |
RegistryConfiguration.Composite.addTopConfig(RegistryConfiguration newConfig)
Add a configuration as the most authoritative place to look.
|
java.util.Map |
RegistryConfiguration.getConfiguration()
getConfiguration returns a mapping of registry
database names to collections of tag-value pairs. |
SequenceDBLite |
Registry.getDatabase(java.lang.String dbName)
getDatabase retrieves a database instance known by
a name String . |
SequenceDBLite |
SequenceDBProvider.getSequenceDB(java.util.Map config)
Get a sequence database.
|
static RegistryConfiguration |
OBDARegistryParser.parseRegistry(java.io.BufferedReader in,
java.lang.String locator)
parseRegistry parses an Open Bioinformatics Database
Access (OBDA) configuration file. |