org.bridgedb.rdb

Class GdbProvider

java.lang.Object

org.bridgedb.rdb.GdbProvider

public class GdbProvider
extends Object

Utility class that maintains a list of synonym databases and the species they apply to. This list can be read from a configuration file with on each line:

 species_latin_name[Tab]database_file_location
 

If a database applies to all species (e.g. metabolites), use "*" as species.

Constructor Summary

Constructors

Constructor and Description
GdbProvider()
GdbProvider(boolean transitive)

Method Summary

Modifier and Type	Method and Description
void	addGlobalGdb(IDMapper gdb)
void	addOrganismGdb(Organism organism, IDMapper gdb)
static GdbProvider	fromConfigFile(File f)
static GdbProvider	fromConfigFile(File f, boolean transitive)
List<IDMapper>	getGdbs(Organism organism) Deprecated. use getStack(organism) instead
Set<Organism>	getOrganisms()
IDMapperStack	getStack(Organism organism)
void	removeGlobalGdb(IDMapper gdb)
void	removeOrganismGdb(Organism organism, IDMapperRdb gdb)

Methods inherited from class java.lang.Object

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

Constructor Detail

GdbProvider

public GdbProvider()

GdbProvider

public GdbProvider(boolean transitive)

Method Detail

getOrganisms

public Set<Organism> getOrganisms()

addOrganismGdb

public void addOrganismGdb(Organism organism,
                           IDMapper gdb)

removeOrganismGdb

public void removeOrganismGdb(Organism organism,
                              IDMapperRdb gdb)

addGlobalGdb

public void addGlobalGdb(IDMapper gdb)

removeGlobalGdb

public void removeGlobalGdb(IDMapper gdb)

getGdbs

public List<IDMapper> getGdbs(Organism organism)

Deprecated. use getStack(organism) instead

getStack

public IDMapperStack getStack(Organism organism)

fromConfigFile

public static GdbProvider fromConfigFile(File f)
                                  throws IDMapperException,
                                         IOException,
                                         ClassNotFoundException

Throws:

IDMapperException

IOException

ClassNotFoundException

fromConfigFile

public static GdbProvider fromConfigFile(File f,
                                         boolean transitive)
                                  throws IDMapperException,
                                         IOException,
                                         ClassNotFoundException

Throws:

IDMapperException

IOException

ClassNotFoundException