A C D F G I M N O Q R S T X
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A

addGlobalGdb(IDMapper) - Method in class org.bridgedb.rdb.GdbProvider

addOrganismGdb(Organism, IDMapper) - Method in class org.bridgedb.rdb.GdbProvider

C

close() - Method in class org.bridgedb.rdb.SimpleGdb

ConfigFile - Class in org.bridgedb.rdb.impl

ConfigFile(File) - Constructor for class org.bridgedb.rdb.impl.ConfigFile

createInstance(String, String) - Static method in class org.bridgedb.rdb.SimpleGdbFactory

Opens a connection to the Gene Database located in the given file.

D

dbName - Variable in class org.bridgedb.rdb.SimpleGdb

F

freeAttributeSearch(String, String, int) - Method in class org.bridgedb.rdb.SimpleGdbImplCommon

free text search for matching symbols.

freeAttributeSearchEx(String, String, int) - Method in class org.bridgedb.rdb.SimpleGdbImplCommon

freeSearch(String, int) - Method in class org.bridgedb.rdb.SimpleGdbImplCommon

fromConfigFile(File) - Static method in class org.bridgedb.rdb.GdbProvider

fromConfigFile(File, boolean) - Static method in class org.bridgedb.rdb.GdbProvider

G

GdbProvider - Class in org.bridgedb.rdb

Utility class that maintains a list of synonym databases and the species they apply to.

GdbProvider() - Constructor for class org.bridgedb.rdb.GdbProvider

GdbProvider(boolean) - Constructor for class org.bridgedb.rdb.GdbProvider

getAttributeSet() - Method in class org.bridgedb.rdb.SimpleGdbImplCommon

getCapabilities() - Method in class org.bridgedb.rdb.SimpleGdbImplCommon

getConnection() - Method in class org.bridgedb.rdb.SimpleGdb

getCrossRefsByAttribute(String, String) - Method in class org.bridgedb.rdb.SimpleGdbImplCommon

getDbName() - Method in class org.bridgedb.rdb.IDMapperRdb

Gets the name of te currently used gene database.

getDbName() - Method in class org.bridgedb.rdb.SimpleGdb

Gets the name of te currently used gene database.

getDrivers() - Method in class org.bridgedb.rdb.impl.ConfigFile

getGdbs(Organism) - Method in class org.bridgedb.rdb.GdbProvider

Deprecated.

use getStack(organism) instead

getGeneCount() - Method in class org.bridgedb.rdb.SimpleGdb

getGeneCount(DataSource) - Method in class org.bridgedb.rdb.SimpleGdb

getIterator() - Method in class org.bridgedb.rdb.SimpleGdbImplCommon

getIterator(DataSource) - Method in class org.bridgedb.rdb.SimpleGdbImplCommon

getLinkCount() - Method in class org.bridgedb.rdb.SimpleGdb

getMappers() - Method in class org.bridgedb.rdb.impl.ConfigFile

getOrganisms() - Method in class org.bridgedb.rdb.GdbProvider

getPrimaryIDCount(DataSource) - Method in class org.bridgedb.rdb.SimpleGdb

getStack(Organism) - Method in class org.bridgedb.rdb.GdbProvider

I

IDMapperRdb - Class in org.bridgedb.rdb

Interface for all classes that provide Gdb-like functionality, such as looking up cross-references and backpage text.

IDMapperRdb() - Constructor for class org.bridgedb.rdb.IDMapperRdb

isConnected() - Method in class org.bridgedb.rdb.SimpleGdb

isFreeAttributeSearchSupported() - Method in class org.bridgedb.rdb.SimpleGdbImplCommon

M

mapID(Collection<Xref>, DataSource...) - Method in class org.bridgedb.rdb.IDMapperRdb

mapID(Xref, DataSource...) - Method in class org.bridgedb.rdb.SimpleGdbImplCommon

N

NO_LIMIT - Static variable in class org.bridgedb.rdb.SimpleGdb

NO_TIMEOUT - Static variable in class org.bridgedb.rdb.SimpleGdb

O

org.bridgedb.rdb - package org.bridgedb.rdb

Driver and helper classes for using relational databases as identifier mapping services.

org.bridgedb.rdb.impl - package org.bridgedb.rdb.impl

Q

QUERY_TIMEOUT - Static variable in class org.bridgedb.rdb.SimpleGdb

R

removeGlobalGdb(IDMapper) - Method in class org.bridgedb.rdb.GdbProvider

removeOrganismGdb(Organism, IDMapperRdb) - Method in class org.bridgedb.rdb.GdbProvider

S

SimpleGdb - Class in org.bridgedb.rdb

SimpleGdb is the main implementation of the Gdb interface, for dealing with single SQL-based pgdb's.

SimpleGdbFactory - Class in org.bridgedb.rdb

Factory class that instantiates the correct SimpleGdb implementation for a new / existing gdb, based on the schema version.

SimpleGdbImplCommon - Class in org.bridgedb.rdb

Some methods and constants that are shared between SimpleGdbImpl2 and SimpleGdbImpl3

T

toString() - Method in class org.bridgedb.rdb.IDMapperRdb

X

xrefExists(Xref) - Method in class org.bridgedb.rdb.SimpleGdbImplCommon

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