A B C D E F G I M O P R S T V X

A

appendLimitConditions(StringBuilder, Integer, Integer) - Method in class org.bridgedb.sql.SQLIdMapper

Adds the limit condition if this is the support method for limitng the number of results.

appendMappingJoinMapping(StringBuilder) - Method in class org.bridgedb.sql.SQLIdMapper

appendSourceIdSysCodePair(StringBuilder, IdSysCodePair) - Method in class org.bridgedb.sql.SQLIdMapper

Add a condition to the query that only mappings with a specific source IdSysCodePair should be used.

appendSourceXref(StringBuilder, String, String) - Method in class org.bridgedb.sql.SQLIdMapper

Add a condition to the query that only mappings with a specific source Xref should be used.

appendTopConditions(StringBuilder, Integer, Integer) - Method in class org.bridgedb.sql.SQLIdMapper

Adds the top condition if this is the support method for limitng the number of results.

autoIncrement - Variable in class org.bridgedb.sql.SQLListener

B

badXref(Xref) - Method in class org.bridgedb.sql.SQLIdMapper

Check if the Xref is invalid in some way.

C

close(Statement, ResultSet) - Method in class org.bridgedb.sql.SQLBase

close() - Method in class org.bridgedb.sql.SQLIdMapper

closeConnection() - Method in class org.bridgedb.sql.SQLBase

closeInput() - Method in interface org.bridgedb.mapping.MappingListener

Closes the input, flushing any links into storage.

closeInput() - Method in class org.bridgedb.sql.SQLListener

codeMapper - Variable in class org.bridgedb.sql.SQLIdMapper

Map between IdSysCodePair and Xref or DataSources

commitTransaction() - Method in class org.bridgedb.sql.SQLBase

configs() - Static method in class org.bridgedb.sql.SqlFactory

createASQLAccess(String) - Static method in class org.bridgedb.sql.SqlFactory

Create a wrapper around the live SQL Database, using the database name, user name and password found in the config file.

createMappingSetTable() - Method in class org.bridgedb.sql.SQLListener

createPreparedStatement(String) - Method in class org.bridgedb.sql.SQLBase

createSQLTables() - Method in class org.bridgedb.sql.SQLListener

Excecutes several SQL statements to create the tables and indexes in the database.

createStatement() - Method in class org.bridgedb.sql.SQLBase

createTheSQLAccess() - Static method in class org.bridgedb.sql.SqlFactory

Create a wrapper around the live SQL Database, using the database name, user name and password found in the config file.

D

DEFAULT_LIMIT - Static variable in class org.bridgedb.sql.SQLIdMapper

dropSQLTables() - Method in class org.bridgedb.sql.SQLListener

Excecutes several SQL statements to drop the tables

dropTable(String) - Method in class org.bridgedb.sql.SQLListener

Drops a single table if it exists.

E

engineSetting() - Static method in class org.bridgedb.sql.SqlFactory

F

freeSearch(String, int) - Method in class org.bridgedb.sql.SQLIdMapper

FULLNAME_LENGTH - Static variable in class org.bridgedb.sql.SQLListener

G

getAutoInc() - Method in class org.bridgedb.sql.SQLListener

getCapabilities() - Method in class org.bridgedb.sql.SQLIdMapper

getConnection() - Method in class org.bridgedb.mysql.MySQLAccess

Retrieve an active connection to the database

getConnection() - Method in interface org.bridgedb.sql.SQLAccess

Allows SQL code to obtain a new Connection without having access to the Database name, user name and password.

getConnection() - Method in class org.bridgedb.virtuoso.VirtuosoAccess

Retrieve an active connection to the database

getDataSourceKey(DataSource) - Method in class org.bridgedb.sql.SQLListener

getKeys() - Method in class org.bridgedb.sql.SQLIdMapper

getProperty(String) - Method in class org.bridgedb.sql.SQLIdMapper

getSupportedSrcDataSources() - Method in class org.bridgedb.sql.SQLIdMapper

getSupportedTgtDataSources() - Method in class org.bridgedb.sql.SQLIdMapper

I

ID_COLUMN_NAME - Static variable in class org.bridgedb.sql.SQLListener

ID_LENGTH - Static variable in class org.bridgedb.sql.SQLListener

IdSysCodePairExists(IdSysCodePair) - Method in class org.bridgedb.sql.SQLIdMapper

insertEscpaeCharacters(String) - Method in class org.bridgedb.sql.SQLBase

insertLink(String, String, int, boolean) - Method in interface org.bridgedb.mapping.MappingListener

Inserts a mapping into the system.

insertLink(String, String, int, boolean) - Method in class org.bridgedb.sql.SQLListener

isConnected() - Method in class org.bridgedb.sql.SQLIdMapper

isFreeSearchSupported() - Method in class org.bridgedb.sql.SQLIdMapper

isMappingSupported(DataSource, DataSource) - Method in class org.bridgedb.sql.SQLIdMapper

M

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

mapID(Xref, DataSource...) - Method in class org.bridgedb.sql.SQLIdMapper

mapID(Xref, DataSource) - Method in class org.bridgedb.sql.SQLIdMapper

Get all cross-references for the given entity, restricting the result to contain only references from the given set of data sources.

MAPPING_SET_ID_COLUMN_NAME - Static variable in class org.bridgedb.sql.SQLListener

MAPPING_SET_TABLE_NAME - Static variable in class org.bridgedb.sql.SQLListener

MAPPING_URI_LENGTH - Static variable in class org.bridgedb.sql.SQLListener

MappingListener - Interface in org.bridgedb.mapping

This interface is used to load Data into the System using Xrefs and DataSources.

MYSQL_ENGINE_PROPERTY - Static variable in class org.bridgedb.sql.SqlFactory

MySQLAccess - Class in org.bridgedb.mysql

MYSQL specific wrapper.

MySQLAccess(String, String, String) - Constructor for class org.bridgedb.mysql.MySQLAccess

Instantiate a connection to the database

O

org.bridgedb.mapping - package org.bridgedb.mapping

org.bridgedb.mysql - package org.bridgedb.mysql

org.bridgedb.sql - package org.bridgedb.sql

org.bridgedb.virtuoso - package org.bridgedb.virtuoso

P

possibleOpenConnection - Variable in class org.bridgedb.sql.SQLBase

putProperty(String, String) - Method in class org.bridgedb.sql.SQLListener

R

registerMappingSet(DataSource, DataSource, boolean) - Method in interface org.bridgedb.mapping.MappingListener

Loads all the meta data for a Mapping Set.

registerMappingSet(DataSource, DataSource, boolean) - Method in class org.bridgedb.sql.SQLListener

rollbackTransaction() - Method in class org.bridgedb.sql.SQLBase

S

setUseMySQL(boolean) - Static method in class org.bridgedb.sql.SqlFactory

SOURCE_DATASOURCE_COLUMN_NAME - Static variable in class org.bridgedb.sql.SQLListener

SQL_COMPAT_VERSION - Static variable in class org.bridgedb.sql.SQLListener

SQL_DATABASE_PROPERTY - Static variable in class org.bridgedb.sql.SqlFactory

SQL_PASSWORD_PROPERTY - Static variable in class org.bridgedb.sql.SqlFactory

SQL_PORT_PROPERTY - Static variable in class org.bridgedb.sql.SqlFactory

Name of the file assumed to hold the SQl configurations.

SQL_USER_PROPERTY - Static variable in class org.bridgedb.sql.SqlFactory

SQLAccess - Interface in org.bridgedb.sql

A wrapper around the individual SQL DataBase Drivers.

sqlAccess - Variable in class org.bridgedb.sql.SQLBase

SQLBase - Class in org.bridgedb.sql

This is the root class of the SQL stack.

SQLBase() - Constructor for class org.bridgedb.sql.SQLBase

SqlFactory - Class in org.bridgedb.sql

Finds the SQL Configuration file and uses it to open the database with the correct database name, user name and password.

SqlFactory() - Constructor for class org.bridgedb.sql.SqlFactory

SQLIdMapper - Class in org.bridgedb.sql

Builds on the SQLListener to implement the Standard BridgeDB functions of IDMapper and IDMapperCapabilities.

SQLIdMapper(boolean, CodeMapper) - Constructor for class org.bridgedb.sql.SQLIdMapper

SQLListener - Class in org.bridgedb.sql

This is the root class of the SQL stack.

SQLListener(boolean) - Constructor for class org.bridgedb.sql.SQLListener

startTransaction() - Method in class org.bridgedb.sql.SQLBase

SYSCODE_LENGTH - Static variable in class org.bridgedb.sql.SQLListener

T

TARGET_DATASOURCE_COLUMN_NAME - Static variable in class org.bridgedb.sql.SQLListener

TEST_SQL_DATABASE_PROPERTY - Static variable in class org.bridgedb.sql.SqlFactory

TEST_SQL_PASSWORD_PROPERTY - Static variable in class org.bridgedb.sql.SqlFactory

TEST_SQL_USER_PROPERTY - Static variable in class org.bridgedb.sql.SqlFactory

toCode(DataSource) - Method in class org.bridgedb.sql.SQLIdMapper

toCodes(DataSource[]) - Method in class org.bridgedb.sql.SQLIdMapper

toIdSysCodePair(Xref) - Method in class org.bridgedb.sql.SQLIdMapper

toXrefs(Set<IdSysCodePair>) - Method in class org.bridgedb.sql.SQLIdMapper

V

VirtuosoAccess - Class in org.bridgedb.virtuoso

Virtuosos specific wrapper.

VirtuosoAccess() - Constructor for class org.bridgedb.virtuoso.VirtuosoAccess

Instantiate a connection to the database

X

xrefExists(Xref) - Method in class org.bridgedb.sql.SQLIdMapper

A B C D E F G I M O P R S T V X