Bio::DB::DBContextI - Interface for a class implementing a database context
# obtain a DBContextI implementing object somehow, usually through # a factory, for example use Bio::DB::BioDB; $dbcontext = Bio::DB::BioDB->new( -database => 'biosql' -user => 'root', -pass => 'mypasswd', -dbname => 'pog', -host => 'caldy', -port => 3306, # optional -driver => 'mysql', ); # obtain other adaptors as needed $dbadp = $dbc->dbadaptor(); $seq_adaptor = $dbadp->get_adaptor('Bio::PrimarySeqI');
This object represents the context of a database that is implemented somehow.
Hilmar Lapp, hlapp at gmx.net
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : dsn Usage : $obj->dsn($newval) Function: Get/set the DSN for the database connection. The DSN typically contains all non-credential information necessary to connect to the database, like driver, database or instance name, host, etc. Therefore, setting the DSN overrides any other individual properties set before. An implementation should make an attempt to parse those properties out of the DSN string but is not mandated to do so. Modules that use a DBContextI compliant object to construct a DSN should instead use the value of this property verbatim for connecting to the database, if it is defined. I.e., if you set this property, setting any other individual properties will not alter the DSN used for connecting to the database. If you query the property, a value will not be automatically constructed if only individual properties have been set. This is so because constructing the proper DSN from individual properties is driver-specific, and therefore cannot be done in a driver-neutral module. Example : Returns : value of dsn (a scalar) Args : on set, new value (a scalar or undef, optional)
Title : dbname Usage : $obj->dbname($newval) Function: Example : Returns : value of dbname (a scalar) Args : new value (a scalar, optional)
Title : driver Usage : $obj->driver($newval) Function: Example : Returns : value of driver (a scalar) Args : new value (a scalar, optional)
Title : username Usage : $obj->username($newval) Function: Example : Returns : value of username (a scalar) Args : new value (a scalar, optional)
Title : password Usage : $obj->password($newval) Function: Example : Returns : value of password (a scalar) Args : new value (a scalar, optional)
Title : host Usage : $obj->host($newval) Function: Example : Returns : value of host (a scalar) Args : new value (a scalar, optional)
Title : port Usage : $obj->port($newval) Function: Example : Returns : value of port (a scalar) Args : new value (a scalar, optional)
Title : dbadaptor Usage : $dbadp = $dbc->dbadaptor(); Function: Example : Returns : An Bio::DB::DBAdaptorI implementing object (an object adaptor factory). Args : Optionally, on set an Bio::DB::DBAdaptorI implementing object (to be used as the object adaptor factory for the respective database)
Title : dbi Usage : Function: Example : Returns : A Bio::DB::DBI implementing object Args : Optionally, on set a Bio::DB::DBI implementing object
Title : schema Usage : $dbc->schema($newval) Function: Get/set the schema in which the database tables reside. A schema is typically equivalent to a namespace for a collection of tables within a database. In Oracle, the notion of a schema is synonymous with that of the user (all database objects of a user belong to the schema of the same name as the user) and hence can be omitted. In PostgreSQL, since v7.4 schemas can delineate collections of tables within a database (which in concept is more similar to a user in Oracle). For most drivers and database instances this will not be needed. Example : Returns : value of schema (a scalar) Args : on set, new value (a scalar or undef, optional)
To install Bio::BioEntry, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::BioEntry
CPAN shell
perl -MCPAN -e shell install Bio::BioEntry
For more information on module installation, please visit the detailed CPAN module installation guide.