15 Apr 2011 19:35:57 UTC
- Distribution: BioPerl-DB
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- License: perl_5
- Perl: v5.6.1
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- Latest versionCJFIELDS Christopher Fieldsand 1 contributors
- BioPerl Team
- AUTHOR - Hilmar Lapp
Bio::DB::DBI::base - base class for drivers implementing Bio::DB::DBI
Don't instantiate this module directly. Instead instantiate one of the derived classes.
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
firstname.lastname@example.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
Email hlapp at gmx.net
Describe contact details here
Juguang Xiao, juguang at tll.org.sg
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : Function: should only be called by derived classes Returns : Args : named parameters with tags -dbcontext (a Bio::DB::DBContextI implementing object) and -sequence_name (the name of the sequence for PK generation)
Title : sequence_name Usage : $obj->sequence_name($newval) Function: Sets/Gets the name of the sequence to be used for PK generation if that name is not passed to the respective method as an argument. Example : Returns : value of sequence_name (a scalar) Args : new value (a scalar, optional)
Title : build_dsn Usage : Function: Constructs the DSN string from the DBContextI object. Since this may be driver-specific, specific implementations may need to override this method. Example : Returns : a string (the DSN) Args : a Bio::DB::DBContextI implementing object
Title : get_connection Usage : Function: Obtains a connection handle to the database represented by the the DBContextI object, passing additional args to the DBI->connect() method if a new connection is created. Contrary to new_connection(), this method will return shared connections from a pool. The implementation makes sure though that the returned handle was opened with the given parameters. In addition, the caller must not disconnect the obtained handle deliberately. Instead, the implementing object will disconnect and dispose of open handles once it is being garbage collected, or once disconnect() is called with the same or no parameters. Specific drivers usually won''t need to override this method but rather build_dsn(). This implementation will call new_connection() to actually get a new connection if needed. Example : Returns : an open DBI database handle Args : A Bio::DB::DBContextI implementing object. Additional hashref parameter to be passed to DBI->connect().
Title : new_connection Usage : Function: Obtains a new connection handle to the database represented by the the DBContextI object, passing additional args to the DBI->connect() method. This method is supposed to always open a new connection. Also, the implementing class is expected to release proper disconnection of the handle entirely to the caller. Specific drivers usually won''t need to override this method but rather build_dsn(). Example : Returns : an open DBI database handle Args : A Bio::DB::DBContextI implementing object. Additional hashref parameter to pass to DBI->connect().
Title : disconnect Usage : Function: Disconnects all or a certain number of connections matching the parameters. The connections affected are those previously obtained through get_connection() (shared connections from a pool). Example : Returns : none Args : Optionally, a Bio::DB::DBContextI implementing object. Additional hashref parameter with settings that were passed to get_connection().
Title : conn_params Usage : $dbi->conn_params($requestor, $newval) Function: Gets/sets connection parameters suitable for the specific driver and the specific requestor. A particular implementation may choose to ignore the requestor, but it may also use it to return different parameters, based on, e.g., which interface the requestor implements. Usually the caller will pass $self as the value $requestor, but an implementation is expected to accept a class or interface name as well. Example : Returns : a hashref to be passed to get_connection() or new_connection() (which would pass it on to DBI->connect()). Args : The requesting object, or alternatively its class name or interface. Optionally, on set the new value (which must be undef or a hashref).
Title : _idsth Usage : $obj->_idsth($newval) Function: Get/set the last/next id value statement handle from/to the cache. Consider this method 'protected' in OO-speak. I.e., call it from derived modules, but not from outside. Example : Returns : a last_id_value or next_id_value prepared statement, or all statements cached under the database handle if the key literal is omitted Args : the database handle for which to cache the statement, a key literal to distinguish between statements (e.g., 'last' and 'next'), and optionall on set the statement handle to cache
Title : _remove_idsths Usage : Function: Un-caches all prepared statement handles cached under the given handle. Example : Returns : the list of previously cached statement handles Args : the database handle
Module Install Instructions
To install Bio::BioEntry, copy and paste the appropriate command in to your terminal.
perl -MCPAN -e shell install Bio::BioEntry
For more information on module installation, please visit the detailed CPAN module installation guide.