NAME
Bio::DB::DBI::base - base class for drivers implementing Bio::DB::DBI
DESCRIPTION
Don't instantiate this module directly. Instead instantiate one of the derived classes.
FEEDBACK
Mailing Lists
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.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing listsSupport
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
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.
Reporting Bugs
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:
http://redmine.open-bio.org/projects/bioperl/AUTHOR - Hilmar Lapp
Email hlapp at gmx.net
Describe contact details here
CONTRIBUTORS
Juguang Xiao, juguang at tll.org.sg
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
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)sequence_name
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)build_dsn
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 objectget_connection
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().new_connection
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().disconnect
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().conn_params
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)._idsth
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_remove_idsths
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