Bio::DB::BioDB - class creating the adaptor factory for a particular database
$dbadp = Bio::DB::BioDB->new( -database => 'biosql', -user => 'root', -dbname => 'pog', -host => 'caldy', -port => 3306, # optional -driver => 'mysql' );
This object represents a database that is implemented somehow (you should not care much as long as you can get the object). From the object you can pull out other adapters, such as the BioSeqAdapter etc.
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 : new Usage : $db = Bio::DB::BioDB->new(-database => 'biosql'); Function: Load and instantiate the encapsulating adaptor for the given database. This module acts as a factory, similar in spirit to Bio::SeqIO, but instead of a sequence stream it returns the adaptor object for the specified database. Example : Returns : a Bio::DB::DBAdaptorI implementing object Args : Named parameters. Currently recognized are -database the name of the database for which the encapsulating adaptor is sought (biosql|markerdb) -dbcontext a Bio::DB::DBContextI implementing object -initrc a scalar denoting a file which when evaluated by perl results in a hash reference or an array reference (to an array with an even number of elements) representing the arguments for this method and for creating an instance of Bio::DB::SimpleDBContext. The special value DEFAULT means to use the file .bioperldb in either the current directory or the home directory, in this order. -printerror whether or not the database and statement handles to be created when necessary should print all errors (the adaptor modules will handle errors themselves, too) Instead of -dbcontext, you can also pass all parameters accepted by Bio::DB::SimpleDBContext::new(), and this module will create the context for you and set the dbadaptor property to the returned value. Note that if you do pass in your own DBContextI object, as a side effect the dbadaptor() property will be changed by this method to reflect the created adaptor. Note also that if using the -initrc argument any separately supplied arguments will override and supplement the arguments defined in that file.
Title : _load_dbadaptor Usage : $self->_load_dbadaptor("Bio::DB::BioSQL::"); Function: Loads up (like use) the DBAdaptorI implementing module for a database at run time on demand. Example : Returns : TRUE on success Args : The prefix of the database implementing modules.
Title : add_db_mapping Usage : $self->add_db_mapping(key, value) Function: Adds another package path mapping to the static private hash %db_map. Example : add_db_mapping("FastBioSQL", "Bio::Das::BioSQL::"); Returns : None Args : key - arbitrary identifier, value - Perl package path ending in "::"