Bio::DB::BioSQL::DBAdapter - Object representing an instance of a bioperl database
$dbcontext = Bio::DB::SimpleContext->new( -user => 'root', -dbname => 'pog', -host => 'caldy', -driver => 'mysql', ); $db = Bio::DB::BioSQL::DBAdaptor->new( -dbcontext => $dbcontext ); # You can also create db adaptor by calling Bio::DB::BioDB constructor. $db = Bio::DB::BioDB->new( -database => 'biosql', -user => 'root', -dbname => 'pog', -host => 'caldy', -driver => 'mysql', );
This object represents a database that is implemented somehow (you shouldn't care much as long as you can get the object). From the object you can pull out other adapters, such as the BioSeqAdapter,
Describe contact details here
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : get_object_adaptor Usage : $objadp = $adaptor->get_object_adaptor("Bio::SeqI"); Function: Obtain an PersistenceAdaptorI compliant object for the given class or object. Example : Returns : The appropriate object adaptor, a Bio::DB::PersistenceAdaptorI implementing object. Args : The class (a string) or object for which the adaptor is to be obtained. Optionally, a DBContextI implementing object to initialize the adaptor with.
Title : _get_object_adaptor_class Usage : $objadpclass = $adaptor->_get_object_adaptor_class("Bio::SeqI"); Function: Obtains and loads the PersistenceAdaptorI compliant class for the given class or object. Example : Returns : The appropriate object adaptor class, a Bio::DB::PersistenceAdaptorI implementing class, or an instantiation of it, if one has been cached. Args : The class (a string) for which the adaptor class is to be obtained.
Title : set_object_adaptor Usage : $adaptor->set_object_adaptor("Bio::SeqI", $bioseqadaptor); Function: Sets the PersistenceAdaptorI compliant object and/or class for the given class or interface. Example : Returns : none Args : The class (a string) or object for which the adaptor is to be set. The PersistenceAdaptorI compliant class or an instance of it to serve as the adaptor.
Title : create_persistent Usage : $dbadaptor->create_persistent($obj) Function: Creates a PersistentObjectI implementing object that adapts the given object to the datastore. Example : Returns : A Bio::DB::PeristentObjectI implementing object Args : An object of a type that can be stored in the datastore adapted by this factory. Alternatively, the class name of such an object. All remaining arguments will be passed to the constructor of the class if the first argument is a class name.
Title : dbcontext Usage : $obj->dbcontext($newval) Function: Get/set the DBContextI object representing the physical database. If this slot is not set, adaptor objects returned by get_adaptor() will not be initialized with a database connection, unless a DBContextI is passed to get_adaptor(). Example : Returns : A DBContextI implementing object Args : on set, the new DBContextI implementing object
Title : _load_object_adaptor Usage : Function: Example : Returns : Args :
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.