/ 
BioPerl-DB-1.006900
River stage zero No dependents
/ Bio::DB::BioSQL::DBAdaptor

NAME

Bio::DB::BioSQL::DBAdapter - Object representing an instance of a bioperl database

SYNOPSIS

    $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',
    );

DESCRIPTION

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,

CONTACT

Describe contact details here

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

get_object_adaptor

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.

_get_object_adaptor_class

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.

set_object_adaptor

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.

create_persistent

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.

dbcontext

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

_load_object_adaptor

Title   : _load_object_adaptor
Usage   :
Function:
Example :
Returns : 
Args    :