BaseAdaptor.pm

#
# BioPerl module for Bio::EnsEMBL::DBSQL::BaseAdaptor
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
#
# Copyright Ewan Birney
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

Bio::EnsEMBL::DBSQL::BaseAdaptor - Base Adaptor for DBSQL adaptors

=head1 SYNOPSIS

    # base adaptor provides
    
    # SQL prepare function
    $adaptor->prepare("sql statement");

    # get of root DBAdaptor object
    $adaptor->db();

    # constructor, ok for inheritence
    $adaptor = Bio::EnsEMBL::DBSQL::SubClassOfBaseAdaptor->new($dbobj)

=head1 DESCRIPTION

This is a true base class for Adaptors in the Ensembl DBSQL
system. Original idea from Arne


Adaptors are expected to have the following functions

    $obj = $adaptor->fetch_by_dbID($internal_id);

which builds the object from the primary key of the object. This
function is crucial because it allows adaptors to collaborate
relatively independently of each other - in other words, we can change
the schema under one adaptor without too many knock on changes through
the other adaptors.

Most adaptors will also have

    $dbid = $adaptor->store($obj);

which stores the object. Currently the storing of an object also causes
the objects to set

    $obj->dbID

correctly and attach the adaptor.


Other fetch functions go by the convention of

    @object_array = @{$adaptor->fetch_all_by_XXXX($arguments_for_XXXX)};

sometimes it returns an array ref denoted by the 'all' in the name of the
method, sometimes an individual object. For example

    $gene = $gene_adaptor->fetch_by_stable_id($stable_id);

or

    @fp  = @{$simple_feature_adaptor->fetch_all_by_Slice($slice)};