Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::DB::ReferenceI - A RandomAccessI-like abstract interface for retrieving Reference
       data from a sequence database and returning Bio::Annotation::Reference objects


         # get a database object somehow using a concrete class

         $ref = $db->get_Reference_by_id('123456');

         # $ref is a Bio::Annotation::Reference object


       This is a pure interface class - in other words, all this does is define methods which
       other (concrete) classes will actually implement.

       The Bio::DB::ReferenceI class defines methods used to retrieve reference data from a
       sequence.  This is returned in the form of Bio::Annotation::Reference objects.

       At the moment it is just the ability to make Bio::Annotation::Reference objects from a
       name or unique id (id), an accession number (acc), and so on.


       Ewan Birney originally wrote Bio::DB::RandomAccessI, from which this class is based.

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

        Title   : get_Reference_by_id
        Usage   : $ref = $db->get_Reference_by_id('123456')
        Function: Gets a Bio::Annotation::Reference-implementing object by its name (id)
        Returns : a Bio::Annotation::Reference object or undef if not found
        Args    : the id (as a string) of a sequence

        Title   : get_Reference_by_acc
        Usage   : $ref = $db->get_Reference_by_acc('X77802');
        Function: Gets a Bio::Annotation::Reference object by accession number
        Returns : A Bio::Annotation::Reference object or undef if not found
        Args    : accession number (as a string)
        Throws  : "more than one sequences correspond to this accession"
                   if the accession maps to multiple primary ids and
                   method is called in a scalar context

        Title   : get_Reference_by_version
        Usage   : $ref = $db->get_Reference_by_version('X77802.1');
        Function: Gets a Bio::Annotation::Reference object by sequence version
        Returns : A Bio::Annotation::Reference object
        Args    : accession.version (as a string)
        Throws  : "acc.version does not exist" exception