Provided by: libbio-perl-perl_1.7.6-3_all bug


       Bio::DB::RandomAccessI - Abstract interface for a sequence database


         # get a database object somehow using a concrete class

         $seq = $db->get_Seq_by_id('ROA1_HUMAN');

         # $seq is a Bio::Seq 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::RandomAccessI class defines what methods a generic database class should
       have. At the moment it is just the ability to make Bio::Seq objects from a name (id) or an
       accession number.


       Ewan Birney <> originally wrote this class.

       Please direct usage questions or support issues to the mailing list:

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their
       resolution. Bug reports can be submitted via the web:


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

        Title   : get_Seq_by_id
        Usage   : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
        Function: Gets a Bio::Seq object by its name
        Returns : a Bio::Seq object or undef if not found
        Args    : the id (as a string) of a sequence,

        Title   : get_Seq_by_acc
        Usage   : $seq = $db->get_Seq_by_acc('X77802');
                  $seq = $db->get_Seq_by_acc(Locus => 'X77802');
        Function: Gets a Bio::Seq object by accession number
        Returns : A Bio::Seq object or undef if not found
        Args    : accession number (as a string), or a two
                      element list consisting of namespace=>accession
        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

       NOTE: The two-element form allows you to choose the namespace for the accession number.

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