Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

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

SYNOPSIS

         #
         # get a database object somehow using a concrete class
         #

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

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

DESCRIPTION

       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.

CONTACT

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

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to one of the Bioperl mailing lists. Your
       participation is much appreciated.

         bioperl-l@lists.open-bio.org               - General discussion
         http://bioperl.org/Support.html  - About the mailing lists

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

       bioperl-l@bioperl.org

       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.

         https://github.com/bioperl/bioperl-live/issues

AUTHOR

       Email cjfields at bioperl dot org

APPENDIX

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

   get_Reference_by_id
        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

   get_Reference_by_acc
        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

   get_Reference_by_version
        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