Provided by: libbio-perl-perl_1.7.2-2_all
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. 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. email@example.com - General discussion http://bioperl.org/Support.html - About the mailing lists Support Please direct usage questions or support issues to the mailing list: firstname.lastname@example.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
Email cjfields at bioperl dot org
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