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