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