| Bio::DB::ReferenceI(3pm) | User Contributed Perl Documentation | Bio::DB::ReferenceI(3pm) |
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.
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.
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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.
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.
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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
| 2021-08-15 | perl v5.32.1 |