Bio::DB ReferenceI
SummaryPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::DB::ReferenceI - A RandomAccessI-like abstract interface for
retrieving Reference data from a sequence database and returning
Bio::Annotation::Reference objects
Package variables
No package variables defined.
# 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.
Methods description
get_Reference_by_idcode    nextTop
 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 = $db->get_Reference_by_version('X77802.1');
Function: Gets a Bio::Annotation::Reference object by sequence version
Returns : A Bio::Annotation::Reference object
Args : accession.version (as a string)
Throws : "acc.version does not exist" exception
Methods code
sub get_Reference_by_id {
   my ($self,@args) = @_;
sub get_Reference_by_acc {
   my ($self,@args) = @_;
sub get_Reference_by_version {
   my ($self,@args) = @_;

## End of Package
General documentation
Ewan Birney originally wrote Bio::DB::RandomAccessI, from which this class
is based.
Mailing ListsTop
User feedback is an integral part of the
evolution of this and other Bioperl modules. Send
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is much appreciated.               - General discussion - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
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 BugsTop
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.
Email cjfields at bioperl dot org
The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _