Bio::DB
ReferenceI
Summary
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.
Synopsis
#
# get a database object somehow using a concrete class
#
$ref = $db->get_Reference_by_id('123456');
#
# $ref is a Bio::Annotation::Reference object
#
Description
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.
Methods
Methods description
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) = @_;
$self->throw_not_implemented(); } | sub get_Reference_by_acc
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | sub get_Reference_by_version
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | General documentation
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.
bioperl-l@lists.open-bio.org - General discussion
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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.
http://bugzilla.open-bio.org/
Email cjfields at uiuc dot edu
The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _