Bio::DB
LocationI
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Summary
Bio::DB::LocationI - A RandomAccessI-like abstract interface for
retrieving location data from a sequence database and returning
Bio::LocationI objects
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
#
# get a database object somehow using a concrete class
#
$loc = $db->get_Location_by_id('123456');
#
# $loc is a Bio::LocationI 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::LocationI class defines methods used to retrieve location data
from a sequence. This is returned in the form of Bio::LocationI objects,
which can include:
Bio::Location::Simple
Bio::Location::Fuzzy
Bio::Location::Split
At the moment it is just the ability to make Bio::LocationI objects
from a name or unique id (id), an accession number (acc), and so on.
Methods
Methods description
Title : get_Location_by_id
Usage : $loc = $db->get_Location_by_id('123456')
Function: Gets a Bio::LocationI-implementing object by its name (id)
Returns : a Bio::LocationI object or undef if not found
Args : the id (as a string) of a sequence |
Title : get_Location_by_acc
Usage : $loc = $db->get_Location_by_acc('X77802');
Function: Gets a Bio::LocationI object by accession number
Returns : A Bio::LocationI 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_Location_by_version
Usage : $loc = $db->get_Location_by_version('X77802.1');
Function: Gets a Bio::LocationI object by sequence version
Returns : A Bio::LocationI object
Args : accession.version (as a string)
Throws : "acc.version does not exist" exception |
Methods code
sub get_Location_by_id
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | sub get_Location_by_acc
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | sub get_Location_by_version
{ my ($self,@args) = @_;
$self->throw_not_implemented();
}
1; } | 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
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is much appreciated.
bioperl-l@lists.open-bio.org - General discussion
http://www.bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
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.
https://redmine.open-bio.org/projects/bioperl/
Email cjfields at bioperl dot org
The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _