Manual Reference Pages - BIO::DB::LOCATIONI (3)
Bio::DB::LocationI - A RandomAccessI-like abstract interface for
retrieving location data from a sequence database and returning
# get a database object somehow using a concrete class
$loc = $db->get_Location_by_id(123456);
# $loc is a Bio::LocationI 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::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:
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.
Ewan Birney originally wrote Bio::DB::RandomAccessI, from which this class
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The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _
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
|perl v5.20.3 ||BIO::DB::LOCATIONI (3) ||2016-04-05 |
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