Bio::DB
RandomAccessI
Summary
Bio::DB::RandomAccessI - Abstract interface for a sequence database
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
#
# get a database object somehow using a concrete class
#
$seq = $db->get_Seq_by_id('ROA1_HUMAN');
#
# $seq is a Bio::Seq 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::RandomAccessI class defines what methods a generic database class
should have. At the moment it is just the ability to make Bio::Seq objects
from a name (id) or a accession number.
Methods
Methods description
Title : get_Seq_by_id
Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
Function: Gets a Bio::Seq object by its name
Returns : a Bio::Seq object or undef if not found
Args : the id (as a string) of a sequence, |
Title : get_Seq_by_acc
Usage : $seq = $db->get_Seq_by_acc('X77802');
$seq = $db->get_Seq_by_acc(Locus => 'X77802');
Function: Gets a Bio::Seq object by accession number
Returns : A Bio::Seq object or undef if not found
Args : accession number (as a string), or a two
element list consisting of namespace=>accession
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
NOTE: The two-element form allows you to choose the namespace for the
accession number. |
Title : get_Seq_by_version
Usage : $seq = $db->get_Seq_by_version('X77802.1');
Function: Gets a Bio::Seq object by sequence version
Returns : A Bio::Seq object
Args : accession.version (as a string)
Throws : "acc.version does not exist" exception |
Methods code
sub get_Seq_by_id
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | sub get_Seq_by_acc
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | sub get_Seq_by_version
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | General documentation
Ewan Birney <birney@ebi.ac.uk> originally wrote this class.
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/
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _