Bio::DB RandomAccessI
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
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Summary
Bio::DB::RandomAccessI - Abstract interface for a sequence database
Package variables
No package variables defined.
Included modules
Bio::Root::RootI
Inherit
Bio::Root::Root
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 an accession number.
Methods
get_Seq_by_idDescriptionCode
get_Seq_by_accDescriptionCode
get_Seq_by_versionDescriptionCode
Methods description
get_Seq_by_idcode    nextTop
 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,
get_Seq_by_acccodeprevnextTop
 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.
get_Seq_by_versioncodeprevnextTop
 Title   : get_Seq_by_version
Usage : $seq = $db->get_Seq_by_version('X77802.1');
Function: Gets a Bio::Seq object by sequence version
Returns : A Bio::Seq object
Args : accession.version (as a string)
Throws : "acc.version does not exist" exception
Methods code
get_Seq_by_iddescriptionprevnextTop
sub get_Seq_by_id {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}
get_Seq_by_accdescriptionprevnextTop
sub get_Seq_by_acc {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}
get_Seq_by_versiondescriptionprevnextTop
sub get_Seq_by_version {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}

## End of Package
1;
}
General documentation
CONTACTTop
Ewan Birney <birney@ebi.ac.uk> originally wrote this class.
Support Top
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.
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:
  https://redmine.open-bio.org/projects/bioperl/
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _