NAME
Bio::DB::BioSeqI - Abstract interface for a sequence database
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::BioSeqI 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.
CONTACT
Ewan Birney originally wrote this class.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:
bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/ APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
get_Seq_by_id
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
Args : the id (as a string) of a sequence
Throws : "id does not exist" exceptionget_Seq_by_acc
Title : get_Seq_by_acc
Usage : $seq = $db->get_Seq_by_acc('X77802');
Function: Gets a Bio::Seq object by accession number
Returns : A Bio::Seq object
Args : accession number (as a string)
Throws : "acc does not exist" exception