Raw content of Bio::DB::SeqI # # $Id: SeqI.pm,v 1.7 2002/10/22 07:38:29 lapp Exp $ # # BioPerl module for Bio::DB::SeqI.pm # # Cared for by Ewan Birney <birney@ebi.ac.uk> # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::SeqI - Abstract Interface for Sequence databases =head1 SYNOPSIS # get a Bio::DB::SeqI somehow $seq = $seqdb->get_Seq_by_id('some-id'); $seq = $seqdb->get_Seq_by_acc('some-accession-number'); @ids = $seqdb->get_all_ids(); $stream = $seqdb->get_PrimarySeq_stream(); while((my $seq = $stream->next_seq()) { # $seq is a PrimarySeqI compliant object } =head1 DESCRIPTION Abstract interface for a sequence database =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - About the mailing lists =head2 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://bugzilla.bioperl.org/ =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk Describe contact details here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::SeqI; use vars qw(@ISA); use strict; # Object preamble - inherits from Bio::Root::Object use Bio::DB::RandomAccessI; @ISA = qw(Bio::DB::RandomAccessI); =head1 Methods inherieted from Bio::DB::RandomAccessI =head2 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" exception =cut =head2 get_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 =cut =head1 Methods [that were] specific for Bio::DB::SeqI =head2 get_PrimarySeq_stream Title : get_PrimarySeq_stream Usage : $stream = get_PrimarySeq_stream Function: Makes a Bio::SeqIO compliant object which provides a single method, next_seq Returns : Bio::SeqIO Args : none =cut sub get_PrimarySeq_stream{ my ($self,@args) = @_; $self->throw("Object did not provide a PrimarySeq stream object"); } =head2 get_all_primary_ids Title : get_all_ids Usage : @ids = $seqdb->get_all_primary_ids() Function: gives an array of all the primary_ids of the sequence objects in the database. These maybe ids (display style) or accession numbers or something else completely different - they *are not* meaningful outside of this database implementation. Example : Returns : an array of strings Args : none =cut sub get_all_primary_ids{ my ($self,@args) = @_; $self->throw("Object did not provide a get_all_ids method"); } =head2 get_Seq_by_primary_id Title : get_Seq_by_primary_id Usage : $seq = $db->get_Seq_by_primary_id($primary_id_string); Function: Gets a Bio::Seq object by the primary id. The primary id in these cases has to come from $db->get_all_primary_ids. There is no other way to get (or guess) the primary_ids in a database. The other possibility is to get Bio::PrimarySeqI objects via the get_PrimarySeq_stream and the primary_id field on these objects are specified as the ids to use here. Returns : A Bio::Seq object Args : accession number (as a string) Throws : "acc does not exist" exception =cut sub get_Seq_by_primary_id { my ($self,@args) = @_; $self->throw("Abstract database call of get_Seq_by_primary_id. Your database has not implemented this method!"); } 1;