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remove DB::Biocorba

svn path=/bioperl-corba-client/trunk/; revision=53
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194 Bio/DB/Biocorba.pm
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-# $Id$
-#
-# BioPerl module for Bio::DB::Biocorba
-#
-# Cared for by Ewan Birney <birney@ebi.ac.uk>,
-# Jason Stajich <jason@chg.mc.duke.edu>
-#
-# Copyright Ewan Birney, Jason Stajich
-#
-# You may distribute this module under the same terms as perl itself
-
-# POD documentation - main docs before the code
-
-=head1 NAME
-
-Bio::DB::Biocorba.pm - Wrapper to make Biocorba DB interface
-
-=head1 SYNOPSIS
-
-=head1 DESCRIPTION
-
-This is a wrapper which maps the Biocorba DB to a Bioperl DB module making it
-available within the Bioperl framework. It does not have to do a great deal...
-
-=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 Bioperl discussion
- biocorba-l@biocorba.org - General Biocorba discussion
- http://www.bioperl.org/MailList.html - About the bioperl mailing list
- http://www.biocorba.org/MailList.shtml - About the biocorba mailing list
-
-=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://bio.perl.org/bioperl-bugs/
-
-=head1 AUTHOR - Ewan Birney, Jason Stajich
-
-Email birney@ebi.ac.uk, jason@chg.mc.duke.edu
-
-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
-
-package Bio::DB::Biocorba;
-use vars qw(@ISA);
-use strict;
-
-use Bio::CorbaClient::Base;
-use Bio::CorbaClient::Seq;
-use Bio::SeqIO;
-use Bio::DB::SeqI;
-
-@ISA = qw(Bio::CorbaClient::Base Bio::DB::SeqI);
-
-=head1 Bio::DB::RandomAccessI Functions not provided by the IDL
-
-=head2 get_Seq_by_id
-
- Title : get_Seq_by_id
- Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
- Function: Gets a Bio::Seq object by its name
- Returns : a Bio::Seq object
- Args : the id (as a string) of a sequence
- Throws : "id does not exist" exception
-
-=cut
-
-sub get_Seq_by_id {
- my ($self,$id) = shift;
- my $corbaref = $self->corbaref->get_Seq($id);
- return Bio::CorbaClient::Seq->new('-corbaref' => $corbaref) if( defined $corbaref );
- $self->throw("DB::Biocorba could not find a seq for id=$id\n");
- return undef;
-}
-
-=head2 get_Seq_by_acc
-
- Title : get_Seq_by_acc
- Usage : $seq = $db->get_Seq_by_acc('X77802');
- Function: Gets a Bio::CorbaClient::Seq object by accession number
- Returns : A Bio::CorbaClient::Seq object
- Args : accession number (as a string)
- Throws : "acc does not exist" exception
-
-=cut
-
-sub get_Seq_by_acc {
- my ($self,$id) = @_;
- # can you really get this by acc ?
- my $corbaref = $self->corbaref->get_Seq($id);
- return Bio::CorbaClient::Seq->new('-corbaref' => $corbaref)
- if( defined $corbaref );
- $self->throw("DB::Biocorba could not find a seq for acc=$id\n");
- return undef;
-}
-
-=head1 Bio::DB::SeqI methods not provided by biocorba.idl
-
-=head2 get_PrimarySeq_stream
-
- Title : get_PrimarySeq_stream
- Usage : $stream = get_PrimarySeq_stream
- Function: Makes a Bio::SeqIO compliant object
- which provides a single method, next_primary_seq
- Returns : Bio::SeqIO
- Args : none
-
-
-=cut
-
-sub get_PrimarySeq_stream{
- my ($self) = @_;
-# I'm not sure this will work?
- eval {
- my $vectorref = $self->corbaref->get_PrimarySeqVector;
- my $seqioref = new Bio::SeqIO('-format' => 'biocorba',
- '-iterator' => $vectorref->iterator());
- return $seqioref;
- };
- if( $@ ) {
- $self->throw("get_PrimarySeq_stream failed -- $@\n");
- }
-
-}
-
-=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) = @_;
- if( ! $self->corbaref->isa('org::biocorba::seqcore::SeqDB')) {
- return ();
- }
- $self->throw("method get_all_primary_ids is not supported at this time");
-# my $ids = $self->corbaref->get_primaryidList();
-# return @$ids;
-}
-
-
-=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 $db->get_all_primary_ids.
- There is no other way to get (or guess) the primary_ids
- in a database.
-
- The other possibility is to get Bio::PrimarySeqI objects
- via the get_PrimarySeq_stream and the primary_id field
- on these objects are specified as the ids to use here.
- Returns : A Bio::CorbaClient::Seq object
- Args : accession number (as a string)
- Throws : "acc does not exist" exception
-
-
-=cut
-
-sub get_Seq_by_primary_id {
- my ($self,@args) = @_;
- return Bio::CorbaClient::Seq->new('-corbaref' =>
- $self->corbaref->get_Seq(shift @args));
-}
-
-1;
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