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# $Id: HIVAnnotProcessor.pm 221 2008-12-11 13:05:24Z maj $
#
# BioPerl module for HIVAnnotProcessor
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Mark A. Jensen <maj@fortinbras.us>
#
# Copyright Mark A. Jensen
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
HIVAnnotProcessor - Adds HIV-specific annotations to Bio::SeqIO streams
=head1 SYNOPSIS
sub get_Stream_by_query {
my ($self, $query ) = @_;
my $stream = $self->get_seq_stream('-query' => $query, '-mode'=>'query');
return new Bio::DB::HIV::HIVAnnotProcessor( -hiv_query=>$query,
-source_stream=>$stream );
}
=head1 DESCRIPTION
Bio::DB::HIV::HIVAnnotProcessor is chained to the C<next_seq> of a sequence stream returned from a query to the Los Alamos HIV sequence database made using L<Bio::DB::HIV> and L<Bio::DB::Query::HIVQuery>. It adds the annotations obtained in the C<Bio::DB::Query::HIVQuery> to the Bio::Seq objects themselves via the C<$seq-E<gt>annotation> method.
=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
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Mark A. Jensen
Email maj@fortinbras.us
=head1 CONTRIBUTORS
Mark A. Jensen
=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::HIV::HIVAnnotProcessor;
use strict;
# Object preamble - inherits from Bio::Root::Root
use Bio::Root::Root;
use base qw( Bio::Root::Root);
=head1 Constructor
=head2 new
Title : new
Usage : my $obj = new HIVAnnotProcessor();
Function: Builds a new HIVAnnotProcessor object
Returns : an instance of HIVAnnotProcessor
Args :
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($hiv_query, $source_stream) =
$self->_rearrange([qw(HIV_QUERY SOURCE_STREAM)], @args);
$hiv_query && $self->hiv_query($hiv_query);
$source_stream && $self->source_stream($source_stream);
return $self;
}
=head1 Bio::Factory::SequenceProcessorI compliance
=head2 source_stream
Title : source_stream
Usage : $hap->source_stream($newval)
Function:
Example :
Returns : value of source_stream (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub source_stream{
my $self = shift;
if (@_) {
$self->throw(-class=>'Bio::Root::BadParameter',
-text=>'Requires a Bio::SeqIO as argument',
-value=>$_[0]) unless $_[0]->isa('Bio::SeqIO');
}
return $self->{'source_stream'} = shift if @_;
return $self->{'source_stream'};
}
=head2 next_seq
Title : next_seq
Usage : $seqobj = stream->next_seq
Function: Reads the next sequence object from the stream,
: adds annotations from the HIVQuery object according
: to the sequence id, and returns sequence object
Returns : a Bio::Seq sequence object
Args : none
=cut
sub next_seq {
my $self = shift;
my $q = $self->hiv_query;
my $seqo = $self->source_stream->next_seq;
return $seqo unless ($q && $seqo);
my $ac = $q->get_annotations_by_id($seqo->primary_id);
$seqo->annotation($ac) if $ac;
my $acc = $q->get_accessions_by_id($seqo->primary_id);
$seqo->accession_number($acc) if $acc;
return $seqo;
}
=head2 write_seq
Title : write_seq
Usage : $seqobj->write_seq
Function: for HIVAnnotProcessor, throw an exception
Example :
Returns : Bio::Root::IOException
Args :
=cut
sub write_seq{
my ($self,@args) = @_;
$self->throw(-class=>'Bio::Root::IOException',
-text=>'This stream is read-only',
-value=>"");
}
=head1 HIVAnnotProcessor-specific methods
=head2 hiv_query
Title : hiv_query
Usage : $obj->hiv_query($newval)
Function:
Example :
Returns : value of hiv_query (a Bio::DB::Query::HIVQuery object)
Args : on set, new value (an HIVQuery object, optional)
=cut
sub hiv_query{
my $self = shift;
if (@_) {
$self->throw(-class=>'Bio::Root::BadParameter',
-text=>'Requires a Bio::DB::Query::HIVQuery as argument',
-value=>$_[0]) unless ref $_[0] && $_[0]->isa('Bio::DB::Query::HIVQuery');
}
return $self->{'hiv_query'} = shift if @_;
return $self->{'hiv_query'};
}
1;
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