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Summary

HIVAnnotProcessor - Adds HIV-specific annotations to Bio::SeqIO streams

Package variables

Included modules

Inherit

Bio::Root::Root

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 );
   }

Description

Bio::DB::HIV::HIVAnnotProcessor is chained to the next_seq of a sequence stream returned from a query to the Los Alamos HIV sequence database made using Bio::DB::HIV and Bio::DB::Query::HIVQuery. It adds the annotations obtained in the Bio::DB::Query::HIVQuery to the Bio::Seq objects themselves via the $seq-E<gt>annotation method.

Methods

Methods description

 Title   : new
 Usage   : my $obj = new HIVAnnotProcessor();
 Function: Builds a new HIVAnnotProcessor object 
 Returns : an instance of HIVAnnotProcessor
 Args    :

 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)

 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

 Title   : write_seq
 Usage   : $seqobj->write_seq
 Function: for HIVAnnotProcessor, throw an exception
 Example :
 Returns : Bio::Root::IOException
 Args    :

 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)

Methods code

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;

}

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'};

}

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;

}

sub write_seq {

   my ($self,@args) = @_;
   $self->throw(-class=>'Bio::Root::IOException',
		-text=>'This stream is read-only',
		-value=>"");

}

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;

}

General documentation

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
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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.

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://redmine.open-bio.org/projects/bioperl/

Email maj@fortinbras.us

Mark A. Jensen

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _