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Bio::DB::HIV::HIVAnnotProcessor(3pm) User Contributed Perl Documentation Bio::DB::HIV::HIVAnnotProcessor(3pm)


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


   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 );


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->annotation" method.


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AUTHOR - Mark A. Jensen



Mark A. Jensen


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



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

Bio::Factory::SequenceProcessorI compliance


 Title   : source_stream
 Usage   : $hap->source_stream($newval)
 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    :

HIVAnnotProcessor-specific methods


 Title   : hiv_query
 Usage   : $obj->hiv_query($newval)
 Example : 
 Returns : value of hiv_query (a Bio::DB::Query::HIVQuery object)
 Args    : on set, new value (an HIVQuery object, optional)
2018-10-27 perl v5.26.2