NAME

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

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->annotation"
       method.

FEEDBACK

   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

   Support
       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.

   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

AUTHOR - Mark A. Jensen

       Email maj@fortinbras.us

CONTRIBUTORS

       Mark A. Jensen

APPENDIX

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

Constructor

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

Bio::Factory::SequenceProcessorI compliance

   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)

   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

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

HIVAnnotProcessor-specific methods

   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)