| 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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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 _
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)
| 2018-10-27 | perl v5.26.2 |