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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" HIVAnnotProcessor \- Adds HIV\-specific annotations to Bio::SeqIO streams .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 6 \& sub get_Stream_by_query { \& my ($self, $query ) = @_; \& my $stream = $self\->get_seq_stream(\*(Aq\-query\*(Aq => $query, \*(Aq\-mode\*(Aq=>\*(Aqquery\*(Aq); \& return new Bio::DB::HIV::HIVAnnotProcessor( \-hiv_query=>$query, \& \-source_stream=>$stream ); \& } .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" Bio::DB::HIV::HIVAnnotProcessor is chained to the \f(CW\*(C`next_seq\*(C'\fR of a sequence stream returned from a query to the Los Alamos \s-1HIV\s0 sequence database made using Bio::DB::HIV and Bio::DB::Query::HIVQuery. It adds the annotations obtained in the \f(CW\*(C`Bio::DB::Query::HIVQuery\*(C'\fR to the Bio::Seq objects themselves via the \f(CW\*(C`$seq\->annotation\*(C'\fR method. .SH "FEEDBACK" .IX Header "FEEDBACK" .SS "Mailing Lists" .IX Subsection "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. .PP .Vb 2 \& bioperl\-l@bioperl.org \- General discussion \& http://bioperl.org/wiki/Mailing_lists \- About the mailing lists .Ve .SS "Support" .IX Subsection "Support" Please direct usage questions or support issues to the mailing list: .PP \&\fIbioperl\-l@bioperl.org\fR .PP 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. .SS "Reporting Bugs" .IX Subsection "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: .PP .Vb 1 \& https://github.com/bioperl/bioperl\-live/issues .Ve .SH "AUTHOR \- Mark A. Jensen" .IX Header "AUTHOR - Mark A. Jensen" Email maj@fortinbras.us .SH "CONTRIBUTORS" .IX Header "CONTRIBUTORS" Mark A. Jensen .SH "APPENDIX" .IX Header "APPENDIX" The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ .SH "Constructor" .IX Header "Constructor" .SS "new" .IX Subsection "new" .Vb 5 \& Title : new \& Usage : my $obj = new HIVAnnotProcessor(); \& Function: Builds a new HIVAnnotProcessor object \& Returns : an instance of HIVAnnotProcessor \& Args : .Ve .SH "Bio::Factory::SequenceProcessorI compliance" .IX Header "Bio::Factory::SequenceProcessorI compliance" .SS "source_stream" .IX Subsection "source_stream" .Vb 6 \& 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) .Ve .SS "next_seq" .IX Subsection "next_seq" .Vb 7 \& 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 .Ve .SS "write_seq" .IX Subsection "write_seq" .Vb 6 \& Title : write_seq \& Usage : $seqobj\->write_seq \& Function: for HIVAnnotProcessor, throw an exception \& Example : \& Returns : Bio::Root::IOException \& Args : .Ve .SH "HIVAnnotProcessor-specific methods" .IX Header "HIVAnnotProcessor-specific methods" .SS "hiv_query" .IX Subsection "hiv_query" .Vb 6 \& 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) .Ve