/ 
BioPerl-1.007001
River stage two • 60 direct dependents • 65 total dependents
/ Bio::DB::HIV::HIVAnnotProcessor

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)