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Manual Reference Pages  -  BIO::DB::HIV::HIVANNOTPROCESSOR (3)

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NAME

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

CONTENTS

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)



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perl v5.20.3 BIO::DB::HIV::HIVANNOTPROCESSOR (3) 2016-04-05

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