Bio::DB::HIV::HIVAnnotUsereContributed Perl Bio::DB::HIV::HIVAnnotProcessor(3)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=>$stream );
}
DESCRIPTIONBio::DB::HIV::HIVAnnotProcessor is chained to the "next_seq" of a
sequence stream returned from a query to the Los Alamos HIV sequence
database made using Bio::DB::HIV and Bio::DB::Query::HIVQuery. It adds
the annotations obtained in the "Bio::DB::Query::HIVQuery" to the
Bio::Seq objects themselves via the "$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:
http://bugzilla.open-bio.org/
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)
perl v5.14.12011-07-22Bio::DB::HIV::HIVAnnotProcessor(3)
