Bio::Search::Result hmmer3Result
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Summary
Bio::Search::Result::hmmer3Result - DESCRIPTION of Object
Package variables
No package variables defined.
Inherit
Bio::Search::Result::GenericResult
Synopsis
Give standard usage here
Description
Describe the object here
Methods
newDescriptionCode
hmm_nameDescriptionCode
sequence_fileDescriptionCode
next_modelDescriptionCode
modelsDescriptionCode
rewindDescriptionCode
Methods description
newcode    nextTop
 Title   : new
 Usage   : my $obj = new Bio::Search::Result::hmmer3Result.pm();
 Function: Builds a new Bio::Search::Result::hmmer3Result.pm object 
 Returns : an instance of Bio::Search::Result::hmmer3Result.pm
 Args    : -hmm_name => string, name of hmm file
           -sequence_file => name of the sequence file
hmm_namecodeprevnextTop
 Title   : hmm_name
 Usage   : $obj->hmm_name($newval)
 Function: Get/Set the value of hmm_name
 Returns : value of hmm_name
 Args    : newvalue (optional)
sequence_filecodeprevnextTop
 Title   : sequence_file
 Usage   : $obj->sequence_file($newval)
 Function: Get/Set the value of sequence_file
 Returns : value of sequence_file
 Args    : newvalue (optional)
next_modelcodeprevnextTop
 Title   : next_model
 Usage   : my $domain = $result->next_model
 Function: Returns the next domain - this
           is an alias for next_hit
 Returns : Bio::Search::Hit::HitI object
 Args    : none
modelscodeprevnextTop
 Title   : models
 Usage   : my @domains = $result->models;
 Function: Returns the list of HMM models seen - this
           is an alias for hits()
 Returns : Array of Bio::Search::Hit::HitI objects
 Args    : none
rewindcodeprevnextTop
 Title   : rewind
 Usage   : $result->rewind;
 Function: Allow one to reset the Hit iteration to the beginning
           Since this is an in-memory implementation
 Returns : none
 Args    : none
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;
  my $self = $class->SUPER::new(@args);

  my ($hmm,$seqfile) = $self->_rearrange([qw(HMM_NAME SEQUENCE_FILE)],
					 @args);
  defined( $seqfile ) && $self->sequence_file( $seqfile );
  defined( $hmm ) && $self->hmm_name( $hmm );

  return $self;
}
hmm_namedescriptionprevnextTop
sub hmm_name {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'_hmm_name'} = $value;
    }
    return $self->{'_hmm_name'};
}
sequence_filedescriptionprevnextTop
sub sequence_file {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'_sequence_file'} = $value;
    }
    return $self->{'_sequence_file'};
}
next_modeldescriptionprevnextTop
sub next_model {
shift->next_hit
}
modelsdescriptionprevnextTop
sub models {
shift->hits
}
rewinddescriptionprevnextTop
sub rewind {
   my ($self) = @_;
   $self->{'_hitindex'} = 0;
}



1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
SupportTop
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Thomas SharptonTop
Email thomas.sharpton@gmail.com
Describe contact details here
CONTRIBUTORSTop
Additional contributors names and emails here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _