# $Id: bioperl.lisp 15559 2009-02-23 12:11:20Z maj $
#
# BioPerl module for Bio::Search::Result::hmmer3Result
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Thomas Sharpton <thomas.sharpton@gmail.com>
#
# Copyright Thomas Sharpton
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Search::Result::hmmer3Result - DESCRIPTION of Object
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
Describe the object here
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
L<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.
=head2 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
=head1 AUTHOR - Thomas Sharpton
Email thomas.sharpton@gmail.com
Describe contact details here
=head1 CONTRIBUTORS
Additional contributors names and emails here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Search::Result::hmmer3Result;
use strict;
use base qw(Bio::Search::Result::GenericResult);
=head2 new
Title : new
Usage : my $obj = new Bio::Search::Result::hmmer3Result.pm();
Function: Builds a new Bio::Search::Result::hmmer3Result.pm object
Returns : an instance of Bio::Search::Result::hmmer3Result.pm
Args : -hmm_name => string, name of hmm file
-sequence_file => name of the sequence file
=cut
sub new {
my($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;
}
=head2 hmm_name
Title : hmm_name
Usage : $obj->hmm_name($newval)
Function: Get/Set the value of hmm_name
Returns : value of hmm_name
Args : newvalue (optional)
=cut
sub hmm_name{
my ($self,$value) = @_;
if( defined $value) {
$self->{'_hmm_name'} = $value;
}
return $self->{'_hmm_name'};
}
=head2 sequence_file
Title : sequence_file
Usage : $obj->sequence_file($newval)
Function: Get/Set the value of sequence_file
Returns : value of sequence_file
Args : newvalue (optional)
=cut
sub sequence_file{
my ($self,$value) = @_;
if( defined $value) {
$self->{'_sequence_file'} = $value;
}
return $self->{'_sequence_file'};
}
=head2 next_model
Title : next_model
Usage : my $domain = $result->next_model
Function: Returns the next domain - this
is an alias for next_hit
Returns : L<Bio::Search::Hit::HitI> object
Args : none
=cut
sub next_model{ shift->next_hit }
=head2 models
Title : models
Usage : my @domains = $result->models;
Function: Returns the list of HMM models seen - this
is an alias for hits()
Returns : Array of L<Bio::Search::Hit::HitI> objects
Args : none
=cut
sub models{ shift->hits }
=head2 rewind
Title : rewind
Usage : $result->rewind;
Function: Allow one to reset the Hit iteration to the beginning
Since this is an in-memory implementation
Returns : none
Args : none
=cut
sub rewind{
my ($self) = @_;
$self->{'_hitindex'} = 0;
}
1;