#
# BioPerl module for Bio::Search::Result::INFERNALResult.pm
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Paul Cantalupo
#
# Copyright Paul Cantalupo
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Search::Result::INFERNALResult - A Result object for INFERNAL results
=head1 SYNOPSIS
# typically one gets Results from a SearchIO stream
use Bio::SearchIO;
my $io = Bio::SearchIO->new(-format => 'infernal',
-file => 't/data/cmsearch_output.txt');
while( my $result = $io->next_result ) {
while( my $hit = $result->next_hit ) {
print join(" ", $result->query_name, $result->algorithm, $result->num_hits), "\n";
}
}
=head1 DESCRIPTION
This object is a specialization of L<Bio::Search::Result::GenericResult>. There
is one extra method called L<cm_name>.
=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:
I<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 - Paul Cantalupo
=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::INFERNALResult;
use strict;
use warnings;
use base qw(Bio::Search::Result::GenericResult);
=head2 new
Title : new
Usage : my $obj = Bio::Search::Result::INFERNALResult->new();
Function: Builds a new Bio::Search::Result::INFERNALResult object
Returns : Bio::Search::Result::INFERNALResult
Args : -cm_name => string, name of covariance model (CM) file.
plus Bio::Search::Result::GenericResult parameters
=cut
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($cm) = $self->_rearrange([qw(CM_NAME)], @args);
if (defined $cm) { $self->cm_name($cm) }
return $self;
}
=head2 cm_name
Title : cm_name
Usage : $obj->cm_name($newvalue)
Function: Get/Set value of the covariance model file name (cm_name)
Returns : value of cm_name
Args : newvalue (optional)
=cut
sub cm_name {
my ($self, $value) = @_;
if (defined $value) {
$self->{'_cm_name'} = $value;
}
return $self->{'_cm_name'};
}
1;