Raw content of Bio::Tools::HMMER::Set
<![CDATA[# $Id: Set.pm,v 1.13 2002/10/22 07:45:23 lapp Exp $
#
# BioPerl module for Bio::Tools::HMMER::Set
#
# Cared for by Ewan Birney <birney@sanger.ac.uk>
#
# Copyright Ewan Birney
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::HMMER::Set - Set of identical domains from HMMER matches
=head1 SYNOPSIS
# get a Set object probably from the results object
print "Bits score over set ",$set->bits," evalue ",$set->evalue,"\n";
foreach $domain ( $set->each_Domain ) {
print "Domain start ",$domain->start," end ",$domain->end,"\n";
}
=head1 DESCRIPTION
Represents a set of HMMER domains hitting one sequence. HMMER reports two
different scores, a per sequence total score (and evalue) and a per
domain score and evalue. This object represents a collection of the same
domain with the sequence bits score and evalue. (these attributes are also
on the per domain scores, which you can get there).
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://www.bioperl.org/MailList.html - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:
bioperl-bugs@bioperl.org
http://www.bugzilla.bioperl.org/
=head1 AUTHOR - Ewan Birney
Email birney@sanger.ac.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::HMMER::Set;
use vars qw(@ISA);
use strict;
use Bio::Root::Root;
use Bio::Tools::HMMER::Domain;
@ISA = qw( Bio::Root::Root );
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($name,$acc,$desc) = $self->_rearrange([qw(NAME ACCESSION DESC)],
@args);
$name && $self->name($name);
$acc && $self->accession($acc);
$desc && $self->desc($desc);
$self->{'domains'} = [];
$self->{'domainnames'} = {};
return $self;
}
=head2 add_Domain
Title : add_Domain
Usage : $set->add_Domain($domain)
Function: adds the domain to the list
Returns : nothing
Args : A Bio::Tools::HMMER::Domain object
=cut
sub add_Domain{
my ($self,$domain) = @_;
if( ! defined $domain || ! $domain->isa("Bio::Tools::HMMER::Domain") ) {
$self->throw("[$domain] is not a Bio::Tools::HMMER::Domain. aborting");
}
return if $self->{'domainnames'}->{$domain->get_nse}++;
push(@{$self->{'domains'}},$domain);
}
=head2 each_Domain
Title : each_Domain
Usage : foreach $domain ( $set->each_Domain() )
Function: returns an array of domain objects in this set
Returns : array
Args : none
=cut
sub each_Domain{
my ($self,@args) = @_;
return @{$self->{'domains'}};
}
=head2 name
Title : name
Usage : $obj->name($newval)
Function:
Example :
Returns : value of name
Args : newvalue (optional)
=cut
sub name{
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'name'} = $value;
}
return $obj->{'name'};
}
=head2 desc
Title : desc
Usage : $obj->desc($newval)
Function:
Example :
Returns : value of desc
Args : newvalue (optional)
=cut
sub desc{
my ($self,$value) = @_;
if( defined $value) {
$self->{'desc'} = $value;
}
return $self->{'desc'};
}
=head2 accession
Title : accession
Usage : $obj->accession($newval)
Function:
Example :
Returns : value of accession
Args : newvalue (optional)
=cut
sub accession{
my ($self,$value) = @_;
if( defined $value) {
$self->{'accession'} = $value;
}
return $self->{'accession'};
}
=head2 bits
Title : bits
Usage : $obj->bits($newval)
Function:
Example :
Returns : value of bits
Args : newvalue (optional)
=cut
sub bits{
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'bits'} = $value;
}
return $obj->{'bits'};
}
=head2 evalue
Title : evalue
Usage : $obj->evalue($newval)
Function:
Example :
Returns : value of evalue
Args : newvalue (optional)
=cut
sub evalue{
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'evalue'} = $value;
}
return $obj->{'evalue'};
}
sub addHMMUnit {
my $self = shift;
my $unit = shift;
$self->warn("Using old addHMMUnit call on Bio::Tools::HMMER::Set. Should replace with add_Domain");
return $self->add_Domain($unit);
}
sub eachHMMUnit {
my $self = shift;
$self->warn("Using old eachHMMUnit call on Bio::Tools::HMMER::Set. Should replace with each_Domain");
return $self->each_Domain();
}
1; # says use was ok
__END__
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