Raw content of Bio::EnsEMBL::Pipeline::GeneDuplication::Result
<![CDATA[package Bio::EnsEMBL::Pipeline::GeneDuplication::Result;
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::Root;
@ISA = qw(Bio::EnsEMBL::Root);
sub new {
my ($class, @args) = @_;
my $self = bless {}, $class;
my ($id,
$distance_method) = $self->_rearrange([qw(ID
DISTANCE_METHOD)],@args);
$id && $self->query_id($id);
$distance_method && $self->distance_method($distance_method);
return $self;
}
sub query_id {
my $self = shift;
if (@_) {
$self->{_query_id} = shift;
}
return $self->{_query_id}
}
sub distance_method {
my $self = shift;
if (@_) {
$self->{_distance_method} = shift;
}
return $self->{_distance_method}
}
sub matrix {
my $self = shift;
if (@_) {
$self->{_matrix} = shift;
}
return $self->{_matrix}
}
sub otus {
my $self = shift;
if (@_) {
$self->{_otus} = shift;
}
return $self->{_otus}
}
sub add_match {
my ($self,
$query_id,
$match_id,
$dn,
$ds,
$n,
$s,
$lnL) = @_;
die "Dont have a match identifier to store with match."
unless $match_id;
die "Dont have nonsynonymous and synonymous values to store with match."
unless defined $dn & defined $ds;
my %match_hash;
$match_hash{query_id} = $query_id;
$match_hash{match_id} = $match_id;
$match_hash{dN} = $dn;
$match_hash{dS} = $ds;
$match_hash{N} = $n;
$match_hash{S} = $s;
$match_hash{lnL} = $lnL ? $lnL : 0; #Set to zero if no defined.
push @{$self->{_matches}}, \%match_hash;
return 1;
}
sub matches {
my $self = shift;
return $self->{_matches}
}
return 1;
]]>