/usr/share/perl5/GO/Model/LogicalDefinition.pm is in libgo-perl 0.15-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#
# This GO module is maintained by Chris Mungall <cjm@fruitfly.org>
#
# see also - http://www.geneontology.org
# - http://www.godatabase.org/dev
#
# You may distribute this module under the same terms as perl itself
package GO::Model::LogicalDefinition;
=head1 NAME
GO::Model::LogicalDefinition - logical definition
=head1 SYNOPSIS
=head1 DESCRIPTION
=cut
use Carp qw(cluck confess);
use Exporter;
use GO::Utils qw(rearrange);
use GO::Model::Root;
use strict;
use vars qw(@ISA);
@ISA = qw(GO::Model::Root Exporter);
sub _valid_params {
return qw(intersection_list);
}
=head2 intersection_list
Usage -
Returns -
Args -
Each element of the list is itself a list
This list is of length 1 or 2.
[$generic_term_acc]
[$relation,$differentiating_term_acc]
=cut
=head2 generic_term_acc
Usage -
Synonyms - genus_acc
Returns -
Args -
the ID of the generic term, also known as 'genus'
=cut
sub generic_term_acc {
my $self = shift;
if (@_) {
my $acc = shift;
my $diffs = $self->differentia;
push(@{$self->intersection_list},$acc);
return $acc;
}
my @direct_accs =
grep {scalar(@$_) == 1} @{$self->intersection_list};
if (@direct_accs > 1) {
$self->throw("multiple generic terms");
}
if (@direct_accs) {
return $direct_accs[0]->[0];
}
# no genus
return;
}
*genus_acc = \&generic_term_acc;
=head2 differentia
Usage -
Returns -
Args -
=cut
sub differentia {
my $self = shift;
if (@_) {
my $diffs = shift;
my $genus = $self->generic_term_acc;
$self->intersection_list([$genus, $diffs]);
return $diffs;
}
my @diffs =
grep {scalar(@$_) > 1} @{$self->intersection_list};
return \@diffs;
}
1;
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