/usr/share/perl5/GO/Model/Relationship.pm is in libgo-perl 0.13-3.
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::Relationship;
=head1 NAME
GO::Model::Relationship - relationship between two terms
=head1 SYNOPSIS
=head1 DESCRIPTION
a relationship between two GO::Model::Terms
relationships can be thought of as B<statements> or sentences of the form
SUBJECT-TERM PREDICATE OBJECT-TERM
for example,
"dog" IS_A "animal"
"G-Protein coupled receptor" IS_A "transmembrane receptor"
Statements have a B<subject> (i.e. the subject of the
sentence/statement), a predicate/relationship-type and an B<object>
(i.e. the object of the sentence/statement)
Relationships can also be seen as arcs in a directed graph, with the
subject being equivalent to the child, and the object equivalent to
the parent. The arc is labeled with the predicate/relationship-type.
A Relationship object currently does not contain an actual pointer to
a GO::Model::Term object. Instead it stores the ID of that term. This
is intended to be used in conjunction with the Graph object, or with
the database.
=cut
use Carp;
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(acc1 acc2 is_inheritance complete type);
}
sub _initialize {
my $self = shift;
$self->SUPER::_initialize(@_);
}
sub acc1 {
my $self = shift;
$self->{"acc1"} = shift if @_;
return $self->{"acc1"};
}
*obj_acc = \&acc1;
*object_acc = \&acc1;
*parent_acc = \&acc1;
sub acc2 {
my $self = shift;
$self->{"acc2"} = shift if @_;
return $self->{"acc2"};
}
*subj_acc = \&acc2;
*subject_acc = \&acc2;
*child_acc = \&acc2;
=head2 subject_acc
Title : subject_acc
Usage : $obj->subject_acc($newid)
Usage : $currid = $obj->subject_acc()
Synonyms: subj_acc, acc2, child_acc
Function: gets or sets the identifier for the child/subject term
Example :
Returns : value of subject_acc (string)
Args : on set, new value (string)
All Relationships can be thought of "subject-predicate-object"
statements. The statement is *about* the subject, and states something
about the relationship *to* the object.
For example, the if we have a Relationship:
cell
^
|
| [part_of]
|
cell nucleus
This is a statement about cell nuclei in general, so "cell nucleus" is
the subject (sometimes called the child node). The Relationship tells
us that all cell nuclei are part_of some cell, so the object of the
relationship (sometimes called the parent node) is "cell"
=cut
=head2 object_acc
Title : object_acc
Usage : $obj->object_acc($newid)
Usage : $currid = $obj->object_acc()
Synonyms: obj_acc, acc1, parent_acc
Function: gets or sets the identifier for the parent/object term
Example :
Returns : value of object_acc (string)
Args : on set, new value (string)
See Also: subj_acc
=cut
=head2 type
Title : type
Usage : $obj->type($newval)
Usage : $currval = $obj->type()
Synonyms:
Function: gets or sets the relationship type (a string)
Example :
Returns : value of type (string)
Args : on set, new value (string)
Currently any string is allowed; in future the type string may be
constrained to come from a controlled vocabulary of relationship types
=cut
sub type {
my $self = shift;
if (@_) {
my $type = shift;
if ($type) {
$self->{type} = $type;
}
}
return $self->{type} || "unknown";
}
sub is_obsolete {
my $self = shift;
$self->{is_obsolete} = shift if @_;
return $self->{is_obsolete} ? 1:0;
}
sub as_str {
my $self = shift;
sprintf("%s:%s:%s", $self->type, $self->acc1, $self->acc2);
}
sub to_ptuples {
my $self = shift;
warn("deprecated");
my ($th) =
rearrange([qw(tuples)], @_);
(["rel", $self->type, $self->acc1, $self->acc2]);
}
sub is_inheritance {
my $self = shift;
warn("deprecated");
if (@_) {
my $is = shift;
$is && $self->type("isa");
!$is && $self->type("partof");
}
return $self->type eq "isa";
}
1;
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