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GOBO/Graph.pm  view on Meta::CPAN

 - Returns: ArrayRef[GOBO::InstanceNode], where each member is an instance belonging to this graph

=cut

sub instances {
    my $self = shift;
    #$self->node_index->nodes_by_metaclass('instance');
    return [values %{$self->instance_h}];
}

=head2 add_term

 - Arguments: Str or GOBO::Node
 - Returns: GOBO::TermNode
 - Side effects: adds the object to the list of terms referenced in this graph. Forces the class to be GOBO::TermNode

=cut

sub add_term {
    my $self = shift;
    my $n = $self->term_noderef(@_);
    $self->term_h->{$n->id} = $n;
    return $n;
}

=head2 add_relation

 - Arguments: Str or GOBO::Node
 - Returns: GOBO::RelationNode
 - Side effects: adds the object to the list of relations referenced in this graph. Forces the class to be GOBO::RelationNode

=cut

sub add_relation {
    my $self = shift;
    my $n = $self->relation_noderef(@_);
    $self->relation_h->{$n->id} = $n;
    return $n;
}

=head2 add_instance

 - Arguments: Str or GOBO::Node
 - Returns: GOBO::InstanceNode

adds the object to the list of instances referenced in this
graph. Forces the class to be GOBO::InstanceNode

=cut

sub add_instance {
    my $self = shift;
    my $n = $self->instance_noderef(@_);
    $self->instance_h->{$n->id} = $n;
    return $n;
}

=head2 remove_node

 - Arguments: node GOBO::Node, cascade Bool[OPT]

unlinks the node from this graph

If cascade is 0 or undef, any links to or from this node will remain as dangling links.

If cascade is set, then links to and from this node will also be deleted

=cut

sub remove_node {
    my $self = shift;
    my $n = shift;
    my $cascade = shift;
    #my $id = ref($n) ? $n->id : $n;
    my $id = $n->id;

    if ($self->term_h->{$id}) {
        delete $self->term_h->{$id};
    }
    if ($self->instance_h->{$id}) {
        delete $self->instance_h->{$id};
    }
    if ($self->relation_h->{$id}) {
        delete $self->relation_h->{$id};
    }
    if ($cascade) {
        $self->remove_link($_) foreach @{$self->get_outgoing_links($n)};
        $self->remove_link($_) foreach @{$self->get_incoming_links($n)};
    }

    return $self->node_index->remove_node($n);
}

sub add_formula { my $self = shift; push(@{$self->formulae},@_) }

=head2 get_outgoing_links (subject GOBO::Node, relation GOBO::RelationNode OPTIONAL)

given a subject (child), get target (parent) links

if relation is specified, also filters results on relation

=cut

sub get_outgoing_links {
    my $self = shift;
    my $n = shift;
    my $rel = shift;
    my @sl = @{$self->link_ix->statements_by_node_id(ref($n) ? $n->id : $n) || []};
    # if x = a AND r(b), then x r b
    if (ref($n) && $n->isa('GOBO::ClassExpression::Intersection')) {
        foreach (@{$n->arguments}) {
            if ($_->isa('GOBO::ClassExpression::RelationalExpression')) {
                push(@sl, new GOBO::LinkStatement(node=>$n,relation=>$_->relation,target=>$_->target));
            }
            else {
                push(@sl, new GOBO::LinkStatement(node=>$n,relation=>'is_a',target=>$_));
            }
        }
    }
    if ($rel) {
        # TODO: use indexes to make this faster
        my $rid = ref($rel) ? $rel->id : $rel;
        @sl = grep {$_->relation->id eq $rid} @sl;
    }
    return \@sl;
}

# @Deprecated
*get_target_links = \&get_outgoing_links;

=head2 get_incoming_links (subject GOBO::Node, relation GOBO::RelationNode OPTIONAL)

given a subject (child), get target (parent) links

if relation is specified, also filters results on relation

=cut

sub get_incoming_links {
    my $self = shift;
    my $n = shift;
    my $rel = shift;
    my @sl = @{$self->link_ix->statements_by_target_id(ref($n) ? $n->id : $n) || []};
    if ($rel) {
        # TODO: use indexes to make this faster
        my $rid = ref($rel) ? $rel->id : $rel;