#
# BioPerl module for Bio::Ontology::RelationshipType
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Christian M. Zmasek <czmasek-at-burnham.org> or <cmzmasek@yahoo.com>
#
# (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Ontology::RelationshipType - a relationship type for an ontology
=head1 SYNOPSIS
#
=head1 DESCRIPTION
This class can be used to model various types of relationships
(such as "IS_A", "PART_OF", "CONTAINS", "FOUND_IN", "RELATED_TO").
This class extends L<Bio::Ontology::Term>, so it essentially is-a
L<Bio::Ontology::TermI>. In addition, all methods are overridden such
as to make the object immutable.
=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 the
Bioperl mailing lists Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=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
the web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR
Christian M. Zmasek
Email: czmasek-at-burnham.org or cmzmasek@yahoo.com
WWW: http://monochrome-effect.net/
Address:
Genomics Institute of the Novartis Research Foundation
10675 John Jay Hopkins Drive
San Diego, CA 92121
=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::Ontology::RelationshipType;
use strict;
use constant PART_OF => "PART_OF";
use constant RELATED_TO => "RELATED_TO";
use constant IS_A => "IS_A";
use constant CONTAINS => "CONTAINS";
use constant FOUND_IN => "FOUND_IN";
use constant REGULATES => "REGULATES";
use constant POSITIVELY_REGULATES => "POSITIVELY_REGULATES";
use constant NEGATIVELY_REGULATES => "NEGATIVELY_REGULATES";
use base qw(Bio::Ontology::Term);
#
# cache for terms
#
my %term_name_map = ();
=head2 get_instance
Title : get_instance
Usage : $IS_A = Bio::Ontology::RelationshipType->get_instance( "IS_A" );
$PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" );
$RELATED_TO = Bio::Ontology::RelationshipType->get_instance( "RELATED_TO" );
$CONTAINS = Bio::Ontology::RelationshipType->get_instance( "CONTAINS" );
$FOUND_IN = Bio::Ontology::RelationshipType->get_instance( "FOUND_IN" );
Function: Factory method to create instances of RelationshipType
Returns : [Bio::Ontology::RelationshipType]
Args : "IS_A" or "PART_OF" or "CONTAINS" or "FOUND_IN" or
"RELATED_TO" [scalar]
the ontology [Bio::Ontology::OntologyI] (optional)
=cut
sub get_instance {
my ( $class, $name, $ont ) = @_;
$class->throw("must provide predicate name") unless $name;
# is one in the cache?
my $reltype = $term_name_map{$name};
if($reltype &&
# check whether ontologies match
(($ont && $reltype->ontology() &&
($ont->name() eq $reltype->ontology->name())) ||
(! ($reltype->ontology() || $ont)))) {
# we're done, return cached type
return $reltype;
}
# valid relationship type?
#
#see the cell ontology. this code is too strict, even for dag-edit files. -allen
#
# if ( ! (($name eq IS_A) || ($name eq PART_OF) ||
# ($name eq CONTAINS) || ( $name eq FOUND_IN ))) {
# my $msg = "Found unknown type of relationship: [" . $name . "]\n";
# $msg .= "Known types are: [" . IS_A . "], [" . PART_OF . "], [" . CONTAINS . "], [" . FOUND_IN . "]";
# $class->throw( $msg );
# }
# if we get here we need to create the rel.type
$reltype = $class->new(-name => $name,
-ontology => $ont);
# cache it (FIXME possibly overrides one from another ontology)
$term_name_map{$name} = $reltype;
return $reltype;
} # get_instance
=head2 init
Title : init()
Usage : $type->init();
Function: Initializes this to all undef and empty lists.
Returns :
Args :
=cut
sub init {
my $self = shift;
$self->SUPER::init();
# at this point we don't really need to do anything special for us
} # init
=head2 equals
Title : equals
Usage : if ( $type->equals( $other_type ) ) { ...
Function: Compares this type to another one, based on string "eq" of
the "identifier" field, if at least one of the two types has
the identifier set, or string eq of the name otherwise.
Returns : true or false
Args : [Bio::Ontology::RelationshipType]
=cut
sub equals {
my( $self, $type ) = @_;
$self->_check_class( $type, "Bio::Ontology::RelationshipType" );
if ( $self->identifier() xor $type->identifier() ) {
$self->warn("comparing relationship types when only ".
"one has an identifier will always return false" );
}
return
($self->identifier() || $type->identifier()) ?
$self->identifier() eq $type->identifier() :
$self->name() eq $type->name();
} # equals
=head2 identifier
Title : identifier
Usage : $term->identifier( "IS_A" );
or
print $term->identifier();
Function: Set/get for the immutable identifier of this Type.
Returns : The identifier [scalar].
Args : The identifier [scalar] (optional).
=cut
sub identifier {
my $self = shift;
my $ret = $self->SUPER::identifier();
if(@_) {
$self->throw($self->veto_change("identifier",$ret,$_[0]))
if $ret && ($ret ne $_[0]);
$ret = $self->SUPER::identifier(@_);
}
return $ret;
} # identifier
=head2 name
Title : name
Usage : $term->name( "is a type" );
or
print $term->name();
Function: Set/get for the immutable name of this Type.
Returns : The name [scalar].
Args : The name [scalar] (optional).
=cut
sub name {
my $self = shift;
my $ret = $self->SUPER::name();
if(@_) {
$self->throw($self->veto_change("name",$ret,$_[0]))
if $ret && ($ret ne $_[0]);
$ret = $self->SUPER::name(@_);
}
return $ret;
} # name
=head2 definition
Title : definition
Usage : $term->definition( "" );
or
print $term->definition();
Function: Set/get for the immutable definition of this Type.
Returns : The definition [scalar].
Args : The definition [scalar] (optional).
=cut
sub definition {
my $self = shift;
my $ret = $self->SUPER::definition();
if(@_) {
$self->veto_change("definition",$ret,$_[0])
if $ret && ($ret ne $_[0]);
$ret = $self->SUPER::definition(@_);
}
# let's be nice and return something readable here
return $ret if $ret;
return $self->name()." relationship predicate (type)" if $self->name();
} # definition
=head2 ontology
Title : ontology
Usage : $term->ontology( $top );
or
$top = $term->ontology();
Function: Set/get for the ontology this relationship type lives in.
Returns : The ontology [Bio::Ontology::OntologyI].
Args : On set, the ontology [Bio::Ontology::OntologyI] (optional).
=cut
sub ontology {
my $self = shift;
my $ret = $self->SUPER::ontology();
if(@_) {
my $ont = shift;
if($ret) {
$self->throw($self->veto_change("ontology",$ret->name,
$ont ? $ont->name : $ont))
unless $ont && ($ont->name() eq $ret->name());
}
$ret = $self->SUPER::ontology($ont,@_);
}
return $ret;
} # category
=head2 version
Title : version
Usage : $term->version( "1.00" );
or
print $term->version();
Function: Set/get for immutable version information.
Returns : The version [scalar].
Args : The version [scalar] (optional).
=cut
sub version {
my $self = shift;
my $ret = $self->SUPER::version();
if(@_) {
$self->throw($self->veto_change("version",$ret,$_[0]))
if $ret && ($ret ne $_[0]);
$ret = $self->SUPER::version(@_);
}
return $ret;
} # version
=head2 is_obsolete
Title : is_obsolete
Usage : $term->is_obsolete( 1 );
or
if ( $term->is_obsolete() )
Function: Set/get for the immutable obsoleteness of this Type.
Returns : the obsoleteness [0 or 1].
Args : the obsoleteness [0 or 1] (optional).
=cut
sub is_obsolete {
my $self = shift;
my $ret = $self->SUPER::is_obsolete();
if(@_) {
$self->throw($self->veto_change("is_obsolete",$ret,$_[0]))
if $ret && ($ret != $_[0]);
$ret = $self->SUPER::is_obsolete(@_);
}
return $ret;
} # is_obsolete
=head2 comment
Title : comment
Usage : $term->comment( "..." );
or
print $term->comment();
Function: Set/get for an arbitrary immutable comment about this Type.
Returns : A comment.
Args : A comment (optional).
=cut
sub comment {
my $self = shift;
my $ret = $self->SUPER::comment();
if(@_) {
$self->throw($self->veto_change("comment",$ret,$_[0]))
if $ret && ($ret ne $_[0]);
$ret = $self->SUPER::comment(@_);
}
return $ret;
} # comment
=head1 Private methods
May be overridden in a derived class, but should never be called from
outside.
=cut
sub _check_class {
my ( $self, $value, $expected_class ) = @_;
if ( ! defined( $value ) ) {
$self->throw( "Found [undef] where [$expected_class] expected" );
}
elsif ( ! ref( $value ) ) {
$self->throw( "Found [scalar] where [$expected_class] expected" );
}
elsif ( ! $value->isa( $expected_class ) ) {
$self->throw( "Found [" . ref( $value ) . "] where [$expected_class] expected" );
}
} # _check_type
=head2 veto_change
Title : veto_change
Usage :
Function: Called if an attribute is changed. Setting an attribute is
considered a change if it had a value before and the attempt
to set it would change the value.
This method returns the message to be printed in the exception.
Example :
Returns : A string
Args : The name of the attribute that was attempted to change.
Optionally, the old value and the new value for reporting
purposes only.
=cut
sub veto_change{
my ($self,$attr,$old,$new) = @_;
my $changetype = $old ? ($new ? "change" : "unset") : "change";
my $msg = "attempt to $changetype attribute $attr in ".ref($self).
", which is immutable";
$msg .= " (\"$old\" to \"$new\")" if $old && $new;
return $msg;
}
1;