Raw content of Bio::Ontology::PathI # $Id: PathI.pm,v 1.1.2.2 2003/03/27 10:07:56 lapp Exp $ # # BioPerl module for PathI # # Cared for by Hilmar Lapp <hlapp at gmx.net> # # (c) Hilmar Lapp, hlapp at gmx.net, 2003. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2003. # # 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 PathI - Interface for a path between ontology terms =head1 SYNOPSIS # see documentation of methods and an implementation, e.g., # Bio::Ontology::Path =head1 DESCRIPTION This is the minimal interface for a path between two terms in an ontology. Ontology engines may use this. Essentially this is a very thin extension of the L<Bio::Ontology::RelationshipI> interface. It basically adds an attribute distance(). For a RelationshipI, you can think of distance as equal to zero (subject == object) or 1 (subject != object). =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 list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net =head1 CONTRIBUTORS Additional contributors names and emails here =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::PathI; use vars qw(@ISA); use strict; use Bio::Ontology::RelationshipI; @ISA = qw( Bio::Ontology::RelationshipI ); =head2 distance Title : distance Usage : $obj->distance($newval) Function: Get (and set if the implementation allows it) the distance between the two terms connected by this path. Example : Returns : value of distance (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub distance{ return shift->throw_not_implemented(); } =head1 Bio::Ontology::RelationshipI Methods =cut =head2 subject_term Title : subject_term Usage : $subj = $rel->subject_term(); Function: Set/get for the subject term of this Relationship. The common convention for ontologies is to express relationships between terms as triples (subject, predicate, object). Returns : The subject term [Bio::Ontology::TermI]. Args : =cut =head2 object_term Title : object_term Usage : $object = $rel->object_term(); Function: Set/get for the object term of this Relationship. The common convention for ontologies is to express relationships between terms as triples (subject, predicate, object). Returns : The object term [Bio::Ontology::TermI]. Args : =cut =head2 predicate_term Title : predicate_term Usage : $type = $rel->predicate_term(); Function: Set/get for the predicate of this relationship. For a path the predicate (relationship type) is defined as the greatest common denominator of all predicates (relationship types) encountered along the path. I.e., if predicate A is-a predicate B, the greatest common denominator for a path containing both predicates A and B is B Returns : The predicate term [Bio::Ontology::TermI]. Args : =cut =head2 ontology Title : ontology Usage : $ont = $obj->ontology() Function: Get the ontology that defined this relationship. Example : Returns : an object implementing L<Bio::Ontology::OntologyI> Args : =cut 1;