diff variant_effect_predictor/Bio/Ontology/PathI.pm @ 0:1f6dce3d34e0

Uploaded

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+++ b/variant_effect_predictor/Bio/Ontology/PathI.pm	Thu Apr 11 02:01:53 2013 -0400
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+# $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.
+
+  [e-mail]              - 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:
+
+  [e-mail]
+  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;