diff variant_effect_predictor/Bio/Ontology/OntologyI.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

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+++ b/variant_effect_predictor/Bio/Ontology/OntologyI.pm	Thu Apr 11 06:29:17 2013 -0400
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+# $Id: OntologyI.pm,v 1.2.2.4 2003/03/27 10:07:56 lapp Exp $
+#
+# BioPerl module for Bio::Ontology::OntologyI
+#
+# Cared for by Hilmar Lapp <hlapp at gmx.net>
+#
+# Copyright Hilmar Lapp
+#
+# You may distribute this module under the same terms as perl itself
+
+#
+# (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.
+#
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Ontology::OntologyI - Interface for an ontology implementation
+
+=head1 SYNOPSIS
+
+    # see method documentation
+
+=head1 DESCRIPTION
+
+This describes the minimal interface an ontology implementation must
+provide. In essence, it represents a namespace with description on top
+of the query interface OntologyEngineI.
+
+This interface inherits from L<Bio::Ontology::OntologyEngineI>.
+
+=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:
+
+  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::OntologyI;
+use vars qw(@ISA);
+use strict;
+
+use Bio::Ontology::OntologyEngineI;
+
+@ISA = qw( Bio::Ontology::OntologyEngineI );
+
+=head1  Methods defined in this interface.
+
+=cut
+
+=head2 name
+
+ Title   : name
+ Usage   : $obj->name($newval)
+ Function: Get/set the name of this ontology.
+ Example :
+ Returns : value of name (a scalar)
+ Args    :
+
+
+=cut
+
+sub name{
+    shift->throw_not_implemented();
+}
+
+=head2 authority
+
+ Title   : authority
+ Usage   : $auth = $obj->authority()
+ Function: Get/set the authority for this ontology, for instance the
+           DNS base for the organization granting the name of the
+           ontology and identifiers for the terms.
+
+           This attribute is optional and should not generally
+           expected by applications to have been set. It is here to
+           follow the rules for namespaces, which ontologies serve as
+           for terms.
+
+ Example :
+ Returns : value of authority (a scalar)
+ Args    :
+
+
+=cut
+
+sub authority{
+    shift->throw_not_implemented();
+}
+
+=head2 identifier
+
+ Title   : identifier
+ Usage   : $id = $obj->identifier()
+ Function: Get an identifier for this ontology.
+
+           This is primarily intended for look-up purposes. Clients
+           should not expect the value to be modifiable, and it may
+           not be allowed to set its value from outside. Also, the
+           identifier's uniqueness may only hold within the scope of a
+           particular application's run time, i.e., it may be a memory
+           location.
+
+ Example :
+ Returns : value of identifier (a scalar)
+ Args    :
+
+
+=cut
+
+sub identifier{
+    shift->throw_not_implemented();
+}
+
+=head2 definition
+
+ Title   : definition
+ Usage   : $def = $obj->definition()
+ Function: Get a descriptive definition for this ontology.
+ Example :
+ Returns : value of definition (a scalar)
+ Args    :
+
+
+=cut
+
+sub definition{
+    shift->throw_not_implemented();
+}
+
+=head2 close
+
+ Title   : close
+ Usage   :
+ Function: Release any resources this ontology may occupy. In order
+           to efficiently release used memory or file handles, you
+           should call this method once you are finished with an
+           ontology.
+
+ Example :
+ Returns : TRUE on success and FALSE otherwise
+ Args    : none
+
+
+=cut
+
+sub close{
+    shift->throw_not_implemented();
+}
+
+=head1 Methods inherited from L<Bio::Ontology::OntologyEngineI>
+
+Their documentations are copied here for completeness. In most use
+cases, you will want to access the query methods of an ontology, not
+just the name and description ...
+
+=cut
+
+=head2 add_term
+
+ Title   : add_term
+ Usage   : add_term(TermI term): TermI
+ Function: Adds TermI object to the ontology engine term store.
+
+           For ease of use, if the ontology property of the term
+           object was not set, an implementation is encouraged to set
+           it to itself upon adding the term.
+
+ Example : $oe->add_term($term)
+ Returns : its argument.
+ Args    : object of class TermI.
+
+
+=cut
+
+=head2 add_relationship
+
+ Title   : add_relationship
+ Usage   : add_relationship(RelationshipI relationship): RelationshipI
+ Function: Adds a relationship object to the ontology engine.
+ Example :
+ Returns : Its argument.
+ Args    : A RelationshipI object.
+
+
+=cut
+
+=head2 get_relationships
+
+ Title   : get_relationships
+ Usage   : get_relationships(TermI term): RelationshipI[]
+ Function: Retrieves all relationship objects from this ontology engine,
+           or all relationships of a term if a term is supplied.
+ Example :
+ Returns : Array of Bio::Ontology::RelationshipI objects
+ Args    : None, or a Bio::Ontology::TermI compliant object for which
+           to retrieve the relationships.
+
+
+=cut
+
+=head2 get_predicate_terms
+
+ Title   : get_predicate_terms
+ Usage   : get_predicate_terms(): TermI[]
+ Function:
+ Example :
+ Returns :
+ Args    :
+
+
+=cut
+
+=head2 get_child_terms
+
+ Title   : get_child_terms
+ Usage   : get_child_terms(TermI term, TermI[] predicate_terms): TermI[]
+ Function: Retrieves all child terms of a given term, that satisfy a
+           relationship among those that are specified in the second
+           argument or undef otherwise. get_child_terms is a special
+           case of get_descendant_terms, limiting the search to the
+           direct descendants.
+
+ Example :
+ Returns : Array of TermI objects.
+ Args    : First argument is the term of interest, second is the list
+           of relationship type terms.
+
+
+=cut
+
+=head2 get_descendant_terms
+
+ Title   : get_descendant_terms
+ Usage   : get_descendant_terms(TermI term, TermI[] rel_types): TermI[]
+ Function: Retrieves all descendant terms of a given term, that
+           satisfy a relationship among those that are specified in
+           the second argument or undef otherwise.
+ Example :
+ Returns : Array of TermI objects.
+ Args    : First argument is the term of interest, second is the list
+           of relationship type terms.
+
+
+=cut
+
+=head2 get_parent_terms
+
+ Title   : get_parent_terms
+ Usage   : get_parent_terms(TermI term, TermI[] predicate_terms): TermI[]
+ Function: Retrieves all parent terms of a given term, that satisfy a
+           relationship among those that are specified in the second
+           argument or undef otherwise. get_parent_terms is a special
+           case of get_ancestor_terms, limiting the search to the
+           direct ancestors.
+
+ Example :
+ Returns : Array of TermI objects.
+ Args    : First argument is the term of interest, second is the list
+           of relationship type terms.
+
+
+=cut
+
+=head2 get_ancestor_terms
+
+ Title   : get_ancestor_terms
+ Usage   : get_ancestor_terms(TermI term, TermI[] predicate_terms): TermI[]
+ Function: Retrieves all ancestor terms of a given term, that satisfy
+           a relationship among those that are specified in the second
+           argument or undef otherwise.
+
+ Example :
+ Returns : Array of TermI objects.
+ Args    : First argument is the term of interest, second is the list
+           of relationship type terms.
+
+
+=cut
+
+=head2 get_leaf_terms
+
+ Title   : get_leaf_terms
+ Usage   : get_leaf_terms(): TermI[]
+ Function: Retrieves all leaf terms from the ontology. Leaf term is a
+           term w/o descendants.
+
+ Example : @leaf_terms = $obj->get_leaf_terms()
+ Returns : Array of TermI objects.
+ Args    :
+
+
+=cut
+
+=head2 get_root_terms()
+
+ Title   : get_root_terms
+ Usage   : get_root_terms(): TermI[]
+ Function: Retrieves all root terms from the ontology. Root term is a
+           term w/o descendants.
+
+ Example : @root_terms = $obj->get_root_terms()
+ Returns : Array of TermI objects.
+ Args    :
+
+
+=cut
+
+=head2 get_all_terms
+
+ Title   : get_all_terms
+ Usage   : get_all_terms: TermI[]
+ Function: Retrieves all terms from the ontology.
+
+           We do not mandate an order here in which the terms are
+           returned. In fact, the default implementation will return
+           them in unpredictable order.
+
+ Example : @terms = $obj->get_all_terms()
+ Returns : Array of TermI objects.
+ Args    :
+
+
+=cut
+
+
+=head2 find_terms
+
+ Title   : find_terms
+ Usage   : ($term) = $oe->find_terms(-identifier => "SO:0000263");
+ Function: Find term instances matching queries for their attributes.
+
+           An implementation may not support querying for arbitrary
+           attributes, but can generally be expected to accept
+           -identifier and -name as queries. If both are provided,
+           they are implicitly intersected.
+
+ Example :
+ Returns : an array of zero or more Bio::Ontology::TermI objects
+ Args    : Named parameters. The following parameters should be recognized
+           by any implementation:
+
+              -identifier    query by the given identifier
+              -name          query by the given name
+
+
+=cut
+
+=head1 Factory for relationships and terms
+
+=cut
+
+=head2 relationship_factory
+
+ Title   : relationship_factory
+ Usage   : $fact = $obj->relationship_factory()
+ Function: Get (and set, if the implementation supports it) the object
+           factory to be used when relationship objects are created by
+           the implementation on-the-fly.
+
+ Example : 
+ Returns : value of relationship_factory (a Bio::Factory::ObjectFactoryI
+           compliant object)
+ Args    : 
+
+
+=cut
+
+sub relationship_factory{
+    return shift->throw_not_implemented();
+}
+
+=head2 term_factory
+
+ Title   : term_factory
+ Usage   : $fact = $obj->term_factory()
+ Function: Get (and set, if the implementation supports it) the object
+           factory to be used when term objects are created by
+           the implementation on-the-fly.
+
+ Example : 
+ Returns : value of term_factory (a Bio::Factory::ObjectFactoryI
+           compliant object)
+ Args    : 
+
+
+=cut
+
+sub term_factory{
+    return shift->throw_not_implemented();
+}
+
+1;