Bio::Ontology PathI
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Summary
Bio::Ontology::PathI - Interface for a path between ontology terms
Package variables
No package variables defined.
Inherit
Bio::Ontology::RelationshipI
Synopsis
    # see documentation of methods and an implementation, e.g.,
# Bio::Ontology::Path
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
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).
Methods
distanceDescriptionCode
Methods description
distancecode    nextTop
 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)
Methods code
distancedescriptionprevnextTop
sub distance {
    return shift->throw_not_implemented();
}
General documentation
FEEDBACKTop
Mailing ListsTop
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/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
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.
Reporting BugsTop
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
the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Hilmar LappTop
Email hlapp at gmx.net
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Bio::Ontology::RelationshipI MethodsTop
subject_termTop
 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 :
object_termTop
 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 :
predicate_termTop
 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 :
ontologyTop
 Title   : ontology
Usage : $ont = $obj->ontology()
Function: Get the ontology that defined this relationship.
Example :
Returns : an object implementing Bio::Ontology::OntologyI
Args :
See Bio::Ontology::OntologyI.