Bio::Ontology::Path(3)User Contributed Perl DocumentatioBio::Ontology::Path(3)NAMEBio::Ontology::Path - a path for an ontology term graph
SYNOPSIS
$path = Bio::Ontology::Path->new( -identifier => "16847",
-subject_term => $subj,
-object_term => $obj,
-predicate_term => $pred,
-distance => 3 );
DESCRIPTION
This is a basic implementation of Bio::Ontology::PathI.
Essiantially this is a very thin extension of
Bio::Ontology::Relationship. It basically adds a method distance().
FEEDBACK
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
Support
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 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:
http://bugzilla.open-bio.org/
AUTHOR
Hilmar Lapp <hlapp@gmx.net>
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
new
Title : new
Usage : $rel = Bio::Ontology::Path->new(-identifier => "16847",
-subject_term => $subject,
-object_term => $object,
-predicate_term => $type );
-distance => 3 );
Function: Creates a new Bio::Ontology::Path.
Returns : A new Bio::Ontology::Path object.
Args : -identifier => the identifier of this relationship [scalar]
-subject_term => the subject term [Bio::Ontology::TermI]
-object_term => the object term [Bio::Ontology::TermI]
-predicate_term => the predicate term [Bio::Ontology::TermI]
-distance => the distance between subject and object
init
Title : init()
Usage : $rel->init();
Function: Initializes this Path to all undef.
Returns :
Args :
distance
Title : distance
Usage : $obj->distance($newval)
Function: Get/set the distance between the two terms connected
by this path.
Note that modifying the distance may not be meaningful. The
implementation here is not connected to any graph engine,
so changing an existing value may simply render the
attribute's value wrong.
Example :
Returns : value of distance (a scalar)
Args : on set, new value (a scalar or undef, optional)
to_string
Title : to_string()
Usage : print $rel->to_string();
Function: to_string method for Path.
Returns : A string representation of this Path.
Args :
perl v5.14.1 2011-07-22 Bio::Ontology::Path(3)
