NAME

Bio::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:

https://github.com/bioperl/bioperl-live/issues

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    :