++ed by:
THALJEF YUSRIDEB PINGAN DEMIAN GENEHACK

11 PAUSE users
14 non-PAUSE users.

Christopher Fields
and 1 contributors

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

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    :