Bio::Ontology::Path - a path for an ontology term graph

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

Top

Bio::Ontology::Path - a path for an ontology term graph

SYNOPSIS

Top

  $path = Bio::Ontology::Path->new( -identifier     => "16847",
                                    -subject_term   => $subj,
                                    -object_term    => $obj,
                                    -predicate_term => $pred,
                                    -distance       => 3 );

DESCRIPTION

Top

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

Top

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://redmine.open-bio.org/projects/bioperl/

AUTHOR

Top

 Hilmar Lapp <hlapp@gmx.net>

APPENDIX

Top

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    :
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Path
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Hilmar Lapp <hlapp at gmx.net> 
#
# (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.
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code



# Let the code begin...


package Bio::Ontology::Path;
use strict;

use base qw(Bio::Ontology::Relationship Bio::Ontology::PathI);





sub new {

    my( $class, @args ) = @_;
    
    my $self = $class->SUPER::new( @args );
   
    my ( $distance ) = 
	$self->_rearrange( [qw( DISTANCE)
			    ], @args );
   
    $distance      && $self->distance($distance);
                                                    
    return $self;
    
} # new




sub init {
    my $self = shift;
    
    $self->SUPER::init(@_);
    $self->{ "_distance" } = undef;
   
} # init



sub distance{
    my $self = shift;

    return $self->{'_distance'} = shift if @_;
    return $self->{'_distance'};
}


sub to_string {
    my( $self ) = @_;
    
    my $s = $self->SUPER::to_string();
    $s .= "-- Distance:\n";
    $s .= $self->distance() if defined($self->distance());
    $s .= "\n";
    
    return $s;
    
} # to_string



1;