Raw content of Bio::Ontology::Path
<![CDATA[# $Id: Path.pm,v 1.1.2.2 2003/03/27 10:07:56 lapp Exp $
#
# BioPerl module for Path
#
# 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
=head1 NAME
Path - a path for an ontology term graph
=head1 SYNOPSIS
$path = Bio::Ontology::Path->new( -identifier => "16847",
-subject_term => $subj,
-object_term => $obj,
-predicate_term => $pred,
-distance => 3 );
=head1 DESCRIPTION
This is a basic implementation of Bio::Ontology::PathI.
Essiantially this is a very thin extension of
L<Bio::Ontology::Relationship>. It basically adds a method distance().
=head1 FEEDBACK
=head2 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://bio.perl.org/MailList.html - About the mailing lists
=head2 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
email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR
Hilmar Lapp <hlapp@gmx.net>
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Ontology::Path;
use vars qw( @ISA );
use strict;
use Bio::Ontology::PathI;
use Bio::Ontology::Relationship;
@ISA = qw( Bio::Ontology::Relationship
Bio::Ontology::PathI );
=head2 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
=cut
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
=head2 init
Title : init()
Usage : $rel->init();
Function: Initializes this Path to all undef.
Returns :
Args :
=cut
sub init {
my $self = shift;
$self->SUPER::init(@_);
$self->{ "_distance" } = undef;
} # init
=head2 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)
=cut
sub distance{
my $self = shift;
return $self->{'_distance'} = shift if @_;
return $self->{'_distance'};
}
=head2 to_string
Title : to_string()
Usage : print $rel->to_string();
Function: to_string method for Path.
Returns : A string representation of this Path.
Args :
=cut
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;
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