diff variant_effect_predictor/Bio/Ontology/Path.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Ontology/Path.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,194 @@
+# $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.
+
+  [e-mail]                         - 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:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR
+
+ Hilmar Lapp <[e-mail]>
+
+=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;