Bio/Ontology/Path.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Path
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Hilmar Lapp <hlapp at gmx.net>
   8 #
   9 # (c) Hilmar Lapp, hlapp at gmx.net, 2003.
  10 # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2003.
  11 #
  12 # You may distribute this module under the same terms as perl itself.
  13 # Refer to the Perl Artistic License (see the license accompanying this
  14 # software package, or see http://www.perl.com/language/misc/Artistic.html)
  15 # for the terms under which you may use, modify, and redistribute this module.
  16 #
  17 # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
  18 # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
  19 # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
  20 #
  21 # You may distribute this module under the same terms as perl itself
  22
  23 # POD documentation - main docs before the code
  24
  25 =head1 NAME
  26
  27 Bio::Ontology::Path - a path for an ontology term graph
  28
  29 =head1 SYNOPSIS
  30
  31   $path = Bio::Ontology::Path->new( -identifier     => "16847",
  32                                     -subject_term   => $subj,
  33                                     -object_term    => $obj,
  34                                     -predicate_term => $pred,
  35                                     -distance       => 3 );
  36
  37 =head1 DESCRIPTION
  38
  39 This is a basic implementation of Bio::Ontology::PathI.
  40
  41 Essiantially this is a very thin extension of
  42 L<Bio::Ontology::Relationship>. It basically adds a method distance().
  43
  44 =head1 FEEDBACK
  45
  46 =head2 Mailing Lists
  47
  48 User feedback is an integral part of the evolution of this and other
  49 Bioperl modules. Send your comments and suggestions preferably to the
  50 Bioperl mailing lists  Your participation is much appreciated.
  51
  52   bioperl-l@bioperl.org                  - General discussion
  53   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  54
  55 =head2 Support
  56
  57 Please direct usage questions or support issues to the mailing list:
  58
  59 L<bioperl-l@bioperl.org>
  60
  61 rather than to the module maintainer directly. Many experienced and
  62 reponsive experts will be able look at the problem and quickly
  63 address it. Please include a thorough description of the problem
  64 with code and data examples if at all possible.
  65
  66 =head2 Reporting Bugs
  67
  68 Report bugs to the Bioperl bug tracking system to help us keep track
  69 the bugs and their resolution.  Bug reports can be submitted via
  70 the web:
  71
  72   http://bugzilla.open-bio.org/
  73
  74 =head1 AUTHOR
  75
  76  Hilmar Lapp <hlapp@gmx.net>
  77
  78 =head1 APPENDIX
  79
  80 The rest of the documentation details each of the object
  81 methods. Internal methods are usually preceded with a _
  82
  83 =cut
  84
  85
  86 # Let the code begin...
  87
  88
  89 package Bio::Ontology::Path;
  90 use strict;
  91
  92 use base qw(Bio::Ontology::Relationship Bio::Ontology::PathI);
  93
  94
  95
  96
  97 =head2 new
  98
  99  Title   : new
 100  Usage   : $rel = Bio::Ontology::Path->new(-identifier   => "16847",
 101                                            -subject_term => $subject,
 102                                            -object_term  => $object,
 103                                            -predicate_term => $type );
 104                                            -distance     => 3 );
 105  Function: Creates a new Bio::Ontology::Path.
 106  Returns : A new Bio::Ontology::Path object.
 107  Args    : -identifier     => the identifier of this relationship [scalar]
 108            -subject_term   => the subject term [Bio::Ontology::TermI]
 109            -object_term    => the object term [Bio::Ontology::TermI]
 110            -predicate_term => the predicate term [Bio::Ontology::TermI]
 111            -distance       => the distance between subject and object
 112
 113 =cut
 114
 115 sub new {
 116
 117     my( $class, @args ) = @_;
 118
 119     my $self = $class->SUPER::new( @args );
 120
 121     my ( $distance ) =
 122         $self->_rearrange( [qw( DISTANCE)
 123                             ], @args );
 124
 125     $distance      && $self->distance($distance);
 126
 127     return $self;
 128
 129 } # new
 130
 131
 132
 133 =head2 init
 134
 135  Title   : init()
 136  Usage   : $rel->init();
 137  Function: Initializes this Path to all undef.
 138  Returns :
 139  Args    :
 140
 141 =cut
 142
 143 sub init {
 144     my $self = shift;
 145
 146     $self->SUPER::init(@_);
 147     $self->{ "_distance" } = undef;
 148
 149 } # init
 150
 151
 152 =head2 distance
 153
 154  Title   : distance
 155  Usage   : $obj->distance($newval)
 156  Function: Get/set the distance between the two terms connected
 157            by this path.
 158
 159            Note that modifying the distance may not be meaningful. The
 160            implementation here is not connected to any graph engine,
 161            so changing an existing value may simply render the
 162            attribute's value wrong.
 163
 164  Example :
 165  Returns : value of distance (a scalar)
 166  Args    : on set, new value (a scalar or undef, optional)
 167
 168 =cut
 169
 170 sub distance{
 171     my $self = shift;
 172
 173     return $self->{'_distance'} = shift if @_;
 174     return $self->{'_distance'};
 175 }
 176
 177 =head2 to_string
 178
 179  Title   : to_string()
 180  Usage   : print $rel->to_string();
 181  Function: to_string method for Path.
 182  Returns : A string representation of this Path.
 183  Args    :
 184
 185 =cut
 186
 187 sub to_string {
 188     my( $self ) = @_;
 189
 190     my $s = $self->SUPER::to_string();
 191     $s .= "-- Distance:\n";
 192     $s .= $self->distance() if defined($self->distance());
 193     $s .= "\n";
 194
 195     return $s;
 196
 197 } # to_string
 198
 199
 200
 201 1;