Bio/Ontology/Path.pm

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