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1 # $Id: Path.pm,v 1.1.2.2 2003/03/27 10:07:56 lapp Exp $
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2 #
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3 # BioPerl module for Path
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4 #
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5 # Cared for by Hilmar Lapp <hlapp at gmx.net>
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6 #
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7 # (c) Hilmar Lapp, hlapp at gmx.net, 2003.
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8 # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2003.
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9 #
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10 # You may distribute this module under the same terms as perl itself.
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11 # Refer to the Perl Artistic License (see the license accompanying this
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12 # software package, or see http://www.perl.com/language/misc/Artistic.html)
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13 # for the terms under which you may use, modify, and redistribute this module.
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14 #
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15 # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
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16 # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
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17 # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
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18 #
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19 # You may distribute this module under the same terms as perl itself
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20
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21 # POD documentation - main docs before the code
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22
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23 =head1 NAME
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24
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25 Path - a path for an ontology term graph
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26
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27 =head1 SYNOPSIS
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28
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29 $path = Bio::Ontology::Path->new( -identifier => "16847",
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30 -subject_term => $subj,
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31 -object_term => $obj,
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32 -predicate_term => $pred,
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33 -distance => 3 );
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34
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35 =head1 DESCRIPTION
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36
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37 This is a basic implementation of Bio::Ontology::PathI.
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38
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39 Essiantially this is a very thin extension of
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40 L<Bio::Ontology::Relationship>. It basically adds a method distance().
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41
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42 =head1 FEEDBACK
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43
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44 =head2 Mailing Lists
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45
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46 User feedback is an integral part of the evolution of this and other
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47 Bioperl modules. Send your comments and suggestions preferably to the
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48 Bioperl mailing lists Your participation is much appreciated.
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49
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50 bioperl-l@bioperl.org - General discussion
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51 http://bio.perl.org/MailList.html - About the mailing lists
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52
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53 =head2 Reporting Bugs
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54
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55 report bugs to the Bioperl bug tracking system to help us keep track
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56 the bugs and their resolution. Bug reports can be submitted via
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57 email or the web:
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58
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59 bioperl-bugs@bio.perl.org
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60 http://bugzilla.bioperl.org/
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61
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62 =head1 AUTHOR
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63
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64 Hilmar Lapp <hlapp@gmx.net>
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65
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66 =head1 APPENDIX
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67
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68 The rest of the documentation details each of the object
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69 methods. Internal methods are usually preceded with a _
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70
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71 =cut
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72
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73
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74 # Let the code begin...
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75
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76
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77 package Bio::Ontology::Path;
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78 use vars qw( @ISA );
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79 use strict;
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80 use Bio::Ontology::PathI;
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81 use Bio::Ontology::Relationship;
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82
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83 @ISA = qw( Bio::Ontology::Relationship
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84 Bio::Ontology::PathI );
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85
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86
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87
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88
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89 =head2 new
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90
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91 Title : new
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92 Usage : $rel = Bio::Ontology::Path->new(-identifier => "16847",
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93 -subject_term => $subject,
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94 -object_term => $object,
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95 -predicate_term => $type );
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96 -distance => 3 );
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97 Function: Creates a new Bio::Ontology::Path.
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98 Returns : A new Bio::Ontology::Path object.
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99 Args : -identifier => the identifier of this relationship [scalar]
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100 -subject_term => the subject term [Bio::Ontology::TermI]
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101 -object_term => the object term [Bio::Ontology::TermI]
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102 -predicate_term => the predicate term [Bio::Ontology::TermI]
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103 -distance => the distance between subject and object
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104
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105 =cut
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106
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107 sub new {
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108
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109 my( $class, @args ) = @_;
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110
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111 my $self = $class->SUPER::new( @args );
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112
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113 my ( $distance ) =
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114 $self->_rearrange( [qw( DISTANCE)
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115 ], @args );
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116
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117 $distance && $self->distance($distance);
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118
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119 return $self;
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120
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121 } # new
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122
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123
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124
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125 =head2 init
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126
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127 Title : init()
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128 Usage : $rel->init();
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129 Function: Initializes this Path to all undef.
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130 Returns :
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131 Args :
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132
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133 =cut
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134
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135 sub init {
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136 my $self = shift;
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137
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138 $self->SUPER::init(@_);
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139 $self->{ "_distance" } = undef;
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140
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141 } # init
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142
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143
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144 =head2 distance
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145
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146 Title : distance
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147 Usage : $obj->distance($newval)
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148 Function: Get/set the distance between the two terms connected
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149 by this path.
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150
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151 Note that modifying the distance may not be meaningful. The
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152 implementation here is not connected to any graph engine,
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153 so changing an existing value may simply render the
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154 attribute's value wrong.
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155
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156 Example :
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157 Returns : value of distance (a scalar)
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158 Args : on set, new value (a scalar or undef, optional)
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159
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160
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161 =cut
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162
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163 sub distance{
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164 my $self = shift;
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165
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166 return $self->{'_distance'} = shift if @_;
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167 return $self->{'_distance'};
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168 }
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169
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170 =head2 to_string
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171
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172 Title : to_string()
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173 Usage : print $rel->to_string();
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174 Function: to_string method for Path.
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175 Returns : A string representation of this Path.
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176 Args :
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177
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178 =cut
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179
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180 sub to_string {
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181 my( $self ) = @_;
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182
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183 my $s = $self->SUPER::to_string();
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184 $s .= "-- Distance:\n";
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185 $s .= $self->distance() if defined($self->distance());
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186 $s .= "\n";
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187
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188 return $s;
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189
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190 } # to_string
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191
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192
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193
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194 1;
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