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1 # $Id: PathI.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 PathI
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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 PathI - Interface for a path between ontology terms
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26
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27 =head1 SYNOPSIS
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28
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29 # see documentation of methods and an implementation, e.g.,
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30 # Bio::Ontology::Path
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31
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32 =head1 DESCRIPTION
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33
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34 This is the minimal interface for a path between two terms in
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35 an ontology. Ontology engines may use this.
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36
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37 Essentially this is a very thin extension of the
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38 L<Bio::Ontology::RelationshipI> interface. It basically adds an
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39 attribute distance(). For a RelationshipI, you can think of distance as
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40 equal to zero (subject == object) or 1 (subject != object).
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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
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48 the Bioperl mailing list. 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://bioperl.org/MailList.shtml - 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 of 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@bioperl.org
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60 http://bugzilla.bioperl.org/
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61
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62 =head1 AUTHOR - Hilmar Lapp
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63
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64 Email hlapp at gmx.net
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65
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66 =head1 CONTRIBUTORS
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67
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68 Additional contributors names and emails here
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69
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70 =head1 APPENDIX
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71
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72 The rest of the documentation details each of the object methods.
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73 Internal methods are usually preceded with a _
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74
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75 =cut
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76
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77
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78 # Let the code begin...
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79
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80
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81 package Bio::Ontology::PathI;
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82 use vars qw(@ISA);
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83 use strict;
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84 use Bio::Ontology::RelationshipI;
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85
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86 @ISA = qw( Bio::Ontology::RelationshipI );
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87
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88
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89 =head2 distance
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90
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91 Title : distance
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92 Usage : $obj->distance($newval)
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93 Function: Get (and set if the implementation allows it) the distance
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94 between the two terms connected by this path.
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95
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96 Example :
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97 Returns : value of distance (a scalar)
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98 Args : on set, new value (a scalar or undef, optional)
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99
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100
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101 =cut
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102
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103 sub distance{
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104 return shift->throw_not_implemented();
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105 }
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106
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107 =head1 Bio::Ontology::RelationshipI Methods
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108
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109 =cut
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110
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111 =head2 subject_term
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112
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113 Title : subject_term
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114 Usage : $subj = $rel->subject_term();
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115 Function: Set/get for the subject term of this Relationship.
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116
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117 The common convention for ontologies is to express
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118 relationships between terms as triples (subject, predicate,
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119 object).
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120
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121 Returns : The subject term [Bio::Ontology::TermI].
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122 Args :
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123
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124 =cut
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125
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126 =head2 object_term
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127
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128 Title : object_term
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129 Usage : $object = $rel->object_term();
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130 Function: Set/get for the object term of this Relationship.
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131
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132 The common convention for ontologies is to express
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133 relationships between terms as triples (subject, predicate,
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134 object).
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135
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136 Returns : The object term [Bio::Ontology::TermI].
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137 Args :
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138
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139 =cut
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140
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141 =head2 predicate_term
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142
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143 Title : predicate_term
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144 Usage : $type = $rel->predicate_term();
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145 Function: Set/get for the predicate of this relationship.
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146
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147 For a path the predicate (relationship type) is defined as
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148 the greatest common denominator of all predicates
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149 (relationship types) encountered along the path. I.e., if
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150 predicate A is-a predicate B, the greatest common
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151 denominator for a path containing both predicates A and B is B
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152
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153 Returns : The predicate term [Bio::Ontology::TermI].
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154 Args :
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155
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156 =cut
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157
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158 =head2 ontology
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159
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160 Title : ontology
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161 Usage : $ont = $obj->ontology()
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162 Function: Get the ontology that defined this relationship.
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163 Example :
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164 Returns : an object implementing L<Bio::Ontology::OntologyI>
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165 Args :
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166
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167
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168 =cut
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169
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170 1;
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