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1 # $Id: OntologyStore.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 Bio::Ontology::OntologyStore
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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 # Copyright Hilmar Lapp
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::Ontology::OntologyStore - A repository of ontologies
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16
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17 =head1 SYNOPSIS
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18
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19 # see documentation of methods
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20
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21 =head1 DESCRIPTION
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22
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23 The primary purpose of this module is that of a singleton repository
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24 of L<Bio::Ontology::OntologyI> instances from which an Ontology
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25 instance can be retrieved by name or identifier. This enables TermI
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26 implementations to return their corresponding OntologyI through using
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27 this singleton store instead of storing a direct reference to the
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28 Ontology object. The latter would almost inevitably lead to memory
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29 cycles, and would therefore potentially blow up an application.
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30
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31 As a user of Ontology objects and Term objects you almost certainly
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32 will not need to deal with this module.
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33
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34 =head1 FEEDBACK
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35
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36 =head2 Mailing Lists
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37
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38 User feedback is an integral part of the evolution of this and other
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39 Bioperl modules. Send your comments and suggestions preferably to
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40 the Bioperl mailing list. Your participation is much appreciated.
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41
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42 bioperl-l@bioperl.org - General discussion
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43 http://bioperl.org/MailList.shtml - About the mailing lists
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44
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45 =head2 Reporting Bugs
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46
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47 Report bugs to the Bioperl bug tracking system to help us keep track
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48 of the bugs and their resolution. Bug reports can be submitted via
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49 the web:
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50
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51 http://bugzilla.bioperl.org/
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52
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53 =head1 AUTHOR - Hilmar Lapp
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54
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55 Email hlapp at gmx.net
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56
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57 =head1 CONTRIBUTORS
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58
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59 Additional contributors names and emails here
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60
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61 =head1 APPENDIX
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62
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63 The rest of the documentation details each of the object methods.
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64 Internal methods are usually preceded with a _
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65
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66 =cut
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67
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68
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69 # Let the code begin...
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70
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71
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72 package Bio::Ontology::OntologyStore;
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73 use vars qw(@ISA);
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74 use strict;
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75
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76 # Object preamble - inherits from Bio::Root::Root
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77
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78 use Bio::Root::Root;
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79
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80
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81 @ISA = qw(Bio::Root::Root );
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82
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83 # these are the static ontology stores by name and by identifier - there is
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84 # only one of each in any application
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85 my %ont_store_by_name = ();
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86 my %ont_store_by_id = ();
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87 # also, this is really meant as a singleton object, so we try to enforce it
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88 my $instance = undef;
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89
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90 =head2 new
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91
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92 Title : new
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93 Usage : my $obj = new Bio::Ontology::OntologyStore();
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94 Function: Returns the Bio::Ontology::OntologyStore object.
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95
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96 Unlike usual implementations of new, this implementation
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97 will try to return a previously instantiated store, if
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98 there is any. It is just a synonym for get_instance. In
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99 order to avoid ambiguities in your code, you may rather
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100 want to call rather get_instance explicitly, which also
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101 usually is better associated with this kind of behaviour.
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102
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103 Returns : an instance of Bio::Ontology::OntologyStore
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104 Args :
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105
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106
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107 =cut
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108
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109 sub new {
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110 return shift->get_instance(@_);
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111 }
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112
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113 =head2 get_instance
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114
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115 Title : get_instance
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116 Usage :
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117 Function: Get an instance of this class for perusal.
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118
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119 Since by design this class is meant to be used as a
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120 singleton, the implementation will return a previously
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121 instantianted store if there is one, and instantiate a new
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122 one otherwise. In order to use this class by means of an
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123 instance, call this method for added code clarity, not
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124 new().
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125
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126 Example :
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127 Returns : an instance of this class
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128 Args : named parameters, if any (currently, there are no
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129 class-specific parameters other than those accepted by
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130 L<Bio::Root::Root>.
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131
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132
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133 =cut
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134
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135 sub get_instance{
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136 my ($self,@args) = @_;
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137
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138 if(! $instance) {
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139 $instance = $self->SUPER::new(@args);
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140 }
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141 return $instance;
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142 }
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143
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144 =head2 get_ontology
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145
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146 Title : get_ontology
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147 Usage :
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148 Function: Get a previously instantiated and registered instance of
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149 this class by name or by identifier.
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150
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151 One of the main purposes of this class is to enable TermI
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152 implementations to return their respective ontology without
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153 keeping a strong reference to the respective ontology
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154 object. Only objects previously registered objects can be
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155 retrieved.
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156
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157 This is a class method, hence you can call it on the class
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158 name, without dereferencing an object.
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159
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160 Example :
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161 Returns : a L<Bio::Ontology::OntologyI> implementing object, or undef
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162 if the query could not be satisfied
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163 Args : Named parameters specifying the query. The following parameters
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164 are recognized:
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165 -name query the store for an ontology with the given name
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166 -id query for an ontology with the given identifier
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167 If both are specified, an implicit AND logical operator is
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168 assumed.
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169
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170 =cut
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171
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172 sub get_ontology{
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173 my ($self,@args) = @_;
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174 my $ont;
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175
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176 my ($name,$id) = $self->_rearrange([qw(NAME ID)], @args);
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177 if($id) {
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178 $ont = $ont_store_by_id{$id};
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179 return unless $ont; # no AND can be satisfied in this case
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180 }
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181 if($name) {
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182 my $o = $ont_store_by_name{$name};
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183 if((! $ont) || ($ont->identifier() eq $o->identifier())) {
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184 $ont = $o;
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185 } else {
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186 $ont = undef;
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187 }
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188 }
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189 return $ont;
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190 }
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191
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192 =head2 register_ontology
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193
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194 Title : register_ontology
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195 Usage :
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196 Function: Registers the given Ontology object for later retrieval
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197 by name and identifier.
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198
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199 Example :
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200 Returns : TRUE on success and FALSE otherwise
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201 Args : the L<Bio::Ontology::OntologyI> object(s) to register
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202
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203
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204 =cut
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205
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206 sub register_ontology{
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207 my ($self,@args) = @_;
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208 my $ret = 1;
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209
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210 foreach my $ont (@args) {
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211 if(! (ref($ont) && $ont->isa("Bio::Ontology::OntologyI"))) {
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212 $self->throw((ref($ont) ? ref($ont) : $ont)." does not implement ".
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213 "Bio::Ontology::OntologyI or is not an object");
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214 }
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215 if($self->get_ontology(-name => $ont->name())) {
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216 $self->warn("ontology with name \"".$ont->name().
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217 "\" already exists in the store, ignoring new one");
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218 $ret = 0;
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219 next;
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220 }
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221 if($self->get_ontology(-id => $ont->identifier())) {
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222 $self->warn("ontology with id \"".$ont->identifier().
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223 "\" already exists in the store, ignoring new one");
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224 $ret = 0;
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225 next;
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226 }
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227 $ont_store_by_name{$ont->name()} = $ont;
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228 $ont_store_by_id{$ont->identifier()} = $ont;
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229 }
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230 return $ret;
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231 }
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232
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233 =head2 remove_ontology
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234
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235 Title : remove_ontology
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236 Usage :
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237 Function: Remove the specified ontology from the store.
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238 Example :
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239 Returns : TRUE on success and FALSE otherwise
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240 Args : the L<Bio::Ontology::OntologyI> implementing object(s)
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241 to be removed from the store
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242
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243
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244 =cut
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245
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246 sub remove_ontology{
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247 my $self = shift;
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248 my $ret = 1;
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249
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250 foreach my $ont (@_) {
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251 $self->throw(ref($ont)." does not implement Bio::Ontology::OntologyI")
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252 unless $ont && ref($ont) && $ont->isa("Bio::Ontology::OntologyI");
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253 # remove it from both the id hash and the name hash
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254 delete $ont_store_by_id{$ont->identifier()};
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255 delete $ont_store_by_name{$ont->name()} if $ont->name();
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256 }
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257 return 1;
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258 }
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259
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260 1;
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