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1 # $Id: IdentifiableI.pm,v 1.6 2002/10/23 18:07:49 lapp Exp $
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2
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3 #
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4 # This module is licensed under the same terms as Perl itself. You use,
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5 # modify, and redistribute it under the terms of the Perl Artistic License.
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6 #
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7
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8 =head1 NAME
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9
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10 Bio::IdentifiableI - interface for objects with identifiers
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11
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12 =head1 SYNOPSIS
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13
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14
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15 # to test this is an identifiable object
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16
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17 $obj->isa("Bio::IdentifiableI") ||
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18 $obj->throw("$obj does not implement the Bio::IdentifiableI interface");
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19
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20 # accessors
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21
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22 $object_id = $obj->object_id();
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23 $namespace = $obj->namespace();
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24 $authority = $obj->authority();
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25 $version = $obj->version();
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26
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27 # utility function
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28
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29 $lsid = $obj->lsid_string(); # gives authority:namespace:object_id
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30 $ns_string = $obj->namespace_string(); # gives namespace:object_id.version
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31
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32
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33 =head1 DESCRIPTION
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34
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35 This interface describes methods expected on identifiable objects, ie
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36 ones which have identifiers expected to make sense across a number of
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37 instances and/or domains. This interface is modeled after pretty much
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38 ubiquitous ideas for names in bioinformatics being
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39
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40 databasename:object_id.version
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41
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42 examples being
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43
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44 swissprot:P012334.2
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45
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46 or
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47
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48 GO:0007048
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49
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50 We also work well with LSID proposals which adds in the concept of an
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51 authority, being the DNS name of the organisation assigning the namespace.
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52 Helper functions are provided to make useful strings being
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53
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54
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55 lsid_string - string complying to the LSID standard
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56 namespace_string - string complying to the usual convention of
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57 namespace:object_id.version
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58
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59 =head1 FEEDBACK
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60
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61 =head2 Mailing Lists
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62
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63 User feedback is an integral part of the evolution of this and other
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64 Bioperl modules. Send your comments and suggestions preferably to one
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65 of the Bioperl mailing lists. Your participation is much appreciated.
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66
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67 bioperl-l@bioperl.org - General discussion
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68 http://bio.perl.org/MailList.html - About the mailing lists
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69
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70 =head2 Reporting Bugs
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71
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72 Report bugs to the Bioperl bug tracking system to help us keep track
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73 the bugs and their resolution. Bug reports can be submitted via email
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74 or the web:
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75
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76 bioperl-bugs@bio.perl.org
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77 http://bugzilla.bioperl.org/
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78
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79 =head1 AUTHOR - Ewan Birney
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80
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81 Email birney@sanger.ac.uk
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82
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83 =cut
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84
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85 package Bio::IdentifiableI;
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86 use vars qw(@ISA );
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87 use strict;
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88 use Bio::Root::RootI;
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89
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90
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91 @ISA = qw(Bio::Root::RootI);
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92
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93 =head1 Implementation Specific Functions
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94
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95 These functions are the ones that a specific implementation must
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96 define.
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97
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98 =head2 object_id
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99
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100 Title : object_id
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101 Usage : $string = $obj->object_id()
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102 Function: a string which represents the stable primary identifier
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103 in this namespace of this object. For DNA sequences this
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104 is its accession_number, similarly for protein sequences
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105
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106 Returns : A scalar
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107 Status : Virtual
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108
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109 =cut
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110
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111 sub object_id {
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112 my ($self) = @_;
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113 $self->throw_not_implemented();
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114 }
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115
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116 =head2 version
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117
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118 Title : version
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119 Usage : $version = $obj->version()
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120 Function: a number which differentiates between versions of
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121 the same object. Higher numbers are considered to be
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122 later and more relevant, but a single object described
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123 the same identifier should represent the same concept
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124
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125 Returns : A number
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126 Status : Virtual
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127
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128 =cut
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129
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130 sub version {
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131 my ($self) = @_;
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132 $self->throw_not_implemented();
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133 }
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134
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135
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136 =head2 authority
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137
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138 Title : authority
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139 Usage : $authority = $obj->authority()
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140 Function: a string which represents the organisation which
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141 granted the namespace, written as the DNS name for
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142 organisation (eg, wormbase.org)
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143
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144 Returns : A scalar
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145 Status : Virtual
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146
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147 =cut
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148
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149 sub authority {
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150 my ($self) = @_;
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151 $self->throw_not_implemented();
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152 }
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153
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154
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155 =head2 namespace
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156
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157 Title : namespace
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158 Usage : $string = $obj->namespace()
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159 Function: A string representing the name space this identifier
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160 is valid in, often the database name or the name
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161 describing the collection
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162
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163 Returns : A scalar
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164 Status : Virtual
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165
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166 =cut
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167
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168 sub namespace {
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169 my ($self) = @_;
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170 $self->throw_not_implemented();
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171 }
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172
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173
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174
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175 =head1 Implementation optional functions
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176
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177 These functions are helper functions that are provided by
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178 the interface but can be overridden if so wished
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179
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180 =head2 lsid_string
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181
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182 Title : lsid_string
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183 Usage : $string = $obj->lsid_string()
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184 Function: a string which gives the LSID standard
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185 notation for the identifier of interest
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186
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187
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188 Returns : A scalar
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189
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190 =cut
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191
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192 sub lsid_string {
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193 my ($self) = @_;
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194
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195 return $self->authority.":".$self->namespace.":".$self->object_id;
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196 }
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197
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198
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199
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200 =head2 namespace_string
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201
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202 Title : namespace_string
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203 Usage : $string = $obj->namespace_string()
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204 Function: a string which gives the common notation of
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205 namespace:object_id.version
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206
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207 Returns : A scalar
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208
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209 =cut
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210
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211 sub namespace_string {
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212 my ($self) = @_;
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213
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214 return $self->namespace.":".$self->object_id .
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215 (defined($self->version()) ? ".".$self->version : '');
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216 }
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217
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218 1;
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