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1 # $Id: DBLink.pm,v 1.12 2002/10/23 18:07:49 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Annotation::Link
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4 #
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5 # Cared for by Ewan Birney <birney@ebi.ac.uk>
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6 #
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7 # Copyright Ewan Birney
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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::Annotation::DBLink - DESCRIPTION of Object
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16
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17 =head1 SYNOPSIS
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18
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19 $link1 = new Bio::Annotation::DBLink(-database => 'TSC',
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20 -primary_id => 'TSC0000030'
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21 );
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22
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23 #or
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24
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25 $link2 = new Bio::Annotation::DBLink();
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26 $link2->database('dbSNP');
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27 $link2->primary_id('2367');
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28
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29 # DBLink is-a Bio::AnnotationI object, can be added to annotation
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30 # collections, e.g. the one on features or seqs
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31 $feat->annotation->add_Annotation('dblink', $link2);
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32
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33
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34 =head1 DESCRIPTION
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35
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36 Provides an object which represents a link from one object to something
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37 in another database without prescribing what is in the other database
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38
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39 =head1 AUTHOR - Ewan Birney
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40
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41 Ewan Birney - birney@ebi.ac.uk
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42
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43 =head1 APPENDIX
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44
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45 The rest of the documentation details each of the object
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46 methods. Internal methods are usually preceded with a _
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47
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48 =cut
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49
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50
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51 # Let the code begin...
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52
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53 package Bio::Annotation::DBLink;
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54 use vars qw(@ISA);
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55 use strict;
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56
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57 use Bio::Root::Root;
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58 use Bio::AnnotationI;
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59 use Bio::IdentifiableI;
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60
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61 @ISA = qw(Bio::Root::Root Bio::AnnotationI Bio::IdentifiableI);
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62
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63
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64 sub new {
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65 my($class,@args) = @_;
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66
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67 my $self = $class->SUPER::new(@args);
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68
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69 my ($database, $primary_id, $optional_id, $comment, $tag, $ns, $auth, $v) =
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70 $self->_rearrange([qw(DATABASE
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71 PRIMARY_ID
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72 OPTIONAL_ID
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73 COMMENT
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74 TAGNAME
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75 NAMESPACE
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76 AUTHORITY
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77 VERSION
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78 )], @args);
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79
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80 $database && $self->database($database);
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81 $primary_id && $self->primary_id($primary_id);
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82 $optional_id && $self->optional_id($optional_id);
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83 $comment && $self->comment($comment);
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84 $tag && $self->tagname($tag);
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85 # Bio::IdentifiableI parameters:
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86 $ns && $self->namespace($ns); # this will override $database
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87 $auth && $self->authority($auth);
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88 defined($v) && $self->version($v);
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89
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90 return $self;
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91 }
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92
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93 =head1 AnnotationI implementing functions
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94
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95 =cut
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96
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97
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98 =head2 as_text
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99
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100 Title : as_text
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101 Usage :
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102 Function:
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103 Example :
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104 Returns :
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105 Args :
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106
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107
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108 =cut
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109
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110 sub as_text{
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111 my ($self) = @_;
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112
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113 return "Direct database link to ".$self->primary_id." in database ".$self->database;
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114 }
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115
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116 =head2 hash_tree
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117
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118 Title : hash_tree
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119 Usage :
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120 Function:
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121 Example :
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122 Returns :
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123 Args :
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124
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125
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126 =cut
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127
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128 sub hash_tree{
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129 my ($self) = @_;
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130
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131 my $h = {};
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132 $h->{'database'} = $self->database;
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133 $h->{'primary_id'} = $self->primary_id;
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134 if( defined $self->optional_id ) {
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135 $h->{'optional_id'} = $self->optional_id;
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136 }
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137 if( defined $self->comment ) {
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138 # we know that comments have hash_tree methods
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139 $h->{'comment'} = $self->comment;
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140 }
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141
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142 return $h;
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143 }
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144
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145 =head2 tagname
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146
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147 Title : tagname
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148 Usage : $obj->tagname($newval)
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149 Function: Get/set the tagname for this annotation value.
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150
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151 Setting this is optional. If set, it obviates the need to
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152 provide a tag to Bio::AnnotationCollectionI when adding
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153 this object. When obtaining an AnnotationI object from the
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154 collection, the collection will set the value to the tag
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155 under which it was stored unless the object has a tag
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156 stored already.
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157
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158 Example :
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159 Returns : value of tagname (a scalar)
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160 Args : new value (a scalar, optional)
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161
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162
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163 =cut
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164
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165 sub tagname{
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166 my ($self,$value) = @_;
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167 if( defined $value) {
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168 $self->{'tagname'} = $value;
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169 }
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170 return $self->{'tagname'};
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171 }
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172
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173 =head1 Specific accessors for DBLinks
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174
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175 =cut
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176
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177 =head2 database
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178
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179 Title : database
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180 Usage : $self->database($newval)
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181 Function: set/get on the database string. Databases are just
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182 a string here which can then be interpretted elsewhere
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183 Example :
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184 Returns : value of database
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185 Args : newvalue (optional)
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186
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187 =cut
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188
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189 sub database{
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190 my ($self,$value) = @_;
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191
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192 if( defined $value) {
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193 $self->{'database'} = $value;
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194 }
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195 return $self->{'database'};
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196
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197 }
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198
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199 =head2 primary_id
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200
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201 Title : primary_id
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202 Usage : $self->primary_id($newval)
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203 Function: set/get on the primary id (a string)
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204 The primary id is the main identifier used for this object in
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205 the database. Good examples would be accession numbers. The id
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206 is meant to be the main, stable identifier for this object
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207 Example :
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208 Returns : value of primary_id
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209 Args : newvalue (optional)
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210
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211 =cut
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212
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213 sub primary_id{
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214 my ($self,$value) = @_;
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215 if( defined $value) {
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216 $self->{'primary_id'} = $value;
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217 }
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218 return $self->{'primary_id'};
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219
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220 }
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221
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222 =head2 optional_id
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223
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224 Title : optional_id
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225 Usage : $self->optional_id($newval)
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226 Function: get/set for the optional_id (a string)
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227
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228 optional id is a slot for people to use as they wish. The
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229 main issue is that some databases do not have a clean
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230 single string identifier scheme. It is hoped that the
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231 primary_id can behave like a reasonably sane "single string
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232 identifier" of objects, and people can use/abuse optional
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233 ids to their heart's content to provide precise mappings.
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234
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235 Example :
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236 Returns : value of optional_id
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237 Args : newvalue (optional)
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238
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239 =cut
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240
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241 #'
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242
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243 sub optional_id{
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244 my ($self,$value) = @_;
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245 if( defined $value) {
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246 $self->{'optional_id'} = $value;
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247 }
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248 return $self->{'optional_id'};
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249
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250 }
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251
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252 =head2 comment
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253
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254 Title : comment
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255 Usage : $self->comment($newval)
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256 Function: get/set of comments (comment object)
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257 Sets or gets comments of this dblink, which is sometimes relevant
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258 Example :
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259 Returns : value of comment (Bio::Annotation::Comment)
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260 Args : newvalue (optional)
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261
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262 =cut
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263
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264 sub comment {
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265 my ($self,$value) = @_;
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266 if( defined $value) {
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267 $self->{'comment'} = $value;
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268 }
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269 return $self->{'comment'};
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270 }
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271
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272 =head1 Methods for Bio::IdentifiableI compliance
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273
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274 =head2 object_id
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275
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276 Title : object_id
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277 Usage : $string = $obj->object_id()
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278 Function: a string which represents the stable primary identifier
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279 in this namespace of this object. For DNA sequences this
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280 is its accession_number, similarly for protein sequences
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281
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282 This is aliased to primary_id().
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283 Returns : A scalar
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284
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285
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286 =cut
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287
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288 sub object_id {
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289 return shift->primary_id(@_);
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290 }
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291
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292 =head2 version
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293
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294 Title : version
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295 Usage : $version = $obj->version()
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296 Function: a number which differentiates between versions of
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297 the same object. Higher numbers are considered to be
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298 later and more relevant, but a single object described
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299 the same identifier should represent the same concept
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300
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301 Returns : A number
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302
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303 =cut
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304
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305 sub version{
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306 my ($self,$value) = @_;
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307 if( defined $value) {
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308 $self->{'_version'} = $value;
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309 }
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310 return $self->{'_version'};
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311 }
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312
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313
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314 =head2 authority
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315
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316 Title : authority
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317 Usage : $authority = $obj->authority()
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318 Function: a string which represents the organisation which
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319 granted the namespace, written as the DNS name for
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320 organisation (eg, wormbase.org)
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321
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322 Returns : A scalar
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323
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324 =cut
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325
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326 sub authority {
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327 my ($obj,$value) = @_;
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328 if( defined $value) {
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329 $obj->{'authority'} = $value;
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330 }
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331 return $obj->{'authority'};
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332 }
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333
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334 =head2 namespace
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335
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336 Title : namespace
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337 Usage : $string = $obj->namespace()
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338 Function: A string representing the name space this identifier
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339 is valid in, often the database name or the name
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340 describing the collection
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341
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342 For DBLink this is the same as database().
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343 Returns : A scalar
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344
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345
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346 =cut
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347
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348 sub namespace{
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349 return shift->database(@_);
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350 }
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351
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352 1;
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