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1 # $Id: Ref.pm,v 1.5 2002/10/22 07:45:11 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Biblio::Ref
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4 #
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5 # Cared for by Martin Senger <senger@ebi.ac.uk>
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6 # For copyright and disclaimer see below.
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7
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8 # POD documentation - main docs before the code
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9
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10 =head1 NAME
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11
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12 Bio::Biblio::Ref - Representation of a bibliographic reference
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13
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14 =head1 SYNOPSIS
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15
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16 $obj = new Bio::Biblio::Ref (-type => 'Letter',
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17 -title => 'Onegin to Tatiana');
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18 --- OR ---
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19
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20 $obj = new Bio::Biblio::Ref;
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21 $obj->type ('Letter');
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22
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23 =head1 DESCRIPTION
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24
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25 A storage object for a general bibliographic reference (a citation).
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26 See its place in the class hierarchy in
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27 http://industry.ebi.ac.uk/openBQS/images/bibobjects_perl.gif
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28
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29 =head2 Attributes
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30
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31 The following attributes are specific to this class,
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32 and they are inherited by all citation types.
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33
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34 author_list_complete values: 'Y' (default) or 'N'
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35 authors type: array ref of Bio::Biblio::Provider's
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36 cross_references type: array ref of Bio::Annotation::DBLink's
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37 cross_references_list_complete values: 'Y' (default) or 'N'
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38 abstract
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39 abstract_language
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40 abstract_type
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41 codes type: hash ref
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42 contributors type: array ref of Bio::Biblio::Provider's
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43 date
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44 date_completed
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45 date_created
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46 date_revised
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47 format
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48 identifier
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49 keywords
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50 language
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51 last_modified_date
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52 publisher type: Bio::Biblio::Provider
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53 repository_subset
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54 rights
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55 spatial_location
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56 subject_headings type: hash ref
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57 subject_headings_source
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58 temporal_period
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59 title
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60 toc
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61 toc_type
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62 type
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63
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64 =head1 SEE ALSO
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65
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66 =over
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67
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68 =item *
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69
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70 OpenBQS home page: http://industry.ebi.ac.uk/openBQS
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71
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72 =item *
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73
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74 Comments to the Perl client: http://industry.ebi.ac.uk/openBQS/Client_perl.html
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75
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76 =back
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77
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78 =head1 FEEDBACK
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79
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80 =head2 Mailing Lists
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81
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82 User feedback is an integral part of the evolution of this and other
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83 Bioperl modules. Send your comments and suggestions preferably to
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84 the Bioperl mailing list. Your participation is much appreciated.
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85
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86 bioperl-l@bioperl.org - General discussion
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87 http://bioperl.org/MailList.shtml - About the mailing lists
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88
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89 =head2 Reporting Bugs
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90
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91 Report bugs to the Bioperl bug tracking system to help us keep track
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92 of the bugs and their resolution. Bug reports can be submitted via
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93 email or the web:
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94
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95 bioperl-bugs@bioperl.org
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96 http://bugzilla.bioperl.org/
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97
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98 =head1 AUTHORS
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99
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100 Heikki Lehvaslaiho (heikki@ebi.ac.uk),
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101 Martin Senger (senger@ebi.ac.uk)
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102
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103 =head1 COPYRIGHT
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104
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105 Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved.
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106
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107 This module is free software; you can redistribute it and/or modify
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108 it under the same terms as Perl itself.
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109
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110 =head1 DISCLAIMER
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111
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112 This software is provided "as is" without warranty of any kind.
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113
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114 =head1 APPENDIX
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115
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116 The rest of the documentation details each of the object
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117 methods. Internal methods are preceded with a _
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118
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119 =cut
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120
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121
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122 # Let the code begin...
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123
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124
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125 package Bio::Biblio::Ref;
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126 use strict;
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127 use vars qw(@ISA $AUTOLOAD);
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128
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129 use Bio::Biblio::BiblioBase;
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130 use Bio::Annotation::DBLink;
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131
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132 @ISA = qw(Bio::Biblio::BiblioBase);
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133
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134 #
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135 # a closure with a list of allowed attribute names (these names
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136 # correspond with the allowed 'get' and 'set' methods); each name also
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137 # keep what type the attribute should be (use 'undef' if it is a
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138 # simple scalar)
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139 #
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140 {
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141 my %_allowed =
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142 (
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143 _author_list_complete => undef,
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144 _authors => 'ARRAY', # of Bio::Biblio::Provider
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145 _cross_references => 'ARRAY', # of Bio::Annotation::DBLink
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146 _cross_references_list_complete => undef,
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147 _abstract => undef,
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148 _abstract_language => undef,
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149 _abstract_type => undef,
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150 _codes => 'HASH',
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151 _contributors => 'ARRAY', # of Bio::Biblio::Provider
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152 _date => undef,
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153 _date_completed => undef,
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154 _date_created => undef,
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155 _date_revised => undef,
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156 _format => undef,
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157 _identifier => undef,
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158 _keywords => 'HASH',
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159 _language => undef,
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160 _last_modified_date => undef,
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161 _publisher => 'Bio::Biblio::Provider',
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162 _repository_subset => undef,
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163 _rights => undef,
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164 _spatial_location => undef,
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165 _subject_headings => 'HASH',
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166 _subject_headings_source => undef,
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167 _temporal_period => undef,
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168 _title => undef,
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169 _toc => undef,
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170 _toc_type => undef,
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171 _type => undef,
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172 );
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173
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174 # return 1 if $attr is allowed to be set/get in this class
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175 sub _accessible {
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176 my ($self, $attr) = @_;
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177 exists $_allowed{$attr};
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178 }
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179
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180 # return an expected type of given $attr
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181 sub _attr_type {
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182 my ($self, $attr) = @_;
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183 $_allowed{$attr};
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184 }
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185 }
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186
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187
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188 =head2 add_cross_reference
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189
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190 Usage : $self->add_cross_reference
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191 (new Bio::Annotation::DBLink (-database => 'EMBL',
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192 -primary_id => 'V00808');
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193 Function: adding a link to a database entry
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194 Returns : new value of 'cross_references'
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195 Args : an object of type Bio::Annotation::DBLink
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196
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197 =cut
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198
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199 sub add_cross_reference {
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200 my ($self, $value) = @_;
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201 $self->throw ($self->_wrong_type_msg (ref $value, 'Bio::Annotation::DBLink'))
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202 unless (UNIVERSAL::isa ($value, 'Bio::Annotation::DBLink'));
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203 (defined $self->cross_references) ?
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204 push (@{ $self->cross_references }, $value) :
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205 return $self->cross_references ( [$value] );
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206 return $self->cross_references;
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207 }
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208
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209
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210 =head2 add_author
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211
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212 Usage : $self->add_author (new Bio::Biblio::Person (-lastname => 'Novak');
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213 Function: adding an author to a list of authors
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214 Returns : new value of 'authors' (a full list)
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215 Args : an object of type Bio::Biblio::Provider
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216
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217 =cut
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218
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219
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220 sub add_author {
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221 my ($self, $value) = @_;
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222 $self->throw ($self->_wrong_type_msg (ref $value, 'Bio::Biblio::Provider'))
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223 unless (UNIVERSAL::isa ($value, 'Bio::Biblio::Provider'));
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224 (defined $self->authors) ?
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225 push (@{ $self->authors }, $value) :
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226 return $self->authors ( [$value] );
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227 return $self->authors;
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228 }
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229
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230 =head2 add_contributor
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231
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232 Usage : $self->add_contributor (new Bio::Biblio::Person (-lastname => 'Novak');
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233 Function: adding a contributor to a list of contributors
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234 Returns : new value of 'contributors' (a full list)
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235 Args : an object of type Bio::Biblio::Provider
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236
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237 =cut
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238
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239 sub add_contributor {
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240 my ($self, $value) = @_;
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241 $self->throw ($self->_wrong_type_msg (ref $value, 'Bio::Biblio::Provider'))
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242 unless (UNIVERSAL::isa ($value, 'Bio::Biblio::Provider'));
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243 (defined $self->contributors) ?
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244 push (@{ $self->contributors }, $value) :
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245 return $self->contributors ( [$value] );
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246 return $self->contributors;
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247 }
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248
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249
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250 1;
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251 __END__
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