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1 # $Id: Reference.pm,v 1.18 2002/09/25 18:11:33 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Annotation::Reference
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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::Reference - Specialised DBLink object for Literature References
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16
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17 =head1 SYNOPSIS
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18
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19 $reg = Bio::Annotation::Reference->new( -title => 'title line',
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20 -location => 'location line',
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21 -authors => 'author line',
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22 -medline => 998122 );
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23
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24 =head1 DESCRIPTION
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25
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26 Object which presents a literature reference. This is considered to be
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27 a specialised form of database link. The additional methods provided
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28 are all set/get methods to store strings commonly associated with
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29 references, in particular title, location (ie, journal page) and
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30 authors line.
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31
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32 There is no attempt to do anything more than store these things as
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33 strings for processing elsewhere. This is mainly because parsing these
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34 things suck and generally are specific to the specific format one is
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35 using. To provide an easy route to go format --E<gt> object --E<gt> format
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36 without losing data, we keep them as strings. Feel free to post the
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37 list for a better solution, but in general this gets very messy very
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38 fast...
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39
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40 =head1 CONTACT
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41
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42 Describe contact details here
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43
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44 =head1 APPENDIX
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45
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46 The rest of the documentation details each of the object 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::Reference;
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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::Annotation::DBLink;
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58 use Bio::AnnotationI;
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59
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60 @ISA = qw(Bio::Annotation::DBLink);
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61
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62 =head2 new
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63
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64 Title : new
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65 Usage : $ref = Bio::Annotation::Reference->new( -title => 'title line',
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66 -authors => 'author line',
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67 -location => 'location line',
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68 -medline => 9988812);
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69 Function:
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70 Example :
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71 Returns : a new Bio::Annotation::Reference object
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72 Args : a hash with optional title, authors, location, medline, start and end
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73 attributes
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74
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75
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76 =cut
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77
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78 sub new{
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79 my ($class,@args) = @_;
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80
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81 my $self = $class->SUPER::new(@args);
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82
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83 my ($start,$end,$authors,$location,$title,$medline,$tag) =
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84 $self->_rearrange([qw(START
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85 END
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86 AUTHORS
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87 LOCATION
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88 TITLE
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89 MEDLINE
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90 TAGNAME
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91 )],@args);
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92
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93 defined $start && $self->start($start);
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94 defined $end && $self->end($end);
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95 defined $authors && $self->authors($authors);
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96 defined $location && $self->location($location);
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97 defined $title && $self->title($title);
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98 defined $medline && $self->medline($medline);
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99 defined $tag && $self->tagname($tag);
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100
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101 return $self;
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102 }
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103
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104
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105 =head1 AnnotationI implementing functions
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106
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107 =cut
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108
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109 =head2 as_text
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110
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111 Title : as_text
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112 Usage :
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113 Function:
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114 Example :
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115 Returns :
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116 Args :
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117
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118
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119 =cut
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120
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121 sub as_text{
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122 my ($self) = @_;
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123
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124 # this could get out of hand!
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125 return "Reference: ".$self->title;
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126 }
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127
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128
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129 =head2 hash_tree
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130
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131 Title : hash_tree
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132 Usage :
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133 Function:
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134 Example :
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135 Returns :
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136 Args :
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137
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138
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139 =cut
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140
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141 sub hash_tree{
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142 my ($self) = @_;
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143
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144 my $h = {};
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145 $h->{'title'} = $self->title;
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146 $h->{'authors'} = $self->authors;
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147 $h->{'location'} = $self->location;
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148 if( defined $self->start ) {
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149 $h->{'start'} = $self->start;
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150 }
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151 if( defined $self->end ) {
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152 $h->{'end'} = $self->end;
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153 }
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154 $h->{'medline'} = $self->medline;
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155
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156 return $h;
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157 }
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158
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159 =head2 tagname
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160
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161 Title : tagname
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162 Usage : $obj->tagname($newval)
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163 Function: Get/set the tagname for this annotation value.
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164
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165 Setting this is optional. If set, it obviates the need to provide
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166 a tag to Bio::AnnotationCollectionI when adding this object. When
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167 obtaining an AnnotationI object from the collection, the collection
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168 will set the value to the tag under which it was stored unless the
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169 object has a tag stored already.
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170 Example :
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171 Returns : value of tagname (a scalar)
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172 Args : new value (a scalar, optional)
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173
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174
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175 =cut
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176
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177 sub tagname{
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178 my ($self,$value) = @_;
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179 if( defined $value) {
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180 $self->{'tagname'} = $value;
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181 }
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182 return $self->{'tagname'};
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183 }
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184
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185
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186 =head1 Specific accessors for References
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187
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188 =cut
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189
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190
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191 =head2 start
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192
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193 Title : start
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194 Usage : $self->start($newval)
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195 Function: Gives the reference start base
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196 Example :
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197 Returns : value of start
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198 Args : newvalue (optional)
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199
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200
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201 =cut
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202
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203 sub start {
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204 my ($self,$value) = @_;
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205 if( defined $value) {
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206 $self->{'start'} = $value;
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207 }
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208 return $self->{'start'};
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209
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210 }
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211
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212 =head2 end
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213
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214 Title : end
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215 Usage : $self->end($newval)
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216 Function: Gives the reference end base
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217 Example :
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218 Returns : value of end
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219 Args : newvalue (optional)
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220
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221
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222 =cut
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223
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224 sub end {
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225 my ($self,$value) = @_;
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226 if( defined $value) {
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227 $self->{'end'} = $value;
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228 }
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229 return $self->{'end'};
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230 }
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231
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232 =head2 rp
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233
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234 Title : rp
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235 Usage : $self->rp($newval)
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236 Function: Gives the RP line. No attempt is made to parse this line.
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237 Example :
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238 Returns : value of rp
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239 Args : newvalue (optional)
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240
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241
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242 =cut
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243
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244 sub rp{
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245 my ($self,$value) = @_;
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246 if( defined $value) {
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247 $self->{'rp'} = $value;
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248 }
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249 return $self->{'rp'};
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250
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251 }
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252
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253 =head2 authors
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254
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255 Title : authors
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256 Usage : $self->authors($newval)
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257 Function: Gives the author line. No attempt is made to parse the author line
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258 Example :
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259 Returns : value of authors
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260 Args : newvalue (optional)
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261
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262
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263 =cut
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264
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265 sub authors{
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266 my ($self,$value) = @_;
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267 if( defined $value) {
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268 $self->{'authors'} = $value;
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269 }
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270 return $self->{'authors'};
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271
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272 }
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273
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274 =head2 location
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275
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276 Title : location
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277 Usage : $self->location($newval)
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278 Function: Gives the location line. No attempt is made to parse the location line
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279 Example :
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280 Returns : value of location
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281 Args : newvalue (optional)
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282
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283
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284 =cut
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285
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286 sub location{
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287 my ($self,$value) = @_;
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288 if( defined $value) {
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289 $self->{'location'} = $value;
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290 }
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291 return $self->{'location'};
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292
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293 }
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294
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295 =head2 title
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296
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297 Title : title
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298 Usage : $self->title($newval)
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299 Function: Gives the title line (if exists)
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300 Example :
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301 Returns : value of title
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302 Args : newvalue (optional)
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303
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304
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305 =cut
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306
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307 sub title{
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308 my ($self,$value) = @_;
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309 if( defined $value) {
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310 $self->{'title'} = $value;
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311 }
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312 return $self->{'title'};
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313
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314 }
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315
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316 =head2 medline
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317
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318 Title : medline
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319 Usage : $self->medline($newval)
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320 Function: Gives the medline number
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321 Example :
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322 Returns : value of medline
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323 Args : newvalue (optional)
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324
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325
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326 =cut
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327
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328 sub medline{
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329 my ($self,$value) = @_;
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330 if( defined $value) {
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331 $self->{'medline'} = $value;
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332 }
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333 return $self->{'medline'};
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334 }
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335
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336 =head2 pubmed
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337
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338 Title : pubmed
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339 Usage : $refobj->pubmed($newval)
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340 Function: Get/Set the PubMed number, if it is different from the MedLine
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341 number.
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342 Example :
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343 Returns : value of medline
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344 Args : newvalue (optional)
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345
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346
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347 =cut
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348
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349 sub pubmed {
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350 my ($self,$value) = @_;
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351 if( defined $value) {
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352 $self->{'pubmed'} = $value;
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353 }
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354 return $self->{'pubmed'};
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355 }
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356
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357 =head2 database
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358
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359 Title : database
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360 Usage :
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361 Function: Overrides DBLink database to be hard coded to 'MEDLINE', unless
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362 the database has been set explicitely before.
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363 Example :
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364 Returns :
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365 Args :
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366
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367
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368 =cut
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369
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370 sub database{
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371 my ($self, @args) = @_;
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372
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373 return $self->SUPER::database(@args) || 'MEDLINE';
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374 }
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375
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376 =head2 primary_id
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377
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378 Title : primary_id
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379 Usage :
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380 Function: Overrides DBLink primary_id to provide medline number
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381 Example :
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382 Returns :
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383 Args :
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384
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385
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386 =cut
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387
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388 sub primary_id{
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389 my ($self, @args) = @_;
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390
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391 return $self->medline(@args);
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392 }
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393
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394 =head2 optional_id
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395
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396 Title : optional_id
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397 Usage :
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398 Function: Overrides DBLink optional_id to provide the PubMed number.
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399 Example :
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400 Returns :
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401 Args :
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402
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403
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404 =cut
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405
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406 sub optional_id{
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407 my ($self, @args) = @_;
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408
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409 return $self->pubmed(@args);
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410 }
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411
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412 =head2 publisher
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413
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414 Title : publisher
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415 Usage : $self->publisher($newval)
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416 Function: Gives the publisher line. No attempt is made to parse the publisher line
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417 Example :
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418 Returns : value of publisher
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419 Args : newvalue (optional)
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420
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421
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422 =cut
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423
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424 sub publisher {
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425 my ($self,$value) = @_;
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426 if( defined $value) {
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427 $self->{'publisher'} = $value;
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428 }
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429 return $self->{'publisher'};
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430 }
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431
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432
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433 =head2 editors
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434
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435 Title : editors
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436 Usage : $self->editors($newval)
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437 Function: Gives the editors line. No attempt is made to parse the editors line
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438 Example :
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439 Returns : value of editors
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440 Args : newvalue (optional)
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441
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442
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443 =cut
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444
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445 sub editors {
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446 my ($self,$value) = @_;
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447 if( defined $value) {
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448 $self->{'editors'} = $value;
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449 }
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450 return $self->{'editors'};
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451 }
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452
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453
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454 =head2 encoded_ref
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455
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456 Title : encoded_ref
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457 Usage : $self->encoded_ref($newval)
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458 Function: Gives the encoded_ref line. No attempt is made to parse the encoded_ref line
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459 (this is added for reading PDB records (REFN record), where this contains
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460 ISBN/ISSN/ASTM code)
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461 Example :
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462 Returns : value of encoded_ref
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463 Args : newvalue (optional)
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464
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465
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466 =cut
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467
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468 sub encoded_ref {
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469 my ($self,$value) = @_;
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470 if( defined $value) {
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471 $self->{'encoded_ref'} = $value;
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472 }
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473 return $self->{'encoded_ref'};
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474 }
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475
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476
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477 1;
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