annotate variant_effect_predictor/Bio/Biblio/Article.pm @ 1:d6778b5d8382 draft default tip

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author willmclaren
date Fri, 03 Aug 2012 10:05:43 -0400
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1 # $Id: Article.pm,v 1.7 2002/10/22 07:45:11 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Biblio::Article
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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::Article - Representation of a general article
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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::Article (-identifier => '123abc',
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17 -first_page => 23,
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18 -last_page => 68);
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19 --- OR ---
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20
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21 $obj = new Bio::Biblio::Article;
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22 $obj->identifier ('123abc');
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23 $obj->first_page (23);
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24 $obj->last_page (68);
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25
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26 =head1 DESCRIPTION
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27
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28 A storage object for a general article.
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29 See its place in the class hierarchy in
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30 http://industry.ebi.ac.uk/openBQS/images/bibobjects_perl.gif
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31
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32 =head2 Attributes
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33
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34 The following attributes are specific to this class
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35 (however, you can also set and get all attributes defined in the parent classes):
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36
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37 first_page
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38 last_page
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39
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40
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41 =head1 SEE ALSO
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42
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43 =over
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44
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45 =item *
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46
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47 OpenBQS home page: http://industry.ebi.ac.uk/openBQS
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48
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49 =item *
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50
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51 Comments to the Perl client: http://industry.ebi.ac.uk/openBQS/Client_perl.html
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52
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53 =back
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54
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55 =head1 FEEDBACK
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56
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57 =head2 Mailing Lists
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58
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59 User feedback is an integral part of the evolution of this and other
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60 Bioperl modules. Send your comments and suggestions preferably to
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61 the Bioperl mailing list. Your participation is much appreciated.
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62
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63 bioperl-l@bioperl.org - General discussion
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64 http://bioperl.org/MailList.shtml - About the mailing lists
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65
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66 =head2 Reporting Bugs
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67
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68 Report bugs to the Bioperl bug tracking system to help us keep track
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69 of the bugs and their resolution. Bug reports can be submitted via
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70 email or the web:
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71
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72 bioperl-bugs@bioperl.org
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73 http://bugzilla.bioperl.org/
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74
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75 =head1 AUTHORS
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76
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77 Heikki Lehvaslaiho (heikki@ebi.ac.uk),
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78 Martin Senger (senger@ebi.ac.uk)
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79
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80 =head1 COPYRIGHT
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81
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82 Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved.
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83
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84 This module is free software; you can redistribute it and/or modify
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85 it under the same terms as Perl itself.
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86
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87 =head1 DISCLAIMER
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88
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89 This software is provided "as is" without warranty of any kind.
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90
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91 =cut
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92
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93
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94 # Let the code begin...
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95
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96
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97 package Bio::Biblio::Article;
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98 use strict;
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99 use vars qw(@ISA);
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100
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101 use Bio::Biblio::Ref;
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102
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103 @ISA = qw( Bio::Biblio::Ref);
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104
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105 #
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106 # a closure with a list of allowed attribute names (these names
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107 # correspond with the allowed 'get' and 'set' methods); each name also
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108 # keep what type the attribute should be (use 'undef' if it is a
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109 # simple scalar)
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110 #
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111 {
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112 my %_allowed =
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113 (
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114 _first_page => undef,
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115 _last_page => undef,
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116 );
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117
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118 # return 1 if $attr is allowed to be set/get in this class
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119 sub _accessible {
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120 my ($self, $attr) = @_;
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121 exists $_allowed{$attr} or $self->SUPER::_accessible ($attr);
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122 }
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123
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124 # return an expected type of given $attr
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125 sub _attr_type {
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126 my ($self, $attr) = @_;
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127 if (exists $_allowed{$attr}) {
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128 return $_allowed{$attr};
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129 } else {
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130 return $self->SUPER::_attr_type ($attr);
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131 }
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132 }
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133 }
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134
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135
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136 1;
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137 __END__