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1 #
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2 # Ensembl module for Bio::EnsEMBL::Funcgen::ArrayChip
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3 #
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4 # You may distribute this module under the same terms as Perl itself
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5
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6 =head1 LICENSE
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7
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8 Copyright (c) 1999-2011 The European Bioinformatics Institute and
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9 Genome Research Limited. All rights reserved.
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10
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11 This software is distributed under a modified Apache license.
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12 For license details, please see
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13
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14 http://www.ensembl.org/info/about/code_licence.html
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15
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16 =head1 CONTACT
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17
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18 Please email comments or questions to the public Ensembl
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19 developers list at <ensembl-dev@ebi.ac.uk>.
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20
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21 Questions may also be sent to the Ensembl help desk at
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22 <helpdesk@ensembl.org>.
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23
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24
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25 =head1 NAME
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26
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27 Bio::EnsEMBL::Funcgen::ArrayChip - A simple module to represent the concept/template of
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28 a chip/slide within an array, of which the physical manifestation is an ExperimentalChip.
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29
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30 =head1 SYNOPSIS
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31
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32 use Bio::EnsEMBL::Funcgen::ArrayChip;
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33
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34 my $ec = Bio::EnsEMBL::Funcgen::ArrayChip->new(
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35 -ARRAY_ID => $array->dbID(),
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36 -NAME => $desc,
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37 -DESIGN_ID => $design_id,
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38 );
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39
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40 #add more methods here?
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41
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42
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43 =head1 DESCRIPTION
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44
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45 An ArrayChip object represent the concept of an array chip/slide withing a given array/chipset.
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46 The data for ArrayChips is stored in the array_chip table.
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47
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48
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49 =cut
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50
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51 use strict;
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52 use warnings;
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53
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54
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55 package Bio::EnsEMBL::Funcgen::ArrayChip;
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56
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57
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58 use Bio::EnsEMBL::Utils::Argument qw( rearrange );
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59 use Bio::EnsEMBL::Utils::Exception qw( throw warning );
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60 use Bio::EnsEMBL::Funcgen::Storable;
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61
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62 use vars qw(@ISA);
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63 @ISA = qw(Bio::EnsEMBL::Funcgen::Storable);
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64
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65
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66 =head2 new
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67
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68 Arg [-ARRAY_ID] : int - the dbID of the parent array
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69 Arg [-ARRAY] : Bio::EnsEMBL::Funcgen::Array
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70 Arg [-DESIGN_ID] : string - the unqiue deisng ID defined by the array vendor
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71 Arg [-NAME] : string - the name of the array chip
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72
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73
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74 Example : my $array_chip = Bio::EnsEMBL::Funcgen::ArrayChip->new(
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75 -ARRAY_ID => $array->dbID(),
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76 -NAME => $desc,
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77 -DESIGN_ID => $design_id,
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78 ); );
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79 Description: Creates a new Bio::EnsEMBL::Funcgen::ArrayChip object.
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80 Returntype : Bio::EnsEMBL::Funcgen::ArrayChip
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81 Exceptions : None ? should throw if mandaotry params not set
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82 Caller : General
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83 Status : Medium Risk
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84
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85 =cut
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86
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87 sub new {
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88 my $caller = shift;
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89
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90 my $class = ref($caller) || $caller;
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91 my $self = $class->SUPER::new(@_);
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92
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93 my ($array_id, $name, $design_id, $array)
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94 = rearrange( ['ARRAY_ID', 'NAME', 'DESIGN_ID', 'ARRAY'], @_ );
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95
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96
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97 #Remove array_id so we can remove checking below?
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98
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99 throw("Must define a name($name) and design_id($design_id)") if(! $name || ! $design_id);
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100
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101
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102 #Make these mutually exclusive to avoid checking
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103 if($array_id && $array){
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104 throw('Must provide either -array or -array_id but not both');
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105 }
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106
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107 if(defined $array){
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108
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109 if(!(ref($array) && $array->isa('Bio::EnsEMBL::Funcgen::Array'))){
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110 throw('array paramter must be a valid Bio::EnsEMBL::Funcgen::Array');
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111 }
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112
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113 $self->{'array'} = $array;
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114 }
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115
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116
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117
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118 $self->array_id($array_id) if defined $array_id;
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119 $self->name($name);
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120 $self->design_id($design_id);
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121
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122 return $self;
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123 }
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124
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125
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126 =head2 array_id
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127
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128 Arg [1] : (optional) int - the parent array dbID
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129 Example : my $array_id = $array_chip->array_id();
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130 Description: Getter, setter array_id attribute.
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131 Returntype : int
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132 Exceptions : None
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133 Caller : General
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134 Status : At Risk
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135
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136 =cut
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137
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138 sub array_id {
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139 my $self = shift;
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140 $self->{'array_id'} = shift if @_;
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141 return $self->{'array_id'};
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142 }
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143
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144 =head2 name
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145
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146 Arg [1] : (optional) string - the array chip name
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147 Example : my $ac_name = $array_chip->name();
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148 Description: Getter, setter for the name attribute
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149 Returntype : string
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150 Exceptions : None
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151 Caller : General
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152 Status : Medium Risk
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153
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154 =cut
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155
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156 sub name {
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157 my $self = shift;
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158 $self->{'name'} = shift if @_;
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159 return $self->{'name'};
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160 }
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161
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162 =head2 design_id
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163
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164 Arg [1] : (optional) string - the array_chip unique design id as deinfed by the array vendor
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165 Example : my $design_id = $array_chip->design_id();
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166 Description: Getter, setter for the design_id attribute
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167 Returntype : string
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168 Exceptions : None
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169 Caller : General
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170 Status : At Risk
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171
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172 =cut
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173
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174 sub design_id {
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175 my $self = shift;
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176 $self->{'design_id'} = shift if @_;
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177 return $self->{'design_id'};
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178 }
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179
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180
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181 =head2 get_Array
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182
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183 Example : my $array = $array_chip->get_array();
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184 Description: Getter for the array attribute
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185 Returntype : Bio::EnsEMBL::Funcgen::Array
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186 Exceptions : None
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187 Caller : General
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188 Status : At Risk
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189
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190 =cut
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191
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192 sub get_Array {
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193 my $self = shift;
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194
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195 if(! defined $self->{'array'}){
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196 $self->{'array'} = $self->adaptor->db->get_ArrayAdaptor()->fetch_by_dbID($self->array_id());
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197 }
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198
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199 return $self->{'array'};
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200 }
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201
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202
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203
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204 1;
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205
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