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1 =head1 LICENSE
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2
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3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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4 Genome Research Limited. All rights reserved.
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5
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6 This software is distributed under a modified Apache license.
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7 For license details, please see
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8
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9 http://www.ensembl.org/info/about/code_licence.html
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10
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11 =head1 CONTACT
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12
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13 Please email comments or questions to the public Ensembl
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14 developers list at <dev@ensembl.org>.
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15
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16 Questions may also be sent to the Ensembl help desk at
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17 <helpdesk@ensembl.org>.
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18
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19 =head1 AUTHOR
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20
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21 Originally from Steve Chervitz. Refactored by Ewan Birney.
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22
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23 =cut
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24
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25 =head1 NAME
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26
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27 Bio::EnsEMBL::Root
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28
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29 =head1 DESCRIPTION
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30
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31 Do not use Bio::EnsEMBL::Root anymore. It is included for backwards
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32 compatibility (every object in EnsEMBL used to inherit from this class)
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33 but will eventually be phased out. The replacement for the _rearrage
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34 method is the rearrange method which can be imported in the following
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35 way:
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36
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37 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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38
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39 # can now call rearrange as a class method (instead as object method)
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40 my ( $start, $end ) = rearrange( [ 'START', 'END' ], @args );
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41
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42 If you want to use the throw or warn methods the replacement use the
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43 class methods throw and warning from the Bio::EnsEMBL::Utils::Exception
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44 class:
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45
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46 use Bio::EnsEMBL::Utils::Exception qw(throw warning);
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47
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48 # can now call throw or warning even without blessed reference
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49 warning('This is a warning');
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50 throw('This is an exception');
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51
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52 This module was stolen from BioPerl to avoid problems with moving to
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53 BioPerl 1 from 0.7
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54
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55 =head1 METHODS
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56
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57 =cut
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58
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59 package Bio::EnsEMBL::Root;
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60
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61 use strict;
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62 use vars qw($VERBOSITY);
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63 use Bio::EnsEMBL::Utils::Exception qw( );
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64 use Bio::EnsEMBL::Utils::Argument qw( );
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65
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66
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67 $VERBOSITY = 0;
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68
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69 sub new{
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70 my($caller,@args) = @_;
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71
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72 my $class = ref($caller) || $caller;
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73 return bless({}, $class);
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74 }
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75
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76
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77 =head2 throw
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78
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79 DEPRECATED
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80
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81 =cut
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82
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83 sub throw{
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84 my ($self,$string) = @_;
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85
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86 Bio::EnsEMBL::Utils::Exception->warning("\n------------------ DEPRECATED ---------------------\n".
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87 "Bio::EnsEMBL::Root::throw has been deprecated\n".
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88 "use Bio::EnsEMBL::Utils::Exception qw(throw); \n".
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89 "throw('message'); #instead\n".
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90 "\n---------------------------------------------------\n");
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91
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92 Bio::EnsEMBL::Utils::Exception->throw($string);
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93
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94
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95 }
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96
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97 =head2 warn
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98
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99 DEPRECATED
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100
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101 =cut
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102
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103 sub warn{
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104 my ($self,$string) = @_;
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105
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106
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107
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108 Bio::EnsEMBL::Utils::Exception->warning("\n------------------ DEPRECATED ---------------------\n".
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109 "Bio::EnsEMBL::Root::warn has been deprecated\n".
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110 "use Bio::EnsEMBL::Utils::Exception qw(warning); \n".
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111 "warning('message'); #instead\n".
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112 "\n---------------------------------------------------\n");
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113
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114 Bio::EnsEMBL::Utils::Exception->warning($string);
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115
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116 }
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117
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118
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119
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120
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121 =head2 verbose
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122
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123 DEPRECATED
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124
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125 =cut
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126
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127 sub verbose{
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128 my ($self,$value) = @_;
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129
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130 Bio::EnsEMBL::Utils::Exception->warning("\n------------------ DEPRECATED ---------------------\n".
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131 "Bio::EnsEMBL::Root::verbose has been deprecated\n".
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132 "use Bio::EnsEMBL::Utils::Exception qw(verbose); \n".
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133 "verbose(value); #instead\n".
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134 "\n---------------------------------------------------\n");
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135
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136 Bio::EnsEMBL::Utils::Exception->verbose($value);
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137
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138 }
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139
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140 =head2 stack_trace_dump
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141
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142 DEPRECATED
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143
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144 =cut
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145
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146 sub stack_trace_dump{
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147 my ($self) = @_;
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148
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149 Bio::EnsEMBL::Utils::Exception->warning("\n------------------ DEPRECATED ---------------------\n".
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150 "Bio::EnsEMBL::Root::stack_trace_dump has been deprecated\n".
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151 "use Bio::EnsEMBL::Utils::Exception qw(stack_trace_dump); \n".
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152 "stack_trace_dump(); #instead\n".
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153 "\n---------------------------------------------------\n");
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154
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155 Bio::EnsEMBL::Utils::Exception->stack_trace_dump();
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156
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157 }
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158
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159
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160 =head2 stack_trace
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161
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162 DEPRECATED
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163
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164 =cut
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165
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166 sub stack_trace{
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167 my ($self) = @_;
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168
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169 Bio::EnsEMBL::Utils::Exception->warning("\n------------------ DEPRECATED ---------------------\n".
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170 "Bio::EnsEMBL::Root::stack_trace has been deprecated\n".
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171 "use Bio::EnsEMBL::Utils::Exception qw(stack_trace); \n".
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172 "stack_trace(); #instead\n".
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173 "\n---------------------------------------------------\n");
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174
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175 Bio::EnsEMBL::Utils::Exception->stack_trace();
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176
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177 }
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178
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179
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180 =head2 _rearrange
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181
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182 DEPRECATED
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183
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184 =cut
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185
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186 #----------------'
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187 sub _rearrange {
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188 #----------------
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189 my($self,$order,@param) = @_;
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190
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191 my $mess = "use Bio::EnsEMBL::Utils::Argument qw(rearrange); \n";
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192 $mess .= "rearrange(order, list); #instead\n";
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193
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194 Bio::EnsEMBL::Utils::Exception->deprecate($mess);
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195
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196 return Bio::EnsEMBL::Utils::Argument->rearrange($order,@param);
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197
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198 }
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199
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200 1;
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