Mercurial > repos > cpt > cpt_psm_recombine

annotate lib/CPT/ParameterCollection.pm @ 1:97ef96676b48 draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:51:26 +0000
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1 package CPT::ParameterCollection;
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2 use Carp;
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3 use Moose;
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4 use strict;
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5 use warnings;
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6 use autodie;
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7 use Data::Dumper;
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8
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9 # A collection of parameters
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10
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11 has 'params' => ( is => 'rw', isa => 'ArrayRef', default => sub{[]});
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12
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13
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14 sub validate {
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15 my ( $self, $getopt_obj) = @_;
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16 my $issue_count = 0;
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17 for my $item ( @{ $self->params() } ) {
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18 my $type = ref($item);
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19 # We now check that getopt has supplied a value (we don't want to validate values that were NOT supplied. That'd be dumb)
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20 # If it's defined AND it doesn't validate, then we add an error on the stack for that.
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21 if(defined $item->name() && defined $getopt_obj->{$item->name()} && !$item->validate()){
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22 carp join("\n", @{$item->errors()});
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23 $issue_count++;
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24 }
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25 }
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26 return $issue_count == 0;
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27 }
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28
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29
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30
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31 sub push_group {
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32 my ( $self, $group ) = @_;
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33 $self->push_params($group->flattenOptionsArray());
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34 }
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35
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36
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37 sub push_param {
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38 my ( $self, $param ) = @_;
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39 $self->_push($self->_coerce_param($_));
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40 }
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41
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42
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43 sub push_params {
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44 my ( $self, $array_ref ) = @_;
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45 foreach(@{$array_ref}){
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46 my $result = $self->_coerce_param($_);
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47 if($result){
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48 $self->_push($result);
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49 }
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50 }
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51 }
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52
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53 sub _push{
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54 my ( $self, $array_ref ) = @_;
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55 my @arr;
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56 if($self->params()){
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57 @arr = @{$self->params()};
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58 }
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59 push(@arr, $array_ref);
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60 $self->params(\@arr);
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61 }
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62
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63
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64 sub parse_short_name {
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65 my ( $self, $parameter ) = @_;
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66 if ( index( $parameter, '|' ) > -1 ) {
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67 return substr( $parameter, index( $parameter, '|' ) + 1 );
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68 }
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69 else {
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70 return "";
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71 }
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72 }
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73
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74
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75 sub parse_long_name {
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76 my ( $self, $parameter ) = @_;
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77 if ( index( $parameter, '|' ) > -1 ) {
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78 return substr( $parameter, 0, index( $parameter, '|' ) );
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79 }
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80 else {
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81 return $parameter;
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82 }
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83 }
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84
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85
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86 sub _coerce0 {
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87 my ($self) = @_;
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88 require CPT::Parameter::Empty;
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89 my $p = CPT::Parameter::Empty->new();
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90 return $p;
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91 }
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92 sub _coerce1 {
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93 my ($self, @parts) = @_;
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94 require CPT::Parameter::Label;
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95 my $p = CPT::Parameter::Label->new(label=> $parts[0]);
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96 return $p;
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97 }
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98 sub _coerce2 {
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99 my ($self, @parts) = @_;
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100 require CPT::Parameter::Flag;
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101 my $p = CPT::Parameter::Flag->new(
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102 name => $self->parse_long_name( $parts[0] ),
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103 short => $self->parse_short_name( $parts[0] ),
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104 multiple => 0,
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105 description => $parts[1],
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106 );
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107 return $p;
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108 }
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109 sub _coerce3 {
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110 my ($self, @parts) = @_;
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111 # Three parameter case
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112 my %attr = (
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113 name => $self->parse_long_name( $parts[0] ),
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114 short => $self->parse_short_name( $parts[0] ),
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115 multiple => 0,
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116 description => $parts[1],
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117 );
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118
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119 # create the attr
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120 my %set_attr = %{ $parts[2] };
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121
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122 # Check if various things are set, if so, copy them.
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123 foreach (qw(default options required hidden implies multiple _show_in_galaxy _galaxy_specific data_format default_format file_format)) {
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124 if ( defined $set_attr{$_} ) {
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125 $attr{$_} = $set_attr{$_};
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126 }
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127 }
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128
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129 # Now, if validate is set, we can choose a type and possibly do other coersion.
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130 if ( $set_attr{'validate'} ) {
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131 my $validate = $set_attr{'validate'};
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132 my $p;
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133 if ( $validate eq 'Flag' ) {
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134 require CPT::Parameter::Flag;
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135 $p = CPT::Parameter::Flag->new(%attr);
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136 }
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137 elsif ( $validate eq 'Float' ) {
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138 foreach (qw(min max)) {
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139 if ( $set_attr{$_} ) {
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140 $attr{$_} = $set_attr{$_};
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141 }
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142 }
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143 require CPT::Parameter::Float;
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144 $p = CPT::Parameter::Float->new(%attr);
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145 }
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146 elsif ( $validate eq 'Int' ) {
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147 foreach (qw(min max)) {
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148 if ( $set_attr{$_} ) {
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149 $attr{$_} = $set_attr{$_};
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150 }
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151 }
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152 require CPT::Parameter::Int;
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153 $p = CPT::Parameter::Int->new(%attr);
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154 }
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155 elsif ( $validate eq 'Option' ) {
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parents:
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156 foreach (qw(options)) {
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parents:
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157 if ( $set_attr{$_} ) {
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158 $attr{$_} = $set_attr{$_};
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159 }
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160 }
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161 require CPT::Parameter::Option::Generic;
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162 $p = CPT::Parameter::Option::Generic->new(%attr);
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163 }
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parents:
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164 elsif ( $validate eq 'String' ) {
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parents:
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165 require CPT::Parameter::String;
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parents:
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166 $p = CPT::Parameter::String->new(%attr);
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parents:
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167 }
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parents:
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168 elsif ( $validate eq 'File/Input' ) {
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parents:
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169 require CPT::Parameter::File::Input;
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170 $p = CPT::Parameter::File::Input->new(%attr);
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parents:
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171 }
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parents:
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172 elsif ( $validate eq 'File/Output' ) {
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parents:
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173 require CPT::Parameter::File::Output;
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parents:
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174 $p = CPT::Parameter::File::Output->new(%attr);
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parents:
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175 }
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parents:
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176 elsif ( $validate eq 'File/OutputFormat' ) {
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parents:
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177 require CPT::Parameter::File::OutputFormat;
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178 $p = CPT::Parameter::File::OutputFormat->new(%attr);
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parents:
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179 }
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180 elsif ( $validate eq 'Genomic/Tag' ) {
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parents:
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181 require CPT::Parameter::Option::Genomic_Tag;
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182 $p = CPT::Parameter::Option::Genomic_Tag->new(%attr);
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parents:
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183 }
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parents:
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184 else {
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185 die 'Unknown validation type: ' . $validate;
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parents:
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186 }
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parents:
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187 return $p;
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parents:
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188 }
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parents:
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189 else {
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190 require CPT::Parameter::Flag;
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191 my $p = CPT::Parameter::Flag->new(%attr);
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192 return $p;
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parents:
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193 }
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parents:
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194 }
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parents:
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195
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196 sub _coerce_param {
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parents:
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197 my ( $self, $param ) = @_;
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parents:
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198 if ( ref($param) eq 'ARRAY' ) {
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parents:
diff changeset
199 my @parts = @{$param};
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parents:
diff changeset
200 if ( scalar @parts == 0 ) {
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parents:
diff changeset
201 return $self->_coerce0(@parts);
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parents:
diff changeset
202 }
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parents:
diff changeset
203 elsif ( scalar @parts == 1 ) {
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parents:
diff changeset
204 return $self->_coerce1(@parts);
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parents:
diff changeset
205 }
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parents:
diff changeset
206 elsif ( scalar @parts == 2 ) {
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parents:
diff changeset
207 return $self->_coerce2(@parts);
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parents:
diff changeset
208 }
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parents:
diff changeset
209 else {
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parents:
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210 return $self->_coerce3(@parts);
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parents:
diff changeset
211 }
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parents:
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212 }
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parents:
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213 else {
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parents:
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214 die 'A non-array type was attempted to be coerced...';
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parents:
diff changeset
215 }
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parents:
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216 }
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cpt
parents:
diff changeset
217
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parents:
diff changeset
218
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parents:
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219 sub get_by_name {
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parents:
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220 my ( $self, $name ) = @_;
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parents:
diff changeset
221 for my $item ( @{ $self->params() } ) {
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parents:
diff changeset
222 if ( defined $item->name() && $item->name() eq $name ) {
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parents:
diff changeset
223 return $item;
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parents:
diff changeset
224 }
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parents:
diff changeset
225 }
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parents:
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226 return;
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parents:
diff changeset
227 }
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parents:
diff changeset
228
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parents:
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229
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230 sub getopt {
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parents:
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231 my ($self) = @_;
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parents:
diff changeset
232 my @clean_opt_spec;
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parents:
diff changeset
233
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parents:
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234 # Loop through each item
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parents:
diff changeset
235 for my $item ( @{ $self->params() } ) {
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parents:
diff changeset
236 my $type = ref($item);
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parents:
diff changeset
237
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parents:
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238 # If it's an array, that means it's definitely an old style
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parents:
diff changeset
239 if ( $type eq 'ARRAY' ) {
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parents:
diff changeset
240
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parents:
diff changeset
241 # And we can push it through without any issues
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parents:
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242 push( @clean_opt_spec, $item );
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parents:
diff changeset
243 }
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parents:
diff changeset
244
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parents:
diff changeset
245 # If it's a hash, it's probably one of the { one_of/xor/etc }
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parents:
diff changeset
246 elsif ( $type eq 'CPT::ParameterGroup' ) {
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parents:
diff changeset
247
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248 # D:
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parents:
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249 push( @clean_opt_spec, $item->flattenOptionsArray() );
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parents:
diff changeset
250 }
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parents:
diff changeset
251
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parents:
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252 # Otherwise it's one of our CPT::Parameter stuff
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parents:
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253 else {
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254
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255 # Otherwise, we'll use the method to transform our complex object into a GetOpt compatible item
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256 push( @clean_opt_spec, $item->getOptionsArray() );
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257 }
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258 }
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259 return @clean_opt_spec;
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260 }
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261
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262
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263 sub populate_from_getopt {
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264 my ( $self, $opt ) = @_;
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265 # Loop through each item
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266 for my $item ( @{ $self->params() } ) {
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267 # If it's has a name, and options supplies a value for that name
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268 if ( defined($item->name()) && defined ($opt->{$item->name()})){
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269 $item->value($opt->{ $item->name() });
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270 }
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271 }
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272 }
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273
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274 no Moose;
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275 1;
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276
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277 __END__
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278
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279 =pod
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280
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281 =encoding UTF-8
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282
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283 =head1 NAME
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284
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285 CPT::ParameterCollection
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286
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287 =head1 VERSION
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288
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289 version 1.99.4
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290
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291 =head2 validate
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292
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293 $pC->validate();
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294
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295 calls the validate method, which loops through and checks that user values line
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296 up with the validate method in each and every slot.
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297
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298 =head2 push_group
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299
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300 $pC->push_group(CPT::Parameter::Flag->new( <snip> ));
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301
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302 Push a new groupeter onto the array
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303
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304 =head2 push_param
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305
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306 $pC->push_param(CPT::Parameter::Flag->new( <snip> ));
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307
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308 Push a new parameter onto the array
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309
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310 =head2 push_params
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311
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312 $pC->push_param([
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313 <snip some params>
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314 ]);
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315
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316 Pushes a lot of params at once onto the array
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317
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318 =head2 parse_short_name
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319
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320 $pc->parse_short_name("file|f");
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321 # would return "f"
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322
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323 =head2 parse_long_name
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324
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325 $pc->parse_long_name("file|f");
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326 # would return "file"
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327
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328 =head2 _coerce_param
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329
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330 $pc->_coerce_param(["file|f","input file",{validate=>'File/Input'}]);
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331
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332 would return a CPT::Parameter::File::Input object.
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333
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334 =head2 get_by_name
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335
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336 $pC->get_by_name('format');
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337
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338 returns the CPT::Parameter object with that key.
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339
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340 =head2 getopt
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341
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342 my @getopt_compatible_array = $pC->getopt()
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343
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344 Returns a getopt compatible array by looping through the array and simply returning array objects, and calling the getOptionsArray method on CPT::Parameter::* objects
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345
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346 =head2 populate_from_getopt
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347
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348 $parameterCollection->populate_from_getopt($opt);
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349
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350 Populate the ->value() from getopt.
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351
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352 =head1 AUTHOR
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353
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354 Eric Rasche <rasche.eric@yandex.ru>
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355
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356 =head1 COPYRIGHT AND LICENSE
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357
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358 This software is Copyright (c) 2014 by Eric Rasche.
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359
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360 This is free software, licensed under:
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361
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362 The GNU General Public License, Version 3, June 2007
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363
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364 =cut