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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 =cut
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20
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21 =head1 NAME
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22
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23 Bio::EnsEMBL::Utils::Eprof - Bespoke Ensembl profiler
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24
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25 =head1 SYNOPSIS
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26
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27 use Bio::EnsEMBL::Utils::Eprof( 'eprof_start', 'eprof_end',
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28 'eprof_dump' );
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29
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30 &eprof_start('function-a');
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31 # ... do something
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32 &eprof_end('function-a');
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33
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34 &eprof_dump( \*STDERR );
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35
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36 # there is an object based set for above as well, for running
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37 # multiple concurrent profilers
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38
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39 =head1 DESCRIPTION
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40
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41 This is an Ensembl profiler as we broke the Perl profilers.
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42
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43 =head1 METHODS
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44
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45 =cut
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46
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47 package Bio::EnsEMBL::Utils::Eprof;
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48
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49 use strict;
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50 use warnings;
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51
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52 use Bio::EnsEMBL::Utils::Exception ('throw');
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53 use Bio::EnsEMBL::Utils::EprofStack;
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54
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55 use base qw( Exporter );
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56
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57 our @EXPORT_OK =
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58 ( 'eprof_start', 'eprof_end', 'eprof_dump', 'eprof_reset' );
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59
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60 my $global;
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61
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62 sub new {
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63 my ($proto) = @_;
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64
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65 my $class = ref($proto) || $proto;
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66 my $self = bless( { '_tags' => {} }, $class );
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67
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68 return $self;
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69 }
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70
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71 =head2 eprof_start
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72
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73 Title : eprof_start
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74 Usage :
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75 Function:
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76 Example :
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77 Returns :
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78 Args :
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79
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80
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81 =cut
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82
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83 sub eprof_start {
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84 my ($tag) = @_;
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85
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86 if ( !defined($global) ) {
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87 $global = Bio::EnsEMBL::Utils::Eprof->new();
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88 }
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89
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90 $global->start($tag);
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91 }
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92
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93 =head2 eprof_end
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94
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95 Title : eprof_end
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96 Usage :
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97 Function:
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98 Example :
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99 Returns :
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100 Args :
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101
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102
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103 =cut
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104
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105 sub eprof_end {
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106 my ($tag) = @_;
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107
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108 if ( !defined($global) ) {
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109 $global = Bio::EnsEMBL::Utils::Eprof->new();
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110 }
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111
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112 $global->end($tag);
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113 }
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114
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115 sub eprof_dump {
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116 my ($fh) = @_;
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117
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118 if ( !defined($global) ) { return }
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119
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120 $global->dump($fh);
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121 }
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122
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123 =head2 eprof_reset
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124
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125 Title : eprof_reset
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126 Usage :
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127 Function:
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128 Example :
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129 Returns :
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130 Args :
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131
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132
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133 =cut
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134
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135 sub eprof_reset { undef($global) }
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136
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137 =head2 dump
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138
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139 Title : dump
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140 Usage :
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141 Function:
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142 Example :
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143 Returns :
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144 Args :
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145
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146
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147 =cut
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148
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149 sub dump {
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150 my ( $self, $fh ) = @_;
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151
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152 my @tags = sort {
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153 $self->_tags()->{$a}->total_time()
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154 <=> $self->_tags()->{$b}->total_time()
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155 } keys %{ $self->_tags() };
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156
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157 foreach my $tag (@tags) {
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158 my $st = $self->_tags->{$tag};
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159
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160 if ( $st->number() == 0 ) { next }
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161
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162 my $STD = '---';
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163
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164 if ( $st->number() > 1 ) {
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165 my $SS =
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166 $st->total_time_time() -
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167 $st->total_time()*$st->total_time()/$st->number();
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168
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169 if ( $SS > 0 ) {
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170 $STD = sprintf( "%6f",
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171 sqrt( $SS/$st->number()/( $st->number() - 1 ) )
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172 );
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173 }
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174 }
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175
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176 print( $fh sprintf( "Eprof: %20s %6f %6f %d %s [%6f,%6f]\n",
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177 $st->tag(), $st->total_time(),
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178 $st->total_time()/$st->number(), $st->number(),
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179 $STD, $st->min_time(),
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180 $st->max_time() ) );
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181 } ## end foreach my $tag (@tags)
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182 } ## end sub dump
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183
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184 =head2 start
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185
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186 Title : start
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187 Usage : $eprof->start('this_tag');
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188 Function:
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189 Example :
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190 Returns :
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191 Args :
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192
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193
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194 =cut
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195
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196 sub start {
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197 my ( $self, $tag ) = @_;
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198
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199 if ( !defined($tag) ) {
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200 $self->throw("No tag, can't start.");
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201 }
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202
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203 if ( !defined( $self->_tags()->{$tag} ) ) {
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204 $self->_tags()->{$tag} = Bio::EnsEMBL::Utils::EprofStack->new($tag);
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205 }
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206
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207 $self->_tags()->{$tag}->push_stack();
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208 }
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209
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210 =head2 end
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211
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212 Title : end
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213 Usage : $eprof->end('this_tag');
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214 Function:
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215 Example :
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216 Returns :
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217 Args :
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218
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219
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220 =cut
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221
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222 sub end {
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223 my ( $self, $tag ) = @_;
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224
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225 if ( !defined($tag) ) {
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226 $self->throw("No tag, can't end.");
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227 }
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228
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229 if ( !defined( $self->_tags()->{$tag} ) ) {
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230 $self->throw(
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231 sprintf( "Ending with a nonexistant tag '%s'", $tag ) );
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232 }
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233
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234 $self->_tags->{$tag}->pop_stack();
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235 }
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236
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237 =head2 _tags
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238
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239 Title : _tags
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240 Usage : $obj->_tags($newval)
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241 Function:
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242 Returns : value of _tags
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243 Args : newvalue (optional)
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244
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245
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246 =cut
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247
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248 sub _tags {
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249 my ($obj) = @_;
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250 return $obj->{'_tags'};
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251 }
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252
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253 1;
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254
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