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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:48:47 +0000
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1
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1 package CPT::Analysis::PAUSE::SVG;
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2
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3 # ABSTRACT: Library for use in PAUSE analysis
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4 use strict;
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5 use warnings;
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6 use Moose;
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7 use Data::Dumper;
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8 use List::MoreUtils qw(each_array);
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9 use SVG;
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10
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11 has 'svg' => ( is => 'rw' );
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12 has 'width' => ( is => 'rw', isa => 'Int' );
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13 has 'height' => ( is => 'rw', isa => 'Int' );
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14 has 'vertical_offset' => ( is => 'rw', isa => 'Int' );
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15 has 'start_end_max_num' => ( is => 'rw', isa => 'Int' );
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16 has 'num_rows' => ( is => 'rw', isa => 'Int' );
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17 has 'row_size' => ( is => 'rw', isa => 'Int' );
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18 has 'row_width' => ( is => 'rw', isa => 'Int' );
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19 has 'x_border' => ( is => 'rw', isa => 'Int' );
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20 has 'y_border' => ( is => 'rw', isa => 'Int' );
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21 has 'line_height' => ( is => 'rw', isa => 'Int' );
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22 has 'inter_line_spacing' => ( is => 'rw', isa => 'Int' );
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23 has 'max' => ( is => 'rw', isa => 'Int' );
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24 has 'fasta_id' => ( is => 'rw', isa => 'Any' );
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25
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26 sub setup {
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27 my ($self) = @_;
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28 $self->svg(
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29 SVG->new(
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30 width => $self->width(),
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31 height => $self->height(),
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32 )
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33 );
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34 }
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35
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36 sub add_header {
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37 my ( $self, @refs ) = @_;
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38
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39 $self->plot_title( 'Plot of ' . $self->fasta_id() );
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40
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41 my $i = 0;
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42 foreach (@refs) {
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43 my @subrefs = @{$_};
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44 foreach (@subrefs) {
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45 $i++;
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46 my %d = %{$_};
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47 $self->plot_key( $d{name}, $d{line}, $d{fill}, $i );
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48 }
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49 }
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50 $self->vertical_offset( $self->vertical_offset() - ( $i - 1 ) * 20 );
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51 }
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52
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53 my $global_pline_idx = 0;
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54
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55 sub plot_track {
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56 my ( $self, $points_ref, $stroke, $fill, $id ) = @_;
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57
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58 $global_pline_idx++;
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59 $self->svg()->polyline(
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60 %{$points_ref},
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61 id => 'pline_' . $id . '-' . $global_pline_idx,
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62 style => {
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63 'fill-opacity' => .5,
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64 'stroke' => $stroke,
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65 'fill' => $fill,
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66 }
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67 )
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68
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69 }
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70
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71 sub make_scale {
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72 my ( $self, $i, $start, $stop ) = @_;
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73
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74 # Left axis label, must be rotated
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75 my $tmp_x = $self->fix_x_value(-30); #$self->x_border()-30;
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76 my $tmp_y = $self->fix_y_value($i) + 50;
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77 $self->svg()->text(
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78 id => 'left_side_label_row_' . $i,
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79 x => $tmp_x - 20,
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80 y => $tmp_y - 20,
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81 'font-family' => 'Helvetica, sans-serif',
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82 'transform' => sprintf( 'rotate(-90 %s %s)', $tmp_x, $tmp_y ),
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83 )->cdata('Start/End Hit Count Scale');
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84
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85 # Right axis label, must be rotated
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86 $tmp_x = $self->fix_x_value( $self->row_width() + 60 );
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87 $tmp_y = $self->fix_y_value($i);
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88 $self->svg()->text(
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89 id => 'right_side_label_row_' . $i,
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90 x => $tmp_x - 20,
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91 y => $tmp_y,
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92 'font-family' => 'Helvetica, sans-serif',
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93 'transform' => sprintf( 'rotate(-90 %s %s)', $tmp_x, $tmp_y ),
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94 )->cdata('Coverage Density');
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95
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96 # Horizontal increments
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97 for ( my $k = -4 ; $k <= 4 ; $k++ ) {
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98
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99 # Left side label
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100 my $y_position = $k / 4 * $self->line_height();
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101 $self->svg()->text(
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102 id => sprintf( 'label_left_side_row_%s_%s', $i, $k ),
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103 x => $self->fix_x_value(-30),
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104 y => $self->fix_y_value( $i, $y_position ),
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105 'font-family' => 'Helvetica, sans-serif',
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106 )->cdata( int( $self->start_end_max_num() * abs( $k / 4 ) ) );
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107
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108 # Right side label
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109 $self->svg()->text(
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110 id => sprintf( 'label_right_side_row_%s_%s', $i, $k ),
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111 x => $self->fix_x_value( $self->row_width() + 10 ),
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112 y => $self->fix_y_value( $i, $y_position ),
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113 'font-family' => 'Helvetica, sans-serif',
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114 )->cdata( int( $self->max() * abs( $k / 4 ) ) );
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115
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116 # Vertical lines
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117 $self->svg()->line(
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118 x1 => $self->fix_x_value( $self->row_width() ),
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119 x2 => $self->fix_x_value(0),
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120 y1 => $self->fix_y_value( $i, $y_position ),
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121 y2 => $self->fix_y_value( $i, $y_position ),
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122 id => sprintf( 'vertical_increment_row_%s_%s', $i, $k ),
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123 opacity => .25,
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124 stroke => 'rgb(0,0,0)',
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125 'stroke-width' => '2',
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126 );
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127 }
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128
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129 # Vertical Increments
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130 my $number_of_increments = 10;
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131 for (
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132 my $k = 0 ;
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133 $k <= $self->row_width() ;
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134 $k += ( $self->row_width() / $number_of_increments )
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135 )
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136 {
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137 # We get % of way across (k/num_inc) and we multiply by the width value, to get % of width which we adjust with start to get correct value
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138 my $b =
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139 ( $k / $self->row_width() ) * ( $stop - $start ) + $start;
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140 my $kb = $b / 1000;
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141 $self->svg()->text(
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142 id =>
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143 sprintf( 'vertical_line_label_row_%s_%s', $i, $k ),
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144 x => $self->fix_x_value($k),
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145 y =>
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146 $self->fix_y_value( $i, $self->line_height() + 20 ),
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147 'font-family' => 'Helvetica, sans-serif',
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148 )->cdata( ($kb) . ' kb' );
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149
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150 $self->svg()->line(
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151 x1 => $self->fix_x_value($k),
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152 x2 => $self->fix_x_value($k),
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153 y1 => $self->fix_y_value( $i, -$self->line_height() ),
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154 y2 => $self->fix_y_value( $i, $self->line_height() ),
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155 id => sprintf( 'vertical_line_row_%s_%s', $i, $k ),
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156 opacity => .5,
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157 stroke => 'rgb(0,0,0)',
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158 'stroke-width' => '1',
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159 );
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160 }
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161 }
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162
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163 sub plot_title {
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164 my ( $self, $string ) = @_;
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165 $self->svg()->text(
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166 id => 'label_plot_title',
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167 x => $self->x_border(),
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168 y => 50 + $self->vertical_offset(),
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169 'font-family' => 'Helvetica, sans-serif',
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170 'font-size' => '150%',
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171 )->cdata($string);
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172 $self->vertical_offset( $self->vertical_offset() + 25 );
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173 }
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174
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175 sub plot_key {
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176 my ( $self, $text, $stroke, $colour, $i ) = @_;
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177
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178 $self->svg()->rectangle(
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179 x => $self->x_border(),
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180 y => 50 + $self->vertical_offset() - 15,
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181 width => 15,
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182 height => 15,
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183 id => 'label_key_example' . $i,
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184 'fill-opacity' => .5,
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185 'stroke' => $stroke,
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186 'fill' => $colour,
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187 );
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188 $self->svg()->text(
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189 id => 'label_key_string' . $i,
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190 x => $self->x_border() + 20,
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191 y => 50 + $self->vertical_offset(),
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192 'font-family' => 'Helvetica, sans-serif',
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193 )->cdata($text);
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194 $self->vertical_offset( $self->vertical_offset + 20 );
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195 }
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196
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197 sub xmlify {
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198 my ($self) = @_;
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199 return $self->svg()->xmlify();
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200 }
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201
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202 sub x_values_for_range_scaled {
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203 my ( $self, $start, $end, $pieces ) = @_;
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204 my @vals = ($start);
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205 my $by = ( $end - $start ) / $pieces;
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206 ## For all values from the x_border to xborder+row_width, add a value of row_width split/row_size (i.e., how far for EACH INDIVIDUAL value)
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207 for ( my $i = $start ; $i < $end ; $i += $by ) {
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208 push( @vals, $i );
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209 }
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210 push( @vals, $end );
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211 return @vals;
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212 }
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213
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214 sub fix_x_values {
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215 my ( $self, @values ) = @_;
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216 return map { $self->fix_x_value($_) } @values;
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217 }
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218
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219 sub fix_x_value {
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220 my ( $self, $val ) = @_;
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221 return $val + $self->x_border();
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222 }
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223
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224 sub fix_y_value {
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225 my ( $self, $i, $val ) = @_;
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226 return (
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227 $self->vertical_offset() + $val - $self->line_height() + (
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228 ( ( 2 + $i ) * $self->line_height() ) +
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229 ( $i * $self->inter_line_spacing() ) +
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230 $self->y_border()
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231 )
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232 );
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233 }
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234
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235 sub fix_all_y_values {
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236 my ( $self, $i, @arrays_to_fix, ) = @_;
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237 for ( my $j = 0 ; $j < scalar @arrays_to_fix ; $j++ ) {
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238
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239 # For each array in postive_y (AoA)
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240 #
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241 # we cast to array, then we map this, then we have this
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242 # in an anonymous array which means we can just
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243 # replace. This is probably not as efficient as looking
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244 # at every value directly and doing "in place"
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245 # replacement, but I don't know how that would be
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246 # written here...
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247 $arrays_to_fix[$j] =
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248 [ map { $self->fix_y_value( $i, $_ ) }
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249 @{ $arrays_to_fix[$j] } ];
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250 }
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251 return @arrays_to_fix;
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252 }
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253
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254 sub copy_data {
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255 my ( $self, $start, $stop, $data_to_ref, $data_from_ref, $max ) = @_;
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256
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257 # Copy data from the original array to the new one, transforming out
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258 # the subset of interest. This is done across an AoA
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259 my @data_to = @{$data_to_ref};
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260 my @data_from = @{$data_from_ref};
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261 for ( my $k = 0 ; $k < scalar @data_from ; $k++ ) {
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262 foreach ( my $j = $start ; $j < $stop ; $j++ )
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263 { #1 to 10_000 in the genome
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264 if ( defined ${ $data_from[$k] }[$j] ) {
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265 push(
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266 @{ $data_to[$k] },
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267 -(
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268 $self->line_height() *
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269 ${ $data_from[$k] }[$j] /
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270 $max
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271 )
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272 );
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273 }
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274 else {
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275 push( @{ $data_to[$k] }, 0 );
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276 }
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277 }
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278 }
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279 return @data_to;
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280 }
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281
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282 sub plot_individual_row {
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283 my ( $self, $start, $stop, $i, $regular_ref, $rescale_ref ) = @_;
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284
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285 my @regular = map { ${$_}{data} } @{$regular_ref};
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286 my @rescale = map { ${$_}{data} } @{$rescale_ref};
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287 my @regular_y;
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288 my @rescale_y;
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289 ## Ensure we duplicate the number of arrays.
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290 foreach (@regular) {
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291 push( @regular_y, [] );
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292 }
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293 foreach (@rescale) {
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294 push( @rescale_y, [] );
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295 }
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296
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297 # Determine bounds of row
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298 $self->push_all( \@regular_y, 0 );
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299 $self->push_all( \@rescale_y, 0 );
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300
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301 @regular_y =
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302 $self->copy_data( $start, $stop, \@regular_y, \@regular,
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303 $self->start_end_max_num() );
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304 @rescale_y =
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305 $self->copy_data( $start, $stop, \@rescale_y, \@rescale,
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306 $self->max() );
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307
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308 #print @rescale_y;
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309
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310 # Set up our X values
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311 my @x_values = $self->fix_x_values(
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312 $self->x_values_for_range_scaled(
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313 0, $self->row_width(), ( $stop - $start )
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314 )
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315 );
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316
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317 #my @x_values_rescale = $self->fix_x_values( $self->x_values_for_range_scaled(0, $self->row_width(), ( $stop - $start )));
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318
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319 $self->push_all( \@regular_y, 0 );
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320 $self->push_all( \@rescale_y, 0 );
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321
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322 # Fix the ys
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323 @regular_y = $self->fix_all_y_values( $i, @regular_y );
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324 @rescale_y = $self->fix_all_y_values( $i, @rescale_y );
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325
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326 # Prepare our styling
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327 my @regular_line = map { ${$_}{line} } @{$regular_ref};
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328 my @rescale_line = map { ${$_}{line} } @{$rescale_ref};
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329 my @regular_fill = map { ${$_}{fill} } @{$regular_ref};
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330 my @rescale_fill = map { ${$_}{fill} } @{$rescale_ref};
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331
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332 # Add data to plot
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333 $self->svg_add_track(
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334 \@x_values, \@regular_y, \@regular_line,
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335 \@regular_fill, "$i-$start-$stop"
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336 );
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337 $self->svg_add_track(
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338 \@x_values, \@rescale_y, \@rescale_line,
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339 \@rescale_fill, "$i-$start-$stop"
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340 );
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341
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342 # scale
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343 $self->make_scale( $i, $start, $stop );
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344 }
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345
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346 sub debug {
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347 my ( $self, $title, @arrs ) = @_;
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348 print "=" x 16 . "\n";
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349 foreach (@arrs) {
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350 my @arr = @{$_};
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351 printf "Array %s : %s\n", $title, scalar @arr;
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352 print "\t"
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353 . join( ',',
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354 map { sprintf( '%-10d', int($_) ) } @arr[ 0 .. 10 ] )
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355 . "\n";
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356 my $a = scalar(@arr) - 11;
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357 my $b = scalar(@arr) - 1;
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358 print "\t"
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359 . join( ',',
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360 map { sprintf( '%-10d', int($_) ) } @arr[ $a .. $b ] )
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361 . "\n";
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362 }
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363 }
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364
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365 sub svg_add_track {
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366 my (
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367 $self, $x_values_ref, $data_ref,
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368 $line_ref, $fill_ref, $base_track_id
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369 ) = @_;
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370 my @x_values = @{$x_values_ref};
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371 my @data = @{$data_ref};
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372 my @lines = @{$line_ref};
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373 my @fills = @{$fill_ref};
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374
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375 my $it = each_array( @data, @lines, @fills );
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376 while ( my ( $pry, $prl, $prf ) = $it->() ) {
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377 my $plot_data = $self->svg()->get_path(
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378 x => \@x_values,
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379 y => $pry,
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380 -type => 'polyline',
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381 -closed => 'false' #specify that the polyline is closed.
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382 );
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383 $self->plot_track( $plot_data, $prl, $prf, "$base_track_id" );
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384 }
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385 }
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386
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387 sub plot_data {
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388 my ( $self, %d ) = @_;
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389 $self->add_header( $d{regular}, $d{rescale} );
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390
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391 ##loop through rows
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392 foreach ( my $i = 0 ; $i < $self->num_rows() ; $i++ ) {
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393 my ( $start, $stop ) =
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394 ( $i * $self->row_size(), ( $i + 1 ) * $self->row_size() );
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395 $self->plot_individual_row( $start, $stop, $i, $d{regular},
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396 $d{rescale}, );
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397 }
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398 }
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399
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400 sub plot_data_subset {
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401 my ( $self, %d ) = @_;
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402
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403 $self->add_header( $d{regular}, $d{rescale} );
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404 ##loop through rows
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405 $self->plot_individual_row( $d{from}, $d{to}, 0, $d{regular},
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406 $d{rescale}, );
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407 }
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408
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409 sub push_all {
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410 my ( $self, $array_ref, @values ) = @_;
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411 foreach ( @{$array_ref} ) {
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412 push( @{$_}, @values );
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413 }
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414 }
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415
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416 no Moose;
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417 1;
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418
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419 __END__
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420
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421 =pod
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422
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423 =encoding UTF-8
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424
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425 =head1 NAME
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426
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427 CPT::Analysis::PAUSE::SVG - Library for use in PAUSE analysis
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428
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429 =head1 VERSION
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430
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431 version 1.96
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432
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433 =head1 AUTHOR
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parents:
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434
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parents:
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435 Eric Rasche <rasche.eric@yandex.ru>
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436
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437 =head1 COPYRIGHT AND LICENSE
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438
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439 This software is Copyright (c) 2014 by Eric Rasche.
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440
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441 This is free software, licensed under:
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442
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443 The GNU General Public License, Version 3, June 2007
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444
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445 =cut