Mercurial > repos > cpt > cpt_psm_comparison_table

annotate lib/CPT/Plot/Base.pm @ 1:f093e08f21f3 draft default tip

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:47:24 +0000
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1 package CPT::Plot::Base;
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2 use Data::Dumper;
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3 use CPT::Plot::Label;
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4 use CPT::Plot::Class;
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5 use CPT::Plot::Gene;
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6 use CPT::Plot::Colours;
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7 use Bio::SeqIO;
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8 use SVG;
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9 use Moose;
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10
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11 # ABSTRACT: Main plotting class for genome mapper
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12
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13 has 'svg' => ( is => 'rw', isa => 'Any' );
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14 has 'line_count' => ( is => 'rw', isa => 'Num', default => 1 );
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15 has '_ft_count' => ( is => 'rw', isa => 'Num', default => 0 );
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16 has 'classes' => ( is => 'rw', isa => 'HashRef' );
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17
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18 # Labels
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19 has 'label' => ( is => 'rw', isa => 'Bool' );
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20
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21 has 'label_pos' => ( is => 'rw', isa => 'Any' );
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22 has 'label_shrink_mode' => ( is => 'rw', isa => 'Any' );
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23 has 'label_callouts' => ( is => 'rw', isa => 'Any' );
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24 has 'label_from' => ( is => 'rw', isa => 'Any' );
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25 has 'label_text_source' => ( is => 'rw', isa => 'Any' );
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26 has 'label_numeric_features' => ( is => 'rw', isa => 'Any' );
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27 has 'label_query' => ( is => 'rw', isa => 'Any' );
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28 has 'label_numbering_count' => ( is => 'rw', isa => 'Any', default => 1 );
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29
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30 has 'justified' => ( is => 'rw', isa => 'Str' );
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31
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32 # CHanged to any b/c unpassed = undef
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33 has 'separate_strands' => ( is => 'rw', isa => 'Any' );
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34 has 'double_line_for_overlap' => ( is => 'rw', isa => 'Any' );
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35 has 'opacity' => ( is => 'rw', isa => 'Str' );
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36 has 'view' => ( is => 'rw', isa => 'Str' );
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37
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38 has 'color_scheme' => ( is => 'rw', isa => 'HashRef' );
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39 has 'wanted_tags' => ( is => 'rw', isa => 'HashRef' );
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40 has 'genome_length' => ( is => 'rw', isa => 'Int' );
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41 has 'features' => ( is => 'rw', isa => 'ArrayRef' );
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42 has 'start' => ( is => 'rw', isa => 'Int' );
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43 has 'end' => ( is => 'rw', isa => 'Int' );
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44
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45 has 'avgRowLength' => ( is => 'rw', isa => 'Int' );
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46 has 'calc_height' => ( is => 'rw', isa => 'Int' );
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47 has 'calc_width' => ( is => 'rw', isa => 'Int' );
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48 has 'x_offset' => ( is => 'rw', isa => 'Num' );
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49 has 'y_offset' => ( is => 'rw', isa => 'Num' );
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50 has 'ils' => ( is => 'rw', isa => 'Num' );
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51 has 'width_mode' => ( is => 'rw', isa => 'Str' );
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52 has 'width_value' => ( is => 'rw', isa => 'Num' );
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53 has 'rows' => ( is => 'rw', isa => 'Num' );
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54 has 'split_factor' => ( is => 'rw', isa => 'Num' );
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55
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56 has 'rowdata' => ( is => 'rw', isa => 'HashRef' );
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57 has '_internal_maxrowlength' => ( is => 'rw', isa => 'Num' );
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58
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59 my $color_spec = CPT::Plot::Colours->new( 'default' => '#000000' );
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60 our ( $parser, $tree, $cb );
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61
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62 sub init {
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63 my ($self) = @_;
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64 my %classes;
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65 my %cs = %{ $self->color_scheme() };
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66 foreach my $key ( keys %cs ) {
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67 $classes{$key} = CPT::Plot::Class->new(
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68 'key' => $key,
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69 'color' => $cs{$key}{color},
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70 'border' => $cs{$key}{border},
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71 'plot' => $cs{$key}{plot},
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72 'included' => 1,
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73 );
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74 }
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75 $self->classes( \%classes );
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76 $self->init_label_stuff();
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77 $self->filterFeatues();
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78 }
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79
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80 sub init_label_stuff {
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81 my ($self) = @_;
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82
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83 if ( $self->{'label_from'} eq 'custom' ) {
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84 use Parse::BooleanLogic;
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85 $parser = new Parse::BooleanLogic( operators => [ '', 'OR' ] );
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86 $tree = $parser->as_array( $self->label_query );
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87 print $parser;
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88
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89 #foreach bio feature,
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90 #if solve == 1, then add to our return,
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91 #else doesn't match
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92 #endforeach
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93 #my $new_tree = $parser->solve($tree,$filter);
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94 $cb = sub {
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95 my $query = $_[0]->{'operand'};
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96 my $feature = $_[1];
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97
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98 my $negate = 0;
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99 if ( substr( $query, 0, 1 ) eq '!' ) { #negate
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100 $negate = 1;
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101 $query = substr( $query, 1 );
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102 }
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103 if ( $query =~ m/([^:]+):["']{0,1}([^'"]*)["']{0,1}/ ) {
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104 my ( $k, $v ) = ( $1, $2 );
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105 my $result;
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106 if ( $k eq 'contains' ) {
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107 my $values = join(
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108 "\t",
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109 map {
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110 if ( $_ ne
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111 "translation" )
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112 {
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113 join(
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114 '',
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115 $feature
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116 ->get_tag_values
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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 }
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122 } $feature->get_all_tags()
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123 );
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124 if ( $values =~ m/$v/i ) {
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125 $result = 1;
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126 }
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127 else {
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128 $result = 0;
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129 }
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130 }
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131 elsif ( $k eq 'key' ) {
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132 if ( $v =~ m/,/ ) {
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133 $result = 0;
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134 foreach ( split( /,/, $v ) ) {
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135 if ( $feature
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136 ->primary_tag
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137 eq $_ )
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138 {
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139 $result = 1;
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140 }
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141 }
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142 }
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143 else {
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144 $result =
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145 $feature->primary_tag eq $v;
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146 }
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147 }
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148 elsif ( $k eq 'tag' ) {
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149 if ( $v =~ m/([^=]+)=(.*)/ ) {
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150 my ( $tag_name, $tag_match ) =
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151 ( $1, $2 );
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152 if ( $feature->has_tag($1) ) {
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153 if (
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154 join(
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155 '',
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156 $feature
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157 ->get_tag_values
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158 (
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159 $1
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160 )
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161 ) =~ /$2/i
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162 )
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163 {
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164 $result = 1;
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165 }
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166 else {
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167 $result = 0;
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168 }
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169 }
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170 else {
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171 $result = 0;
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172 }
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173 }
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174 else {
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175 $result = $feature->has_tag($v);
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176 }
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177 }
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178 else {
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179
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180 #error
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181 $result = 0;
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182 }
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183 return ( $negate xor $result );
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184 }
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185 else {
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186
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187 #error
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188 return 0;
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189 }
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190
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191 #error
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192 return 0;
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193 };
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194 }
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195 }
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196
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197 sub filterFeatues {
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198 my ($self) = @_;
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199
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200 #$self->{'wanted_tags'} = map { $_ => 1 } split(/,/,$self->{'q'});
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201 my %tags = map { $_ => 1 } split( /,/, "tRNA,CDS" );
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202 $self->wanted_tags( \%tags );
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203 my @feats = @{ $self->features() };
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204 for my $feat_object (@feats) {
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205 my $should_add = 1;
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206 if ( $feat_object->primary_tag eq 'source' ) {
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207 $should_add = 0;
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208 }
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209 if ( $feat_object->primary_tag eq 'gene' ) {
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210 $should_add = 0;
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211 }
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212 if ( defined $self->start()
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213 && $feat_object->start < $self->start() )
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214 {
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215 $should_add = 0;
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216 }
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217 if ( defined $self->end()
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218 && $feat_object->end > $self->end() )
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219 {
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220 $should_add = 0;
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221 }
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222 if ($should_add) {
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223 $self->addGene($feat_object);
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224 }
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225 }
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226 }
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227
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228 sub addGene {
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229 my ( $self, $feat_object ) = @_;
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230 my $tag = $feat_object->primary_tag;
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231 my $label = "";
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232 if ( $self->label() ) {
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233
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234 #If it meets the criteria specified for labelling an object, set the label, else don't set a label
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235 if ( $self->label_from() eq 'custom' ) {
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236 if ( $parser->solve( $tree, $cb, $feat_object ) ) {
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237 if (
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238 $feat_object->has_tag(
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239 $self->label_text_source()
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240 )
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241 )
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242 {
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243 $label = join(
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244 ' ',
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245 $feat_object->get_tag_values(
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246 $self
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247 ->label_text_source(
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248 )
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249 )
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250 );
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251 }
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252 else {
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253 $label = '[]';
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254 }
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255 }
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256
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257 #if($feat_object->has_tag($self->label_text_source())){
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258 #$label = ' '.join(' ', $feat_object->get_tag_values($self->label_text_source()));
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259 #}
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260 }
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261 elsif ( $self->label_from() eq 'numeric' ) {
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262 if ( ${ $self->wanted_tags() }{$tag} ) {
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263 $label = $self->label_numbering_count();
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264 $self->label_numbering_count(
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265 $self->label_numbering_count() + 1 );
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266 }
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267 }
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268 else {
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269 die $self->label_from();
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270 }
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271 }
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272 my @color_arr;
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273 my $color;
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274 if ( $feat_object->has_tag('color') ) {
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275 push( @color_arr, $feat_object->get_tag_values('color') );
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276 }
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277 if ( $feat_object->has_tag('color') ) {
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278 push( @color_arr, $feat_object->get_tag_values('color') );
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279 }
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280 if ( scalar @color_arr ) {
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281 $color = $color_arr[0];
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282 }
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283
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284 my $gene = CPT::Plot::Gene->new(
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285 'tag' => $tag,
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286 'label' => $label,
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287 'start' => $feat_object->start,
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288 'end' => $feat_object->end,
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289 'strand' => $feat_object->strand,
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290 'color' => $color,
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291 );
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292
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293 #This is a "failsafe" addition of classes, in case the user didn't specify a color
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294 if ( !defined ${ $self->classes() }{$tag} ) {
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295 ${ $self->classes() }{$tag} = CPT::Plot::Class->new(
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296 'key' => $tag,
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297 'color' => '#000000',
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298 'border' => 1,
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299 'plot' => 1,
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300 'included' => 1,
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301 );
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302 }
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303 else {
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304 ${ $self->classes() }{$tag}->addObject($gene);
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305 }
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306 }
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307
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308 sub partitionLines {
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309 my ($self) = @_;
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310
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311 # To use when I finally get partitioning.pm working
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312 #sub partitionLines{
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313 # my ($self) = @_;
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314 #
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315 # my $partioner = Partitioning->new(
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316 # genome_length => $self->genome_length(),
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317 # rows => $self->rows(),
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318 # justified => $self->justified(),
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319 # );
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320 #
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321 # # Add data to it
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322 # foreach(keys %classes){
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323 # if($classes{$_}->isIncludedInPartioning()){
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324 # $partioner->add($classes{$_}->getItemList());
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325 # }
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326 # }
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327 # # Run && get Results
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328 # my %result = %{$partioner->run()};
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329 # # . . .
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330 # print Dupmer %results;
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331 # # Profit
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332 # exit 1;
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333 # # This is supposed to merge two hashes. [http://perldoc.perl.org/perlfaq4.html#How-do-I-merge-two-hashes%3f]
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334 # @self{keys %result} = values %result;
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335
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336 my @items;
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337
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338 $self->avgRowLength(
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339 int(
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340 $self->genome_length() /
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341 $self->rows() *
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342 $self->split_factor()
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343 )
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344 )
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345 ; #TODO, allow adjusting or just re-calc? need to benchmark first I guess.
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346 $self->calc_height( int( ( 1 + $self->rows() ) * $self->ils() ) );
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347
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348 if ( $self->width_mode() eq 'dynamic' ) {
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349 $self->calc_width(
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350 int( $self->avgRowLength() / $self->width_value() ) );
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351 }
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352 else {
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353 $self->calc_width( $self->width_value() );
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354 }
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355
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356 my $fake_count = 100;
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357 if ($fake_count) {
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358 for ( my $i = 0 ; $i <= $fake_count ; $i++ ) {
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359 my $key =
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360 int( $self->genome_length() * $i / $fake_count );
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361 push( @items, [ $key, $key, 1 ] );
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362 }
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363 }
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364
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365 my %classes = %{ $self->classes() };
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366 foreach ( keys %classes ) {
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367 if ( $classes{$_}->included() ) {
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368 push( @items, @{ $classes{$_}->getItemList() } );
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369 }
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370 }
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371
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diff changeset
372 #Sort based on where each item starts
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373 @items = sort { ${$a}[0] <=> ${$b}[0] } @items;
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374
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375 #my $z = '(' . join('),(',map { "${$_}[0],${$_}[1]" } @items ) . ')';
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376 #print join("\n",split(/(.{1,120})/msxog, $z)) . "\n";
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377 my %rowdata;
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378
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379 my ( $longest_last_object, $thisRowEnd, $currentRow ) =
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380 ( 1, 1 + $self->avgRowLength(), 1 );
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381 $rowdata{1}{start} = 1;
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382 foreach my $item_ref (@items) {
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383 my ( $item_start, $item_end ) = @{$item_ref};
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384
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385 #print "\t$item_start\t$item_end\t$thisRowEnd\n";
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386 if ( $item_start >= $thisRowEnd || $item_end > $thisRowEnd ) {
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387
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388 # This was just cleaned up from the following commented out piece of code
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389 if ( $self->justified() eq 'justify'
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390 || $item_start >= $rowdata{$currentRow}{end} )
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391 {
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392 $rowdata{$currentRow}{end} = $thisRowEnd;
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393 }
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394 else {
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395 $rowdata{$currentRow}{end} =
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396 max( $longest_last_object, $item_start );
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397 }
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398
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399 # There was a corner case here:
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400 # O represents the end of a gene,
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401 # --- represents a gene
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402 # | represents $thisRowEnd
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403 #
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404 #
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405 # ------O | O---------
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406 # In this case, the second end would be chosen as
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407 # max($longest_last_object,$item_start), which is NOT what we
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408 # want. You want | to be chosen, not O, so in the case that
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409 # item_start is >= current row end (or should that be >?), we
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410 # use this.
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411 #
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412 # ------O |
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413 # O--+--------
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414 # This case works fine
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parents:
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415 #
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416 #
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417 # ------O |
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418 # O--------+--------
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419 # This case also works fine
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parents:
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420 #
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parents:
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421 #
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422 # if($self->justified()){
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423 # $rowdata{$currentRow}end() = $thisRowEnd;
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parents:
diff changeset
424 # }else{
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parents:
diff changeset
425 # if($item_start <= $rowdata{$currentRow}end()){
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parents:
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426 # $rowdata{$currentRow}end() = max($longest_last_object,$item_start);
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parents:
diff changeset
427 # }else{
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parents:
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428 # $rowdata{$currentRow}end() = $thisRowEnd;
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parents:
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429 # }
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430 # }
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parents:
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431 $self->_internal_maxrowlength(
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parents:
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432 max(
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parents:
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433 $self->_internal_maxrowlength(),
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parents:
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434 $rowdata{$currentRow}{end} -
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parents:
diff changeset
435 $rowdata{$currentRow}{start}
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parents:
diff changeset
436 )
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parents:
diff changeset
437 );
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parents:
diff changeset
438 $currentRow++;
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parents:
diff changeset
439
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parents:
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440 #print "$item_start $rowdata{$currentRow-1}{end}\n";
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parents:
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441 if ( $item_start <= $rowdata{ $currentRow - 1 }{end} ) {
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parents:
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442 $rowdata{$currentRow}{start} = $item_start;
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parents:
diff changeset
443 }
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parents:
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444 else { #nonjustified never encounters the following line
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parents:
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445 $rowdata{$currentRow}{start} =
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parents:
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446 $rowdata{ $currentRow - 1 }{end} + 1;
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parents:
diff changeset
447 }
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parents:
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448 $thisRowEnd =
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parents:
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449 $self->avgRowLength() + $rowdata{$currentRow}{start};
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parents:
diff changeset
450 }
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parents:
diff changeset
451 }
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cpt
parents:
diff changeset
452
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cpt
parents:
diff changeset
453 # if($self->justified()){
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cpt
parents:
diff changeset
454 # foreach my $item_ref(@items){
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cpt
parents:
diff changeset
455 # my ($item_start, $item_end) = @{$item_ref};
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cpt
parents:
diff changeset
456 # # If the item starts OR ends after this row is supposed to end
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cpt
parents:
diff changeset
457 # # print "\t$item_start\t$item_end\t$thisrowend\n";
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cpt
parents:
diff changeset
458 # if($item_start >= $thisRowEnd || $item_end > $thisRowEnd){
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cpt
parents:
diff changeset
459 # $rowdata{$currentRow}end() = $thisRowEnd;
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cpt
parents:
diff changeset
460 # #Internal max row length is the length of the longest row
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cpt
parents:
diff changeset
461 # $self->_internal_maxrowlength'} = max($self->{'_internal_maxrowlength'},$rowdata{$currentRow}{'end'}-$rowdata{$currentRow}{'start());
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cpt
parents:
diff changeset
462 # #Update which row we're on (so we aren't using +1s everywhere)
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cpt
parents:
diff changeset
463 # $currentRow++;
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cpt
parents:
diff changeset
464 # if($item_start <= $rowdata{$currentRow-1}end()){
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cpt
parents:
diff changeset
465 # $rowdata{$currentRow}start() = $item_start;
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cpt
parents:
diff changeset
466 # }else{
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
467 # $rowdata{$currentRow}start'} = $rowdata{$currentRow-1}{'end() + 1;
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cpt
parents:
diff changeset
468 # }
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parents:
diff changeset
469 # #tracks where the current row ends
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cpt
parents:
diff changeset
470 # #print Dumper $rowdata;
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cpt
parents:
diff changeset
471 # #print ">>$thisRowEnd\t".$self->avgRowLength'}." + ".$rowdata{$currentRow}{'start()."\n";
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cpt
parents:
diff changeset
472 # $thisRowEnd = $self->avgRowLength'} + $rowdata{$currentRow}{'start();
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cpt
parents:
diff changeset
473 # #print ">>$thisRowEnd\t".$self->avgRowLength'}." + ".$rowdata{$currentRow}{'start()."\n";
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parents:
diff changeset
474 # }
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parents:
diff changeset
475 # }
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parents:
diff changeset
476 # }else{#Non justified, raggedright
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cpt
parents:
diff changeset
477 # foreach my $item_ref(@items){
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cpt
parents:
diff changeset
478 # my ($item_start, $item_end) = @{$item_ref};
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cpt
parents:
diff changeset
479 # #print "\t$item_start\t$item_end\t$thisrowend\n";
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cpt
parents:
diff changeset
480 # if($item_start >= $thisRowEnd || $item_end > $thisRowEnd){
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cpt
parents:
diff changeset
481 ## print "\t> $item_start\t$item_end\t$thisRowEnd\n";
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
482 ## print "Candidate for ending [" . ($item_start >= $thisRowEnd) ."]\t[" .($item_end >= $thisRowEnd) . "]\n";
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cpt
parents:
diff changeset
483 ## # If we have ``justified'' rulers, they all need to the be the SAME length (until the last)
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
484 ## print " -- $rowdata{$currentRow}end()$thisRowEnd\n";
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cpt
parents:
diff changeset
485 # $rowdata{$currentRow}end() = max($longest_last_object,$item_start);
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
486 # #Internal max row length is the length of the longest row
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
487 # $self->_internal_maxrowlength'} = max($self->{'_internal_maxrowlength'},$rowdata{$currentRow}{'end'}-$rowdata{$currentRow}{'start());
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
488 # #Update which row we're on (so we aren't using +1s everywhere)
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
489 # $currentRow++;
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
490 # #if($item_start <= $rowdata{$currentRow-1}end()){
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
491 # $rowdata{$currentRow}start() = $item_start;
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
492 # #}
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
493 # #tracks where the current row ends
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
494 # $thisRowEnd = $self->avgRowLength'} + $rowdata{$currentRow}{'start();
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
495 # }
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cpt
parents:
diff changeset
496 # $longest_last_object = max($longest_last_object,$item_end);
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
497 # }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
498 # }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
499 #make sure the final row length is set, in addition to the _int_max_rowlength
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
500 $thisRowEnd = $rowdata{$currentRow}{end} =
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
501 $self->genome_length() + 1; #Putative
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cpt
parents:
diff changeset
502 $self->_internal_maxrowlength(
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
503 max(
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
504 $self->_internal_maxrowlength(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
505 $rowdata{$currentRow}{end} -
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
506 $rowdata{$currentRow}{start}
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
507 )
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
508 );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
509 $rowdata{max} = $currentRow;
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
510
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cpt
parents:
diff changeset
511 if ( defined $self->{start} && defined $self->{end} ) {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
512 %rowdata = (
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
513 '1' =>
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
514 { 'end' => $self->{end}, 'start' => $self->{start} },
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cpt
parents:
diff changeset
515 'max' => 1,
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
516 );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
diff changeset
517 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
518
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cpt
parents:
diff changeset
519 $self->rowdata( \%rowdata );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
520
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
521 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
522
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
523 sub getSVG {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
524 my ($self) = @_;
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
525 return $self->svg();
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
526 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
527
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
528 # SVG
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
529 sub createSVG {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
530 my ($self) = @_;
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
531 my %rowdata = %{ $self->rowdata() };
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
532 $self->calc_height( int( ( 1 + $rowdata{max} ) * $self->ils() ) );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
533 if ( $self->width_mode() eq 'dynamic' ) {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
534 $self->calc_width(
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
535 int( $self->avgRowLength() / $self->width_value() ) );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
536 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
537 else {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
538 $self->calc_width( $self->width_value() );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
539 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
540
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
541 $self->svg(
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
542 SVG->new(
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
543 width => $self->calc_width() + 2 * $self->x_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
544 height => $self->calc_height() + 2 * $self->y_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
545 )
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
546 );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
547
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
548 #$self->svg()->title( id => 'documenfeatures from t-title' )->cdata("Genome Map of [$file_name]");
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
549
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
550 my $ui_group = $self->svg()->tag(
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
551 'g',
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
552 id => 'group_ui',
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
553 style => {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
554 stroke => '#000000',
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
555 fill => '#000000',
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
556 'fill-opacity' => 1,
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
557 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
558 );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
559
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
560 foreach ( my $i = 1 ; $i <= $rowdata{max} ; $i++ ) {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
561 $self->_addRuler( $i, $ui_group );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
562 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
563
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
564 my %classes = %{ $self->classes() };
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
565 foreach my $class_key ( keys %classes ) {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
566
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
567 #print "Adding features from $class_key\n";
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
568 my $class = $classes{$class_key};
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
569 if ( !$class->plot() ) {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
570 next;
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
571 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
572 my $group = $self->svg()->tag(
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
573 'g',
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
574 id => 'group_' . $class->key(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
575 style => {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
576 stroke => (
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
577 $class->plot()
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
578 ? (
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
579 $class->border()
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
580 ? "black"
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
581 : "none"
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
582 )
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
583 : 'none'
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
584 ),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
585 fill => $class->color(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
586 'fill-opacity' => $self->opacity(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
587 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
588 );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
589 my @data = @{ $class->getObjects() };
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
590 foreach my $gene (@data) {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
591 my ( $start, $end ) =
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
592 ( $gene->start(), $gene->end() );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
593 my $row = calculateRow( $self, $start, $end );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
594 addFeature(
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
595 $self,
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
596 group => $group,
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
597 row => $row,
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
598 start => $start,
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
599 end => $end,
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
600 key => $gene->tag(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
601 strand => $gene->strand(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
602 label => $gene->label(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
603 ui_group => $ui_group,
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
604 color => $gene->color(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
605 );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
606
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
607 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
608 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
609
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
610 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
611
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
612 sub calculateRow {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
613 my ( $self, $start, $end ) = @_;
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
614 my %rowdata = %{ $self->rowdata() };
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
615 for ( my $i = 1 ; $i <= $rowdata{max} ; $i++ ) {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
616 if (
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
617 $start > $rowdata{$i}{start} - 1
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
618 && $start < $rowdata{$i}{end} + 1
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
619 && $end > $rowdata{$i}{start} - 1
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
620 && $end < $rowdata{$i}{end} + 1
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
621
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
622 )
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
623 {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
624 return $i;
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
625 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
626 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
627
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
628 #print "<b>$start,$end,".$self->rowdata'}{$i}{'start'}.",".$self->{'rowdata'}{$i}{'end()."<\/b>\n";
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
629 return 1.5;
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
630 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
631
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
632 sub _addRuler {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
633 my ( $self, $row, $ui_group ) = @_;
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
634 my $y_fix = $self->ils() * ( $row - 1 );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
635
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
636 # my @d = (
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
637 # $self->calc_width(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
638 # $self->rowdata'}{$row}{'end(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
639 # $self->rowdata'}{$row}{'start(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
640 # ($self->rowdata'}{$row}{'end'}-$self->{'rowdata'}{$row}{'start()),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
641 # $self->_internal_maxrowlength(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
642 # );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
643 # print join("\t",@d),"\n";
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
644 my %rowdata = %{ $self->rowdata() };
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
645 my $line_width =
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
646 $self->calc_width() *
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
647 ( $rowdata{$row}{end} - $rowdata{$row}{start} ) /
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
648 $self->_internal_maxrowlength();
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
649
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
650 #print "Adding ruler\t".$self->rowdata'}{$row}{'start'}."\t".$self->{'rowdata'}{$row}{'end'}."\t" . ($self->{'rowdata'}{$row}{'end'} - $self->{'rowdata'}{$row}{'start()) . "\n";
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
651
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
652 $ui_group->line(
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
653 id => 'ui_element_' . ( $self->line_count() + rand() ),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
654 x1 => 0 + $self->x_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
655 x2 => $line_width + $self->x_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
656 y1 => $y_fix + $self->y_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
657 y2 => $y_fix + $self->y_offset()
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
658 );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
659
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
660 # print "Ruler is being plotted from $y_fix to $line_width\n";
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
661 if ( $self->separate_strands() ) {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
662
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
663 #$ui_group->rectangle(
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
664 #id => 'ui_element_' . ( $self->line_count() + rand() ) . "_" . rand(1),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
665 #x => 0 + $self->x_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
666 #y => $y_fix - 2.5 + $self->y_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
667 #width => $line_width,
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
668 #height => 5
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
669 #);
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
670
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
671 #$y_fix += 100;
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
672 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
673
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
674 if ( $self->double_line_for_overlap() && $row > 1 )
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
675 { #This shows any duplicated part of the scale
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
676 if ( $rowdata{ $row - 1 }{end} - $rowdata{$row}{start} >= 0 )
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
677 { #Equal to zero indicates ONE base of overlap
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
678 $ui_group->line(
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
679 id => 'ui_element_'
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
680 . ( $self->line_count() + rand() ),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
681 y1 => $y_fix - 5 + $self->y_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
682 y2 => $y_fix - 5 + $self->y_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
683 x1 => 0 + $self->x_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
684 x2 => $self->calc_width() * (
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
685 $rowdata{ $row - 1 }{end} -
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
686 $rowdata{$row}{start}
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
687 ) / $self->_internal_maxrowlength() +
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
688 $self->x_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
689
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
690 #$calc_width*($rowdata{$row-1}end'}-$rowdata{$row}{'start'})/$self->{'_internal_maxrowlength'} + $self->{'x_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
691 );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
692 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
693 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
694 $ui_group->line(
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
695 id => 'ui_element_' . ( $self->line_count() + rand() ),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
696 x1 => 0 + $self->x_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
697 x2 => $line_width + $self->x_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
698 y1 => $y_fix + $self->y_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
699 y2 => $y_fix + $self->y_offset()
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
700 );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
701 foreach ( $rowdata{$row}{start} - 1 .. $rowdata{$row}{end} ) {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
702 if ( $_ % 1000 == 0 && $_ % 10000 != 0 ) {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
703 my $current_location =
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
704 $self->calc_width() *
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
705 ( $_ - $rowdata{$row}{start} ) /
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
706 $self->_internal_maxrowlength();
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
707 $ui_group->line(
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
708 id => 'ui_element_'
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
709 . ( $self->line_count() + rand() ),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
710 x1 => $current_location + $self->x_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
711 x2 => $current_location + $self->x_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
712 y1 => $y_fix + $self->y_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
713 y2 => $y_fix + 5 + $self->y_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
714 );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
715 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
716 if ( $_ % 10000 == 0 ) {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
717 my $current_location =
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
718 $self->calc_width() *
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
719 ( $_ - $rowdata{$row}{start} ) /
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
720 $self->_internal_maxrowlength();
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
721 $ui_group->line(
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
722 id => 'ui_element_'
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
723 . ( $self->line_count() + rand() ),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
724 x1 => $current_location + $self->x_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
725 x2 => $current_location + $self->x_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
726 y1 => $y_fix + $self->y_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
727 y2 => $y_fix + 10 + $self->y_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
728 );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
729 $ui_group->text(
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
730 id => 'ui_text'
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
731 . ( $self->line_count() + rand() ),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
732 x => $current_location + 10 + $self->x_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
733 y => $y_fix + 20 + $self->y_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
734 -cdata => ( $_ / 1000 ) . " kb",
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
735 'fill' => '#000000',
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
736 'fill-opacity' => 1,
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
737 'font-family' => 'mono',
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
738 'stroke' => 'none'
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
739 );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
740 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
741
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
742 if (
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
743 (
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
744 $_ == $rowdata{$row}{start} - 1
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
745 || $_ == $rowdata{$row}{end}
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
746 )
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
747 && ( $_ % 10000 != 0 )
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
748 )
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
749 {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
750 my $current_location =
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
751 $self->calc_width() *
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
752 ( $_ - $rowdata{$row}{start} ) /
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
753 $self->_internal_maxrowlength();
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
754 $ui_group->line(
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
755 id => 'ui_element_'
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
756 . ( $self->line_count() + rand() ),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
757 x1 => $current_location + $self->x_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
758 x2 => $current_location + $self->x_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
759 y1 => $y_fix + $self->y_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
760 y2 => $y_fix + 10 + $self->y_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
761 );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
762 $ui_group->text(
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
763 id => 'ui_text'
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
764 . ( $self->line_count() + rand() ),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
765 x => $current_location + $self->x_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
766 y => $y_fix + 20 + $self->y_offset(),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
767 -cdata => sprintf( '%d kb', ( $_ / 1000 ) ),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
768 'fill' => '#000000',
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
769 'fill-opacity' => 1,
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
770 'font-family' => 'mono',
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
771 'stroke' => 'none'
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
772 );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
773 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
774 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
775 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
776
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
777 sub addFeature {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
778 my ( $self, %data ) = @_;
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
779 my %rowdata = %{ $self->rowdata() };
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
780 my $x =
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
781 $self->calc_width() *
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
782 ( $data{'start'} - $rowdata{ $data{'row'} }{'start'} ) /
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
783 $self->_internal_maxrowlength() + $self->x_offset();
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
784 my $w =
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
785 $self->calc_width() *
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
786 ( $data{'end'} - $data{'start'} ) /
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
787 $self->_internal_maxrowlength();
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
788 my $h = 15;
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
789 my $y =
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
790 ( $data{'row'} - 1 ) * $self->ils() + $self->y_offset() - $h / 2;
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
791
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
792 my $id = "$x$y$w$h" . rand();
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
793
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
794 #print "Item(".$data{'start'}.",".$data{'end'}.",".$data{'row'}.") =\t($x,$y,$w,$h)\n";
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
795
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
796 if ( $self->separate_strands() ) {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
797 $y += -$data{'strand'} * 30;
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
798 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
799
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
800 if ( $self->view() eq 'alt_random' ) { # Max add = 20
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
801 $y += 4 * ( $x % 5 );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
802 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
803 elsif ( $self->view() eq 'alt_every' ) { # Max add = 10
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
804 # We (Sort of like a convolution?) multiply by strand This has
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
805 # the following effect; when on the top strand, we will only
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
806 # ever add a positive to the height of the item (moving it
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
807 # downward and closer to the ruler). On the bottom strand
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
808 # however, we only ever add a negative to the height of the
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
809 # item (moving it upwards towards the ruler). This allows the
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
810 # items on the top and bottom to stay balanced.
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
811 $y +=
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
812 $data{'strand'} * 10 *
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
813 ( ( $self->_ft_count( $self->_ft_count() + 1 ) ) % 2 ) -
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
814 10 * $data{'strand'};
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
815
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
816 # However, This is imperfect, since we add items based on class,
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
817 # not from left to right
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
818 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
819 elsif ( $self->view() eq 'alt_artemis' ) { # Max add = 20?
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
820 # Muwahahahaha. Sorry. Determined coefficient and constant by
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
821 # trial and error, but this matches up with the artemis view
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
822 # without an if/else based on which strand. :D
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
823 $y +=
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
824 10 * ( ( $data{'start'} - 2 * $data{'strand'} + 1 ) % 3 ) -
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
825 10 * $data{'strand'};
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
826 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
827
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
828 my $item_color = $color_spec->getColour( $data{'color'} );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
829 if ($item_color) {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
830 $data{'group'}->rectangle(
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
831 x => ($x),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
832 y => $y,
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
833 width => $w,
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
834 height => $h,
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
835 id => $id,
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
836 fill => $color_spec->getColour( $data{'color'} )
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
837 );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
838 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
839 else {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
840 $data{'group'}->rectangle(
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
841 x => ($x),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
842 y => $y,
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
843 width => $w,
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
844 height => $h,
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
845 id => $id,
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
846 );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
847 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
848 if ( $self->label() && $data{'label'} ) {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
849
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
850 my ( $lx, $ly );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
851 my @char_data = split( //, $data{label} );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
852
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
853 #Exit early if we don't even want to plot.
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
854 my $is_too_small = ( scalar(@char_data) * 2 > $w );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
855 if ( $self->label_shrink_mode() eq 'cutoff' && $is_too_small ) {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
856 return;
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
857 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
858
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
859 #Font Scaling
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
860 my $font_scaling = 100;
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
861 if ( $self->label_shrink_mode() eq 'shrink' ) {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
862 $font_scaling *= $w / ( 8 * scalar(@char_data) );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
863 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
864
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
865 # Horizontal positioning
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
866 $lx =
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
867 $x +
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
868 $w / 2
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
869 ; #Horizontally center it, but this is by the leading edge of the text
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
870 if ( scalar(@char_data) * 8 > $w
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
871 && $self->label_shrink_mode() eq 'shrink' )
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
872 {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
873 $lx -=
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
874 scalar(@char_data) * 4 *
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
875 $font_scaling / 100
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
876 ; #Adjustment for scaled text. Determined by experiment
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
877 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
878 else {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
879 $lx -=
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
880 scalar(@char_data) * 4
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
881 ; #Move four pixels left for every character in the label
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
882 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
883
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
884 # Vertical positioning
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
885 if ( $self->label_pos() eq "above" ) { #Label is ABOVE
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
886 if ( $self->separate_strands()
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
887 && $data{'strand'} == -1 )
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
888 {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
889 $ly =
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
890 $y +
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
891 $h / 2 + 10 + 30
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
892 ; #Need to consider below strand, only one strand.
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
893 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
894 else {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
895 $ly =
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
896 $y +
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
897 $h / 2 - 30
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
898 ; #Need to consider below strand, only one strand.
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
899 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
900 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
901 else { #Label is ON
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
902 $ly = $y + $h / 2 + 5;
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
903 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
904
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
905 if ( $data{'label'} !~ /^gene_[0-9]+$/ ){
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
906 $self->plot_label( $lx, $ly, $font_scaling, $data{'label'},
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
907 $data{'ui_group'} );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
908
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
909 if ( $self->label_callouts()
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
910 && $self->label_pos() eq "above" )
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
911 {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
912 $data{'ui_group'}->line(
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
913 id => 'l' . "_" . rand(1),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
914 x1 => $x + ( $w / 2 ),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
915 x2 => $x + ( $w / 2 ),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
916 y1 => (
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
917 $self->separate_strands()
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
918 && $data{'strand'} eq '-1' ? $y + $h
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
919 : $y
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
920 ),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
921 y2 => (
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
922 $self->separate_strands()
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
923 && $data{'strand'} eq '-1' ? $ly - 12
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
924 : $ly
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
925 )
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
926 );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
927 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
928 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
929
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
930 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
931 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
932
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
933 sub plot_label {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
934 my ( $self, $x, $y, $font_size, $label, $ui_group ) = @_;
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
935 if ( $font_size < 80 ) {
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
936 $font_size = 80;
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
937 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
938 $ui_group->text(
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
939 id => 'text' . rand(1),
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
940 x => $x,
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
941 y => $y,
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
942 -cdata => $label,
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
943 'fill' => '#000000',
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
944 'fill-opacity' => 1,
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
945 'font-family' => 'mono',
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
946 'font-size' => $font_size . '%',
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
947 'stroke' => 'none'
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
948 );
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
949 }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
950
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
951 sub max ($$) { $_[ $_[0] < $_[1] ] }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
952 sub min ($$) { $_[ $_[0] > $_[1] ] }
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
953
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
954 no Moose;
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
955 1;
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
956
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
957 __END__
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
958
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
959 =pod
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
960
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
961 =encoding UTF-8
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
962
f093e08f21f3 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
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963 =head1 NAME
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964
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965 CPT::Plot::Base - Main plotting class for genome mapper
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966
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967 =head1 VERSION
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968
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969 version 1.96
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970
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971 =head1 AUTHOR
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972
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973 Eric Rasche <rasche.eric@yandex.ru>
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974
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975 =head1 COPYRIGHT AND LICENSE
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976
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977 This software is Copyright (c) 2014 by Eric Rasche.
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978
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979 This is free software, licensed under:
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980
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981 The GNU General Public License, Version 3, June 2007
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982
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983 =cut