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1 package Bio::Graphics::Glyph::translation;
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2
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3 use strict;
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4 use Bio::Graphics::Glyph::generic;
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5 use Bio::Graphics::Util qw(frame_and_offset);
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6 use vars '@ISA';
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7 @ISA = qw(Bio::Graphics::Glyph::generic);
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8
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9 my %default_colors = qw(
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10 frame0f cadetblue
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11 frame1f blue
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12 frame2f darkblue
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13 frame0r darkred
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14 frame1r red
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15 frame2r crimson
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16 );
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17
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18 # turn off description
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19 sub description { 0 }
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20
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21 # turn off label
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22 # sub label { 1 }
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23
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24 sub default_color {
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25 my ($self,$key) = @_;
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26 return $self->factory->translate_color($default_colors{$key});
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27 }
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28
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29 sub height {
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30 my $self = shift;
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31 my $font = $self->font;
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32 my $lines = $self->translation_type eq '3frame' ? 3
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33 : $self->translation_type eq '6frame' ? 6
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34 : 1;
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35 return $self->protein_fits ? $lines*$font->height
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36 : $self->SUPER::height;
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37 }
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38
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39 sub pixels_per_base {
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40 my $self = shift;
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41 return $self->scale;
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42 }
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43
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44 sub pixels_per_residue {
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45 my $self = shift;
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46 return $self->scale * 3;
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47 }
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48
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49 sub gridcolor {
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50 my $self = shift;
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51 my $color = $self->option('gridcolor') || 'lightgrey';
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52 $self->factory->translate_color($color);
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53 }
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54
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55 sub protein_fits {
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56 my $self = shift;
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57
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58 my $pixels_per_base = $self->pixels_per_residue;
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59 my $font = $self->font;
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60 my $font_width = $font->width;
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61
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62 return $pixels_per_base >= $font_width;
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63 }
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64
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65 sub translation_type {
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66 my $self = shift;
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67 return $self->option('translation') || '1frame';
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68 }
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69
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70 sub arrow_height {
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71 my $self = shift;
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72 $self->option('arrow_height') || 1;
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73 }
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74
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75 sub show_stop_codons {
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76 my $self = shift;
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77 my $show = $self->option('stop_codons');
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78 return $show if defined $show;
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79 return 1;
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80 }
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81
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82 sub show_start_codons {
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83 my $self = shift;
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84 my $show = $self->option('start_codons');
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85 return $show if defined $show;
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86 return 0;
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87 }
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88
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89 sub strand {
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90 my $self = shift;
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91 return $self->option('strand') || '+1';
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92 }
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93
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94 sub draw_component {
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95 my $self = shift;
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96 my $gd = shift;
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97 my ($x1,$y1,$x2,$y2) = $self->bounds(@_);
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98
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99 my $type = $self->translation_type;
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100 my $strand = $self->strand;
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101
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102 my @strands = $type eq '6frame' ? (1,-1)
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103 : $strand > 0 ? (1)
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104 : -1;
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105 my @phase = (0,2,1); # looks weird, but gives correct effect
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106 for my $s (@strands) {
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107 for (my $i=0; $i < @phase; $i++) {
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108 $self->draw_frame($self->feature,$s,$i,$phase[$i],$gd,$x1,$y1,$x2,$y2);
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109 }
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110 }
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111
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112 }
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113
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114 sub draw_frame {
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115 my $self = shift;
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116 my ($feature,$strand,$base_offset,$phase,$gd,$x1,$y1,$x2,$y2) = @_;
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117 return unless $feature->seq; # no sequence, arggh.
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118 my ($seq,$pos) = $strand < 0 ? ($feature->revcom,$feature->end)
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119 : ($feature,$feature->start);
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120 my ($frame,$offset) = frame_and_offset($pos,$strand,$phase);
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121 ($strand >= 0 ? $x1 : $x2) += $self->pixels_per_base * $offset;
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122 my $lh;
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123 if ($self->translation_type eq '6frame') {
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124 $lh = $self->height / 6;
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125 $y1 += $lh * $frame;
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126 $y1 += $self->height/2 if $strand < 0;
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127 } else {
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128 $lh = $self->height / 3;
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129 $y1 += $lh * $frame;
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130 }
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131
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132 $y2 = $y1;
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133
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134 my $protein = $seq->translate(undef,undef,$base_offset)->seq;
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135 my $k = $strand>=0 ? 'f' : 'r';
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136 my $color = $self->color("frame$frame$k") ||
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137 $self->color("frame$frame") ||
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138 $self->default_color("frame$frame$k") || $self->fgcolor;
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139 if ($self->protein_fits) {
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140 $self->draw_protein(\$protein,$strand,$color,$gd,$x1,$y1,$x2,$y2);
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141 } else {
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142 $self->draw_orfs(\$protein,$strand,$color,$gd,$x1,$y1,$x2,$y2);
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143 }
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144 }
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145
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146 sub draw_protein {
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147 my $self = shift;
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148 my ($protein,$strand,$color,$gd,$x1,$y1,$x2,$y2) = @_;
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149 my $pixels_per_base = $self->pixels_per_base;
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150 my $font = $self->font;
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151
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152 my @residues = split '',$$protein;
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153 for (my $i=0;$i<@residues;$i++) {
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154 my $x = $strand > 0
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155 ? $x1 + 3 * $i * $pixels_per_base
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156 : $x2 - 3 * $i * $pixels_per_base;
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157 next if $x+1 < $x1;
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158 last if $x > $x2;
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159 $gd->char($font,$x,$y1,$residues[$i],$color);
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160 }
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161 }
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162
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163 sub draw_orfs {
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164 my $self = shift;
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165 my ($protein,$strand,$color,$gd,$x1,$y1,$x2,$y2) = @_;
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166 my $pixels_per_base = $self->pixels_per_base * 3;
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167 $y1++;
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168
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169 my $gcolor = $self->gridcolor;
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170 $gd->line($x1,$y1,$x2,$y1,$gcolor);
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171
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172 if ($self->show_stop_codons) {
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173 my $stops = $self->find_codons($protein,'*');
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174
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175 for my $stop (@$stops) {
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176 my $pos = $strand > 0
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177 ? $x1 + $stop * $pixels_per_base
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178 : $x2 - $stop * $pixels_per_base;
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179 next if $pos+1 < $x1;
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180 last if $pos > $x2;
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181 $gd->line($pos,$y1-2,$pos,$y1+2,$color);
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182 }
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183 }
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184
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185 my $arrowhead_height = $self->arrow_height;
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186
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187 if ($self->show_start_codons) {
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188 my $starts = $self->find_codons($protein,'M');
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189
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190 for my $start (@$starts) {
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191 my $pos = $strand > 0
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192 ? $x1 + $start * $pixels_per_base
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193 : $x2 - $start * $pixels_per_base;
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194 next if $pos+1 < $x1;
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195 last if $pos > $x2;
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196
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197 # little arrowheads at the start codons
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198 $strand > 0 ? $self->arrowhead($gd,$pos-$arrowhead_height,$y1,
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199 $arrowhead_height,+1)
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200 : $self->arrowhead($gd,$pos+$arrowhead_height,$y1,
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201 $arrowhead_height,-1)
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202 }
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203 }
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204
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205 $strand > 0 ? $self->arrowhead($gd,$x2-1,$y1,3,+1)
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206 : $self->arrowhead($gd,$x1,$y1,3,-1)
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207 }
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208
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209 sub find_codons {
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210 my $self = shift;
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211 my $protein = shift;
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212 my $codon = shift || '*';
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213 my $pos = -1;
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214 my @stops;
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215 while ( ($pos = index($$protein,$codon,$pos+1)) >= 0) {
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216 push @stops,$pos;
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217 }
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218 \@stops;
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219 }
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220
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221 sub make_key_feature {
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222 my $self = shift;
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223 my @gatc = qw(g a t c);
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224 my $offset = $self->panel->offset;
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225 my $scale = 1/$self->scale; # base pairs/pixel
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226 my $start = $offset;
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227 my $stop = $offset + 100 * $scale;
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228 my $seq = join('',map{$gatc[rand 4]} (1..500));
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229 my $feature =
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230 Bio::Graphics::Feature->new(-start=> $start,
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231 -end => $stop,
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232 -seq => $seq,
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233 -name => $self->option('key')
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234 );
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235 $feature;
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236 }
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237
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238 1;
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239
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240 __END__
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241
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242 =head1 NAME
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243
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244 Bio::Graphics::Glyph::translation - The "6-frame translation" glyph
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245
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246 =head1 SYNOPSIS
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247
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248 See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
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249
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250 =head1 DESCRIPTION
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251
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252 This glyph draws the conceptual translation of DNA sequences. At high
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253 magnifications, it simply draws lines indicating open reading frames.
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254 At low magnifications, it draws a conceptual protein translation.
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255 Options can be used to set 1-frame, 3-frame or 6-frame translations.
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256
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257 =head2 OPTIONS
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258
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259 The following options are standard among all Glyphs. See
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260 L<Bio::Graphics::Glyph> for a full explanation.
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261
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262 Option Description Default
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263 ------ ----------- -------
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264
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265 -fgcolor Foreground color black
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266
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267 -outlinecolor Synonym for -fgcolor
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268
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269 -bgcolor Background color turquoise
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270
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271 -fillcolor Synonym for -bgcolor
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272
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273 -linewidth Line width 1
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274
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275 -height Height of glyph 10
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276
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277 -font Glyph font gdSmallFont
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278
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279 -connector Connector type 0 (false)
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280
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281 -connector_color
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282 Connector color black
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283
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284 -label Whether to draw a label 0 (false)
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285
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286 -description Whether to draw a description 0 (false)
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287
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288 In addition to the common options, the following glyph-specific
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289 options are recognized:
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290
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291 Option Description Default
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292 ------ ----------- -------
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293
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294 -translation Type of translation to 1frame
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295 perform. One of "1frame",
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296 "3frame", or "6frame"
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297
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298 -strand Forward (+1) or reverse (-1) +1
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299 translation.
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300
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301 -frame0 Color for the first frame fgcolor
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302
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303 -frame1 Color for the second frame fgcolor
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304
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305 -frame2 Color for the third frame fgcolor
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306
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307 -gridcolor Color for the horizontal lightgrey
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308 lines of the reading frames
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309
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310 -start_codons Draw little arrowheads 0 (false)
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311 indicating start codons
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312
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313 -stop_codons Draw little vertical ticks 1 (true)
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314 indicating stop codons
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315
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316 -arrow_height Height of the start codon 1
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317 arrowheads
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318
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319 =head1 SUGGESTED STANZA FOR GENOME BROWSER
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320
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321 This produces a nice gbrowse display in which the DNA/GC Content glyph
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322 is sandwiched between the forward and reverse three-frame
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323 translations. The frames are color-coordinated with the example
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324 configuration for the "cds" glyph.
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325
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326 [TranslationF]
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327 glyph = translation
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328 global feature = 1
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329 frame0 = cadetblue
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330 frame1 = blue
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331 frame2 = darkblue
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332 height = 20
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333 fgcolor = purple
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334 strand = +1
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335 translation = 3frame
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336 key = 3-frame translation (forward)
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337
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338 [DNA/GC Content]
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339 glyph = dna
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340 global feature = 1
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341 height = 40
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342 do_gc = 1
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343 fgcolor = red
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344 axis_color = blue
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345
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346 [TranslationR]
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347 glyph = translation
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348 global feature = 1
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349 frame0 = darkred
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350 frame1 = red
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351 frame2 = crimson
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352 height = 20
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353 fgcolor = blue
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354 strand = -1
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355 translation = 3frame
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356 key = 3-frame translation (reverse)
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357
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358 =head1 BUGS
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359
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360 Please report them.
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361
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362 =head1 SEE ALSO
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363
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364
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365 L<Bio::Graphics::Panel>,
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366 L<Bio::Graphics::Glyph>,
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367 L<Bio::Graphics::Glyph::arrow>,
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368 L<Bio::Graphics::Glyph::cds>,
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369 L<Bio::Graphics::Glyph::crossbox>,
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370 L<Bio::Graphics::Glyph::diamond>,
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371 L<Bio::Graphics::Glyph::dna>,
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372 L<Bio::Graphics::Glyph::dot>,
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373 L<Bio::Graphics::Glyph::ellipse>,
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374 L<Bio::Graphics::Glyph::extending_arrow>,
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375 L<Bio::Graphics::Glyph::generic>,
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376 L<Bio::Graphics::Glyph::graded_segments>,
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377 L<Bio::Graphics::Glyph::heterogeneous_segments>,
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378 L<Bio::Graphics::Glyph::line>,
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379 L<Bio::Graphics::Glyph::pinsertion>,
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380 L<Bio::Graphics::Glyph::primers>,
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381 L<Bio::Graphics::Glyph::rndrect>,
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382 L<Bio::Graphics::Glyph::segments>,
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383 L<Bio::Graphics::Glyph::ruler_arrow>,
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384 L<Bio::Graphics::Glyph::toomany>,
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385 L<Bio::Graphics::Glyph::transcript>,
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386 L<Bio::Graphics::Glyph::transcript2>,
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387 L<Bio::Graphics::Glyph::translation>,
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388 L<Bio::Graphics::Glyph::triangle>,
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389 L<Bio::DB::GFF>,
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390 L<Bio::SeqI>,
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391 L<Bio::SeqFeatureI>,
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392 L<Bio::Das>,
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393 L<GD>
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394
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395 =head1 AUTHOR
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396
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397 Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
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398
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399 Copyright (c) 2001 Cold Spring Harbor Laboratory
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400
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401 This library is free software; you can redistribute it and/or modify
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402 it under the same terms as Perl itself. See DISCLAIMER.txt for
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403 disclaimers of warranty.
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404
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405 =cut
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