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1 package Bio::Graphics::Glyph::dna;
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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 vars '@ISA';
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6 @ISA = qw(Bio::Graphics::Glyph::generic);
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7
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8 my %complement = (g=>'c',a=>'t',t=>'a',c=>'g',n=>'n',
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9 G=>'C',A=>'T',T=>'A',C=>'G',N=>'N');
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10
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11 # turn off description
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12 sub description { 0 }
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13
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14 # turn off label
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15 # sub label { 1 }
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16
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17 sub height {
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18 my $self = shift;
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19 my $font = $self->font;
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20 return $self->dna_fits ? 2*$font->height
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21 : $self->do_gc ? $self->SUPER::height
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22 : 0;
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23 }
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24
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25 sub do_gc {
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26 my $self = shift;
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27 my $do_gc = $self->option('do_gc');
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28 return if defined($do_gc) && !$do_gc;
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29 return 1;
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30 }
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31
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32 sub draw_component {
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33 my $self = shift;
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34 my $gd = shift;
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35 my ($x1,$y1,$x2,$y2) = $self->bounds(@_);
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36
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37 my $dna = eval { $self->feature->seq };
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38 $dna = $dna->seq if ref($dna) and $dna->can('seq'); # to catch Bio::PrimarySeqI objects
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39 $dna or return;
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40
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41 # workaround for my misreading of interface -- LS
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42 $dna = $dna->seq if ref($dna) && $dna->can('seq');
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43
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44 if ($self->dna_fits) {
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45 $self->draw_dna($gd,$dna,$x1,$y1,$x2,$y2);
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46 } elsif ($self->do_gc) {
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47 $self->draw_gc_content($gd,$dna,$x1,$y1,$x2,$y2);
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48 }
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49 }
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50
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51 sub draw_dna {
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52 my $self = shift;
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53
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54 my ($gd,$dna,$x1,$y1,$x2,$y2) = @_;
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55 my $pixels_per_base = $self->scale;
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56
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57 my $feature = $self->feature;
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58
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59 my $strand = $feature->strand;
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60 $strand *= -1 if $self->{flip};
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61
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62 my @bases = split '',$strand >= 0 ? $dna : $self->reversec($dna);
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63 my $color = $self->fgcolor;
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64 my $font = $self->font;
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65 my $lineheight = $font->height;
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66 $y1 -= $lineheight/2 - 3;
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67 my $strands = $self->option('strand') || 'auto';
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68
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69 my ($forward,$reverse);
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70 if ($strands eq 'auto') {
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71 $forward = $feature->strand >= 0;
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72 $reverse = $feature->strand <= 0;
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73 } elsif ($strands eq 'both') {
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74 $forward = $reverse = 1;
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75 } elsif ($strands eq 'reverse') {
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76 $reverse = 1;
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77 } else {
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78 $forward = 1;
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79 }
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80
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81 my $start = $self->map_no_trunc($feature->start);
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82 my $end = $self->map_no_trunc($feature->end);
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83
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84 my $offset = int(($x1-$start-1)/$pixels_per_base);
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85
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86 for (my $i=$offset;$i<@bases;$i++) {
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87 my $x = $start + $i * $pixels_per_base;
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88 next if $x+1 < $x1;
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89 last if $x > $x2;
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90 $gd->char($font,$x+1,$y1,$bases[$i],$color) if $forward;
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91 $gd->char($font,$x+1,$y1+($forward ? $lineheight:0),$complement{$bases[$i]}||$bases[$i],$color) if $reverse;
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92 }
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93
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94 }
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95
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96 sub draw_gc_content {
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97 my $self = shift;
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98 my $gd = shift;
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99 my $dna = shift;
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100 my ($x1,$y1,$x2,$y2) = @_;
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101
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102 my $bin_size = length($dna) / ($self->option('gc_bins') || 100);
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103 $bin_size = 100 if $bin_size < 100;
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104
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105 my @bins;
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106 for (my $i = 0; $i < length($dna) - $bin_size; $i+= $bin_size) {
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107 my $subseq = substr($dna,$i,$bin_size);
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108 my $gc = $subseq =~ tr/gcGC/gcGC/;
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109 my $content = $gc/$bin_size;
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110 push @bins,$content;
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111 }
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112 push @bins,0.5 unless @bins; # avoid div by zero
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113 my $bin_width = ($x2-$x1)/@bins;
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114 my $bin_height = $y2-$y1;
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115 my $fgcolor = $self->fgcolor;
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116 my $bgcolor = $self->factory->translate_color($self->panel->gridcolor);
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117 my $axiscolor = $self->color('axis_color') || $fgcolor;
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118
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119 $gd->line($x1, $y1, $x1, $y2, $axiscolor);
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120 $gd->line($x2-2,$y1, $x2-2,$y2, $axiscolor);
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121 $gd->line($x1, $y1, $x1+3,$y1, $axiscolor);
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122 $gd->line($x1, $y2, $x1+3,$y2, $axiscolor);
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123 $gd->line($x1, ($y2+$y1)/2,$x1+3,($y2+$y1)/2,$axiscolor);
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124 $gd->line($x2-4,$y1, $x2-1, $y1, $axiscolor);
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125 $gd->line($x2-4,$y2, $x2-1, $y2, $axiscolor);
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126 $gd->line($x2-4,($y2+$y1)/2,$x2-1,($y2+$y1)/2,$axiscolor);
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127 $gd->line($x1+5,$y2, $x2-5,$y2, $bgcolor);
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128 $gd->line($x1+5,($y2+$y1)/2,$x2-5,($y2+$y1)/2,$bgcolor);
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129 $gd->line($x1+5,$y1, $x2-5,$y1, $bgcolor);
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130 $gd->string($self->font,$x1+5,$y1,'% gc',$axiscolor) if $bin_height > $self->font->height*2;
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131
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132 for (my $i = 0; $i < @bins; $i++) {
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133 my $bin_start = $x1+$i*$bin_width;
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134 my $bin_stop = $bin_start + $bin_width;
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135 my $y = $y2 - ($bin_height*$bins[$i]);
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136 $gd->line($bin_start,$y,$bin_stop,$y,$fgcolor);
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137 $gd->line($bin_stop,$y,$bin_stop,$y2 - ($bin_height*$bins[$i+1]),$fgcolor)
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138 if $i < @bins-1;
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139 }
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140 }
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141
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142 sub make_key_feature {
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143 my $self = shift;
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144 my @gatc = qw(g a t c);
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145 my $offset = $self->panel->offset;
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146 my $scale = 1/$self->scale; # base pairs/pixel
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147
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148 my $start = $offset+1;
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149 my $stop = $offset+100*$scale;
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150 my $feature =
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151 Bio::Graphics::Feature->new(-start=> $start,
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152 -stop => $stop,
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153 -seq => join('',map{$gatc[rand 4]} (1..500)),
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154 -name => $self->option('key'),
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155 -strand => '+1',
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156 );
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157 $feature;
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158 }
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159
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160 1;
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161
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162 __END__
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163
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164 =head1 NAME
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165
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166 Bio::Graphics::Glyph::dna - The "dna" glyph
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167
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168 =head1 SYNOPSIS
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169
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170 See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
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171
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172 =head1 DESCRIPTION
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173
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174 This glyph draws DNA sequences. At high magnifications, this glyph
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175 will draw the actual base pairs of the sequence (both strands). At
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176 low magnifications, the glyph will plot the GC content.
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177
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178 For this glyph to work, the feature must return a DNA sequence string
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179 in response to the dna() method.
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180
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181 =head2 OPTIONS
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182
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183 The following options are standard among all Glyphs. See
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184 L<Bio::Graphics::Glyph> for a full explanation.
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185
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186 Option Description Default
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187 ------ ----------- -------
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188
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189 -fgcolor Foreground color black
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190
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191 -outlinecolor Synonym for -fgcolor
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192
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193 -bgcolor Background color turquoise
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194
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195 -fillcolor Synonym for -bgcolor
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196
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197 -linewidth Line width 1
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198
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199 -height Height of glyph 10
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200
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201 -font Glyph font gdSmallFont
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202
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203 -connector Connector type 0 (false)
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204
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205 -connector_color
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206 Connector color black
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207
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208 -label Whether to draw a label 0 (false)
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209
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210 -description Whether to draw a description 0 (false)
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211
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212 In addition to the common options, the following glyph-specific
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213 options are recognized:
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214
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215 Option Description Default
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216 ------ ----------- -------
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217
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218 -do_gc Whether to draw the GC true
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219 graph at low mags
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220
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221 -gc_bins Fixed number of intervals 100
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222 to sample across the
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223 panel.
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224
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225 -axis_color Color of the vertical axes fgcolor
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226 in the GC content graph
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227
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228 -strand Show both forward and auto
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229 reverse strand, one of
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230 "forward", "reverse",
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231 "both" or "auto".
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232 In "auto" mode,
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233 +1 strand features will
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234 show the plus strand
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235 -1 strand features will
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236 show the reverse complement
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237 and strandless features will
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238 show both
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239
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240 =head1 BUGS
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241
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242 Please report them.
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243
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244 =head1 SEE ALSO
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245
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246 L<Bio::Graphics::Panel>,
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247 L<Bio::Graphics::Glyph>,
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248 L<Bio::Graphics::Glyph::arrow>,
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249 L<Bio::Graphics::Glyph::cds>,
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250 L<Bio::Graphics::Glyph::crossbox>,
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251 L<Bio::Graphics::Glyph::diamond>,
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252 L<Bio::Graphics::Glyph::dna>,
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253 L<Bio::Graphics::Glyph::dot>,
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254 L<Bio::Graphics::Glyph::ellipse>,
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255 L<Bio::Graphics::Glyph::extending_arrow>,
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256 L<Bio::Graphics::Glyph::generic>,
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257 L<Bio::Graphics::Glyph::graded_segments>,
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258 L<Bio::Graphics::Glyph::heterogeneous_segments>,
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259 L<Bio::Graphics::Glyph::line>,
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260 L<Bio::Graphics::Glyph::pinsertion>,
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261 L<Bio::Graphics::Glyph::primers>,
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262 L<Bio::Graphics::Glyph::rndrect>,
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263 L<Bio::Graphics::Glyph::segments>,
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264 L<Bio::Graphics::Glyph::ruler_arrow>,
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265 L<Bio::Graphics::Glyph::toomany>,
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266 L<Bio::Graphics::Glyph::transcript>,
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267 L<Bio::Graphics::Glyph::transcript2>,
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268 L<Bio::Graphics::Glyph::translation>,
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269 L<Bio::Graphics::Glyph::triangle>,
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270 L<Bio::DB::GFF>,
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271 L<Bio::SeqI>,
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272 L<Bio::SeqFeatureI>,
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273 L<Bio::Das>,
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274 L<GD>
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275
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276 =head1 AUTHOR
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277
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278 Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
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279
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280 Copyright (c) 2001 Cold Spring Harbor Laboratory
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281
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282 This library is free software; you can redistribute it and/or modify
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283 it under the same terms as Perl itself. See DISCLAIMER.txt for
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284 disclaimers of warranty.
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285
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286 =cut
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