← Back to branch summary

~ubuntu-branches/ubuntu/saucy/bioperl/saucy-proposed

« back to all changes in this revision

Viewing changes to examples/biographics/all_glyphs.pl

  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2009-03-10 07:19:11 UTC
  • mfrom: (1.2.3 upstream)
  • Revision ID: james.westby@ubuntu.com-20090310071911-fukqzw54pyb1f0bd
Tags: 1.6.0-2
https://launchpad.net/bugs/324001
* Removed patch system (not used):
  - removed instuctions in debian/rules;
  - removed quilt from Build-Depends in debian/control.
* Re-enabled tests:
  - uncommented test command in debian/rules;
  - uncommented previously missing build-dependencies in debian/control.
  - Re-enabled tests and uncommented build-dependencies accordingly.
* Removed libmodule-build-perl and libtest-harness-perl from
  Build-Depends-Indep (provided by perl-modules).
* Better cleaning of empty directories using find -type d -empty -delete
  instead of rmdir in debian/rules (LP: #324001).

Show diffs side-by-side

added added

removed removed

Lines of Context:
examples/biographics/all_glyphs.pl
1
 
#!/usr/bin/perl -w
2
 
# Generate a simple display of all glyphs for comparison testing
3
 
# T. Harris (harris@cshl.org)
4
 
 
5
 
# Usage:
6
 
# ./all_glyphs GD > all.png
7
 
# ./all_glyphs GD 0 1000 > all.png       # output in png with a wide view
8
 
# ./all_glyphs GD::SVG 100 150 > all.svg # output in SVG, zoomed
9
 
 
10
 
use lib '.','../..','./blib/lib','../../blib/lib','../..';
11
 
use strict;
12
 
use Bio::Seq;
13
 
use Bio::Graphics::Panel;
14
 
use Bio::Graphics::Feature;
15
 
 
16
 
chomp (my $CLASS = shift);
17
 
$CLASS or die "\nUsage: lots_of_glyphs IMAGE_CLASS
18
 
\t- where IMAGE_CLASS is one of GD or GD::SVG
19
 
\t- GD generate png output; GD::SVG generates SVG.\n";
20
 
 
21
 
chomp (my $start = shift);
22
 
chomp (my $end   = shift);
23
 
 
24
 
$start ||= -100;
25
 
$end   ||= 1000;
26
 
 
27
 
my $ftr = 'Bio::Graphics::Feature';
28
 
my $segment = $ftr->new(-start=>$start,-end=>$end,-name=>'ZK154',-type=>'clone');
29
 
my $panel = Bio::Graphics::Panel->new(
30
 
                                      -grid => [50,100,150,200,250,300,310,320,330],
31
 
                                      -gridcolor => 'lightcyan',
32
 
                                      -grid => 1,
33
 
                                      -segment => $segment,
34
 
                                    #  -offset => 300,
35
 
                                    #  -length  => 1000,
36
 
                                      -spacing => 15,
37
 
                                      -width   => 600,
38
 
                                      -pad_top  => 20,
39
 
                                      -pad_bottom  => 20,
40
 
                                      -pad_left => 20,
41
 
                                      -pad_right=> 20,
42
 
                                    #  -bgcolor => 'teal',
43
 
                                    #  -key_style => 'between',
44
 
                                      -key_style => 'bottom',
45
 
                                      -image_class => $CLASS,
46
 
                                     );
47
 
 
48
 
my $zk154_1 = $ftr->new(-start=>-50,-end=>800,-name=>'ZK154.1',-type=>'gene',-source=>'predicted');
49
 
my $zk154_2 = $ftr->new(-start=>380,-end=>500,-name=>'ZK154.2',-type=>'gene',-source=>'predicted');
50
 
my $zk154_3 = $ftr->new(-start=>900,-end=>1200,-name=>'ZK154.3',-type=>'gene',-source=>'confirmed');
51
 
my $xyz4 = $ftr->new(-segments=>[[40,80],[100,120],[200,280],[300,320]],
52
 
                     -name   =>'xyz4',
53
 
                     -source =>'mysterious',
54
 
                     -subtype=>'predicted',
55
 
                     -type   =>'alignment');
56
 
 
57
 
# alignment
58
 
add_scores($xyz4);
59
 
$panel->add_track([$zk154_1,[$zk154_2,$xyz4]],
60
 
                  -glyph => 'alignment',
61
 
                  -label => 'alignment',
62
 
                  -key   => 'alignment',
63
 
                  -height => 10,
64
 
                  -font => 'gdSmallFont',
65
 
                  -bump => 1,
66
 
                  -bgcolor   => sub { shift->primary_tag eq 'predicted' ? 'green' : 'blue'},
67
 
                  -connector => sub { my $primary_tag = shift->primary_tag;
68
 
                                      $primary_tag eq 'transcript' ? 'hat'
69
 
                                    : $primary_tag eq 'alignment'  ? 'solid'
70
 
                                    : undef},
71
 
                  -connector_color => 'black',
72
 
                 );
73
 
 
74
 
# anchored_arrow
75
 
my $short_segment = $ftr->new(-start=>200,-end=>1000);
76
 
$panel->add_track($short_segment,
77
 
                  -glyph  => 'anchored_arrow',
78
 
                  -label  => 'anchored_arrow',
79
 
                  -key    => 'anchored_arrow',
80
 
                  -double => 1,
81
 
                  -bump   => 0,
82
 
                  -height => 10,
83
 
                  -linewidth =>1,
84
 
                  -arrowstyle=>'regular',
85
 
                  -tick      =>1,
86
 
                 );
87
 
 
88
 
# arrow
89
 
$panel->add_track($segment,
90
 
                  -glyph  => 'arrow',
91
 
                  -label  => 'arrow-minor ticks',
92
 
                  -key    => 'arrow',
93
 
                  -double => 1,
94
 
                  -fgcolor=> 'red',
95
 
                  -bump   => 0,
96
 
                  -height => 10,
97
 
                  -arrowstyle=>'regular',
98
 
                  -tick      =>1,
99
 
                  -linewidth =>1,
100
 
                 );
101
 
 
102
 
$panel->add_track($segment,
103
 
                  -glyph  => 'arrow',
104
 
                  -label  => 'arrow-major ticks',
105
 
                  -double => 1,
106
 
                  -bump   => 0,
107
 
                  -height => 10,
108
 
                  -linewidth =>1,
109
 
                  -arrowstyle=>'filled',
110
 
                  -tick=>2,
111
 
                 );
112
 
 
113
 
# box
114
 
my $box = $ftr->new(-start=>100,-end=>600,-name=>'JC8',-type=>'clone');
115
 
$panel->add_track($box,
116
 
                  -glyph  => 'box',
117
 
                  -label  => 'box',
118
 
                  -key => 'box',
119
 
                  -bump   => 0,
120
 
                  -height => 10,
121
 
                  -font   => 'gdLargeFont',
122
 
                  -linewidth =>1,
123
 
                  -bgcolor => 'turquoise',
124
 
                  -fgcolor => 'black',
125
 
                 );
126
 
 
127
 
 
128
 
# cds
129
 
my $cds = $ftr->new(-segments=>[[1,50],[100,150],[222,280],[380,400],[520,599],[801,900]],
130
 
                             -name=>'cds',
131
 
                             -type=>'gene',
132
 
                             -strand=>'+1',
133
 
                             -subtype=>'predicted',
134
 
                            );
135
 
 
136
 
my $cds2 = $ftr->new(-segments =>[[23,90],[157,201],[256,375],[439,502],[600,725]],
137
 
                     -name     =>'cds',
138
 
                     -strand   => '-1',
139
 
                     -subtype  =>'predicted',
140
 
                     -type     =>'gene');
141
 
 
142
 
$panel->add_track([$cds],
143
 
                  -glyph    => 'cds',
144
 
                  -label    => 'cds',
145
 
                  -key      => 'cds',
146
 
                  -bump     => 0,
147
 
                  -height   =>30,
148
 
                  -linewidth=>1,
149
 
                  -frame0f => 'blue',
150
 
                  -frame1f => 'green',
151
 
                  -frame2f => 'yellow',
152
 
                  -frame0r => 'red',
153
 
                  -frame1r => 'black',
154
 
                  -frame2r => 'purple',
155
 
                  #  -sixframe => 1,
156
 
                  -require_subparts=>1,
157
 
                 );
158
 
 
159
 
 
160
 
# crossbox
161
 
my $crossbox = $ftr->new(-start=>200,-end=>600);
162
 
$panel->add_track($crossbox,
163
 
                  -glyph  => 'crossbox',
164
 
                  -label  => 'crossbox',
165
 
                  -key    => 'crossbox',
166
 
                  -bump   => 0,
167
 
                  -height => 20,
168
 
                  # -font   => 'gdMediumBold',
169
 
                  -linewidth =>1,
170
 
                  -bgcolor => 'red',
171
 
                  -fgcolor => 'black',
172
 
                 );
173
 
 
174
 
# diamond
175
 
my $diamonds = $ftr->new(-segments=>[[10,11],[100,101],[201,202],[214,215],[237,238],
176
 
                                     [300,301],[350,351],[400,550],[601,602],[775,776]],
177
 
                         -name=>'SNPs');
178
 
$panel->add_track([$diamonds],
179
 
                  -glyph   => 'diamond',
180
 
                  -label   => 'diamond',
181
 
                  -key     => 'diamond',
182
 
                  -height  => 10,
183
 
                  -bgcolor => 'aqua',
184
 
                 );
185
 
 
186
 
 
187
 
 
188
 
# dna
189
 
my $string =
190
 
'tcgtcaaatgtctattgggtcgaaaagaaggtgaacgagtgctcggtgatgcgttcaaaactcaacacaaatcttcacatttcgctccactagtcgactttatcgattttgattatcatgctcaaatgaagatttccaaagaggcaattgtgcagttgaaaaagaaaatgagcccacatatgacaaagcatggatttttctattcaatgggaaaagaaatagtgaaacgacaaactggagtaattcgaacaaattgtctagattgtctggataggacgaatgccgtacaaacagccatcggacttcaaatgtcacatgatcaagttgcatttctgaatttaaacgcgggaaaagtgaatgtagagcaacgagttgaagagattcttcgtgatttgtggcagaaaaatggagatcagtgtagtacgatctacgcgggaactggagctcttgacggaaagagcaagttgaaagacgcgtcgagatcgcttgcaagaactattcagaataatttgatggatggtgcaaagcaggaatcatttgatttatttttgactggagccgcatatgatccgaggcttttcgatagagcatgtaatatattgccacctagtttgatacaagaatacgctgacgccgtatcgcagcttgtcgagcgaagtcccgaaatcgccgaacctcaatccattaaaatattcgttggaacttggaatgtgaatggaggaaagaatattcataatgtggcattccgtaatgaatcgagtctctcccactggatatttgccaattcaatgacacgtctcgtatctgtagaagatgagcaactagctgatattgtagcaattggagttgaagaacttgttgatttgaatgcaagtaatatggttaaagcaagtaccacaaatcaacgaatgtggtgtgaaagtattcgaaaaactctttctgaaaaagctccatttgtgctcattggctccgagcagctcgtcggtgtttgtctattcctcttcgcaagaccacgtgtctcaccatacctgaaagactttgcagtggcttctgtaaagactggaatgggtggagcaactggaaataagggatccgttgccttccgaatcgtcgtattctccacttctatttgttttatttgttctcactttgcagccgggcaaaacgagattcgagacagaaatgaggattttgcgacgacgttgaaaaagattcgattcccgttgggcagagaaattgactcgcatgacgtcatattttggttgggagatttcaactatcgaattaatttgtcgggggatgaagttaagaatgctgttagaaatggagactatgcgaaattagtcgaaaatgatcaattgacacagcagaaagctcttggacagacatttgttggcttcaacgaaggacagctcacgttcgcaccaacatacaaatacgacacattcagtgatgactatgatacgagtgaaaagtgtcgtgcacccgcatggactgatcgaattctttggaaagatcagagaaagaagggaaaaacgcaacttctcagctatgatagatcagaattaaaaacttctgatcatcgacctgttggagctgttttcaaagtggaaacttttaaagttggcggcagaaaatgtgtggagctcatcgaggatgttgtagaatctatgggtccaccggacggaacaatcattgtcagtattgccggaaaacctcgattcccgccgcaaatgtttccgccgattcatgagaagttgaaggaactcggtgctcaagttcagctgagcaaattcgacgatggcgatctatggattgtactgaatagtggagaaatggcattagccgcattaagtatggatgggctgaagatcggaggaacagatcagattaatgtgaagttgaagtcaccggattgggcttatgctttgaagccacatctttcagattttgatttggaatcgtttgaagtgacggcagaggaagaggcattacttggtggtactgatggtgccgtttttgaatttgcagacgaagacgaggacgcaatcagtgtgtctagtctgacgcttactggttcggctcccgatcgacctcgtccaccatcagcaagaagtgaagcgatcagtgtagccaaacttgaatggccaacagaacaaccaaacgtcctctccacatcaatgccaacacgagcttcatcagcttctcttgccaatagttcttggtatgagcatgtaccaccacttgctccacctcaatcaaacaataataaaagccctccacaagcttgtctattcaatccattcactcaatctgcaccatccccggctccaccaccatccacgattcctcttccaccgactcgtggagcatcagttggaccaggtcctccagcggttcccgtcaggaaggcacccccaccgccacctcggcctgtcattccacctagaccaaaaaatatgtag';
191
 
 
192
 
my $fragment = Bio::Seq->new(-seq=>$string);
193
 
my $dna = $ftr->new(-seq=>$fragment,
194
 
                    -start=>$start,-end=>$end);
195
 
$panel->add_track($dna,
196
 
                  -glyph    => 'dna',
197
 
                  -label    => 'dna',
198
 
                  -key      => 'dna',
199
 
                  -height   => 50,
200
 
                  -linewidth=> 1,
201
 
                  -axis_color=>'red',
202
 
                  -gc_bins  => 10,
203
 
                  -strand   => 'both',
204
 
                  );
205
 
 
206
 
 
207
 
# dot
208
 
my $dots = $ftr->new(-segments=>[[10,11],[100,150],[201,232],[214,215],[237,270],
209
 
                                     [280,281],[300,321],[400,550],[601,602],[775,776]]);
210
 
$panel->add_track([$dots],
211
 
                  -glyph   => 'dot',
212
 
                  -label   => 'dot',
213
 
                  -key     => 'dot',
214
 
                  -height  => 10,
215
 
                  -bgcolor => 'red',
216
 
                  -point   => 5,
217
 
                 );
218
 
 
219
 
# ellipse
220
 
my $ellipses = $ftr->new(-segments=>[[100,150],[201,232],[237,270],[300,321],[400,550],[730,776]]);
221
 
$panel->add_track([$ellipses],
222
 
                  -glyph   => 'ellipse',
223
 
                  -label   => 'ellipse',
224
 
                  -key     => 'ellipse',
225
 
                  -height  => 10,
226
 
                  -bgcolor => 'orange',
227
 
                 );
228
 
 
229
 
# ex
230
 
my $ex = $ftr->new(-start=>100,-end=>400);
231
 
$panel->add_track($ex,
232
 
                  -glyph  => 'ex',
233
 
                  -label  => 'ex',
234
 
                  -key    => 'ex',
235
 
                  -bump   => 0,
236
 
                  -height => 20,
237
 
                  # -font   => 'gdMediumBold',
238
 
                  -linewidth =>1,
239
 
                  -bgcolor => 'red',
240
 
                  -fgcolor => 'black',
241
 
                 );
242
 
 
243
 
# graded_segments                               
244
 
my $partial_gene = $ftr->new(-segments=>[[1,50],[100,150],[220,300],
245
 
                                         [380,400],[520,600],[800,900]],
246
 
                             -name   =>'partial_gene',
247
 
                             -strand => '+1',
248
 
                             -type   =>'exon',
249
 
                             -source =>'confirmed');
250
 
 
251
 
add_scores($partial_gene);
252
 
$panel->add_track($partial_gene,
253
 
                  -glyph     => 'graded_segments',
254
 
                  -key       => 'graded_segments',
255
 
                  -label     => 'graded_segments - quill connector',,
256
 
                  -bgcolor   => 'blue',
257
 
                  -connector => 'quill',
258
 
                 );
259
 
 
260
 
$panel->add_track($partial_gene,
261
 
                  -glyph     => 'graded_segments',
262
 
                  -label     => 'graded_segments - hat connector',
263
 
                  -key       => 'graded_segments',
264
 
                  -bgcolor   => 'green',
265
 
                  -connector => 'hat',
266
 
                 );
267
 
 
268
 
$panel->add_track($partial_gene,
269
 
                  -glyph     => 'graded_segments',
270
 
                  -label     => 'graded_segments - solid connector',
271
 
                  -key       => 'graded_segments',
272
 
                  -bgcolor   => 'yellow',
273
 
                  -connector => 'solid',
274
 
                 );
275
 
 
276
 
$panel->add_track($partial_gene,
277
 
                  -glyph     => 'graded_segments',
278
 
                  -label     => 'graded_segments - dashed connector',
279
 
                  -key       => 'graded_segments',
280
 
                  -bgcolor   => 'red',
281
 
                  -connector => 'dashed',
282
 
                 );
283
 
 
284
 
# heterogenous_segments
285
 
$panel->add_track([[$zk154_2,$zk154_3],[$zk154_2,$xyz4]],
286
 
                  -glyph => 'heterogeneous_segments',
287
 
                  -label => 'heterogeneous_segments',
288
 
                  -key   => 'heterogeneous_segments',
289
 
                  -height => 10,
290
 
                  -bump => 1,
291
 
                  -predicted_color=>'orange',
292
 
                  -confirmed_color=>'purple',
293
 
                  -mysterious_color=>'red',
294
 
                  -connector_color => 'black',
295
 
                 );
296
 
 
297
 
# line
298
 
$panel->add_track($short_segment,
299
 
                  -glyph  => 'line',
300
 
                  -label  => 'line',
301
 
                  -key    => 'line',
302
 
                  -bump   => 0,
303
 
                  -height => 20,
304
 
                  # -font   => 'gdMediumBold',
305
 
                  -linewidth =>1,
306
 
                  -bgcolor => 'green',
307
 
                  -fgcolor => 'black',
308
 
                 );
309
 
 
310
 
# pinsertion
311
 
my $pinsertion = $ftr->new(-segments=>[[10,10],[100,100],[200,200],[300,300],[400,400],
312
 
                                       [550,600],[650,650]]);
313
 
$panel->add_track([$pinsertion],
314
 
                  -glyph   => 'pinsertion',
315
 
                  -label   => 'pinsertion',
316
 
                  -key     => 'pinsertion',
317
 
                  -height  => 10,
318
 
                  -bgcolor => 'yellow',
319
 
                 );
320
 
 
321
 
# primers
322
 
my $p = $ftr->new(-start=>200,-end=>600);
323
 
$panel->add_track($p,
324
 
                  -glyph  => 'primers',
325
 
                  -label  => 'primers',
326
 
                  -key    => 'primers',
327
 
                  -height => 10,
328
 
                  -linewidth =>1,
329
 
                 );
330
 
 
331
 
# processed_transcript
332
 
my $trans1 = $ftr->new(-start=>50,-end=>10,-name=>'ZK154.1',-type=>"3'-UTR");
333
 
my $trans2 = $ftr->new(-start=>100,-end=>50,-name=>'ZK154.2',-type=>'CDS');
334
 
my $trans3 = $ftr->new(-start=>350,-end=>225,-name=>'ZK154.3',-type=>'CDS');
335
 
my $trans4 = $ftr->new(-start=>650,-end=>500,-name=>'ZK154.3',-type=>'CDS');
336
 
my $trans5 = $ftr->new(-start=>700,-end=>650,-name=>'ZK154.3',-type=>"5'-UTR");
337
 
my $trans  = $ftr->new(-segments=>[$trans1,$trans2,$trans3,$trans4,$trans5]);
338
 
$panel->add_track($trans,
339
 
                  -glyph     => 'processed_transcript',
340
 
                  -key       => 'processed_transcript',
341
 
                  -label     => 'processed_transcript',
342
 
                  -bgcolor   => 'aqua',
343
 
                  # -height    => 5,
344
 
                 );
345
 
 
346
 
$panel->add_track($trans,
347
 
                  -glyph    => 'processed_transcript',
348
 
                  -key      => 'processed_transcript',
349
 
                  -label    => 'processed_transcript',
350
 
                  -bgcolor  => 'green',
351
 
                  # -height   => 10,
352
 
                  -thin_utr => 1);
353
 
 
354
 
 
355
 
# redgreen_box
356
 
$panel->add_track($partial_gene,
357
 
                  -glyph     => 'redgreen_box',
358
 
                  -label     => 'redgreen_box',
359
 
                  -key       => 'redgreen_box',
360
 
                 );
361
 
 
362
 
# redgreen_segments
363
 
$panel->add_track($partial_gene,
364
 
                  -glyph     => 'redgreen_segment',
365
 
                  -label     => 'redgreen_segment',
366
 
                  -key       => 'redgreen_segment',
367
 
                 );
368
 
 
369
 
# rndrect
370
 
$panel->add_track($partial_gene,
371
 
                  -glyph     => 'rndrect',
372
 
                  -label     => 'rndrect',
373
 
                  -key       => 'rndrect',
374
 
                 );
375
 
 
376
 
# ruler_arrow
377
 
$panel->add_track($partial_gene,
378
 
                  -glyph => 'ruler_arrow',
379
 
                  -label => 1,
380
 
                  -key   => 'ruler_arrow',
381
 
                  -base  => 1,
382
 
                 );
383
 
 
384
 
$panel->add_track($partial_gene,
385
 
                  -glyph => 'ruler_arrow',
386
 
                  -label => 1,
387
 
                  -key   => 'ruler_arrow',
388
 
                  -base  => 1,
389
 
                  -parallel => 0,
390
 
                 );
391
 
 
392
 
# segments
393
 
$panel->add_track([$zk154_1,[$zk154_2,$xyz4]],
394
 
                  -glyph => 'segments',
395
 
                  -label => 'segments',
396
 
                  -key   => 'segments',
397
 
                  -height => 10,
398
 
                  -bump => 1,
399
 
                  -bgcolor   => sub { shift->primary_tag eq 'predicted' ? 'green' : 'blue'},
400
 
                  -connector => sub { my $primary_tag = shift->primary_tag;
401
 
                                      $primary_tag eq 'transcript' ? 'hat'
402
 
                                    : $primary_tag eq 'alignment'  ? 'solid'
403
 
                                    : undef},
404
 
                  -connector_color => 'black',
405
 
                 # -draw_dna => 1,
406
 
                 );
407
 
 
408
 
# span
409
 
my $big_span = $ftr->new(-start=>-400,-end=>3000);
410
 
my $small_span = $ftr->new(-start=>290,-end=>600);
411
 
$panel->add_track([$big_span,$small_span],
412
 
                  -glyph => 'span',
413
 
                  -label => 'span',
414
 
                  -key   => 'span',
415
 
                 );
416
 
 
417
 
# splice_site
418
 
$panel->add_track($partial_gene,
419
 
                  -glyph => 'splice_site',
420
 
                  -label => 'splice_site',
421
 
                  -key   => 'splice_site',
422
 
                  -direction => 'right',
423
 
                 );
424
 
 
425
 
# transcript
426
 
$panel->add_track($trans,
427
 
                  -glyph   => 'transcript',
428
 
                  -label   => 'transcript',
429
 
                  -key     => 'transcript',
430
 
                  -bgcolor =>'yellow',
431
 
                  -arrow_length=>10,
432
 
                 );
433
 
 
434
 
# transcript2
435
 
$panel->add_track($trans,
436
 
                  -glyph   => 'transcript2',
437
 
                  -label   => 'transcript2',
438
 
                  -key     => 'transcript2',
439
 
                  -bgcolor => 'purple',
440
 
                  -arrow_length=>10,
441
 
                 );
442
 
 
443
 
# translation
444
 
$panel->add_track($dna,
445
 
                  -glyph   => 'translation',
446
 
                  -label   => 'translation',
447
 
                  -key     => 'translation',
448
 
                  -translation => '3frame',
449
 
                  -frame0 => 'red',
450
 
                  -frame1 => 'blue',
451
 
                  -frame2 => 'green',
452
 
                  -arrow_length => 10,
453
 
                  -start_codons => 1,
454
 
                  -show_sequence=> 1,
455
 
                 );
456
 
 
457
 
 
458
 
# triangle
459
 
$panel->add_track([$pinsertion],
460
 
                  -glyph   => 'triangle',
461
 
                  -label   => 'triangle',
462
 
                  -key     => 'triangle',
463
 
                  -bgcolor => 'yellow',
464
 
                  -point   => 1,
465
 
                  -orient  => 'E',
466
 
                 );
467
 
 
468
 
 
469
 
# xyplot
470
 
$panel->add_track($partial_gene,
471
 
                  -glyph      => 'xyplot',
472
 
                  -key        => 'xyplot',
473
 
                  -label      => 'xyplot',
474
 
                  -graph_type => 'boxes');
475
 
 
476
 
 
477
 
my $gd   = $panel->gd;
478
 
my $type = ($CLASS eq 'GD') ? 'png' : 'svg';
479
 
print $gd->$type;
480
 
 
481
 
 
482
 
 
483
 
 
484
 
 
485
 
 
486
 
sub add_scores {
487
 
  my $ftr = shift;
488
 
  my $score = 10;
489
 
  my @segs = $ftr->segments;
490
 
  foreach (@segs) {
491
 
    $_->score($score);
492
 
    $score += 10;
493
 
  }
494
 
}
495
 
 
496