line |
stmt |
bran |
cond |
sub |
pod |
time |
code |
1
|
|
|
|
|
|
|
package Tree::Cladogram::Imager; |
2
|
|
|
|
|
|
|
|
3
|
1
|
|
|
1
|
|
142257
|
use parent 'Tree::Cladogram'; |
|
1
|
|
|
|
|
10
|
|
|
1
|
|
|
|
|
8
|
|
4
|
|
|
|
|
|
|
|
5
|
1
|
|
|
1
|
|
91
|
use Imager; |
|
1
|
|
|
|
|
3
|
|
|
1
|
|
|
|
|
11
|
|
6
|
1
|
|
|
1
|
|
763
|
use Imager::Fill; |
|
1
|
|
|
|
|
1362
|
|
|
1
|
|
|
|
|
41
|
|
7
|
|
|
|
|
|
|
|
8
|
1
|
|
|
1
|
|
10
|
use Moo; |
|
1
|
|
|
|
|
3
|
|
|
1
|
|
|
|
|
9
|
|
9
|
|
|
|
|
|
|
|
10
|
1
|
|
|
1
|
|
378
|
use Types::Standard qw/Any Int Str/; |
|
1
|
|
|
|
|
3
|
|
|
1
|
|
|
|
|
12
|
|
11
|
|
|
|
|
|
|
|
12
|
|
|
|
|
|
|
has leaf_font => |
13
|
|
|
|
|
|
|
( |
14
|
|
|
|
|
|
|
default => sub{return ''}, |
15
|
|
|
|
|
|
|
is => 'rw', |
16
|
|
|
|
|
|
|
isa => Any, |
17
|
|
|
|
|
|
|
required => 0, |
18
|
|
|
|
|
|
|
); |
19
|
|
|
|
|
|
|
|
20
|
|
|
|
|
|
|
has title_font => # Internal. |
21
|
|
|
|
|
|
|
( |
22
|
|
|
|
|
|
|
default => sub{return ''}, |
23
|
|
|
|
|
|
|
is => 'rw', |
24
|
|
|
|
|
|
|
isa => Any, |
25
|
|
|
|
|
|
|
required => 0, |
26
|
|
|
|
|
|
|
); |
27
|
|
|
|
|
|
|
|
28
|
|
|
|
|
|
|
our $VERSION = '1.04'; |
29
|
|
|
|
|
|
|
|
30
|
|
|
|
|
|
|
# ------------------------------------------------ |
31
|
|
|
|
|
|
|
|
32
|
|
|
|
|
|
|
sub BUILD |
33
|
|
|
|
|
|
|
{ |
34
|
0
|
|
|
0
|
0
|
|
my($self) = @_; |
35
|
|
|
|
|
|
|
|
36
|
0
|
|
0
|
|
|
|
$self -> leaf_font |
37
|
|
|
|
|
|
|
( |
38
|
|
|
|
|
|
|
Imager::Font -> new |
39
|
|
|
|
|
|
|
( |
40
|
|
|
|
|
|
|
color => Imager::Color -> new($self -> leaf_font_color), |
41
|
|
|
|
|
|
|
file => $self -> leaf_font_file, |
42
|
|
|
|
|
|
|
size => $self -> leaf_font_size, |
43
|
|
|
|
|
|
|
utf8 => 1 |
44
|
|
|
|
|
|
|
) || die "Error. Can't define leaf font: " . Imager -> errstr |
45
|
|
|
|
|
|
|
); |
46
|
0
|
|
0
|
|
|
|
$self -> title_font |
47
|
|
|
|
|
|
|
( |
48
|
|
|
|
|
|
|
Imager::Font -> new |
49
|
|
|
|
|
|
|
( |
50
|
|
|
|
|
|
|
color => Imager::Color -> new($self -> title_font_color), |
51
|
|
|
|
|
|
|
file => $self -> title_font_file, |
52
|
|
|
|
|
|
|
size => $self -> title_font_size, |
53
|
|
|
|
|
|
|
utf8 => 1 |
54
|
|
|
|
|
|
|
) || die "Error. Can't define title font: " . Imager -> errstr |
55
|
|
|
|
|
|
|
); |
56
|
|
|
|
|
|
|
|
57
|
|
|
|
|
|
|
} # End of BUILD. |
58
|
|
|
|
|
|
|
|
59
|
|
|
|
|
|
|
# ------------------------------------------------ |
60
|
|
|
|
|
|
|
|
61
|
|
|
|
|
|
|
sub _calculate_leaf_name_bounds |
62
|
|
|
|
|
|
|
{ |
63
|
0
|
|
|
0
|
|
|
my($self) = @_; |
64
|
0
|
|
|
|
|
|
my($leaf_font_size) = $self -> leaf_font_size; |
65
|
0
|
|
|
|
|
|
my($x_step) = $self -> x_step; |
66
|
|
|
|
|
|
|
|
67
|
0
|
|
|
|
|
|
my($attributes); |
68
|
|
|
|
|
|
|
my(@bounds); |
69
|
|
|
|
|
|
|
|
70
|
|
|
|
|
|
|
$self -> root -> walk_down |
71
|
|
|
|
|
|
|
({ |
72
|
|
|
|
|
|
|
callback => |
73
|
|
|
|
|
|
|
sub |
74
|
|
|
|
|
|
|
{ |
75
|
0
|
|
|
0
|
|
|
my($node) = @_; |
76
|
0
|
|
|
|
|
|
$attributes = $node -> attributes; |
77
|
|
|
|
|
|
|
@bounds = $self -> leaf_font -> align |
78
|
|
|
|
|
|
|
( |
79
|
|
|
|
|
|
|
halign => 'left', |
80
|
|
|
|
|
|
|
image => undef, |
81
|
|
|
|
|
|
|
string => $node -> name, |
82
|
|
|
|
|
|
|
valign => 'baseline', |
83
|
|
|
|
|
|
|
x => $$attributes{x} + $x_step + 4, |
84
|
0
|
|
|
|
|
|
y => $$attributes{y} + int($leaf_font_size / 2), |
85
|
|
|
|
|
|
|
); |
86
|
0
|
|
|
|
|
|
$$attributes{bounds} = [@bounds]; |
87
|
|
|
|
|
|
|
|
88
|
0
|
|
|
|
|
|
$node -> attributes($attributes); |
89
|
|
|
|
|
|
|
|
90
|
0
|
|
|
|
|
|
return 1; # Keep walking. |
91
|
|
|
|
|
|
|
}, |
92
|
0
|
|
|
|
|
|
_depth => 0, |
93
|
|
|
|
|
|
|
}); |
94
|
|
|
|
|
|
|
|
95
|
|
|
|
|
|
|
} # End of _calculate_leaf_name_bounds. |
96
|
|
|
|
|
|
|
|
97
|
|
|
|
|
|
|
# ------------------------------------------------ |
98
|
|
|
|
|
|
|
|
99
|
|
|
|
|
|
|
sub _calculate_title_metrics |
100
|
|
|
|
|
|
|
{ |
101
|
0
|
|
|
0
|
|
|
my($self, $image, $maximum_x, $maximum_y) = @_; |
102
|
0
|
|
|
|
|
|
my(@metrics) = $self -> title_font -> align |
103
|
|
|
|
|
|
|
( |
104
|
|
|
|
|
|
|
halign => 'left', |
105
|
|
|
|
|
|
|
image => undef, |
106
|
|
|
|
|
|
|
string => $self -> title, |
107
|
|
|
|
|
|
|
valign => 'baseline', |
108
|
|
|
|
|
|
|
x => 0, |
109
|
|
|
|
|
|
|
y => 0, |
110
|
|
|
|
|
|
|
); |
111
|
|
|
|
|
|
|
|
112
|
0
|
|
|
|
|
|
$self -> title_width($metrics[2] + 1); |
113
|
|
|
|
|
|
|
|
114
|
|
|
|
|
|
|
} # End of _calculate_title_metrics. |
115
|
|
|
|
|
|
|
|
116
|
|
|
|
|
|
|
# ------------------------------------------------ |
117
|
|
|
|
|
|
|
|
118
|
|
|
|
|
|
|
sub create_image |
119
|
|
|
|
|
|
|
{ |
120
|
0
|
|
|
0
|
0
|
|
my($self, $maximum_x, $maximum_y) = @_; |
121
|
0
|
|
|
|
|
|
my($image) = Imager -> new(xsize => $maximum_x, ysize => $maximum_y); |
122
|
0
|
|
|
|
|
|
my($frame_color) = Imager::Color -> new($self -> frame_color); |
123
|
0
|
|
|
|
|
|
my($white) = Imager::Color -> new(255, 255, 255); |
124
|
|
|
|
|
|
|
|
125
|
0
|
|
|
|
|
|
$image -> box(color => $white, filled => 1); |
126
|
0
|
0
|
|
|
|
|
$self -> _calculate_title_metrics($image, $maximum_x, $maximum_y) if (length($self -> title) ); |
127
|
0
|
0
|
|
|
|
|
$image -> box(color => $frame_color) if ($self -> draw_frame); |
128
|
|
|
|
|
|
|
|
129
|
0
|
|
|
|
|
|
return $image; |
130
|
|
|
|
|
|
|
|
131
|
|
|
|
|
|
|
} # End of create_image. |
132
|
|
|
|
|
|
|
|
133
|
|
|
|
|
|
|
# ------------------------------------------------ |
134
|
|
|
|
|
|
|
|
135
|
|
|
|
|
|
|
sub draw_horizontal_branch |
136
|
|
|
|
|
|
|
{ |
137
|
0
|
|
|
0
|
0
|
|
my($self, $image, $middle_attributes, $daughter_attributes, $final_offset) = @_; |
138
|
0
|
|
|
|
|
|
my($branch_color) = $self -> branch_color; |
139
|
0
|
|
|
|
|
|
my($branch_width) = $self -> branch_width - 1; |
140
|
0
|
|
|
|
|
|
my($x_step) = $self -> x_step; |
141
|
|
|
|
|
|
|
|
142
|
|
|
|
|
|
|
$image -> box |
143
|
|
|
|
|
|
|
( |
144
|
|
|
|
|
|
|
box => |
145
|
|
|
|
|
|
|
[ |
146
|
|
|
|
|
|
|
$$middle_attributes{x}, |
147
|
|
|
|
|
|
|
$$daughter_attributes{y}, |
148
|
|
|
|
|
|
|
$$daughter_attributes{x} + $x_step + $final_offset, |
149
|
0
|
|
|
|
|
|
$$daughter_attributes{y} + $branch_width, |
150
|
|
|
|
|
|
|
], |
151
|
|
|
|
|
|
|
color => $branch_color, |
152
|
|
|
|
|
|
|
filled => 1, |
153
|
|
|
|
|
|
|
); |
154
|
|
|
|
|
|
|
|
155
|
|
|
|
|
|
|
} # End of draw_horizontal_branch. |
156
|
|
|
|
|
|
|
|
157
|
|
|
|
|
|
|
# ------------------------------------------------ |
158
|
|
|
|
|
|
|
|
159
|
|
|
|
|
|
|
sub draw_leaf_name |
160
|
|
|
|
|
|
|
{ |
161
|
0
|
|
|
0
|
0
|
|
my($self, $image, $name, $daughter_attributes, $final_offset) = @_; |
162
|
|
|
|
|
|
|
|
163
|
0
|
0
|
0
|
|
|
|
if ( (length($name) > 0) && ($name !~ /^\d+$/) ) |
164
|
|
|
|
|
|
|
{ |
165
|
0
|
|
|
|
|
|
my($bounds) = $$daughter_attributes{bounds}; |
166
|
0
|
|
|
|
|
|
$$bounds[0] += $final_offset; |
167
|
0
|
|
|
|
|
|
$$bounds[2] += $final_offset; |
168
|
|
|
|
|
|
|
|
169
|
0
|
|
|
|
|
|
$image -> string |
170
|
|
|
|
|
|
|
( |
171
|
|
|
|
|
|
|
align => 0, |
172
|
|
|
|
|
|
|
font => $self -> leaf_font, |
173
|
|
|
|
|
|
|
string => $name, |
174
|
|
|
|
|
|
|
x => $$bounds[0], |
175
|
|
|
|
|
|
|
y => $$bounds[1], |
176
|
|
|
|
|
|
|
); |
177
|
|
|
|
|
|
|
|
178
|
0
|
0
|
|
|
|
|
if ($self -> debug) |
179
|
|
|
|
|
|
|
{ |
180
|
0
|
|
|
|
|
|
my($fuchsia) = Imager::Color -> new(0xff, 0, 0xff); |
181
|
|
|
|
|
|
|
|
182
|
0
|
|
|
|
|
|
$image -> box |
183
|
|
|
|
|
|
|
( |
184
|
|
|
|
|
|
|
box => $bounds, |
185
|
|
|
|
|
|
|
color => $fuchsia, |
186
|
|
|
|
|
|
|
filled => 0, |
187
|
|
|
|
|
|
|
); |
188
|
|
|
|
|
|
|
} |
189
|
|
|
|
|
|
|
} |
190
|
|
|
|
|
|
|
|
191
|
|
|
|
|
|
|
} # End of draw_leaf_name. |
192
|
|
|
|
|
|
|
|
193
|
|
|
|
|
|
|
# ------------------------------------------------ |
194
|
|
|
|
|
|
|
|
195
|
|
|
|
|
|
|
sub draw_root_branch |
196
|
|
|
|
|
|
|
{ |
197
|
0
|
|
|
0
|
0
|
|
my($self, $image) = @_; |
198
|
0
|
|
|
|
|
|
my($branch_color) = $self -> branch_color; |
199
|
0
|
|
|
|
|
|
my($branch_width) = $self -> branch_width - 1; |
200
|
0
|
|
|
|
|
|
my($attributes) = $self -> root -> attributes; |
201
|
0
|
|
|
|
|
|
my(@daughters) = $self -> root -> daughters; |
202
|
0
|
|
|
|
|
|
my($daughter_attributes) = $daughters[0] -> attributes; |
203
|
|
|
|
|
|
|
|
204
|
|
|
|
|
|
|
$image -> box |
205
|
|
|
|
|
|
|
( |
206
|
|
|
|
|
|
|
box => |
207
|
|
|
|
|
|
|
[ |
208
|
|
|
|
|
|
|
$$daughter_attributes{x}, |
209
|
|
|
|
|
|
|
$$daughter_attributes{y}, |
210
|
|
|
|
|
|
|
$self -> left_margin, |
211
|
0
|
|
|
|
|
|
$$attributes{y} + $branch_width, |
212
|
|
|
|
|
|
|
], |
213
|
|
|
|
|
|
|
color => $branch_color, |
214
|
|
|
|
|
|
|
filled => 1, |
215
|
|
|
|
|
|
|
); |
216
|
|
|
|
|
|
|
|
217
|
|
|
|
|
|
|
} # End of draw_root_branch. |
218
|
|
|
|
|
|
|
|
219
|
|
|
|
|
|
|
# ------------------------------------------------ |
220
|
|
|
|
|
|
|
|
221
|
|
|
|
|
|
|
sub draw_title |
222
|
|
|
|
|
|
|
{ |
223
|
0
|
|
|
0
|
0
|
|
my($self, $image, $maximum_x, $maximum_y) = @_; |
224
|
0
|
|
|
|
|
|
my($title) = $self -> title; |
225
|
|
|
|
|
|
|
|
226
|
0
|
0
|
|
|
|
|
if (length($title) > 0) |
227
|
|
|
|
|
|
|
{ |
228
|
0
|
|
|
|
|
|
$image -> string |
229
|
|
|
|
|
|
|
( |
230
|
|
|
|
|
|
|
align => 0, |
231
|
|
|
|
|
|
|
font => $self -> title_font, |
232
|
|
|
|
|
|
|
string => $title, |
233
|
|
|
|
|
|
|
x => int( ($maximum_x - $self -> title_width) / 2), |
234
|
|
|
|
|
|
|
y => $maximum_y - $self -> top_margin, |
235
|
|
|
|
|
|
|
); |
236
|
|
|
|
|
|
|
} |
237
|
|
|
|
|
|
|
|
238
|
|
|
|
|
|
|
} # End of draw_title. |
239
|
|
|
|
|
|
|
|
240
|
|
|
|
|
|
|
# ------------------------------------------------ |
241
|
|
|
|
|
|
|
|
242
|
|
|
|
|
|
|
sub draw_vertical_branch |
243
|
|
|
|
|
|
|
{ |
244
|
0
|
|
|
0
|
0
|
|
my($self, $image, $middle_attributes, $daughter_attributes) = @_; |
245
|
0
|
|
|
|
|
|
my($branch_color) = $self -> branch_color; |
246
|
0
|
|
|
|
|
|
my($branch_width) = $self -> branch_width - 1; |
247
|
|
|
|
|
|
|
|
248
|
|
|
|
|
|
|
$image -> box |
249
|
|
|
|
|
|
|
( |
250
|
|
|
|
|
|
|
box => |
251
|
|
|
|
|
|
|
[ |
252
|
|
|
|
|
|
|
$$middle_attributes{x}, |
253
|
|
|
|
|
|
|
$$middle_attributes{y}, |
254
|
|
|
|
|
|
|
$$middle_attributes{x} + $branch_width, |
255
|
|
|
|
|
|
|
$$daughter_attributes{y}, |
256
|
0
|
|
|
|
|
|
], |
257
|
|
|
|
|
|
|
color => $branch_color, |
258
|
|
|
|
|
|
|
filled => 1, |
259
|
|
|
|
|
|
|
); |
260
|
|
|
|
|
|
|
|
261
|
|
|
|
|
|
|
} # End of draw_vertical_branch. |
262
|
|
|
|
|
|
|
|
263
|
|
|
|
|
|
|
# ------------------------------------------------ |
264
|
|
|
|
|
|
|
|
265
|
|
|
|
|
|
|
sub write |
266
|
|
|
|
|
|
|
{ |
267
|
0
|
|
|
0
|
0
|
|
my($self, $image, $file_name) = @_; |
268
|
|
|
|
|
|
|
|
269
|
0
|
|
|
|
|
|
$image -> write(file => $file_name); |
270
|
0
|
|
|
|
|
|
$self -> log('Wrote ' . $file_name); |
271
|
|
|
|
|
|
|
|
272
|
|
|
|
|
|
|
} # End of write. |
273
|
|
|
|
|
|
|
|
274
|
|
|
|
|
|
|
# ------------------------------------------------ |
275
|
|
|
|
|
|
|
|
276
|
|
|
|
|
|
|
1; |
277
|
|
|
|
|
|
|
|
278
|
|
|
|
|
|
|
=pod |
279
|
|
|
|
|
|
|
|
280
|
|
|
|
|
|
|
=head1 NAME |
281
|
|
|
|
|
|
|
|
282
|
|
|
|
|
|
|
C - Render a cladogram using Imager or Image::Magick |
283
|
|
|
|
|
|
|
|
284
|
|
|
|
|
|
|
=head1 Synopsis |
285
|
|
|
|
|
|
|
|
286
|
|
|
|
|
|
|
See L. |
287
|
|
|
|
|
|
|
|
288
|
|
|
|
|
|
|
=head1 Description |
289
|
|
|
|
|
|
|
|
290
|
|
|
|
|
|
|
See L. |
291
|
|
|
|
|
|
|
|
292
|
|
|
|
|
|
|
=head1 Distributions |
293
|
|
|
|
|
|
|
|
294
|
|
|
|
|
|
|
See L. |
295
|
|
|
|
|
|
|
|
296
|
|
|
|
|
|
|
=head1 Constructor and Initialization |
297
|
|
|
|
|
|
|
|
298
|
|
|
|
|
|
|
See L. |
299
|
|
|
|
|
|
|
|
300
|
|
|
|
|
|
|
=head1 Methods |
301
|
|
|
|
|
|
|
|
302
|
|
|
|
|
|
|
See L. |
303
|
|
|
|
|
|
|
|
304
|
|
|
|
|
|
|
=head1 FAQ |
305
|
|
|
|
|
|
|
|
306
|
|
|
|
|
|
|
See L. |
307
|
|
|
|
|
|
|
|
308
|
|
|
|
|
|
|
=head1 See Also |
309
|
|
|
|
|
|
|
|
310
|
|
|
|
|
|
|
See L. |
311
|
|
|
|
|
|
|
|
312
|
|
|
|
|
|
|
=head1 Machine-Readable Change Log |
313
|
|
|
|
|
|
|
|
314
|
|
|
|
|
|
|
The file Changes was converted into Changelog.ini by L. |
315
|
|
|
|
|
|
|
|
316
|
|
|
|
|
|
|
=head1 Version Numbers |
317
|
|
|
|
|
|
|
|
318
|
|
|
|
|
|
|
Version numbers < 1.00 represent development versions. From 1.00 up, they are production versions. |
319
|
|
|
|
|
|
|
|
320
|
|
|
|
|
|
|
=head1 Repository |
321
|
|
|
|
|
|
|
|
322
|
|
|
|
|
|
|
L |
323
|
|
|
|
|
|
|
|
324
|
|
|
|
|
|
|
=head1 Support |
325
|
|
|
|
|
|
|
|
326
|
|
|
|
|
|
|
Bugs should be reported via the CPAN bug tracker at |
327
|
|
|
|
|
|
|
|
328
|
|
|
|
|
|
|
L |
329
|
|
|
|
|
|
|
|
330
|
|
|
|
|
|
|
=head1 Author |
331
|
|
|
|
|
|
|
|
332
|
|
|
|
|
|
|
L was written by Ron Savage Iron@savage.net.auE> in 2015. |
333
|
|
|
|
|
|
|
|
334
|
|
|
|
|
|
|
My homepage: L |
335
|
|
|
|
|
|
|
|
336
|
|
|
|
|
|
|
=head1 Copyright |
337
|
|
|
|
|
|
|
|
338
|
|
|
|
|
|
|
Australian copyright (c) 2015, Ron Savage. |
339
|
|
|
|
|
|
|
|
340
|
|
|
|
|
|
|
All Programs of mine are 'OSI Certified Open Source Software'; |
341
|
|
|
|
|
|
|
you can redistribute them and/or modify them under the terms of |
342
|
|
|
|
|
|
|
The Artistic License 2.0, a copy of which is available at: |
343
|
|
|
|
|
|
|
http://opensource.org/licenses/alphabetical. |
344
|
|
|
|
|
|
|
|
345
|
|
|
|
|
|
|
=cut |