2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2010 Christian M. Zmasek
6 // Copyright (C) 2008-2010 Burnham Institute for Medical Research
7 // Copyright (C) 2003-2010 Ethalinda K.S. Cannon
10 // This library is free software; you can redistribute it and/or
11 // modify it under the terms of the GNU Lesser General Public
12 // License as published by the Free Software Foundation; either
13 // version 2.1 of the License, or (at your option) any later version.
15 // This library is distributed in the hope that it will be useful,
16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
18 // Lesser General Public License for more details.
20 // You should have received a copy of the GNU Lesser General Public
21 // License along with this library; if not, write to the Free Software
22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 // Contact: phylosoft @ gmail . com
25 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
27 package org.forester.archaeopteryx;
29 import java.awt.Color;
32 import org.forester.util.ForesterUtil;
34 public final class TreeColorSet {
36 public static final String ANNOTATION = "Annotation";
37 public static final String BACKGROUND = "Background";
38 public static final String BACKGROUND_GRADIENT_BOTTOM = "Background Gradient Bottom";
39 public static final String BINARY_DOMAIN_COMBINATIONS = "Binary Domain Combinations";
40 public static final String BRANCH = "Branch";
41 public static final String BRANCH_LENGTH = "Branch Length";
42 public static final String COLLAPSED = "Collapsed";
43 public static final String CONFIDENCE = "Confidence";
44 public static final String DOMAIN_LABEL = "Domain Label";
45 public static final String DOMAIN_BASE = "Domain Base";
46 public static final String DUPLICATION = "Duplication";
47 public static final String DUPLICATION_OR_SPECATION = "Duplication or Specation";
48 public static final String MATCHING_NODES_A = "Matching A";
49 public static final String MATCHING_NODES_A_AND_B = "Matching A and B";
50 public static final String MATCHING_NODES_B = "Matching B";
51 public static final String NODE_BOX = "Node Box";
52 public static final String OVERVIEW = "Overview";
53 public static final String SEQUENCE = "Sequence";
54 public static final String SPECIATION = "Speciation";
55 public static final String TAXONOMY = "Taxonomy";
56 static final String[] COLOR_FIELDS = { BACKGROUND, BACKGROUND_GRADIENT_BOTTOM, SEQUENCE,
57 TAXONOMY, CONFIDENCE, BRANCH_LENGTH, BRANCH, NODE_BOX, COLLAPSED, MATCHING_NODES_A, MATCHING_NODES_B,
58 MATCHING_NODES_A_AND_B, DUPLICATION, SPECIATION, DUPLICATION_OR_SPECATION, DOMAIN_LABEL, DOMAIN_BASE,
59 BINARY_DOMAIN_COMBINATIONS, ANNOTATION, OVERVIEW };
60 static final String[] SCHEME_NAMES = { "Default", "Black", "Black & White", "Silver", "Green",
61 "White & Blue", "Cyan", "Orange", "Blue", "Blue & White", "Neon" };
62 private int _color_scheme;
63 private final Color[][] _color_schemes = { { new Color( 0, 0, 0 ), // background_color
64 new Color( 0, 100, 100 ), // background_color_gradient_bottom
65 new Color( 230, 230, 230 ), // sequence __ Default (same as Black)
66 new Color( 180, 180, 180 ), // taxonomy
67 new Color( 180, 180, 180 ), // support
68 new Color( 140, 140, 140 ), // branch_length_color
69 new Color( 255, 255, 255 ), // branch_color
70 new Color( 255, 255, 255 ), // box_color
71 new Color( 255, 255, 255 ), // collapesed_fill_color
72 new Color( 0, 255, 0 ), // found_color 0
73 new Color( 255, 0, 0 ), // found_color 1
74 new Color( 255, 255, 0 ), // found_color 1 + 2
75 new Color( 255, 0, 0 ), // duplication_box_color
76 new Color( 0, 255, 0 ), // speciation_box_color
77 new Color( 255, 255, 0 ), // duplication_speciation_color
78 new Color( 230, 230, 230 ), // domain_label
79 new Color( 100, 100, 100 ), // domains_base
80 new Color( 65, 105, 255 ), // binary_domain_combinations_color
81 new Color( 173, 255, 47 ) // annotation
82 , new Color( 130, 130, 130 ) // overview
83 }, { new Color( 0, 0, 0 ), // background_color
84 new Color( 0, 255, 255 ), // background_color_gradient_bottom
85 new Color( 230, 230, 230 ), // sequence __ Black
86 new Color( 180, 180, 180 ), // taxonomy
87 new Color( 180, 180, 180 ), // support
88 new Color( 140, 140, 140 ), // branch_length_color
89 new Color( 255, 255, 255 ), // branch_color
90 new Color( 255, 255, 255 ), // box_color
91 new Color( 255, 255, 255 ), // collapesed_fill_color
92 new Color( 0, 255, 0 ), // found_color 0
93 new Color( 255, 0, 0 ), // found_color 1
94 new Color( 255, 255, 0 ), // found_color 1 + 2
95 new Color( 255, 0, 0 ), // duplication_box_color
96 new Color( 0, 255, 0 ), // speciation_box_color
97 new Color( 255, 255, 0 ), // duplication_speciation_color
98 new Color( 230, 230, 230 ), // domain_label
99 new Color( 100, 100, 100 ), // domains_base
100 new Color( 65, 105, 255 ), // binary_domain_combinations_color
101 new Color( 173, 255, 47 ) // annotation
102 , new Color( 130, 130, 130 ) // ov
103 }, { new Color( 255, 255, 255 ), // background_color
104 new Color( 0, 255, 255 ), // background_color_gradient_bottom
105 new Color( 0, 0, 0 ), // sequence __ Black & White
106 new Color( 0, 0, 0 ), // taxonomy
107 new Color( 0, 0, 0 ), // support
108 new Color( 0, 0, 0 ), // branch_length_color
109 new Color( 0, 0, 0 ), // branch_color
110 new Color( 0, 0, 0 ), // box_color
111 new Color( 0, 0, 0 ), // collapesed_fill_color
112 new Color( 255, 0, 0 ), // found_color 0
113 new Color( 0, 255, 0 ), // found_color 1
114 new Color( 0, 0, 255 ), // found_color 1 + 2
115 new Color( 255, 0, 0 ), // duplication_box_color
116 new Color( 0, 255, 0 ), // speciation_box_color
117 new Color( 255, 255, 0 ), // duplication_speciation_color
118 new Color( 0, 0, 0 ), // domain_label
119 new Color( 100, 100, 100 ), // domains_base
120 new Color( 0, 0, 0 ), // binary_domain_combinations_color
121 new Color( 0, 0, 0 ) // annotation
122 , new Color( 220, 220, 220 ) // ov
123 }, { new Color( 0, 0, 0 ), // background_color
124 new Color( 0, 255, 255 ), // background_color_gradient_bottom
125 new Color( 220, 220, 220 ), // sequence __ Silver
126 new Color( 180, 180, 180 ), // taxonomy
127 new Color( 140, 140, 140 ), // support
128 new Color( 140, 140, 140 ), // branch_length_color
129 new Color( 240, 240, 240 ), // branch_color
130 new Color( 140, 140, 140 ), // box_color
131 new Color( 240, 240, 240 ), // collapesed_fill_color
132 new Color( 255, 0, 0 ), // found_color 0
133 new Color( 0, 255, 0 ), // found_color 1
134 new Color( 255, 255, 0 ), // found_color 1 + 2
135 new Color( 255, 0, 0 ), // duplication_box_color
136 new Color( 0, 255, 0 ), // speciation_box_color
137 new Color( 255, 255, 0 ), // duplication_speciation_color
138 new Color( 230, 230, 230 ), // domain_label
139 new Color( 100, 100, 100 ), // domains_base
140 new Color( 180, 180, 180 ), // binary_domain_combinations_color
141 new Color( 140, 140, 140 ) // annotation
142 , new Color( 40, 40, 40 ) // ov
143 }, { new Color( 0, 10, 0 ), // background_color
144 new Color( 0, 255, 255 ), // background_color_gradient_bottom
145 new Color( 0, 255, 0 ), // sequence __ the Matrix
146 new Color( 30, 200, 30 ), // taxonomy
147 new Color( 0, 155, 0 ), // support
148 new Color( 0, 100, 0 ), // branch_length_color
149 new Color( 0, 155, 0 ), // branch_color
150 new Color( 0, 255, 0 ), // box_color
151 new Color( 0, 155, 0 ), // collapesed_fill_color
152 new Color( 255, 0, 0 ), // found_color 0
153 new Color( 0, 255, 0 ), // found_color 1
154 new Color( 255, 255, 0 ), // found_color 1 + 2
155 new Color( 255, 0, 0 ), // duplication_box_color
156 new Color( 0, 255, 0 ), // speciation_box_color
157 new Color( 255, 255, 0 ), // duplication_speciation_color
158 new Color( 230, 230, 230 ), // domain_label
159 new Color( 100, 100, 100 ), // domains_base
160 new Color( 0, 235, 0 ), // binary_domain_combinations_color
161 new Color( 0, 235, 0 ) // annotation
162 , new Color( 40, 40, 40 ) // ov
163 }, { new Color( 255, 255, 255 ), // background_color
164 new Color( 0, 255, 255 ), // background_color_gradient_bottom
165 new Color( 0, 0, 0 ), //sequence __ White & Blue
166 new Color( 40, 40, 40 ), // taxonomy
167 new Color( 0, 125, 0 ), // support
168 new Color( 70, 70, 0 ), // branch_length_color
169 new Color( 0, 20, 200 ), // branch_color
170 new Color( 0, 20, 200 ), // box_color
171 new Color( 0, 20, 200 ), // collapesed_fill_color
172 new Color( 0, 255, 0 ), // found_color 0
173 new Color( 255, 0, 0 ), // found_color 1
174 new Color( 0, 0, 255 ), // found_color 0 + 1
175 new Color( 255, 0, 0 ), // duplication_box_color
176 new Color( 0, 255, 0 ), // speciation_box_color
177 new Color( 255, 255, 0 ), // duplication_speciation_color
178 new Color( 0, 0, 0 ), // domain_label
179 new Color( 50, 50, 50 ), // domains_base
180 new Color( 65, 105, 225 ), // binary_domain_combinations_color
181 new Color( 173, 255, 47 ) // annotation
182 , new Color( 220, 220, 220 ) // ov
183 }, { new Color( 0, 0, 0 ), // background_color
184 new Color( 0, 255, 255 ), // background_color_gradient_bottom
185 new Color( 255, 255, 255 ), // sequence __ Cyan
186 new Color( 200, 200, 200 ), // taxonomy
187 new Color( 255, 255, 255 ), // support
188 new Color( 200, 200, 200 ), // branch_length_color
189 new Color( 0, 255, 255 ), // branch_color
190 new Color( 0, 255, 255 ), // box_color
191 new Color( 0, 255, 255 ), // collapesed_fill_color
192 new Color( 0, 255, 0 ), // found_color 0
193 new Color( 0, 0, 255 ), // found_color 1
194 new Color( 0, 255, 255 ), // found_color 0 + 1
195 new Color( 255, 0, 0 ), // duplication_box_color
196 new Color( 0, 255, 0 ), // speciation_box_color
197 new Color( 255, 255, 0 ), // duplication_speciation_color
198 new Color( 230, 230, 230 ), // domain_label
199 new Color( 100, 100, 100 ), // domains_base
200 new Color( 65, 105, 225 ), // binary_domain_combinations_color
201 new Color( 173, 255, 47 ) // annotation
202 , new Color( 0, 120, 120 ) // ov
203 }, { new Color( 0, 0, 0 ), // background_color
204 new Color( 0, 255, 255 ), // background_color_gradient_bottom
205 new Color( 255, 200, 0 ), // sequence __ Clockwork
206 new Color( 255, 200, 0 ), // taxonomy
207 new Color( 255, 200, 0 ), // support
208 new Color( 255, 200, 0 ), // branch_length_color
209 new Color( 255, 200, 0 ), // branch_color
210 new Color( 255, 200, 0 ), // box_color
211 new Color( 255, 200, 0 ), // collapesed_fill_color
212 new Color( 255, 255, 0 ), // found_color 0
213 new Color( 0, 255, 255 ), // found_color 1
214 new Color( 255, 255, 255 ), // found_color 0 + 1
215 new Color( 255, 0, 0 ), // duplication_box_color
216 new Color( 0, 255, 0 ), // speciation_box_color
217 new Color( 255, 255, 0 ), // duplication_speciation_color
218 new Color( 255, 200, 0 ), // domain_label
219 new Color( 255, 200, 0 ), // domains_base
220 new Color( 150, 150, 150 ), // binary_domain_combinations_color
221 new Color( 150, 150, 150 ) // annotation
222 , new Color( 150, 150, 150 ) // ov
223 }, { new Color( 0, 0, 100 ), // background_color
224 new Color( 0, 255, 255 ), // background_color_gradient_bottom
225 new Color( 255, 255, 255 ), // sequence __ Blue
226 new Color( 255, 255, 255 ), // taxonomy
227 new Color( 255, 0, 0 ), // support
228 new Color( 255, 0, 0 ), // branch_length_color
229 new Color( 255, 0, 0 ), // branch_color
230 new Color( 255, 0, 0 ), // box_color
231 new Color( 255, 0, 0 ), // collapesed_fill_color
232 new Color( 0, 255, 0 ), // found_color
233 new Color( 255, 0, 0 ), // found_color 1
234 new Color( 255, 255, 0 ), // found_color 1 + 2
235 new Color( 255, 0, 0 ), // duplication_box_color
236 new Color( 0, 255, 0 ), // speciation_box_color
237 new Color( 255, 255, 0 ), // duplication_speciation_color
238 new Color( 255, 255, 255 ), // domain_label
239 new Color( 100, 100, 100 ), // domains_base
240 new Color( 255, 255, 255 ), // binary_domain_combinations_color
241 new Color( 255, 255, 255 ) // annotation
242 , new Color( 77, 77, 255 ) // ov
243 }, { new Color( 0, 0, 0 ), // background_color
244 new Color( 0, 255, 255 ), // background_color_gradient_bottom
245 new Color( 255, 255, 255 ), // sequence __ blue & white
246 new Color( 255, 255, 255 ), // taxonomy
247 new Color( 255, 255, 255 ), // support
248 new Color( 0, 191, 255 ), // branch_length_color
249 new Color( 0, 191, 255 ), // branch_color
250 new Color( 0, 191, 255 ), // box_color
251 new Color( 0, 191, 255 ), // collapesed_fill_color
252 new Color( 255, 0, 0 ), // found_color 0
253 new Color( 0, 255, 0 ), // found_color 1
254 new Color( 255, 255, 0 ), // found_color 0 + 1
255 new Color( 255, 0, 0 ), // duplication_box_color
256 new Color( 0, 255, 0 ), // speciation_box_color
257 new Color( 255, 255, 0 ), // duplication_speciation_color
258 new Color( 255, 255, 255 ), // domain_label
259 new Color( 150, 150, 150 ), // domains_base
260 new Color( 255, 255, 255 ), // binary_domain_combinations_color
261 new Color( 255, 255, 255 ) // annotation
262 , new Color( 170, 187, 204 ) // ov
263 }, { new Color( 0, 0, 0 ), // background_color
264 new Color( 255, 255, 0 ), // background_color_gradient_bottom
265 new Color( 127, 255, 0 ), // sequence __ Neon
266 new Color( 255, 110, 199 ), // taxonomy
267 new Color( 234, 173, 234 ), // support
268 new Color( 77, 77, 255 ), // branch_length_color
269 new Color( 234, 173, 234 ), // branch_color
270 new Color( 77, 77, 255 ), // box_color
271 new Color( 234, 173, 234 ), // collapsed_fill_color
272 new Color( 243, 243, 21 ), // found_color 0
273 new Color( 255, 20, 147 ), // found_color 1
274 new Color( 255, 255, 255 ), // found_color 1 + 2
275 new Color( 255, 0, 0 ), // duplication_box_color
276 new Color( 0, 255, 0 ), // speciation_box_color
277 new Color( 255, 255, 0 ), // duplication_speciation_color
278 new Color( 127, 255, 0 ), // domain_label
279 new Color( 234, 173, 234 ), // domains_base
280 new Color( 27, 255, 0 ), // binary_domain_combinations_color
281 new Color( 27, 255, 0 ) // annotation
282 , new Color( 77, 77, 255 ) // ov
284 private Color annotation_color;
285 private Color background_color;
286 private Color background_color_gradient_bottom;
287 private Color binary_domain_combinations_color;
288 private Color bootstrap_color;
289 private Color box_color;
290 private Color branch_color;
291 private Color branch_length_color;
292 private Color collapse_fill_color;
293 private Color domain_label_color;
294 private Color domain_base_color;
295 private Color dup_box_color;
296 private Color duplication_or_specation_color;
297 private Color found_color_0;
298 private Color found_color_0_and_1;
299 private Color found_color_1;
300 private Color ov_color;
301 // The drawing colors
302 private Color seq_color;
303 private Color spec_box_color;
304 private Color taxonomy_color;
306 private TreeColorSet() {
307 // Hidden constructor.
310 void cycleColorScheme() {
311 if ( getCurrentColorScheme() >= ( _color_schemes.length - 1 ) ) {
315 setColorSchema( getCurrentColorScheme() + 1 );
319 Color getAnnotationColor() {
320 return annotation_color;
323 Color getBackgroundColor() {
324 return background_color;
327 Color getBackgroundColorGradientBottom() {
328 return background_color_gradient_bottom;
331 Color getBinaryDomainCombinationsColor() {
332 if ( Constants.SPECIAL_CUSTOM ) {
333 return new Color( 50, 50, 50 );
335 return binary_domain_combinations_color;
338 Color getBoxColor() {
342 Color getBranchColor() {
346 Color getBranchColorForPdf() {
350 Color getBranchLengthColor() {
351 return branch_length_color;
354 Color getCollapseFillColor() {
355 return collapse_fill_color;
358 Color[][] getColorSchemes() {
359 return _color_schemes;
362 Color getConfidenceColor() {
363 return bootstrap_color;
366 int getCurrentColorScheme() {
367 return _color_scheme;
370 String getCurrentColorSchemeName() {
371 return SCHEME_NAMES[ getCurrentColorScheme() ];
374 public Color getDomainBaseColor() {
375 return domain_base_color;
378 public Color getDomainLabelColor() {
379 return domain_label_color;
382 Color getDuplicationBoxColor() {
383 return dup_box_color;
386 Color getDuplicationOrSpeciationColor() {
387 return duplication_or_specation_color;
390 Color getFoundColor0() {
391 return found_color_0;
394 Color getFoundColor0and1() {
395 return found_color_0_and_1;
398 Color getFoundColor1() {
399 return found_color_1;
402 Color getGainedCharactersColor() {
406 Color getLostCharactersColor() {
414 Color getSequenceColor() {
418 Color getSpecBoxColor() {
419 return spec_box_color;
422 Color getTaxonomyColor() {
423 return taxonomy_color;
426 void setColorforDefault( final String color_field_name, final Color color ) {
427 final String query = color_field_name.trim().replace( '_', ' ' );
428 boolean found = false;
430 for( final String cf : COLOR_FIELDS ) {
431 if ( query.equalsIgnoreCase( cf ) ) {
433 setColorForDefault( i, color );
439 throw new IllegalArgumentException( "unknown color field name [" + color_field_name + "]" );
444 * Switches colors between different schemes.
446 void setColorSchema( final int scheme ) {
447 _color_scheme = scheme;
448 background_color = _color_schemes[ scheme ][ 0 ];
449 background_color_gradient_bottom = _color_schemes[ scheme ][ 1 ];
450 seq_color = _color_schemes[ scheme ][ 2 ];
451 taxonomy_color = _color_schemes[ scheme ][ 3 ];
452 bootstrap_color = _color_schemes[ scheme ][ 4 ];
453 branch_length_color = _color_schemes[ scheme ][ 5 ];
454 branch_color = _color_schemes[ scheme ][ 6 ];
455 box_color = _color_schemes[ scheme ][ 7 ];
456 collapse_fill_color = _color_schemes[ scheme ][ 8 ];
457 found_color_0 = _color_schemes[ scheme ][ 9 ];
458 found_color_1 = _color_schemes[ scheme ][ 10 ];
459 found_color_0_and_1 = _color_schemes[ scheme ][ 11 ];
460 dup_box_color = _color_schemes[ scheme ][ 12 ];
461 spec_box_color = _color_schemes[ scheme ][ 13 ];
462 duplication_or_specation_color = _color_schemes[ scheme ][ 14 ];
463 domain_label_color = _color_schemes[ scheme ][ 15 ];
464 domain_base_color = _color_schemes[ scheme ][ 16 ];
465 binary_domain_combinations_color = _color_schemes[ scheme ][ 17 ];
466 annotation_color = _color_schemes[ scheme ][ 18 ];
467 ov_color = _color_schemes[ scheme ][ 19 ];
470 void setCurrentColorScheme( final int color_scheme ) {
471 _color_scheme = color_scheme;
474 private void setColorForDefault( final int i, final Color color ) {
475 _color_schemes[ 0 ][ i ] = color;
478 static TreeColorSet createInstance() {
479 final TreeColorSet tcs = new TreeColorSet();
480 tcs.setColorSchema( 0 );
484 static TreeColorSet createInstance( final Configuration configuration ) {
485 final TreeColorSet tcs = new TreeColorSet();
486 if ( ( configuration != null ) && ( configuration.getDisplayColors() != null )
487 && ( configuration.getDisplayColors().size() > 0 ) ) {
488 final Map<String, Color> colors = configuration.getDisplayColors();
489 for( final String field : colors.keySet() ) {
490 final Color color = colors.get( field );
492 tcs.setColorforDefault( field, color );
494 catch ( final IllegalArgumentException ex ) {
495 ForesterUtil.printWarningMessage( Constants.PRG_NAME, ex.getMessage() );
499 tcs.setColorSchema( 0 );