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;
35 public final class TreeColorSet {
37 public static final String ANNOTATION = "Annotation";
38 public static final String BACKGROUND = "Background";
39 public static final String BACKGROUND_GRADIENT_BOTTOM = "Background Gradient Bottom";
40 public static final String BINARY_DOMAIN_COMBINATIONS = "Binary Domain Combinations";
41 public static final String BRANCH = "Branch";
42 public static final String BRANCH_LENGTH = "Branch Length";
43 public static final String COLLAPSED = "Collapsed";
44 public static final String CONFIDENCE = "Confidence";
45 public static final String DOMAIN_LABEL = "Domain Label";
46 public static final String DOMAIN_BASE = "Domain Base";
47 public static final String DUPLICATION = "Duplication";
48 public static final String DUPLICATION_OR_SPECATION = "Duplication or Specation";
49 public static final String MATCHING_NODES_A = "Matching A";
50 public static final String MATCHING_NODES_A_AND_B = "Matching A and B";
51 public static final String MATCHING_NODES_B = "Matching B";
52 public static final String NODE_BOX = "Node Box";
53 public static final String OVERVIEW = "Overview";
54 public static final String SEQUENCE = "Sequence";
55 public static final String SPECIATION = "Speciation";
56 public static final String TAXONOMY = "Taxonomy";
57 static final String[] COLOR_FIELDS = { BACKGROUND, BACKGROUND_GRADIENT_BOTTOM, SEQUENCE,
58 TAXONOMY, CONFIDENCE, BRANCH_LENGTH, BRANCH, NODE_BOX, COLLAPSED, MATCHING_NODES_A, MATCHING_NODES_B,
59 MATCHING_NODES_A_AND_B, DUPLICATION, SPECIATION, DUPLICATION_OR_SPECATION, DOMAIN_LABEL, DOMAIN_BASE,
60 BINARY_DOMAIN_COMBINATIONS, ANNOTATION, OVERVIEW };
61 static final String[] SCHEME_NAMES = { "Default", "Black", "Black & White", "Silver", "Green",
62 "White & Blue", "Cyan", "Orange", "Blue", "Blue & White", "Neon" };
64 private int _color_scheme;
66 private final Color[][] _color_schemes = { { new Color( 0, 0, 0 ), // background_color
67 new Color( 0, 100, 100 ), // background_color_gradient_bottom
68 new Color( 230, 230, 230 ), // sequence __ Default (same as Black)
69 new Color( 180, 180, 180 ), // taxonomy
70 new Color( 180, 180, 180 ), // support
71 new Color( 140, 140, 140 ), // branch_length_color
72 new Color( 255, 255, 255 ), // branch_color
73 new Color( 255, 255, 255 ), // box_color
74 new Color( 255, 255, 255 ), // collapesed_fill_color
75 new Color( 0, 255, 0 ), // found_color 0
76 new Color( 255, 0, 0 ), // found_color 1
77 new Color( 255, 255, 0 ), // found_color 1 + 2
78 new Color( 255, 0, 0 ), // duplication_box_color
79 new Color( 0, 255, 0 ), // speciation_box_color
80 new Color( 255, 255, 0 ), // duplication_speciation_color
81 new Color( 230, 230, 230 ), // domain_label
82 new Color( 100, 100, 100 ), // domains_base
83 new Color( 65, 105, 255 ), // binary_domain_combinations_color
84 new Color( 173, 255, 47 ) // annotation
85 , new Color( 130, 130, 130 ) // overview
86 }, { new Color( 0, 0, 0 ), // background_color
87 new Color( 0, 255, 255 ), // background_color_gradient_bottom
88 new Color( 230, 230, 230 ), // sequence __ Black
89 new Color( 180, 180, 180 ), // taxonomy
90 new Color( 180, 180, 180 ), // support
91 new Color( 140, 140, 140 ), // branch_length_color
92 new Color( 255, 255, 255 ), // branch_color
93 new Color( 255, 255, 255 ), // box_color
94 new Color( 255, 255, 255 ), // collapesed_fill_color
95 new Color( 0, 255, 0 ), // found_color 0
96 new Color( 255, 0, 0 ), // found_color 1
97 new Color( 255, 255, 0 ), // found_color 1 + 2
98 new Color( 255, 0, 0 ), // duplication_box_color
99 new Color( 0, 255, 0 ), // speciation_box_color
100 new Color( 255, 255, 0 ), // duplication_speciation_color
101 new Color( 230, 230, 230 ), // domain_label
102 new Color( 100, 100, 100 ), // domains_base
103 new Color( 65, 105, 255 ), // binary_domain_combinations_color
104 new Color( 173, 255, 47 ) // annotation
105 , new Color( 130, 130, 130 ) // ov
106 }, { new Color( 255, 255, 255 ), // background_color
107 new Color( 0, 255, 255 ), // background_color_gradient_bottom
108 new Color( 0, 0, 0 ), // sequence __ Black & White
109 new Color( 0, 0, 0 ), // taxonomy
110 new Color( 0, 0, 0 ), // support
111 new Color( 0, 0, 0 ), // branch_length_color
112 new Color( 0, 0, 0 ), // branch_color
113 new Color( 0, 0, 0 ), // box_color
114 new Color( 0, 0, 0 ), // collapesed_fill_color
115 new Color( 255, 0, 0 ), // found_color 0
116 new Color( 0, 255, 0 ), // found_color 1
117 new Color( 0, 0, 255 ), // found_color 1 + 2
118 new Color( 255, 0, 0 ), // duplication_box_color
119 new Color( 0, 255, 0 ), // speciation_box_color
120 new Color( 255, 255, 0 ), // duplication_speciation_color
121 new Color( 0, 0, 0 ), // domain_label
122 new Color( 100, 100, 100 ), // domains_base
123 new Color( 0, 0, 0 ), // binary_domain_combinations_color
124 new Color( 0, 0, 0 ) // annotation
125 , new Color( 220, 220, 220 ) // ov
126 }, { new Color( 0, 0, 0 ), // background_color
127 new Color( 0, 255, 255 ), // background_color_gradient_bottom
128 new Color( 220, 220, 220 ), // sequence __ Silver
129 new Color( 180, 180, 180 ), // taxonomy
130 new Color( 140, 140, 140 ), // support
131 new Color( 140, 140, 140 ), // branch_length_color
132 new Color( 240, 240, 240 ), // branch_color
133 new Color( 140, 140, 140 ), // box_color
134 new Color( 240, 240, 240 ), // collapesed_fill_color
135 new Color( 255, 0, 0 ), // found_color 0
136 new Color( 0, 255, 0 ), // found_color 1
137 new Color( 255, 255, 0 ), // found_color 1 + 2
138 new Color( 255, 0, 0 ), // duplication_box_color
139 new Color( 0, 255, 0 ), // speciation_box_color
140 new Color( 255, 255, 0 ), // duplication_speciation_color
141 new Color( 230, 230, 230 ), // domain_label
142 new Color( 100, 100, 100 ), // domains_base
143 new Color( 180, 180, 180 ), // binary_domain_combinations_color
144 new Color( 140, 140, 140 ) // annotation
145 , new Color( 40, 40, 40 ) // ov
146 }, { new Color( 0, 10, 0 ), // background_color
147 new Color( 0, 255, 255 ), // background_color_gradient_bottom
148 new Color( 0, 255, 0 ), // sequence __ the Matrix
149 new Color( 30, 200, 30 ), // taxonomy
150 new Color( 0, 155, 0 ), // support
151 new Color( 0, 100, 0 ), // branch_length_color
152 new Color( 0, 155, 0 ), // branch_color
153 new Color( 0, 255, 0 ), // box_color
154 new Color( 0, 155, 0 ), // collapesed_fill_color
155 new Color( 255, 0, 0 ), // found_color 0
156 new Color( 0, 255, 0 ), // found_color 1
157 new Color( 255, 255, 0 ), // found_color 1 + 2
158 new Color( 255, 0, 0 ), // duplication_box_color
159 new Color( 0, 255, 0 ), // speciation_box_color
160 new Color( 255, 255, 0 ), // duplication_speciation_color
161 new Color( 230, 230, 230 ), // domain_label
162 new Color( 100, 100, 100 ), // domains_base
163 new Color( 0, 235, 0 ), // binary_domain_combinations_color
164 new Color( 0, 235, 0 ) // annotation
165 , new Color( 40, 40, 40 ) // ov
166 }, { new Color( 255, 255, 255 ), // background_color
167 new Color( 0, 255, 255 ), // background_color_gradient_bottom
168 new Color( 0, 0, 0 ), //sequence __ White & Blue
169 new Color( 40, 40, 40 ), // taxonomy
170 new Color( 0, 125, 0 ), // support
171 new Color( 70, 70, 0 ), // branch_length_color
172 new Color( 0, 20, 200 ), // branch_color
173 new Color( 0, 20, 200 ), // box_color
174 new Color( 0, 20, 200 ), // collapesed_fill_color
175 new Color( 0, 255, 0 ), // found_color 0
176 new Color( 255, 0, 0 ), // found_color 1
177 new Color( 0, 0, 255 ), // found_color 0 + 1
178 new Color( 255, 0, 0 ), // duplication_box_color
179 new Color( 0, 255, 0 ), // speciation_box_color
180 new Color( 255, 255, 0 ), // duplication_speciation_color
181 new Color( 0, 0, 0 ), // domain_label
182 new Color( 50, 50, 50 ), // domains_base
183 new Color( 65, 105, 225 ), // binary_domain_combinations_color
184 new Color( 173, 255, 47 ) // annotation
185 , new Color( 220, 220, 220 ) // ov
186 }, { new Color( 0, 0, 0 ), // background_color
187 new Color( 0, 255, 255 ), // background_color_gradient_bottom
188 new Color( 255, 255, 255 ), // sequence __ Cyan
189 new Color( 200, 200, 200 ), // taxonomy
190 new Color( 255, 255, 255 ), // support
191 new Color( 200, 200, 200 ), // branch_length_color
192 new Color( 0, 255, 255 ), // branch_color
193 new Color( 0, 255, 255 ), // box_color
194 new Color( 0, 255, 255 ), // collapesed_fill_color
195 new Color( 0, 255, 0 ), // found_color 0
196 new Color( 0, 0, 255 ), // found_color 1
197 new Color( 0, 255, 255 ), // found_color 0 + 1
198 new Color( 255, 0, 0 ), // duplication_box_color
199 new Color( 0, 255, 0 ), // speciation_box_color
200 new Color( 255, 255, 0 ), // duplication_speciation_color
201 new Color( 230, 230, 230 ), // domain_label
202 new Color( 100, 100, 100 ), // domains_base
203 new Color( 65, 105, 225 ), // binary_domain_combinations_color
204 new Color( 173, 255, 47 ) // annotation
205 , new Color( 0, 120, 120 ) // ov
206 }, { new Color( 0, 0, 0 ), // background_color
207 new Color( 0, 255, 255 ), // background_color_gradient_bottom
208 new Color( 255, 200, 0 ), // sequence __ Clockwork
209 new Color( 255, 200, 0 ), // taxonomy
210 new Color( 255, 200, 0 ), // support
211 new Color( 255, 200, 0 ), // branch_length_color
212 new Color( 255, 200, 0 ), // branch_color
213 new Color( 255, 200, 0 ), // box_color
214 new Color( 255, 200, 0 ), // collapesed_fill_color
215 new Color( 255, 255, 0 ), // found_color 0
216 new Color( 0, 255, 255 ), // found_color 1
217 new Color( 255, 255, 255 ), // found_color 0 + 1
218 new Color( 255, 0, 0 ), // duplication_box_color
219 new Color( 0, 255, 0 ), // speciation_box_color
220 new Color( 255, 255, 0 ), // duplication_speciation_color
221 new Color( 255, 200, 0 ), // domain_label
222 new Color( 255, 200, 0 ), // domains_base
223 new Color( 150, 150, 150 ), // binary_domain_combinations_color
224 new Color( 150, 150, 150 ) // annotation
225 , new Color( 150, 150, 150 ) // ov
226 }, { new Color( 0, 0, 100 ), // background_color
227 new Color( 0, 255, 255 ), // background_color_gradient_bottom
228 new Color( 255, 255, 255 ), // sequence __ Blue
229 new Color( 255, 255, 255 ), // taxonomy
230 new Color( 255, 0, 0 ), // support
231 new Color( 255, 0, 0 ), // branch_length_color
232 new Color( 255, 0, 0 ), // branch_color
233 new Color( 255, 0, 0 ), // box_color
234 new Color( 255, 0, 0 ), // collapesed_fill_color
235 new Color( 0, 255, 0 ), // found_color
236 new Color( 255, 0, 0 ), // found_color 1
237 new Color( 255, 255, 0 ), // found_color 1 + 2
238 new Color( 255, 0, 0 ), // duplication_box_color
239 new Color( 0, 255, 0 ), // speciation_box_color
240 new Color( 255, 255, 0 ), // duplication_speciation_color
241 new Color(255, 255, 255 ), // domain_label
242 new Color( 100, 100, 100 ), // domains_base
243 new Color( 255, 255, 255 ), // binary_domain_combinations_color
244 new Color( 255, 255, 255 ) // annotation
245 , new Color( 77, 77, 255 ) // ov
246 }, { new Color( 0, 0, 0 ), // background_color
247 new Color( 0, 255, 255 ), // background_color_gradient_bottom
248 new Color( 255, 255, 255 ), // sequence __ blue & white
249 new Color( 255, 255, 255 ), // taxonomy
250 new Color( 255, 255, 255 ), // support
251 new Color( 0, 191, 255 ), // branch_length_color
252 new Color( 0, 191, 255 ), // branch_color
253 new Color( 0, 191, 255 ), // box_color
254 new Color( 0, 191, 255 ), // collapesed_fill_color
255 new Color( 255, 0, 0 ), // found_color 0
256 new Color( 0, 255, 0 ), // found_color 1
257 new Color( 255, 255, 0 ), // found_color 0 + 1
258 new Color( 255, 0, 0 ), // duplication_box_color
259 new Color( 0, 255, 0 ), // speciation_box_color
260 new Color( 255, 255, 0 ), // duplication_speciation_color
261 new Color( 255, 255, 255 ), // domain_label
262 new Color( 150, 150, 150 ), // domains_base
263 new Color( 255, 255, 255 ), // binary_domain_combinations_color
264 new Color( 255, 255, 255 ) // annotation
265 , new Color( 170, 187, 204 ) // ov
266 }, { new Color( 0, 0, 0 ), // background_color
267 new Color( 255, 255, 0 ), // background_color_gradient_bottom
268 new Color( 127, 255, 0 ), // sequence __ Neon
269 new Color( 255, 110, 199 ), // taxonomy
270 new Color( 234, 173, 234 ), // support
271 new Color( 77, 77, 255 ), // branch_length_color
272 new Color( 234, 173, 234 ), // branch_color
273 new Color( 77, 77, 255 ), // box_color
274 new Color( 234, 173, 234 ), // collapsed_fill_color
275 new Color( 243, 243, 21 ), // found_color 0
276 new Color( 255, 20, 147 ), // found_color 1
277 new Color( 255, 255, 255 ), // found_color 1 + 2
278 new Color( 255, 0, 0 ), // duplication_box_color
279 new Color( 0, 255, 0 ), // speciation_box_color
280 new Color( 255, 255, 0 ), // duplication_speciation_color
281 new Color( 127, 255, 0 ), // domain_label
282 new Color( 234, 173, 234 ), // domains_base
283 new Color( 27, 255, 0 ), // binary_domain_combinations_color
284 new Color( 27, 255, 0 ) // annotation
285 , new Color( 77, 77, 255 ) // ov
287 private Color annotation_color;
288 private Color background_color;
289 private Color background_color_gradient_bottom;
290 private Color binary_domain_combinations_color;
291 private Color bootstrap_color;
292 private Color box_color;
293 private Color branch_color;
294 private Color branch_length_color;
295 private Color collapse_fill_color;
296 private Color domain_label_color;
297 private Color domain_base_color;
298 private Color dup_box_color;
299 private Color duplication_or_specation_color;
300 private Color found_color_0;
301 private Color found_color_0_and_1;
302 private Color found_color_1;
303 private Color ov_color;
304 // The drawing colors
305 private Color seq_color;
306 private Color spec_box_color;
307 private Color taxonomy_color;
309 private TreeColorSet() {
310 // Hidden constructor.
313 void cycleColorScheme() {
314 if ( getCurrentColorScheme() >= ( _color_schemes.length - 1 ) ) {
318 setColorSchema( getCurrentColorScheme() + 1 );
322 Color getAnnotationColor() {
323 return annotation_color;
326 Color getBackgroundColor() {
327 return background_color;
330 Color getBackgroundColorGradientBottom() {
331 return background_color_gradient_bottom;
334 Color getBinaryDomainCombinationsColor() {
335 if ( Constants.SPECIAL_CUSTOM ) {
336 return new Color( 50, 50, 50 );
338 return binary_domain_combinations_color;
341 Color getBoxColor() {
345 Color getBranchColor() {
349 Color getBranchColorForPdf() {
353 Color getBranchLengthColor() {
354 return branch_length_color;
357 Color getCollapseFillColor() {
358 return collapse_fill_color;
361 Color[][] getColorSchemes() {
362 return _color_schemes;
365 Color getConfidenceColor() {
366 return bootstrap_color;
369 int getCurrentColorScheme() {
370 return _color_scheme;
373 String getCurrentColorSchemeName() {
374 return SCHEME_NAMES[ getCurrentColorScheme() ];
377 public Color getDomainBaseColor() {
378 return domain_base_color;
381 public Color getDomainLabelColor() {
382 return domain_label_color;
385 Color getDuplicationBoxColor() {
386 return dup_box_color;
389 Color getDuplicationOrSpeciationColor() {
390 return duplication_or_specation_color;
393 Color getFoundColor0() {
394 return found_color_0;
397 Color getFoundColor0and1() {
398 return found_color_0_and_1;
401 Color getFoundColor1() {
402 return found_color_1;
405 Color getGainedCharactersColor() {
409 Color getLostCharactersColor() {
417 Color getSequenceColor() {
421 Color getSpecBoxColor() {
422 return spec_box_color;
425 Color getTaxonomyColor() {
426 return taxonomy_color;
429 void setColorforDefault( final String color_field_name, final Color color ) {
430 final String query = color_field_name.trim().replace( '_', ' ' );
431 boolean found = false;
433 for( final String cf : COLOR_FIELDS ) {
434 if ( query.equalsIgnoreCase( cf ) ) {
436 setColorForDefault( i, color );
442 throw new IllegalArgumentException( "unknown color field name [" + color_field_name + "]" );
447 * Switches colors between different schemes.
449 void setColorSchema( final int scheme ) {
450 _color_scheme = scheme;
451 background_color = _color_schemes[ scheme ][ 0 ];
452 background_color_gradient_bottom = _color_schemes[ scheme ][ 1 ];
453 seq_color = _color_schemes[ scheme ][ 2 ];
454 taxonomy_color = _color_schemes[ scheme ][ 3 ];
455 bootstrap_color = _color_schemes[ scheme ][ 4 ];
456 branch_length_color = _color_schemes[ scheme ][ 5 ];
457 branch_color = _color_schemes[ scheme ][ 6 ];
458 box_color = _color_schemes[ scheme ][ 7 ];
459 collapse_fill_color = _color_schemes[ scheme ][ 8 ];
460 found_color_0 = _color_schemes[ scheme ][ 9 ];
461 found_color_1 = _color_schemes[ scheme ][ 10 ];
462 found_color_0_and_1 = _color_schemes[ scheme ][ 11 ];
463 dup_box_color = _color_schemes[ scheme ][ 12 ];
464 spec_box_color = _color_schemes[ scheme ][ 13 ];
465 duplication_or_specation_color = _color_schemes[ scheme ][ 14 ];
466 domain_label_color = _color_schemes[ scheme ][ 15 ];
467 domain_base_color = _color_schemes[ scheme ][ 16 ];
468 binary_domain_combinations_color = _color_schemes[ scheme ][ 17 ];
469 annotation_color = _color_schemes[ scheme ][ 18 ];
470 ov_color = _color_schemes[ scheme ][ 19 ];
473 void setCurrentColorScheme( final int color_scheme ) {
474 _color_scheme = color_scheme;
477 private void setColorForDefault( final int i, final Color color ) {
478 _color_schemes[ 0 ][ i ] = color;
481 static TreeColorSet createInstance() {
482 final TreeColorSet tcs = new TreeColorSet();
483 tcs.setColorSchema( 0 );
487 static TreeColorSet createInstance( final Configuration configuration ) {
488 final TreeColorSet tcs = new TreeColorSet();
489 if ( ( configuration != null ) && ( configuration.getDisplayColors() != null )
490 && ( configuration.getDisplayColors().size() > 0 ) ) {
491 final Map<String, Color> colors = configuration.getDisplayColors();
492 for( final String field : colors.keySet() ) {
493 final Color color = colors.get( field );
495 tcs.setColorforDefault( field, color );
497 catch ( final IllegalArgumentException ex ) {
498 ForesterUtil.printWarningMessage( Constants.PRG_NAME, ex.getMessage() );
502 tcs.setColorSchema( 0 );