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 * Maintains the color schemes and a set of colors for drawing a tree.
37 public final class TreeColorSet {
39 public static final String ANNOTATION = "Annotation";
40 public static final String BACKGROUND = "Background";
41 public static final String BACKGROUND_GRADIENT_BOTTOM = "Background Gradient Bottom";
42 public static final String BINARY_DOMAIN_COMBINATIONS = "Binary Domain Combinations";
43 public static final String BRANCH = "Branch";
44 public static final String BRANCH_LENGTH = "Branch Length";
45 public static final String COLLAPSED = "Collapsed";
46 public static final String CONFIDENCE = "Confidence";
47 public static final String DOMAINS = "Domains";
48 public static final String DUPLICATION = "Duplication";
49 public static final String DUPLICATION_OR_SPECATION = "Duplication or Specation";
50 public static final String MATCHING_NODES_A = "Matching A";
51 public static final String MATCHING_NODES_A_AND_B = "Matching A and B";
52 public static final String MATCHING_NODES_B = "Matching B";
53 public static final String NODE_BOX = "Node Box";
54 public static final String OVERVIEW = "Overview";
55 public static final String SEQUENCE = "Sequence";
56 public static final String SPECIATION = "Speciation";
57 public static final String TAXONOMY = "Taxonomy";
58 static final String[] COLOR_FIELDS = { BACKGROUND, BACKGROUND_GRADIENT_BOTTOM, SEQUENCE,
59 TAXONOMY, CONFIDENCE, BRANCH_LENGTH, BRANCH, NODE_BOX, COLLAPSED, MATCHING_NODES_A, MATCHING_NODES_B,
60 MATCHING_NODES_A_AND_B, DUPLICATION, SPECIATION, DUPLICATION_OR_SPECATION, DOMAINS,
61 BINARY_DOMAIN_COMBINATIONS, ANNOTATION, OVERVIEW };
62 static final String[] SCHEME_NAMES = { "Default", "Black", "Black & White", "Silver", "Green",
63 "White & Blue", "Cyan", "Orange", "Blue", "Blue & White", "Neon" };
65 private int _color_scheme;
66 // All the color sets; better be the same # of sets as there are names!
67 private final Color[][] _color_schemes = { { new Color( 0, 0, 0 ), // background_color
68 new Color( 0, 100, 100 ), // background_color_gradient_bottom
69 new Color( 230, 230, 230 ), // sequence __ Default (same as Black)
70 new Color( 255, 220, 220 ), // taxonomy
71 new Color( 56, 176, 255 ), // support
72 new Color( 140, 140, 140 ), // branch_length_color
73 new Color( 255, 255, 255 ), // branch_color
74 new Color( 255, 255, 255 ), // box_color
75 new Color( 255, 255, 0 ), // collapesed_fill_color
76 new Color( 0, 255, 0 ), // found_color 0
77 new Color( 255, 0, 0 ), // found_color 1
78 new Color( 255, 255, 0 ), // found_color 1 + 2
79 new Color( 255, 0, 0 ), // duplication_box_color
80 new Color( 0, 255, 0 ), // speciation_box_color
81 new Color( 255, 255, 0 ), // duplication_speciation_color
82 new Color( 123, 104, 238 ), // domains_color
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( 255, 220, 220 ), // taxonomy
90 new Color( 56, 176, 255 ), // 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, 0 ), // 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( 123, 104, 238 ), // domains_color
102 new Color( 65, 105, 255 ), // binary_domain_combinations_color
103 new Color( 173, 255, 47 ) // annotation
104 , new Color( 130, 130, 130 ) // ov
105 }, { new Color( 255, 255, 255 ), // background_color
106 new Color( 0, 255, 255 ), // background_color_gradient_bottom
107 new Color( 0, 0, 0 ), // sequence __ Black & White
108 new Color( 0, 0, 0 ), // taxonomy
109 new Color( 0, 0, 0 ), // support
110 new Color( 0, 0, 0 ), // branch_length_color
111 new Color( 0, 0, 0 ), // branch_color
112 new Color( 0, 0, 0 ), // box_color
113 new Color( 0, 0, 0 ), // collapesed_fill_color
114 new Color( 255, 0, 0 ), // found_color 0
115 new Color( 0, 255, 0 ), // found_color 1
116 new Color( 0, 0, 255 ), // found_color 1 + 2
117 new Color( 255, 0, 0 ), // duplication_box_color
118 new Color( 0, 255, 0 ), // speciation_box_color
119 new Color( 255, 255, 0 ), // duplication_speciation_color
120 new Color( 0, 0, 0 ), // domains_color
121 new Color( 0, 0, 0 ), // binary_domain_combinations_color
122 new Color( 0, 0, 0 ) // annotation
123 , new Color( 220, 220, 220 ) // ov
124 }, { new Color( 0, 0, 0 ), // background_color
125 new Color( 0, 255, 255 ), // background_color_gradient_bottom
126 new Color( 220, 220, 220 ), // sequence __ Silver
127 new Color( 180, 180, 180 ), // taxonomy
128 new Color( 140, 140, 140 ), // support
129 new Color( 140, 140, 140 ), // branch_length_color
130 new Color( 240, 240, 240 ), // branch_color
131 new Color( 140, 140, 140 ), // box_color
132 new Color( 140, 140, 140 ), // collapesed_fill_color
133 new Color( 255, 0, 0 ), // found_color 0
134 new Color( 0, 255, 0 ), // found_color 1
135 new Color( 255, 255, 0 ), // found_color 1 + 2
136 new Color( 255, 0, 0 ), // duplication_box_color
137 new Color( 0, 255, 0 ), // speciation_box_color
138 new Color( 255, 255, 0 ), // duplication_speciation_color
139 new Color( 180, 180, 180 ), // domains_color
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, 255, 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( 0, 235, 0 ), // domains_color
159 new Color( 0, 235, 0 ), // binary_domain_combinations_color
160 new Color( 0, 235, 0 ) // annotation
161 , new Color( 40, 40, 40 ) // ov
162 }, { new Color( 255, 255, 255 ), // background_color
163 new Color( 0, 255, 255 ), // background_color_gradient_bottom
164 new Color( 0, 0, 0 ), //sequence __ White & Blue
165 new Color( 40, 40, 40 ), // taxonomy
166 new Color( 0, 125, 0 ), // support
167 new Color( 70, 70, 0 ), // branch_length_color
168 new Color( 0, 20, 200 ), // branch_color
169 new Color( 0, 20, 200 ), // box_color
170 new Color( 255, 255, 0 ), // collapesed_fill_color
171 new Color( 0, 255, 0 ), // found_color 0
172 new Color( 255, 0, 0 ), // found_color 1
173 new Color( 0, 0, 255 ), // found_color 0 + 1
174 new Color( 255, 0, 0 ), // duplication_box_color
175 new Color( 0, 255, 0 ), // speciation_box_color
176 new Color( 255, 255, 0 ), // duplication_speciation_color
177 new Color( 123, 104, 238 ), // domains_color
178 new Color( 65, 105, 225 ), // binary_domain_combinations_color
179 new Color( 173, 255, 47 ) // annotation
180 , new Color( 220, 220, 220 ) // ov
181 }, { new Color( 0, 0, 0 ), // background_color
182 new Color( 0, 255, 255 ), // background_color_gradient_bottom
183 new Color( 255, 255, 255 ), // sequence __ Cyan
184 new Color( 200, 200, 200 ), // taxonomy
185 new Color( 255, 255, 255 ), // support
186 new Color( 200, 200, 200 ), // branch_length_color
187 new Color( 0, 255, 255 ), // branch_color
188 new Color( 0, 255, 255 ), // box_color
189 new Color( 255, 255, 0 ), // collapesed_fill_color
190 new Color( 0, 255, 0 ), // found_color 0
191 new Color( 0, 0, 255 ), // found_color 1
192 new Color( 0, 255, 255 ), // found_color 0 + 1
193 new Color( 255, 0, 0 ), // duplication_box_color
194 new Color( 0, 255, 0 ), // speciation_box_color
195 new Color( 255, 255, 0 ), // duplication_speciation_color
196 new Color( 123, 104, 238 ), // domains_color
197 new Color( 65, 105, 225 ), // binary_domain_combinations_color
198 new Color( 173, 255, 47 ) // annotation
199 , new Color( 0, 120, 120 ) // ov
200 }, { new Color( 0, 0, 0 ), // background_color
201 new Color( 0, 255, 255 ), // background_color_gradient_bottom
202 new Color( 255, 200, 0 ), // sequence __ Clockwork
203 new Color( 255, 200, 0 ), // taxonomy
204 new Color( 255, 200, 0 ), // support
205 new Color( 255, 200, 0 ), // branch_length_color
206 new Color( 255, 200, 0 ), // branch_color
207 new Color( 255, 200, 0 ), // box_color
208 new Color( 255, 255, 255 ), // collapesed_fill_color
209 new Color( 255, 255, 0 ), // found_color 0
210 new Color( 0, 255, 255 ), // found_color 1
211 new Color( 255, 255, 255 ), // found_color 0 + 1
212 new Color( 255, 0, 0 ), // duplication_box_color
213 new Color( 0, 255, 0 ), // speciation_box_color
214 new Color( 255, 255, 0 ), // duplication_speciation_color
215 new Color( 150, 150, 150 ), // domains_color
216 new Color( 150, 150, 150 ), // binary_domain_combinations_color
217 new Color( 150, 150, 150 ) // annotation
218 , new Color( 150, 150, 150 ) // ov
219 }, { new Color( 0, 0, 100 ), // background_color
220 new Color( 0, 255, 255 ), // background_color_gradient_bottom
221 new Color( 255, 255, 255 ), // sequence __ Blue
222 new Color( 255, 255, 255 ), // taxonomy
223 new Color( 255, 0, 0 ), // support
224 new Color( 255, 0, 0 ), // branch_length_color
225 new Color( 255, 0, 0 ), // branch_color
226 new Color( 255, 0, 0 ), // box_color
227 new Color( 0, 0, 0 ), // collapesed_fill_color
228 new Color( 0, 255, 0 ), // found_color
229 new Color( 255, 0, 0 ), // found_color 1
230 new Color( 255, 255, 0 ), // found_color 1 + 2
231 new Color( 255, 0, 0 ), // duplication_box_color
232 new Color( 0, 255, 0 ), // speciation_box_color
233 new Color( 255, 255, 0 ), // duplication_speciation_color
234 new Color( 255, 255, 255 ), // domains_color
235 new Color( 255, 255, 255 ), // binary_domain_combinations_color
236 new Color( 255, 255, 255 ) // annotation
237 , new Color( 77, 77, 255 ) // ov
238 }, { new Color( 0, 0, 0 ), // background_color
239 new Color( 0, 255, 255 ), // background_color_gradient_bottom
240 new Color( 255, 255, 255 ), // sequence __ blue & white
241 new Color( 255, 255, 255 ), // taxonomy
242 new Color( 255, 255, 255 ), // support
243 new Color( 0, 191, 255 ), // branch_length_color
244 new Color( 0, 191, 255 ), // branch_color
245 new Color( 0, 191, 255 ), // box_color
246 new Color( 255, 255, 255 ), // collapesed_fill_color
247 new Color( 255, 0, 0 ), // found_color 0
248 new Color( 0, 255, 0 ), // found_color 1
249 new Color( 255, 255, 0 ), // found_color 0 + 1
250 new Color( 255, 0, 0 ), // duplication_box_color
251 new Color( 0, 255, 0 ), // speciation_box_color
252 new Color( 255, 255, 0 ), // duplication_speciation_color
253 new Color( 255, 255, 255 ), // domains_color
254 new Color( 255, 255, 255 ), // binary_domain_combinations_color
255 new Color( 255, 255, 255 ) // annotation
256 , new Color( 170, 187, 204 ) // ov
257 }, { new Color( 0, 0, 0 ), // background_color
258 new Color( 255, 255, 0 ), // background_color_gradient_bottom
259 new Color( 127, 255, 0 ), // sequence __ Neon
260 new Color( 255, 110, 199 ), // taxonomy
261 new Color( 234, 173, 234 ), // support
262 new Color( 77, 77, 255 ), // branch_length_color
263 new Color( 234, 173, 234 ), // branch_color
264 new Color( 77, 77, 255 ), // box_color
265 new Color( 77, 77, 255 ), // collapsed_fill_color
266 new Color( 243, 243, 21 ), // found_color 0
267 new Color( 255, 20, 147 ), // found_color 1
268 new Color( 255, 255, 255 ), // found_color 1 + 2
269 new Color( 255, 0, 0 ), // duplication_box_color
270 new Color( 0, 255, 0 ), // speciation_box_color
271 new Color( 255, 255, 0 ), // duplication_speciation_color
272 new Color( 27, 255, 0 ), // domains_color
273 new Color( 27, 255, 0 ), // binary_domain_combinations_color
274 new Color( 27, 255, 0 ) // annotation
275 , new Color( 77, 77, 255 ) // ov
277 private Color annotation_color;
278 private Color background_color;
279 private Color background_color_gradient_bottom;
280 private Color binary_domain_combinations_color;
281 private Color bootstrap_color;
282 private Color box_color;
283 private Color branch_color;
284 private Color branch_length_color;
285 private Color collapse_fill_color;
286 private Color domains_color;
287 private Color dup_box_color;
288 private Color duplication_or_specation_color;
289 private Color found_color_0;
290 private Color found_color_0_and_1;
291 private Color found_color_1;
292 private Color ov_color;
293 // The drawing colors
294 private Color seq_color;
295 private Color spec_box_color;
296 private Color taxonomy_color;
298 private TreeColorSet() {
299 // Hidden constructor.
302 void cycleColorScheme() {
303 if ( getCurrentColorScheme() >= ( _color_schemes.length - 1 ) ) {
307 setColorSchema( getCurrentColorScheme() + 1 );
311 Color getAnnotationColor() {
312 return annotation_color;
315 Color getBackgroundColor() {
316 return background_color;
319 Color getBackgroundColorGradientBottom() {
320 return background_color_gradient_bottom;
323 Color getBinaryDomainCombinationsColor() {
324 if ( Constants.SPECIAL_CUSTOM ) {
325 return new Color( 50, 50, 50 );
327 return binary_domain_combinations_color;
330 Color getBoxColor() {
334 Color getBranchColor() {
338 Color getBranchColorForPdf() {
342 Color getBranchLengthColor() {
343 return branch_length_color;
346 Color getCollapseFillColor() {
347 return collapse_fill_color;
350 Color[][] getColorSchemes() {
351 return _color_schemes;
354 Color getConfidenceColor() {
355 return bootstrap_color;
358 int getCurrentColorScheme() {
359 return _color_scheme;
362 String getCurrentColorSchemeName() {
363 return SCHEME_NAMES[ getCurrentColorScheme() ];
366 Color getDomainsColor() {
367 return domains_color;
370 Color getDuplicationBoxColor() {
371 return dup_box_color;
374 Color getDuplicationOrSpeciationColor() {
375 return duplication_or_specation_color;
378 Color getFoundColor0() {
379 return found_color_0;
382 Color getFoundColor0and1() {
383 return found_color_0_and_1;
386 Color getFoundColor1() {
387 return found_color_1;
390 Color getGainedCharactersColor() {
394 Color getLostCharactersColor() {
402 Color getSequenceColor() {
406 Color getSpecBoxColor() {
407 return spec_box_color;
410 Color getTaxonomyColor() {
411 return taxonomy_color;
414 void setColorforDefault( final String color_field_name, final Color color ) {
415 final String query = color_field_name.trim().replace( '_', ' ' );
416 boolean found = false;
418 for( final String cf : COLOR_FIELDS ) {
419 if ( query.equalsIgnoreCase( cf ) ) {
421 setColorForDefault( i, color );
427 throw new IllegalArgumentException( "unknown color field name [" + color_field_name + "]" );
432 * Switches colors between different schemes.
434 void setColorSchema( final int scheme ) {
435 _color_scheme = scheme;
436 background_color = _color_schemes[ scheme ][ 0 ];
437 background_color_gradient_bottom = _color_schemes[ scheme ][ 1 ];
438 seq_color = _color_schemes[ scheme ][ 2 ];
439 taxonomy_color = _color_schemes[ scheme ][ 3 ];
440 bootstrap_color = _color_schemes[ scheme ][ 4 ];
441 branch_length_color = _color_schemes[ scheme ][ 5 ];
442 branch_color = _color_schemes[ scheme ][ 6 ];
443 box_color = _color_schemes[ scheme ][ 7 ];
444 collapse_fill_color = _color_schemes[ scheme ][ 8 ];
445 found_color_0 = _color_schemes[ scheme ][ 9 ];
446 found_color_1 = _color_schemes[ scheme ][ 10 ];
447 found_color_0_and_1 = _color_schemes[ scheme ][ 11 ];
448 dup_box_color = _color_schemes[ scheme ][ 12 ];
449 spec_box_color = _color_schemes[ scheme ][ 13 ];
450 duplication_or_specation_color = _color_schemes[ scheme ][ 14 ];
451 domains_color = _color_schemes[ scheme ][ 15 ];
452 binary_domain_combinations_color = _color_schemes[ scheme ][ 16 ];
453 annotation_color = _color_schemes[ scheme ][ 17 ];
454 ov_color = _color_schemes[ scheme ][ 18 ];
457 void setCurrentColorScheme( final int color_scheme ) {
458 _color_scheme = color_scheme;
461 private void setColorForDefault( final int i, final Color color ) {
462 _color_schemes[ 0 ][ i ] = color;
465 static TreeColorSet createInstance() {
466 final TreeColorSet tcs = new TreeColorSet();
467 tcs.setColorSchema( 0 );
471 static TreeColorSet createInstance( final Configuration configuration ) {
472 final TreeColorSet tcs = new TreeColorSet();
473 if ( ( configuration != null ) && ( configuration.getDisplayColors() != null )
474 && ( configuration.getDisplayColors().size() > 0 ) ) {
475 final Map<String, Color> colors = configuration.getDisplayColors();
476 for( final String field : colors.keySet() ) {
477 final Color color = colors.get( field );
479 tcs.setColorforDefault( field, color );
481 catch ( final IllegalArgumentException ex ) {
482 ForesterUtil.printWarningMessage( Constants.PRG_NAME, ex.getMessage() );
486 tcs.setColorSchema( 0 );