Fixed issue with reading from TreeBase
[jalview.git] / forester / java / src / org / forester / archaeopteryx / TreeColorSet.java
1 // $Id:
2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
4 //
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
8 // All rights reserved
9 //
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.
14 //
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.
19 //
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
23 //
24 // Contact: phylosoft @ gmail . com
25 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
26
27 package org.forester.archaeopteryx;
28
29 import java.awt.Color;
30 import java.util.Map;
31
32 import org.forester.util.ForesterUtil;
33
34 public final class TreeColorSet {
35
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
283             }                                            };
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;
305
306     private TreeColorSet() {
307         // Hidden constructor.
308     }
309
310     public Color getDomainBaseColor() {
311         return domain_base_color;
312     }
313
314     public Color getDomainLabelColor() {
315         return domain_label_color;
316     }
317
318     private void setColorForDefault( final int i, final Color color ) {
319         _color_schemes[ 0 ][ i ] = color;
320     }
321
322     void cycleColorScheme() {
323         if ( getCurrentColorScheme() >= ( _color_schemes.length - 1 ) ) {
324             setColorSchema( 0 );
325         }
326         else {
327             setColorSchema( getCurrentColorScheme() + 1 );
328         }
329     }
330
331     Color getAnnotationColor() {
332         return annotation_color;
333     }
334
335     Color getBackgroundColor() {
336         return background_color;
337     }
338
339     Color getBackgroundColorGradientBottom() {
340         return background_color_gradient_bottom;
341     }
342
343     Color getBinaryDomainCombinationsColor() {
344         if ( AptxConstants.SPECIAL_CUSTOM ) {
345             return new Color( 50, 50, 50 );
346         }
347         return binary_domain_combinations_color;
348     }
349
350     Color getBoxColor() {
351         return box_color;
352     }
353
354     Color getBranchColor() {
355         return branch_color;
356     }
357
358     Color getBranchColorForPdf() {
359         return Color.BLACK;
360     }
361
362     Color getBranchLengthColor() {
363         return branch_length_color;
364     }
365
366     Color getCollapseFillColor() {
367         return collapse_fill_color;
368     }
369
370     Color[][] getColorSchemes() {
371         return _color_schemes;
372     }
373
374     Color getConfidenceColor() {
375         return bootstrap_color;
376     }
377
378     int getCurrentColorScheme() {
379         return _color_scheme;
380     }
381
382     String getCurrentColorSchemeName() {
383         return SCHEME_NAMES[ getCurrentColorScheme() ];
384     }
385
386     Color getDuplicationBoxColor() {
387         return dup_box_color;
388     }
389
390     Color getDuplicationOrSpeciationColor() {
391         return duplication_or_specation_color;
392     }
393
394     Color getFoundColor0() {
395         return found_color_0;
396     }
397
398     Color getFoundColor0and1() {
399         return found_color_0_and_1;
400     }
401
402     Color getFoundColor1() {
403         return found_color_1;
404     }
405
406     Color getGainedCharactersColor() {
407         return Color.GREEN;
408     }
409
410     Color getLostCharactersColor() {
411         return Color.RED;
412     }
413
414     Color getOvColor() {
415         return ov_color;
416     }
417
418     Color getSequenceColor() {
419         return seq_color;
420     }
421
422     Color getSpecBoxColor() {
423         return spec_box_color;
424     }
425
426     Color getTaxonomyColor() {
427         return taxonomy_color;
428     }
429
430     void setColorforDefault( final String color_field_name, final Color color ) {
431         final String query = color_field_name.trim().replace( '_', ' ' );
432         boolean found = false;
433         int i = 0;
434         for( final String cf : COLOR_FIELDS ) {
435             if ( query.equalsIgnoreCase( cf ) ) {
436                 found = true;
437                 setColorForDefault( i, color );
438                 break;
439             }
440             ++i;
441         }
442         if ( !found ) {
443             throw new IllegalArgumentException( "unknown color field name [" + color_field_name + "]" );
444         }
445     }
446
447     /**
448      * Switches colors between different schemes.
449      */
450     void setColorSchema( final int scheme ) {
451         _color_scheme = scheme;
452         background_color = _color_schemes[ scheme ][ 0 ];
453         background_color_gradient_bottom = _color_schemes[ scheme ][ 1 ];
454         seq_color = _color_schemes[ scheme ][ 2 ];
455         taxonomy_color = _color_schemes[ scheme ][ 3 ];
456         bootstrap_color = _color_schemes[ scheme ][ 4 ];
457         branch_length_color = _color_schemes[ scheme ][ 5 ];
458         branch_color = _color_schemes[ scheme ][ 6 ];
459         box_color = _color_schemes[ scheme ][ 7 ];
460         collapse_fill_color = _color_schemes[ scheme ][ 8 ];
461         found_color_0 = _color_schemes[ scheme ][ 9 ];
462         found_color_1 = _color_schemes[ scheme ][ 10 ];
463         found_color_0_and_1 = _color_schemes[ scheme ][ 11 ];
464         dup_box_color = _color_schemes[ scheme ][ 12 ];
465         spec_box_color = _color_schemes[ scheme ][ 13 ];
466         duplication_or_specation_color = _color_schemes[ scheme ][ 14 ];
467         domain_label_color = _color_schemes[ scheme ][ 15 ];
468         domain_base_color = _color_schemes[ scheme ][ 16 ];
469         binary_domain_combinations_color = _color_schemes[ scheme ][ 17 ];
470         annotation_color = _color_schemes[ scheme ][ 18 ];
471         ov_color = _color_schemes[ scheme ][ 19 ];
472     }
473
474     void setCurrentColorScheme( final int color_scheme ) {
475         _color_scheme = color_scheme;
476     }
477
478     static TreeColorSet createInstance() {
479         final TreeColorSet tcs = new TreeColorSet();
480         tcs.setColorSchema( 0 );
481         return tcs;
482     }
483
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 );
491                 try {
492                     tcs.setColorforDefault( field, color );
493                 }
494                 catch ( final IllegalArgumentException ex ) {
495                     ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, ex.getMessage() );
496                 }
497             }
498         }
499         tcs.setColorSchema( 0 );
500         return tcs;
501     }
502 }