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 /*
  35  * Maintains the color schemes and a set of colors for drawing a tree.
  36  */
  37 public final class TreeColorSet {
  38
  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" };
  64     // Color schemes:
  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( 180, 180, 180 ), // 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, 255 ), // 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( 180, 180, 180 ), // 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, 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( 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( 240, 240, 240 ), // 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, 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( 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( 0, 20, 200 ), // 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( 0, 255, 255 ), // 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, 200, 0 ), // 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( 255, 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( 0, 191, 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( 234, 173, 234 ), // 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
 276             }                                            };
 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;
 297
 298     private TreeColorSet() {
 299         // Hidden constructor.
 300     }
 301
 302     void cycleColorScheme() {
 303         if ( getCurrentColorScheme() >= ( _color_schemes.length - 1 ) ) {
 304             setColorSchema( 0 );
 305         }
 306         else {
 307             setColorSchema( getCurrentColorScheme() + 1 );
 308         }
 309     }
 310
 311     Color getAnnotationColor() {
 312         return annotation_color;
 313     }
 314
 315     Color getBackgroundColor() {
 316         return background_color;
 317     }
 318
 319     Color getBackgroundColorGradientBottom() {
 320         return background_color_gradient_bottom;
 321     }
 322
 323     Color getBinaryDomainCombinationsColor() {
 324         if ( Constants.SPECIAL_CUSTOM ) {
 325             return new Color( 50, 50, 50 );
 326         }
 327         return binary_domain_combinations_color;
 328     }
 329
 330     Color getBoxColor() {
 331         return box_color;
 332     }
 333
 334     Color getBranchColor() {
 335         return branch_color;
 336     }
 337
 338     Color getBranchColorForPdf() {
 339         return Color.BLACK;
 340     }
 341
 342     Color getBranchLengthColor() {
 343         return branch_length_color;
 344     }
 345
 346     Color getCollapseFillColor() {
 347         return collapse_fill_color;
 348     }
 349
 350     Color[][] getColorSchemes() {
 351         return _color_schemes;
 352     }
 353
 354     Color getConfidenceColor() {
 355         return bootstrap_color;
 356     }
 357
 358     int getCurrentColorScheme() {
 359         return _color_scheme;
 360     }
 361
 362     String getCurrentColorSchemeName() {
 363         return SCHEME_NAMES[ getCurrentColorScheme() ];
 364     }
 365
 366     Color getDomainsColor() {
 367         return domains_color;
 368     }
 369
 370     Color getDuplicationBoxColor() {
 371         return dup_box_color;
 372     }
 373
 374     Color getDuplicationOrSpeciationColor() {
 375         return duplication_or_specation_color;
 376     }
 377
 378     Color getFoundColor0() {
 379         return found_color_0;
 380     }
 381
 382     Color getFoundColor0and1() {
 383         return found_color_0_and_1;
 384     }
 385
 386     Color getFoundColor1() {
 387         return found_color_1;
 388     }
 389
 390     Color getGainedCharactersColor() {
 391         return Color.GREEN;
 392     }
 393
 394     Color getLostCharactersColor() {
 395         return Color.RED;
 396     }
 397
 398     Color getOvColor() {
 399         return ov_color;
 400     }
 401
 402     Color getSequenceColor() {
 403         return seq_color;
 404     }
 405
 406     Color getSpecBoxColor() {
 407         return spec_box_color;
 408     }
 409
 410     Color getTaxonomyColor() {
 411         return taxonomy_color;
 412     }
 413
 414     void setColorforDefault( final String color_field_name, final Color color ) {
 415         final String query = color_field_name.trim().replace( '_', ' ' );
 416         boolean found = false;
 417         int i = 0;
 418         for( final String cf : COLOR_FIELDS ) {
 419             if ( query.equalsIgnoreCase( cf ) ) {
 420                 found = true;
 421                 setColorForDefault( i, color );
 422                 break;
 423             }
 424             ++i;
 425         }
 426         if ( !found ) {
 427             throw new IllegalArgumentException( "unknown color field name [" + color_field_name + "]" );
 428         }
 429     }
 430
 431     /**
 432      * Switches colors between different schemes.
 433      */
 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 ];
 455     }
 456
 457     void setCurrentColorScheme( final int color_scheme ) {
 458         _color_scheme = color_scheme;
 459     }
 460
 461     private void setColorForDefault( final int i, final Color color ) {
 462         _color_schemes[ 0 ][ i ] = color;
 463     }
 464
 465     static TreeColorSet createInstance() {
 466         final TreeColorSet tcs = new TreeColorSet();
 467         tcs.setColorSchema( 0 );
 468         return tcs;
 469     }
 470
 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 );
 478                 try {
 479                     tcs.setColorforDefault( field, color );
 480                 }
 481                 catch ( final IllegalArgumentException ex ) {
 482                     ForesterUtil.printWarningMessage( Constants.PRG_NAME, ex.getMessage() );
 483                 }
 484             }
 485         }
 486         tcs.setColorSchema( 0 );
 487         return tcs;
 488     }
 489 }