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 OVERVIEW                   = "Overview";
  40     public static final String ANNOTATION                 = "Annotation";
  41     public static final String BINARY_DOMAIN_COMBINATIONS = "Binary Domain Combinations";
  42     public static final String DOMAINS                    = "Domains";
  43     public static final String DUPLICATION_OR_SPECATION   = "Duplication or Specation";
  44     public static final String SPECIATION                 = "Speciation";
  45     public static final String DUPLICATION                = "Duplication";
  46     public static final String MATCHING_NODES             = "Matching Nodes";
  47     public static final String COLLAPSED                  = "Collapsed";
  48     public static final String NODE_BOX                   = "Node Box";
  49     public static final String BRANCH                     = "Branch";
  50     public static final String BRANCH_LENGTH              = "Branch Length";
  51     public static final String CONFIDENCE                 = "Confidence";
  52     public static final String TAXONOMY                   = "Taxonomy";
  53     public static final String SEQUENCE                   = "Sequence";
  54     public static final String BACKGROUND_GRADIENT_BOTTOM = "Background Gradient Bottom";
  55     public static final String BACKGROUND                 = "Background";
  56     static final String[]      SCHEME_NAMES               = { "Default", "Black", "Black & White", "Silver",
  57             "The Matrix", "White & Blue", "Cyan", "Clockwork", "Blue", "Blue & White", "Neon" };
  58     static final String[]      COLOR_FIELDS               = { BACKGROUND, BACKGROUND_GRADIENT_BOTTOM, SEQUENCE,
  59             TAXONOMY, CONFIDENCE, BRANCH_LENGTH, BRANCH, NODE_BOX, COLLAPSED, MATCHING_NODES, DUPLICATION, SPECIATION,
  60             DUPLICATION_OR_SPECATION, DOMAINS, BINARY_DOMAIN_COMBINATIONS, ANNOTATION, OVERVIEW };
  61     // All the color sets; better be the same # of sets as there are names!
  62     private final Color[][]    _color_schemes             = { { new Color( 0, 0, 0 ), // background_color
  63             new Color( 0, 100, 100 ), // background_color_gradient_bottom
  64             new Color( 220, 220, 220 ), // sequence  __ Default (same as Black)
  65             new Color( 180, 180, 180 ), // taxonomy
  66             new Color( 56, 176, 222 ), // support
  67             new Color( 140, 140, 140 ), // branch_length_color
  68             new Color( 255, 255, 255 ), // branch_color
  69             new Color( 255, 255, 255 ), // box_color
  70             new Color( 255, 255, 0 ), // collapesed_fill_color
  71             new Color( 0, 255, 0 ), // found_color 0
  72             new Color( 255, 0, 0 ), // found_color 1
  73             new Color( 255, 255, 0 ), // found_color 1 + 2
  74             new Color( 255, 0, 0 ), // duplication_box_color
  75             new Color( 0, 255, 0 ), // speciation_box_color
  76             new Color( 255, 255, 0 ), // duplication_speciation_color
  77             new Color( 123, 104, 238 ), // domains_color
  78             new Color( 65, 105, 255 ), // binary_domain_combinations_color
  79             new Color( 173, 255, 47 ) // annotation
  80             , new Color( 130, 130, 130 )                 // overview
  81             }, { new Color( 0, 0, 0 ), // background_color
  82             new Color( 0, 255, 255 ), // background_color_gradient_bottom
  83             new Color( 220, 220, 220 ), // sequence  __ Black
  84             new Color( 180, 180, 180 ), // taxonomy
  85             new Color( 56, 176, 222 ), // support
  86             new Color( 140, 140, 140 ), // branch_length_color
  87             new Color( 255, 255, 255 ), // branch_color
  88             new Color( 255, 255, 255 ), // box_color
  89             new Color( 255, 255, 0 ), // collapesed_fill_color
  90             new Color( 0, 255, 0 ), // found_color 0
  91             new Color( 255, 0, 0 ), // found_color 1
  92             new Color( 255, 255, 0 ), // found_color 1 + 2
  93             new Color( 255, 0, 0 ), // duplication_box_color
  94             new Color( 0, 255, 0 ), // speciation_box_color
  95             new Color( 255, 255, 0 ), // duplication_speciation_color
  96             new Color( 123, 104, 238 ), // domains_color
  97             new Color( 65, 105, 255 ), // binary_domain_combinations_color
  98             new Color( 173, 255, 47 ) // annotation
  99             , new Color( 130, 130, 130 ) // ov
 100             }, { new Color( 255, 255, 255 ), // background_color
 101             new Color( 0, 255, 255 ), // background_color_gradient_bottom
 102             new Color( 0, 0, 0 ), // sequence  __ Black & White
 103             new Color( 0, 0, 0 ), // taxonomy
 104             new Color( 0, 0, 0 ), // support
 105             new Color( 0, 0, 0 ), // branch_length_color
 106             new Color( 0, 0, 0 ), // branch_color
 107             new Color( 0, 0, 0 ), // box_color
 108             new Color( 0, 0, 0 ), // collapesed_fill_color
 109             new Color( 255, 0, 0 ), // found_color 0
 110             new Color( 0, 255, 0 ), // found_color 1
 111             new Color( 0, 0, 255 ), // found_color 1 + 2
 112             new Color( 255, 0, 0 ), // duplication_box_color
 113             new Color( 0, 255, 0 ), // speciation_box_color
 114             new Color( 255, 255, 0 ), // duplication_speciation_color
 115             new Color( 0, 0, 0 ), // domains_color
 116             new Color( 0, 0, 0 ), // binary_domain_combinations_color
 117             new Color( 0, 0, 0 ) // annotation
 118             , new Color( 220, 220, 220 ) // ov
 119             }, { new Color( 0, 0, 0 ), // background_color
 120             new Color( 0, 255, 255 ), // background_color_gradient_bottom
 121             new Color( 220, 220, 220 ), // sequence __ Silver
 122             new Color( 180, 180, 180 ), // taxonomy
 123             new Color( 140, 140, 140 ), // support
 124             new Color( 140, 140, 140 ), // branch_length_color
 125             new Color( 240, 240, 240 ), // branch_color
 126             new Color( 140, 140, 140 ), // box_color
 127             new Color( 140, 140, 140 ), // collapesed_fill_color
 128             new Color( 255, 0, 0 ), // found_color 0
 129             new Color( 0, 255, 0 ), // found_color 1
 130             new Color( 255, 255, 0 ), // found_color 1 + 2
 131             new Color( 255, 0, 0 ), // duplication_box_color
 132             new Color( 0, 255, 0 ), // speciation_box_color
 133             new Color( 255, 255, 0 ), // duplication_speciation_color
 134             new Color( 180, 180, 180 ), // domains_color
 135             new Color( 180, 180, 180 ), // binary_domain_combinations_color
 136             new Color( 140, 140, 140 ) // annotation
 137             , new Color( 40, 40, 40 ) // ov
 138             }, { new Color( 0, 10, 0 ), // background_color
 139             new Color( 0, 255, 255 ), // background_color_gradient_bottom
 140             new Color( 0, 255, 0 ), // sequence __ the Matrix
 141             new Color( 30, 200, 30 ), // taxonomy
 142             new Color( 0, 155, 0 ), // support
 143             new Color( 0, 100, 0 ), // branch_length_color
 144             new Color( 0, 155, 0 ), // branch_color
 145             new Color( 0, 255, 0 ), // box_color
 146             new Color( 0, 255, 0 ), // collapesed_fill_color
 147             new Color( 255, 0, 0 ), // found_color 0
 148             new Color(  0, 255, 0 ), // found_color 1
 149             new Color( 255, 255, 0 ), // found_color 1 + 2
 150             new Color( 255, 0, 0 ), // duplication_box_color
 151             new Color( 0, 255, 0 ), // speciation_box_color
 152             new Color( 255, 255, 0 ), // duplication_speciation_color
 153             new Color( 0, 235, 0 ), // domains_color
 154             new Color( 0, 235, 0 ), // binary_domain_combinations_color
 155             new Color( 0, 235, 0 ) // annotation
 156             , new Color( 40, 40, 40 ) // ov
 157             }, { new Color( 255, 255, 255 ), // background_color
 158             new Color( 0, 255, 255 ), // background_color_gradient_bottom
 159             new Color( 0, 0, 0 ), //sequence __ White & Blue
 160             new Color( 40, 40, 40 ), // taxonomy
 161             new Color( 0, 125, 0 ), // support
 162             new Color( 70, 70, 0 ), // branch_length_color
 163             new Color( 0, 20, 200 ), // branch_color
 164             new Color( 0, 20, 200 ), // box_color
 165             new Color( 255, 255, 0 ), // collapesed_fill_color
 166             new Color( 0, 255, 0 ), // found_color 0
 167             new Color( 255, 0, 0 ), // found_color 1
 168             new Color( 0, 0, 255 ), // found_color 0 + 1
 169             new Color( 255, 0, 0 ), // duplication_box_color
 170             new Color( 0, 255, 0 ), // speciation_box_color
 171             new Color( 255, 255, 0 ), // duplication_speciation_color
 172             new Color( 123, 104, 238 ), // domains_color
 173             new Color( 65, 105, 225 ), // binary_domain_combinations_color
 174             new Color( 173, 255, 47 ) // annotation
 175             , new Color( 220, 220, 220 ) // ov
 176             }, { new Color( 0, 0, 0 ), // background_color
 177             new Color( 0, 255, 255 ), // background_color_gradient_bottom
 178             new Color( 255, 255, 255 ), // sequence __ Cyan
 179             new Color( 200, 200, 200 ), // taxonomy
 180             new Color( 255, 255, 255 ), // support
 181             new Color( 200, 200, 200 ), // branch_length_color
 182             new Color( 0, 255, 255 ), // branch_color
 183             new Color( 0, 255, 255 ), // box_color
 184             new Color( 255, 255, 0 ), // collapesed_fill_color
 185             new Color( 0, 255, 0 ), // found_color 0
 186             new Color( 0, 0, 255 ), // found_color 1
 187             new Color( 0, 255, 255 ), // found_color 0 + 1
 188             new Color( 255, 0, 0 ), // duplication_box_color
 189             new Color( 0, 255, 0 ), // speciation_box_color
 190             new Color( 255, 255, 0 ), // duplication_speciation_color
 191             new Color( 123, 104, 238 ), // domains_color
 192             new Color( 65, 105, 225 ), // binary_domain_combinations_color
 193             new Color( 173, 255, 47 ) // annotation
 194             , new Color( 0, 120, 120 ) // ov
 195             }, { new Color( 0, 0, 0 ), // background_color
 196             new Color( 0, 255, 255 ), // background_color_gradient_bottom
 197             new Color( 255, 200, 0 ), // sequence __ Clockwork
 198             new Color( 255, 200, 0 ), // taxonomy
 199             new Color( 255, 200, 0 ), // support
 200             new Color( 255, 200, 0 ), // branch_length_color
 201             new Color( 255, 200, 0 ), // branch_color
 202             new Color( 255, 200, 0 ), // box_color
 203             new Color( 255, 255, 255 ), // collapesed_fill_color
 204             new Color( 255, 255, 0 ), // found_color 0
 205             new Color( 0, 255, 255 ), // found_color 1
 206             new Color( 255, 255, 255 ), // found_color 0 + 1
 207             new Color( 255, 0, 0 ), // duplication_box_color
 208             new Color( 0, 255, 0 ), // speciation_box_color
 209             new Color( 255, 255, 0 ), // duplication_speciation_color
 210             new Color( 150, 150, 150 ), // domains_color
 211             new Color( 150, 150, 150 ), // binary_domain_combinations_color
 212             new Color( 150, 150, 150 ) // annotation
 213             , new Color( 150, 150, 150 ) // ov
 214             }, { new Color( 0, 0, 100 ), // background_color
 215             new Color( 0, 255, 255 ), // background_color_gradient_bottom
 216             new Color( 255, 255, 255 ), // sequence __ Blue
 217             new Color( 255, 255, 255 ), // taxonomy
 218             new Color( 255, 0, 0 ), // support
 219             new Color( 255, 0, 0 ), // branch_length_color
 220             new Color( 255, 0, 0 ), // branch_color
 221             new Color( 255, 0, 0 ), // box_color
 222             new Color( 0, 0, 0 ), // collapesed_fill_color
 223             new Color( 0, 255, 0 ), // found_color
 224             new Color( 255, 0, 0 ), // found_color 1
 225             new Color( 255, 255, 0 ), // found_color 1 + 2
 226             new Color( 255, 0, 0 ), // duplication_box_color
 227             new Color( 0, 255, 0 ), // speciation_box_color
 228             new Color( 255, 255, 0 ), // duplication_speciation_color
 229             new Color( 255, 255, 255 ), // domains_color
 230             new Color( 255, 255, 255 ), // binary_domain_combinations_color
 231             new Color( 255, 255, 255 ) // annotation
 232             , new Color( 77, 77, 255 ) // ov
 233             }, { new Color( 0, 0, 0 ), // background_color
 234             new Color( 0, 255, 255 ), // background_color_gradient_bottom
 235             new Color( 255, 255, 255 ), // sequence __ blue &  white
 236             new Color( 255, 255, 255 ), // taxonomy
 237             new Color( 255, 255, 255 ), // support
 238             new Color( 0, 191, 255 ), // branch_length_color
 239             new Color( 0, 191, 255 ), // branch_color
 240             new Color( 0, 191, 255 ), // box_color
 241             new Color( 255, 255, 255 ), // collapesed_fill_color
 242             new Color( 255, 0, 0 ), // found_color 0
 243             new Color( 0, 255, 0 ), // found_color 1
 244             new Color( 255, 255, 0 ), // found_color 0 + 1
 245             new Color( 255, 0, 0 ), // duplication_box_color
 246             new Color( 0, 255, 0 ), // speciation_box_color
 247             new Color( 255, 255, 0 ), // duplication_speciation_color
 248             new Color( 255, 255, 255 ), // domains_color
 249             new Color( 255, 255, 255 ), // binary_domain_combinations_color
 250             new Color( 255, 255, 255 ) // annotation
 251             , new Color( 170, 187, 204 ) // ov
 252             }, { new Color( 0, 0, 0 ), // background_color
 253             new Color( 255, 255, 0 ), // background_color_gradient_bottom
 254             new Color( 127, 255, 0 ), // sequence __ Neon
 255             new Color( 255, 110, 199 ), // taxonomy
 256             new Color( 234, 173, 234 ), // support
 257             new Color( 77, 77, 255 ), // branch_length_color
 258             new Color( 234, 173, 234 ), // branch_color
 259             new Color( 77, 77, 255 ), // box_color
 260             new Color( 77, 77, 255 ), // collapsed_fill_color
 261             new Color( 243, 243, 21 ), // found_color 0
 262             new Color( 255,20, 147 ), // found_color 1
 263             new Color( 255, 255, 255 ), // found_color 1 + 2
 264             new Color( 255, 0, 0 ), // duplication_box_color
 265             new Color( 0, 255, 0 ), // speciation_box_color
 266             new Color( 255, 255, 0 ), // duplication_speciation_color
 267             new Color( 27, 255, 0 ), // domains_color
 268             new Color( 27, 255, 0 ), // binary_domain_combinations_color
 269             new Color( 27, 255, 0 ) // annotation
 270             , new Color( 77, 77, 255 ) // ov
 271             }                                            };
 272     // Color schemes:
 273     private int                _color_scheme;
 274     // The drawing colors
 275     private Color              seq_color;
 276     private Color              taxonomy_color;
 277     private Color              bootstrap_color;
 278     private Color              branch_length_color;
 279     private Color              branch_color;
 280     private Color              box_color;
 281     private Color              background_color;
 282     private Color              background_color_gradient_bottom;
 283     private Color              dup_box_color;
 284     private Color              spec_box_color;
 285     private Color              collapse_fill_color;
 286     private Color              found_color_0;
 287     private Color              found_color_1;
 288     private Color              found_color_0_and_1;
 289     private Color              duplication_or_specation_color;
 290     private Color              domains_color;
 291     private Color              binary_domain_combinations_color;
 292     private Color              annotation_color;
 293     private Color              ov_color;
 294
 295     private TreeColorSet() {
 296         // Hidden constructor.
 297     }
 298
 299     void cycleColorScheme() {
 300         if ( getCurrentColorScheme() >= ( _color_schemes.length - 1 ) ) {
 301             setColorSchema( 0 );
 302         }
 303         else {
 304             setColorSchema( getCurrentColorScheme() + 1 );
 305         }
 306     }
 307
 308     Color getAnnotationColor() {
 309         return annotation_color;
 310     }
 311
 312     Color getBackgroundColor() {
 313         return background_color;
 314     }
 315
 316     Color getBackgroundColorGradientBottom() {
 317         return background_color_gradient_bottom;
 318     }
 319
 320     Color getBinaryDomainCombinationsColor() {
 321         if ( Constants.SPECIAL_CUSTOM ) {
 322             return new Color( 50, 50, 50 );
 323         }
 324         return binary_domain_combinations_color;
 325     }
 326
 327     Color getBoxColor() {
 328         return box_color;
 329     }
 330
 331     Color getBranchColor() {
 332         return branch_color;
 333     }
 334
 335     Color getBranchColorForPdf() {
 336         return Color.BLACK;
 337     }
 338
 339     Color getBranchLengthColor() {
 340         return branch_length_color;
 341     }
 342
 343     Color getCollapseFillColor() {
 344         return collapse_fill_color;
 345     }
 346
 347     Color[][] getColorSchemes() {
 348         return _color_schemes;
 349     }
 350
 351     Color getConfidenceColor() {
 352         return bootstrap_color;
 353     }
 354
 355     int getCurrentColorScheme() {
 356         return _color_scheme;
 357     }
 358
 359     String getCurrentColorSchemeName() {
 360         return SCHEME_NAMES[ getCurrentColorScheme() ];
 361     }
 362
 363     Color getDomainsColor() {
 364         return domains_color;
 365     }
 366
 367     Color getDuplicationBoxColor() {
 368         return dup_box_color;
 369     }
 370
 371     Color getDuplicationOrSpeciationColor() {
 372         return duplication_or_specation_color;
 373     }
 374
 375     Color getFoundColor0() {
 376         return found_color_0;
 377     }
 378
 379     Color getFoundColor1() {
 380         return found_color_1;
 381     }
 382
 383     Color getFoundColor0and1() {
 384         return found_color_0_and_1;
 385     }
 386
 387     Color getGainedCharactersColor() {
 388         return Color.GREEN;
 389     }
 390
 391     Color getLostCharactersColor() {
 392         return Color.RED;
 393     }
 394
 395     Color getOvColor() {
 396         return ov_color;
 397     }
 398
 399     Color getSequenceColor() {
 400         return seq_color;
 401     }
 402
 403     Color getSpecBoxColor() {
 404         return spec_box_color;
 405     }
 406
 407     Color getTaxonomyColor() {
 408         return taxonomy_color;
 409     }
 410
 411     void setColorforDefault( final String color_field_name, final Color color ) {
 412         final String query = color_field_name.trim().replace( '_', ' ' );
 413         boolean found = false;
 414         int i = 0;
 415         for( final String cf : COLOR_FIELDS ) {
 416             if ( query.equalsIgnoreCase( cf ) ) {
 417                 found = true;
 418                 setColorForDefault( i, color );
 419                 break;
 420             }
 421             ++i;
 422         }
 423         if ( !found ) {
 424             throw new IllegalArgumentException( "unknown color field name [" + color_field_name + "]" );
 425         }
 426     }
 427
 428     private void setColorForDefault( final int i, final Color color ) {
 429         _color_schemes[ 0 ][ i ] = color;
 430     }
 431
 432     /**
 433      * Switches colors between different schemes.
 434      */
 435     void setColorSchema( final int scheme ) {
 436         _color_scheme = scheme;
 437         background_color = _color_schemes[ scheme ][ 0 ];
 438         background_color_gradient_bottom = _color_schemes[ scheme ][ 1 ];
 439         seq_color = _color_schemes[ scheme ][ 2 ];
 440         taxonomy_color = _color_schemes[ scheme ][ 3 ];
 441         bootstrap_color = _color_schemes[ scheme ][ 4 ];
 442         branch_length_color = _color_schemes[ scheme ][ 5 ];
 443         branch_color = _color_schemes[ scheme ][ 6 ];
 444         box_color = _color_schemes[ scheme ][ 7 ];
 445         collapse_fill_color = _color_schemes[ scheme ][ 8 ];
 446         found_color_0 = _color_schemes[ scheme ][ 9 ];
 447
 448         found_color_1 = _color_schemes[ scheme ][ 10 ];
 449
 450         found_color_0_and_1 = _color_schemes[ scheme ][11 ];
 451
 452
 453         dup_box_color = _color_schemes[ scheme ][ 12 ];
 454         spec_box_color = _color_schemes[ scheme ][ 13 ];
 455         duplication_or_specation_color = _color_schemes[ scheme ][ 14 ];
 456         domains_color = _color_schemes[ scheme ][ 15 ];
 457         binary_domain_combinations_color = _color_schemes[ scheme ][ 16 ];
 458         annotation_color = _color_schemes[ scheme ][ 17 ];
 459         ov_color = _color_schemes[ scheme ][ 18 ];
 460     }
 461
 462     void setCurrentColorScheme( final int color_scheme ) {
 463         _color_scheme = color_scheme;
 464     }
 465
 466     static TreeColorSet createInstance() {
 467         final TreeColorSet tcs = new TreeColorSet();
 468         tcs.setColorSchema( 0 );
 469         return tcs;
 470     }
 471
 472     static TreeColorSet createInstance( final Configuration configuration ) {
 473         final TreeColorSet tcs = new TreeColorSet();
 474         if ( ( configuration != null ) && ( configuration.getDisplayColors() != null )
 475                 && ( configuration.getDisplayColors().size() > 0 ) ) {
 476             final Map<String, Color> colors = configuration.getDisplayColors();
 477             for( final String field : colors.keySet() ) {
 478                 final Color color = colors.get( field );
 479                 try {
 480                     tcs.setColorforDefault( field, color );
 481                 }
 482                 catch ( final IllegalArgumentException ex ) {
 483                     ForesterUtil.printWarningMessage( Constants.PRG_NAME, ex.getMessage() );
 484                 }
 485             }
 486         }
 487         tcs.setColorSchema( 0 );
 488         return tcs;
 489     }
 490 }