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