src/jalview/appletgui/FeatureRenderer.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package jalview.appletgui;\r
  20 \r
  21 import java.util.*;\r
  22 \r
  23 import java.awt.*;\r
  24 \r
  25 import java.awt.event.*;\r
  26 \r
  27 \r
  28 import jalview.datamodel.*;\r
  29 \r
  30 /**\r
  31  * DOCUMENT ME!\r
  32  *\r
  33  * @author $author$\r
  34  * @version $Revision$\r
  35  */\r
  36 public class FeatureRenderer\r
  37 {\r
  38   AlignViewport av;\r
  39 \r
  40   Hashtable featureColours = new Hashtable();\r
  41 \r
  42   // A higher level for grouping features of a\r
  43   // particular type\r
  44   Hashtable featureGroups = null;\r
  45 \r
  46   // Holds web links for feature groups and feature types\r
  47   // in the form label|link\r
  48   Hashtable featureLinks = null;\r
  49 \r
  50   // This is actually an Integer held in the hashtable,\r
  51   // Retrieved using the key feature type\r
  52   Object currentColour;\r
  53 \r
  54   String[] renderOrder;\r
  55 \r
  56   FontMetrics fm;\r
  57   int charOffset;\r
  58 \r
  59   float transparency = 1f;\r
  60 \r
  61   TransparencySetter transparencySetter = null;\r
  62 \r
  63   /**\r
  64    * Creates a new FeatureRenderer object.\r
  65    *\r
  66    * @param av DOCUMENT ME!\r
  67    */\r
  68   public FeatureRenderer(AlignViewport av)\r
  69   {\r
  70     this.av = av;\r
  71 \r
  72     if (!System.getProperty("java.version").startsWith("1.1"))\r
  73     {\r
  74       transparencySetter = new TransparencySetter();\r
  75     }\r
  76   }\r
  77 \r
  78   public void transferSettings(FeatureRenderer fr)\r
  79   {\r
  80     renderOrder = fr.renderOrder;\r
  81     featureGroups = fr.featureGroups;\r
  82     featureColours = fr.featureColours;\r
  83     transparency = fr.transparency;\r
  84   }\r
  85 \r
  86 \r
  87   static String lastFeatureAdded;\r
  88   static String lastFeatureGroupAdded;\r
  89   static String lastDescriptionAdded;\r
  90 \r
  91   public boolean createNewFeatures(SequenceI[] sequences,\r
  92                                    SequenceFeature[] features,\r
  93       AlignmentPanel ap)\r
  94   {\r
  95     return amendFeatures(sequences, features, true, ap);\r
  96   }\r
  97 \r
  98 \r
  99   int featureIndex = 0;\r
 100   boolean deleteFeature = false;\r
 101   Panel colourPanel;\r
 102   boolean amendFeatures(final SequenceI[] sequences,\r
 103                         final SequenceFeature[] features,\r
 104                         boolean newFeatures,\r
 105                         final AlignmentPanel ap)\r
 106   {\r
 107     Panel bigPanel = new Panel(new BorderLayout());\r
 108     final TextField name = new TextField(16);\r
 109     final TextField source = new TextField(16);\r
 110     final TextArea description = new TextArea(3, 35);\r
 111     final TextField start = new TextField(8);\r
 112     final TextField end = new TextField(8);\r
 113     final Choice overlaps;\r
 114     Button deleteButton = new Button("Delete");\r
 115     deleteFeature = false;\r
 116 \r
 117     colourPanel = new Panel(null);\r
 118     colourPanel.setSize(110,15);\r
 119     final FeatureRenderer fr = this;\r
 120 \r
 121     Panel panel = new Panel(new GridLayout(3, 1));\r
 122 \r
 123     Panel tmp;\r
 124 \r
 125     ///////////////////////////////////////\r
 126     ///MULTIPLE FEATURES AT SELECTED RESIDUE\r
 127     if(!newFeatures && features.length>1)\r
 128     {\r
 129      panel = new Panel(new GridLayout(4, 1));\r
 130      tmp = new Panel();\r
 131      tmp.add(new Label("Select Feature: "));\r
 132      overlaps = new Choice();\r
 133      for(int i=0; i<features.length; i++)\r
 134      {\r
 135        String item = features[i].getType()\r
 136         +"/"+features[i].getBegin()+"-"+features[i].getEnd();\r
 137 \r
 138        if(features[i].getFeatureGroup()!=null)\r
 139          item += " ("+features[i].getFeatureGroup()+")";\r
 140 \r
 141        overlaps.addItem(item);\r
 142      }\r
 143 \r
 144      tmp.add(overlaps);\r
 145 \r
 146      overlaps.addItemListener(new java.awt.event.ItemListener()\r
 147      {\r
 148        public void itemStateChanged(java.awt.event.ItemEvent e)\r
 149        {\r
 150          int index = overlaps.getSelectedIndex();\r
 151          if (index != -1)\r
 152          {\r
 153            featureIndex = index;\r
 154            name.setText(features[index].getType());\r
 155            description.setText(features[index].getDescription());\r
 156            source.setText(features[index].getFeatureGroup());\r
 157            start.setText(features[index].getBegin()+"");\r
 158            end.setText(features[index].getEnd()+"");\r
 159 \r
 160            SearchResults highlight = new SearchResults();\r
 161            highlight.addResult(sequences[0],\r
 162                                features[index].getBegin(),\r
 163                                features[index].getEnd());\r
 164 \r
 165            ap.seqPanel.seqCanvas.highlightSearchResults(highlight);\r
 166 \r
 167          }\r
 168          Color col = getColour(name.getText());\r
 169          if (col == null)\r
 170          {\r
 171            col = new\r
 172                jalview.schemes.UserColourScheme()\r
 173                .createColourFromName(name.getText());\r
 174          }\r
 175 \r
 176          colourPanel.setBackground(col);\r
 177        }\r
 178      });\r
 179 \r
 180 \r
 181      panel.add(tmp);\r
 182     }\r
 183     //////////\r
 184     //////////////////////////////////////\r
 185 \r
 186 \r
 187     tmp = new Panel();\r
 188     panel.add(tmp);\r
 189     tmp.add(new Label("Name: ", Label.RIGHT));\r
 190     tmp.add(name);\r
 191 \r
 192     tmp = new Panel();\r
 193     panel.add(tmp);\r
 194     tmp.add(new Label("Group: ",Label.RIGHT));\r
 195     tmp.add(source);\r
 196 \r
 197     tmp = new Panel();\r
 198     panel.add(tmp);\r
 199     tmp.add(new Label("Colour: ", Label.RIGHT));\r
 200     tmp.add(colourPanel);\r
 201 \r
 202     bigPanel.add(panel, BorderLayout.NORTH);\r
 203 \r
 204     panel = new Panel();\r
 205     panel.add(new Label("Description: ", Label.RIGHT));\r
 206     panel.add(new ScrollPane().add(description));\r
 207 \r
 208     if (!newFeatures)\r
 209     {\r
 210       bigPanel.add(panel, BorderLayout.SOUTH);\r
 211 \r
 212       panel = new Panel();\r
 213       panel.add(new Label(" Start:", Label.RIGHT));\r
 214       panel.add(start);\r
 215       panel.add(new Label("  End:", Label.RIGHT));\r
 216       panel.add(end);\r
 217       bigPanel.add(panel, BorderLayout.CENTER);\r
 218     }\r
 219     else\r
 220     {\r
 221       bigPanel.add(panel, BorderLayout.CENTER);\r
 222     }\r
 223 \r
 224     if (lastFeatureAdded == null)\r
 225     {\r
 226       if (features[0].type != null)\r
 227       {\r
 228         lastFeatureAdded = features[0].type;\r
 229       }\r
 230       else\r
 231       {\r
 232         lastFeatureAdded = "feature_1";\r
 233       }\r
 234     }\r
 235 \r
 236     if (lastFeatureGroupAdded == null)\r
 237     {\r
 238       if (features[0].featureGroup != null)\r
 239       {\r
 240         lastFeatureGroupAdded = features[0].featureGroup;\r
 241       }\r
 242       else\r
 243       {\r
 244         lastFeatureAdded = "Jalview";\r
 245       }\r
 246     }\r
 247 \r
 248 \r
 249     String title = newFeatures ? "Create New Sequence Feature(s)" :\r
 250         "Amend/Delete Features for "\r
 251         + sequences[0].getName();\r
 252 \r
 253     final JVDialog dialog = new JVDialog(ap.alignFrame,\r
 254                                title,\r
 255                                true,\r
 256                                385,240);\r
 257 \r
 258     dialog.setMainPanel(bigPanel);\r
 259 \r
 260     if(newFeatures)\r
 261     {\r
 262       name.setText(lastFeatureAdded);\r
 263       source.setText(lastFeatureGroupAdded);\r
 264     }\r
 265     else\r
 266     {\r
 267       dialog.ok.setLabel("Amend");\r
 268       dialog.buttonPanel.add(deleteButton, 1);\r
 269       deleteButton.addActionListener(new ActionListener()\r
 270           {\r
 271             public void actionPerformed(ActionEvent evt)\r
 272             {\r
 273               deleteFeature = true;\r
 274               dialog.setVisible(false);\r
 275             }\r
 276           });\r
 277       name.setText(features[0].getType());\r
 278       source.setText(features[0].getFeatureGroup());\r
 279     }\r
 280 \r
 281     start.setText(features[0].getBegin()+"");\r
 282     end.setText(features[0].getEnd()+"");\r
 283     description.setText(features[0].getDescription());\r
 284 \r
 285     Color col = getColour(name.getText());\r
 286     if (col == null)\r
 287     {\r
 288       col = new\r
 289           jalview.schemes.UserColourScheme()\r
 290           .createColourFromName(name.getText());\r
 291     }\r
 292 \r
 293     colourPanel.setBackground(col);\r
 294 \r
 295     dialog.setResizable(true);\r
 296 \r
 297 \r
 298     colourPanel.addMouseListener(new java.awt.event.MouseAdapter()\r
 299     {\r
 300       public void mousePressed(java.awt.event.MouseEvent evt)\r
 301       {\r
 302         new UserDefinedColours(fr, ap.alignFrame);\r
 303       }\r
 304     });\r
 305 \r
 306     dialog.show();\r
 307 \r
 308     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();\r
 309 \r
 310     if (dialog.accept)\r
 311     {\r
 312       //This ensures that the last sequence\r
 313       //is refreshed and new features are rendered\r
 314       lastSeq = null;\r
 315       lastFeatureAdded = name.getText().trim();\r
 316       lastFeatureGroupAdded = source.getText().trim();\r
 317       lastDescriptionAdded = description.getText().replace('\n', ' ');\r
 318     }\r
 319 \r
 320     if(lastFeatureGroupAdded !=null && lastFeatureGroupAdded.length()<1)\r
 321       lastFeatureGroupAdded = null;\r
 322 \r
 323 \r
 324     if (!newFeatures)\r
 325     {\r
 326       SequenceFeature sf = features[featureIndex];\r
 327 \r
 328       if (dialog.accept)\r
 329       {\r
 330         sf.type = lastFeatureAdded;\r
 331         sf.featureGroup = lastFeatureGroupAdded;\r
 332         sf.description = lastDescriptionAdded;\r
 333         setColour(sf.type, colourPanel.getBackground());\r
 334         try\r
 335         {\r
 336           sf.begin = Integer.parseInt(start.getText());\r
 337           sf.end =  Integer.parseInt(end.getText());\r
 338         }\r
 339         catch (NumberFormatException ex)\r
 340         {}\r
 341 \r
 342         ffile.parseDescriptionHTML(sf, false);\r
 343       }\r
 344       if (deleteFeature)\r
 345       {\r
 346         sequences[0].deleteFeature(sf);\r
 347       }\r
 348 \r
 349     }\r
 350     else\r
 351     {\r
 352       if (dialog.accept && name.getText().length()>0)\r
 353       {\r
 354         for (int i = 0; i < sequences.length; i++)\r
 355         {\r
 356           features[i].type = lastFeatureAdded;\r
 357           features[i].featureGroup = lastFeatureGroupAdded;\r
 358           features[i].description = lastDescriptionAdded;\r
 359           sequences[i].addSequenceFeature(features[i]);\r
 360           ffile.parseDescriptionHTML(features[i], false);\r
 361         }\r
 362 \r
 363         if (av.featuresDisplayed == null)\r
 364         {\r
 365           av.featuresDisplayed = new Hashtable();\r
 366         }\r
 367 \r
 368         if (featureGroups == null)\r
 369         {\r
 370           featureGroups = new Hashtable();\r
 371         }\r
 372 \r
 373 \r
 374 \r
 375         col = colourPanel.getBackground();\r
 376         setColour(lastFeatureAdded, col);\r
 377 \r
 378         if(lastFeatureGroupAdded!=null)\r
 379         {\r
 380           featureGroups.put(lastFeatureGroupAdded, new Boolean(true));\r
 381           av.featuresDisplayed.put(lastFeatureGroupAdded,\r
 382                                    new Integer(col.getRGB()));\r
 383         }\r
 384         findAllFeatures();\r
 385 \r
 386         return true;\r
 387       }\r
 388       else\r
 389       {\r
 390         return false;\r
 391       }\r
 392     }\r
 393 \r
 394     findAllFeatures();\r
 395 \r
 396     return true;\r
 397   }\r
 398 \r
 399 \r
 400   public Color findFeatureColour(Color initialCol, SequenceI seq, int i)\r
 401   {\r
 402     overview = true;\r
 403     if (!av.showSequenceFeatures)\r
 404     {\r
 405       return initialCol;\r
 406     }\r
 407 \r
 408     lastSeq = seq;\r
 409     sequenceFeatures = lastSeq.getSequenceFeatures();\r
 410     if (sequenceFeatures == null)\r
 411     {\r
 412       return initialCol;\r
 413     }\r
 414 \r
 415     sfSize = sequenceFeatures.length;\r
 416 \r
 417     if (jalview.util.Comparison.isGap(lastSeq.getCharAt(i)))\r
 418     {\r
 419       return Color.white;\r
 420     }\r
 421 \r
 422     currentColour = null;\r
 423 \r
 424     drawSequence(null, lastSeq, lastSeq.findPosition(i), -1, -1);\r
 425 \r
 426     if (currentColour == null)\r
 427     {\r
 428       return initialCol;\r
 429     }\r
 430 \r
 431     return new Color( ( (Integer) currentColour).intValue());\r
 432   }\r
 433 \r
 434   /**\r
 435    * This is used by the Molecule Viewer to get the accurate colour\r
 436    * of the rendered sequence\r
 437    */\r
 438   boolean overview = false;\r
 439 \r
 440 \r
 441   /**\r
 442    * DOCUMENT ME!\r
 443    *\r
 444    * @param g DOCUMENT ME!\r
 445    * @param seq DOCUMENT ME!\r
 446    * @param sg DOCUMENT ME!\r
 447    * @param start DOCUMENT ME!\r
 448    * @param end DOCUMENT ME!\r
 449    * @param x1 DOCUMENT ME!\r
 450    * @param y1 DOCUMENT ME!\r
 451    * @param width DOCUMENT ME!\r
 452    * @param height DOCUMENT ME!\r
 453    */\r
 454   // String type;\r
 455   // SequenceFeature sf;\r
 456 \r
 457   SequenceI lastSeq;\r
 458   SequenceFeature[] sequenceFeatures;\r
 459   int sfSize, sfindex, spos, epos;\r
 460 \r
 461   public void drawSequence(Graphics g, SequenceI seq,\r
 462                            int start, int end, int y1)\r
 463   {\r
 464     if (seq.getSequenceFeatures() == null\r
 465         || seq.getSequenceFeatures().length == 0)\r
 466     {\r
 467       return;\r
 468     }\r
 469 \r
 470     if (transparencySetter != null && g != null)\r
 471     {\r
 472       transparencySetter.setTransparency(g, transparency);\r
 473     }\r
 474 \r
 475     if (lastSeq == null || seq != lastSeq || sequenceFeatures!=seq.getSequenceFeatures())\r
 476     {\r
 477       lastSeq = seq;\r
 478       sequenceFeatures = seq.getSequenceFeatures();\r
 479       sfSize = sequenceFeatures.length;\r
 480     }\r
 481 \r
 482     if (av.featuresDisplayed == null || renderOrder == null)\r
 483     {\r
 484       findAllFeatures();\r
 485       if (av.featuresDisplayed.size() < 1)\r
 486       {\r
 487         return;\r
 488       }\r
 489 \r
 490       sequenceFeatures = seq.getSequenceFeatures();\r
 491       sfSize = sequenceFeatures.length;\r
 492     }\r
 493     if (!overview)\r
 494     {\r
 495       spos = lastSeq.findPosition(start);\r
 496       epos = lastSeq.findPosition(end);\r
 497       if (g != null)\r
 498       {\r
 499         fm = g.getFontMetrics();\r
 500       }\r
 501     }\r
 502     String type;\r
 503     for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)\r
 504     {\r
 505       type = renderOrder[renderIndex];\r
 506       if (!av.featuresDisplayed.containsKey(type))\r
 507       {\r
 508         continue;\r
 509       }\r
 510 \r
 511       // loop through all features in sequence to find\r
 512       // current feature to render\r
 513       for (sfindex = 0; sfindex < sfSize; sfindex++)\r
 514       {\r
 515         if (!sequenceFeatures[sfindex].type.equals(type))\r
 516         {\r
 517           continue;\r
 518         }\r
 519 \r
 520         if (featureGroups != null\r
 521             && sequenceFeatures[sfindex].featureGroup != null\r
 522             &&\r
 523             featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)\r
 524             &&\r
 525             ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].\r
 526                                             featureGroup)).\r
 527             booleanValue())\r
 528         {\r
 529           continue;\r
 530         }\r
 531 \r
 532         if (!overview && (sequenceFeatures[sfindex].getBegin() > epos\r
 533                           || sequenceFeatures[sfindex].getEnd() < spos))\r
 534         {\r
 535           continue;\r
 536         }\r
 537 \r
 538         if (overview)\r
 539         {\r
 540           if (sequenceFeatures[sfindex].begin <= start &&\r
 541               sequenceFeatures[sfindex].end >= start)\r
 542           {\r
 543             currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].\r
 544                 type);\r
 545           }\r
 546 \r
 547         }\r
 548         else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))\r
 549         {\r
 550 \r
 551           renderFeature(g, seq,\r
 552                         seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 553                         seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 554                         new Color( ( (Integer) av.featuresDisplayed.get(\r
 555                             sequenceFeatures[sfindex].type)).intValue()),\r
 556                         start, end, y1);\r
 557           renderFeature(g, seq,\r
 558                         seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 559                         seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 560                         new Color( ( (Integer) av.featuresDisplayed.get(\r
 561                             sequenceFeatures[sfindex].type)).intValue()),\r
 562                         start, end, y1);\r
 563 \r
 564         }\r
 565         else\r
 566         {\r
 567           renderFeature(g, seq,\r
 568                         seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 569                         seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 570                         getColour(sequenceFeatures[sfindex].type),\r
 571                         start, end, y1);\r
 572         }\r
 573 \r
 574       }\r
 575     }\r
 576 \r
 577     if (transparencySetter != null && g != null)\r
 578     {\r
 579       transparencySetter.setTransparency(g, 1.0f);\r
 580     }\r
 581   }\r
 582 \r
 583   char s;\r
 584   int i;\r
 585   void renderFeature(Graphics g, SequenceI seq,\r
 586                      int fstart, int fend, Color featureColour, int start,\r
 587                      int end, int y1)\r
 588   {\r
 589 \r
 590     if ( ( (fstart <= end) && (fend >= start)))\r
 591     {\r
 592       if (fstart < start)\r
 593       { // fix for if the feature we have starts before the sequence start,\r
 594         fstart = start; // but the feature end is still valid!!\r
 595       }\r
 596 \r
 597       if (fend >= end)\r
 598       {\r
 599         fend = end;\r
 600       }\r
 601 \r
 602       for (i = fstart; i <= fend; i++)\r
 603       {\r
 604         s = seq.getCharAt(i);\r
 605 \r
 606         if (jalview.util.Comparison.isGap(s))\r
 607         {\r
 608           continue;\r
 609         }\r
 610 \r
 611         g.setColor(featureColour);\r
 612 \r
 613         g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);\r
 614 \r
 615         if (!av.validCharWidth)\r
 616         {\r
 617           continue;\r
 618         }\r
 619 \r
 620         g.setColor(Color.white);\r
 621         charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
 622         g.drawString(String.valueOf(s),\r
 623                      charOffset + (av.charWidth * (i - start)),\r
 624                      (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5;\r
 625 \r
 626       }\r
 627     }\r
 628   }\r
 629 \r
 630   void findAllFeatures()\r
 631   {\r
 632     jalview.schemes.UserColourScheme ucs = new\r
 633         jalview.schemes.UserColourScheme();\r
 634 \r
 635     av.featuresDisplayed = new Hashtable();\r
 636     Vector allfeatures = new Vector();\r
 637     for (int i = 0; i < av.alignment.getHeight(); i++)\r
 638     {\r
 639       SequenceFeature[] features = av.alignment.getSequenceAt(i).\r
 640           getSequenceFeatures();\r
 641 \r
 642       if (features == null)\r
 643       {\r
 644         continue;\r
 645       }\r
 646 \r
 647       int index = 0;\r
 648       while (index < features.length)\r
 649       {\r
 650         if (!av.featuresDisplayed.containsKey(features[index].getType()))\r
 651         {\r
 652           if (getColour(features[index].getType()) == null)\r
 653           {\r
 654             featureColours.put(features[index].getType(),\r
 655                                ucs.createColourFromName(features[index].\r
 656                 getType()));\r
 657           }\r
 658 \r
 659           av.featuresDisplayed.put(features[index].getType(),\r
 660                                    new Integer(getColour(features[index].\r
 661               getType()).getRGB()));\r
 662           allfeatures.addElement(features[index].getType());\r
 663         }\r
 664         index++;\r
 665       }\r
 666     }\r
 667 \r
 668     renderOrder = new String[allfeatures.size()];\r
 669     Enumeration en = allfeatures.elements();\r
 670     int i = allfeatures.size() - 1;\r
 671     while (en.hasMoreElements())\r
 672     {\r
 673       renderOrder[i] = en.nextElement().toString();\r
 674       i--;\r
 675     }\r
 676   }\r
 677 \r
 678   public Color getColour(String featureType)\r
 679   {\r
 680     return (Color) featureColours.get(featureType);\r
 681   }\r
 682 \r
 683   public void addNewFeature(String name, Color col)\r
 684   {\r
 685 \r
 686     setColour(name, col);\r
 687     if (av.featuresDisplayed == null)\r
 688     {\r
 689       av.featuresDisplayed = new Hashtable();\r
 690     }\r
 691 \r
 692     av.featuresDisplayed.put(name, "NOGROUP");\r
 693   }\r
 694 \r
 695   public void setColour(String featureType, Color col)\r
 696   {\r
 697     featureColours.put(featureType, col);\r
 698   }\r
 699 \r
 700   public void setFeaturePriority(Object[][] data)\r
 701   {\r
 702     // The feature table will display high priority\r
 703     // features at the top, but theses are the ones\r
 704     // we need to render last, so invert the data\r
 705     if (av.featuresDisplayed != null)\r
 706     {\r
 707       av.featuresDisplayed.clear();\r
 708     }\r
 709 \r
 710     renderOrder = new String[data.length];\r
 711 \r
 712     if (data.length > 0)\r
 713     {\r
 714       for (int i = 0; i < data.length; i++)\r
 715       {\r
 716         String type = data[i][0].toString();\r
 717         setColour(type, (Color) data[i][1]);\r
 718         if ( ( (Boolean) data[i][2]).booleanValue())\r
 719         {\r
 720           av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));\r
 721         }\r
 722 \r
 723         renderOrder[data.length - i - 1] = type;\r
 724       }\r
 725     }\r
 726   }\r
 727 }\r
 728 \r
 729 class TransparencySetter\r
 730 {\r
 731   void setTransparency(Graphics g, float value)\r
 732   {\r
 733      Graphics2D g2 = (Graphics2D) g;\r
 734      g2.setComposite(\r
 735         AlphaComposite.getInstance(\r
 736              AlphaComposite.SRC_OVER, value));\r
 737   }\r
 738 }\r