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