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         ap.paintAlignment(true);\r
 382 \r
 383         return true;\r
 384       }\r
 385       else\r
 386       {\r
 387         return false;\r
 388       }\r
 389     }\r
 390 \r
 391     findAllFeatures();\r
 392 \r
 393     ap.paintAlignment(true);\r
 394 \r
 395     return true;\r
 396   }\r
 397 \r
 398 \r
 399   public Color findFeatureColour(Color initialCol, SequenceI seq, int i)\r
 400   {\r
 401     overview = true;\r
 402     if (!av.showSequenceFeatures)\r
 403     {\r
 404       return initialCol;\r
 405     }\r
 406 \r
 407     lastSeq = seq;\r
 408     sequenceFeatures = lastSeq.getSequenceFeatures();\r
 409     if (sequenceFeatures == null)\r
 410     {\r
 411       return initialCol;\r
 412     }\r
 413 \r
 414     sfSize = sequenceFeatures.length;\r
 415 \r
 416     if (jalview.util.Comparison.isGap(lastSeq.getCharAt(i)))\r
 417     {\r
 418       return Color.white;\r
 419     }\r
 420 \r
 421     currentColour = null;\r
 422 \r
 423     drawSequence(null, lastSeq, lastSeq.findPosition(i), -1, -1);\r
 424 \r
 425     if (currentColour == null)\r
 426     {\r
 427       return initialCol;\r
 428     }\r
 429 \r
 430     return new Color( ( (Integer) currentColour).intValue());\r
 431   }\r
 432 \r
 433   /**\r
 434    * This is used by the Molecule Viewer to get the accurate colour\r
 435    * of the rendered sequence\r
 436    */\r
 437   boolean overview = false;\r
 438 \r
 439 \r
 440   /**\r
 441    * DOCUMENT ME!\r
 442    *\r
 443    * @param g DOCUMENT ME!\r
 444    * @param seq DOCUMENT ME!\r
 445    * @param sg DOCUMENT ME!\r
 446    * @param start DOCUMENT ME!\r
 447    * @param end DOCUMENT ME!\r
 448    * @param x1 DOCUMENT ME!\r
 449    * @param y1 DOCUMENT ME!\r
 450    * @param width DOCUMENT ME!\r
 451    * @param height DOCUMENT ME!\r
 452    */\r
 453   // String type;\r
 454   // SequenceFeature sf;\r
 455 \r
 456   SequenceI lastSeq;\r
 457   SequenceFeature[] sequenceFeatures;\r
 458   int sfSize, sfindex, spos, epos;\r
 459 \r
 460   synchronized public void drawSequence(Graphics g, SequenceI seq,\r
 461                            int start, int end, int y1)\r
 462   {\r
 463     if (seq.getSequenceFeatures() == null\r
 464         || seq.getSequenceFeatures().length == 0)\r
 465     {\r
 466       return;\r
 467     }\r
 468 \r
 469     if (transparencySetter != null && g != null)\r
 470     {\r
 471       transparencySetter.setTransparency(g, transparency);\r
 472     }\r
 473 \r
 474     if (lastSeq == null || seq != lastSeq || sequenceFeatures!=seq.getSequenceFeatures())\r
 475     {\r
 476       lastSeq = seq;\r
 477       sequenceFeatures = seq.getSequenceFeatures();\r
 478       sfSize = sequenceFeatures.length;\r
 479     }\r
 480 \r
 481     if (av.featuresDisplayed == null || renderOrder == null)\r
 482     {\r
 483       findAllFeatures();\r
 484       if (av.featuresDisplayed.size() < 1)\r
 485       {\r
 486         return;\r
 487       }\r
 488 \r
 489       sequenceFeatures = seq.getSequenceFeatures();\r
 490       sfSize = sequenceFeatures.length;\r
 491     }\r
 492     if (!overview)\r
 493     {\r
 494       spos = lastSeq.findPosition(start);\r
 495       epos = lastSeq.findPosition(end);\r
 496       if (g != null)\r
 497       {\r
 498         fm = g.getFontMetrics();\r
 499       }\r
 500     }\r
 501     String type;\r
 502     for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)\r
 503     {\r
 504       type = renderOrder[renderIndex];\r
 505       if (!av.featuresDisplayed.containsKey(type))\r
 506       {\r
 507         continue;\r
 508       }\r
 509 \r
 510       // loop through all features in sequence to find\r
 511       // current feature to render\r
 512       for (sfindex = 0; sfindex < sfSize; sfindex++)\r
 513       {\r
 514         if (!sequenceFeatures[sfindex].type.equals(type))\r
 515         {\r
 516           continue;\r
 517         }\r
 518 \r
 519         if (featureGroups != null\r
 520             && sequenceFeatures[sfindex].featureGroup != null\r
 521             &&\r
 522             featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)\r
 523             &&\r
 524             ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].\r
 525                                             featureGroup)).\r
 526             booleanValue())\r
 527         {\r
 528           continue;\r
 529         }\r
 530 \r
 531         if (!overview && (sequenceFeatures[sfindex].getBegin() > epos\r
 532                           || sequenceFeatures[sfindex].getEnd() < spos))\r
 533         {\r
 534           continue;\r
 535         }\r
 536 \r
 537         if (overview)\r
 538         {\r
 539           if (sequenceFeatures[sfindex].begin <= start &&\r
 540               sequenceFeatures[sfindex].end >= start)\r
 541           {\r
 542             currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].\r
 543                 type);\r
 544           }\r
 545 \r
 546         }\r
 547         else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))\r
 548         {\r
 549 \r
 550           renderFeature(g, seq,\r
 551                         seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 552                         seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 553                         new Color( ( (Integer) av.featuresDisplayed.get(\r
 554                             sequenceFeatures[sfindex].type)).intValue()),\r
 555                         start, end, y1);\r
 556           renderFeature(g, seq,\r
 557                         seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 558                         seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 559                         new Color( ( (Integer) av.featuresDisplayed.get(\r
 560                             sequenceFeatures[sfindex].type)).intValue()),\r
 561                         start, end, y1);\r
 562 \r
 563         }\r
 564         else\r
 565         {\r
 566           renderFeature(g, seq,\r
 567                         seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 568                         seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 569                         getColour(sequenceFeatures[sfindex].type),\r
 570                         start, end, y1);\r
 571         }\r
 572 \r
 573       }\r
 574     }\r
 575 \r
 576     if (transparencySetter != null && g != null)\r
 577     {\r
 578       transparencySetter.setTransparency(g, 1.0f);\r
 579     }\r
 580   }\r
 581 \r
 582   char s;\r
 583   int i;\r
 584   void renderFeature(Graphics g, SequenceI seq,\r
 585                      int fstart, int fend, Color featureColour, int start,\r
 586                      int end, int y1)\r
 587   {\r
 588 \r
 589     if ( ( (fstart <= end) && (fend >= start)))\r
 590     {\r
 591       if (fstart < start)\r
 592       { // fix for if the feature we have starts before the sequence start,\r
 593         fstart = start; // but the feature end is still valid!!\r
 594       }\r
 595 \r
 596       if (fend >= end)\r
 597       {\r
 598         fend = end;\r
 599       }\r
 600 \r
 601       for (i = fstart; i <= fend; i++)\r
 602       {\r
 603         s = seq.getCharAt(i);\r
 604 \r
 605         if (jalview.util.Comparison.isGap(s))\r
 606         {\r
 607           continue;\r
 608         }\r
 609 \r
 610         g.setColor(featureColour);\r
 611 \r
 612         g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);\r
 613 \r
 614         if (!av.validCharWidth)\r
 615         {\r
 616           continue;\r
 617         }\r
 618 \r
 619         g.setColor(Color.white);\r
 620         charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
 621         g.drawString(String.valueOf(s),\r
 622                      charOffset + (av.charWidth * (i - start)),\r
 623                      (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5;\r
 624 \r
 625       }\r
 626     }\r
 627   }\r
 628 \r
 629   void findAllFeatures()\r
 630   {\r
 631     jalview.schemes.UserColourScheme ucs = new\r
 632         jalview.schemes.UserColourScheme();\r
 633 \r
 634     av.featuresDisplayed = new Hashtable();\r
 635     Vector allfeatures = new Vector();\r
 636     for (int i = 0; i < av.alignment.getHeight(); i++)\r
 637     {\r
 638       SequenceFeature[] features = av.alignment.getSequenceAt(i).\r
 639           getSequenceFeatures();\r
 640 \r
 641       if (features == null)\r
 642       {\r
 643         continue;\r
 644       }\r
 645 \r
 646       int index = 0;\r
 647       while (index < features.length)\r
 648       {\r
 649         if (!av.featuresDisplayed.containsKey(features[index].getType()))\r
 650         {\r
 651           if (getColour(features[index].getType()) == null)\r
 652           {\r
 653             featureColours.put(features[index].getType(),\r
 654                                ucs.createColourFromName(features[index].\r
 655                 getType()));\r
 656           }\r
 657 \r
 658           av.featuresDisplayed.put(features[index].getType(),\r
 659                                    new Integer(getColour(features[index].\r
 660               getType()).getRGB()));\r
 661           allfeatures.addElement(features[index].getType());\r
 662         }\r
 663         index++;\r
 664       }\r
 665     }\r
 666 \r
 667     renderOrder = new String[allfeatures.size()];\r
 668     Enumeration en = allfeatures.elements();\r
 669     int i = allfeatures.size() - 1;\r
 670     while (en.hasMoreElements())\r
 671     {\r
 672       renderOrder[i] = en.nextElement().toString();\r
 673       i--;\r
 674     }\r
 675   }\r
 676 \r
 677   public Color getColour(String featureType)\r
 678   {\r
 679     if (!featureColours.containsKey(featureType))\r
 680     {\r
 681       jalview.schemes.UserColourScheme ucs = new\r
 682           jalview.schemes.UserColourScheme();\r
 683       Color col = ucs.createColourFromName(featureType);\r
 684       featureColours.put(featureType, col);\r
 685       return col;\r
 686     }\r
 687     else\r
 688       return (Color) featureColours.get(featureType);\r
 689   }\r
 690 \r
 691 \r
 692   public void setColour(String featureType, Color col)\r
 693   {\r
 694     featureColours.put(featureType, col);\r
 695   }\r
 696 \r
 697   public void setFeaturePriority(Object[][] data)\r
 698   {\r
 699     // The feature table will display high priority\r
 700     // features at the top, but theses are the ones\r
 701     // we need to render last, so invert the data\r
 702     if (av.featuresDisplayed != null)\r
 703     {\r
 704       av.featuresDisplayed.clear();\r
 705     }\r
 706 \r
 707    /* if (visibleNew)\r
 708     {\r
 709       if (av.featuresDisplayed != null)\r
 710       {\r
 711         av.featuresDisplayed.clear();\r
 712       }\r
 713       else\r
 714       {\r
 715         av.featuresDisplayed = new Hashtable();\r
 716       }\r
 717     }\r
 718     if (data == null)\r
 719     {\r
 720       return;\r
 721     }*/\r
 722 \r
 723 \r
 724     renderOrder = new String[data.length];\r
 725 \r
 726     if (data.length > 0)\r
 727     {\r
 728       for (int i = 0; i < data.length; i++)\r
 729       {\r
 730         String type = data[i][0].toString();\r
 731         setColour(type, (Color) data[i][1]);\r
 732         if ( ( (Boolean) data[i][2]).booleanValue())\r
 733         {\r
 734           av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));\r
 735         }\r
 736 \r
 737         renderOrder[data.length - i - 1] = type;\r
 738       }\r
 739     }\r
 740   }\r
 741 }\r
 742 \r
 743 class TransparencySetter\r
 744 {\r
 745   void setTransparency(Graphics g, float value)\r
 746   {\r
 747      Graphics2D g2 = (Graphics2D) g;\r
 748      g2.setComposite(\r
 749         AlphaComposite.getInstance(\r
 750              AlphaComposite.SRC_OVER, value));\r
 751   }\r
 752 }\r