src/jalview/gui/FeatureRenderer.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2006 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.gui;\r
  20 \r
  21 import jalview.datamodel.*;\r
  22 \r
  23 import java.awt.*;\r
  24 \r
  25 import java.util.*;\r
  26 \r
  27 import java.awt.image.*;\r
  28 import javax.swing.*;\r
  29 import javax.swing.JOptionPane;\r
  30 import java.awt.event.*;\r
  31 \r
  32 \r
  33 /**\r
  34  * DOCUMENT ME!\r
  35  *\r
  36  * @author $author$\r
  37  * @version $Revision$\r
  38  */\r
  39 public class FeatureRenderer\r
  40 {\r
  41     AlignViewport av;\r
  42     Color resBoxColour;\r
  43     float transparency = 1.0f;\r
  44     FontMetrics fm;\r
  45     int charOffset;\r
  46 \r
  47     Hashtable featureColours = new Hashtable();\r
  48 \r
  49 \r
  50     // A higher level for grouping features of a\r
  51    // particular type\r
  52     Hashtable featureGroups = null;\r
  53 \r
  54     // This is actually an Integer held in the hashtable,\r
  55     // Retrieved using the key feature type\r
  56     Object currentColour;\r
  57 \r
  58     String [] renderOrder;\r
  59 \r
  60     /**\r
  61      * Creates a new FeatureRenderer object.\r
  62      *\r
  63      * @param av DOCUMENT ME!\r
  64      */\r
  65     public FeatureRenderer(AlignViewport av)\r
  66     {\r
  67         this.av = av;\r
  68     }\r
  69 \r
  70     public void transferSettings(FeatureRenderer fr)\r
  71     {\r
  72       renderOrder = fr.renderOrder;\r
  73       featureGroups = fr.featureGroups;\r
  74       featureColours = fr.featureColours;\r
  75       transparency =  fr.transparency;\r
  76     }\r
  77 \r
  78     BufferedImage offscreenImage;\r
  79     boolean offscreenRender = false;\r
  80     public Color findFeatureColour(Color initialCol, SequenceI seq, int res)\r
  81     {\r
  82       return new Color( findFeatureColour (initialCol.getRGB(),\r
  83                         seq, res ));\r
  84     }\r
  85 \r
  86     /**\r
  87      * This is used by the Molecule Viewer and Overview to\r
  88      * get the accurate colourof the rendered sequence\r
  89      */\r
  90     public int findFeatureColour(int initialCol, SequenceI seq, int column)\r
  91     {\r
  92       if(!av.showSequenceFeatures)\r
  93         return initialCol;\r
  94 \r
  95       if(seq!=lastSeq)\r
  96       {\r
  97         lastSeq = seq;\r
  98         sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();\r
  99         if(sequenceFeatures==null)\r
 100           return initialCol;\r
 101 \r
 102         sfSize = sequenceFeatures.length;\r
 103       }\r
 104 \r
 105       if(jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))\r
 106         return Color.white.getRGB();\r
 107 \r
 108 \r
 109       //Only bother making an offscreen image if transparency is applied\r
 110       if(transparency!=1.0f && offscreenImage==null)\r
 111       {\r
 112         offscreenImage = new BufferedImage(1,1,BufferedImage.TYPE_INT_ARGB);\r
 113       }\r
 114 \r
 115       currentColour = null;\r
 116 \r
 117       offscreenRender = true;\r
 118 \r
 119       if(offscreenImage!=null)\r
 120       {\r
 121         offscreenImage.setRGB(0,0,initialCol);\r
 122         drawSequence(offscreenImage.getGraphics(),\r
 123                      lastSeq,\r
 124                      column,column,0);\r
 125 \r
 126         return offscreenImage.getRGB(0,0);\r
 127       }\r
 128       else\r
 129       {\r
 130         drawSequence(null,\r
 131                     lastSeq,\r
 132                     lastSeq.findPosition(column),\r
 133                     -1, -1);\r
 134 \r
 135         if (currentColour == null)\r
 136           return initialCol;\r
 137         else\r
 138           return  ((Integer)currentColour).intValue();\r
 139       }\r
 140 \r
 141 \r
 142     }\r
 143 \r
 144 \r
 145     /**\r
 146      * DOCUMENT ME!\r
 147      *\r
 148      * @param g DOCUMENT ME!\r
 149      * @param seq DOCUMENT ME!\r
 150      * @param sg DOCUMENT ME!\r
 151      * @param start DOCUMENT ME!\r
 152      * @param end DOCUMENT ME!\r
 153      * @param x1 DOCUMENT ME!\r
 154      * @param y1 DOCUMENT ME!\r
 155      * @param width DOCUMENT ME!\r
 156      * @param height DOCUMENT ME!\r
 157      */\r
 158    // String type;\r
 159    // SequenceFeature sf;\r
 160     SequenceI lastSeq;\r
 161     SequenceFeature [] sequenceFeatures;\r
 162     int sfSize, sfindex, spos, epos;\r
 163 \r
 164     public void drawSequence(Graphics g, SequenceI seq,\r
 165                              int start, int end, int y1)\r
 166     {\r
 167       if ( seq.getDatasetSequence().getSequenceFeatures() == null\r
 168           || seq.getDatasetSequence().getSequenceFeatures().length==0)\r
 169         return;\r
 170 \r
 171       if(g!=null)\r
 172         fm = g.getFontMetrics();\r
 173 \r
 174 \r
 175       if (av.featuresDisplayed == null\r
 176           || renderOrder==null\r
 177           || newFeatureAdded)\r
 178        {\r
 179          findAllFeatures();\r
 180          if(av.featuresDisplayed.size()<1)\r
 181            return;\r
 182 \r
 183          sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
 184          sfSize = sequenceFeatures.length;\r
 185        }\r
 186 \r
 187        if(lastSeq==null || seq!=lastSeq)\r
 188       {\r
 189         lastSeq = seq;\r
 190         sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
 191         sfSize = sequenceFeatures.length;\r
 192       }\r
 193 \r
 194 \r
 195       if (transparency != 1 && g!=null)\r
 196       {\r
 197         Graphics2D g2 = (Graphics2D) g;\r
 198         g2.setComposite(\r
 199             AlphaComposite.getInstance(\r
 200                 AlphaComposite.SRC_OVER, transparency));\r
 201       }\r
 202 \r
 203       if(!offscreenRender)\r
 204       {\r
 205         spos = lastSeq.findPosition(start);\r
 206         epos = lastSeq.findPosition(end);\r
 207       }\r
 208 \r
 209 \r
 210       String type;\r
 211       for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)\r
 212        {\r
 213         type =  renderOrder[renderIndex];\r
 214 \r
 215         if(type==null || !av.featuresDisplayed.containsKey(type))\r
 216           continue;\r
 217 \r
 218         // loop through all features in sequence to find\r
 219         // current feature to render\r
 220         for (sfindex = 0; sfindex < sfSize; sfindex++)\r
 221         {\r
 222           if(sequenceFeatures.length<=sfindex)\r
 223           {\r
 224             continue;\r
 225           }\r
 226           if (!sequenceFeatures[sfindex].type.equals(type))\r
 227             continue;\r
 228 \r
 229           if (featureGroups != null\r
 230               && sequenceFeatures[sfindex].featureGroup != null\r
 231               &&\r
 232               featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)\r
 233               &&\r
 234               ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).\r
 235               booleanValue())\r
 236           {\r
 237             continue;\r
 238           }\r
 239 \r
 240           if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos\r
 241                             || sequenceFeatures[sfindex].getEnd() < spos))\r
 242             continue;\r
 243 \r
 244           if (offscreenRender && offscreenImage==null)\r
 245           {\r
 246             if (sequenceFeatures[sfindex].begin <= start &&\r
 247                 sequenceFeatures[sfindex].end  >= start)\r
 248             {\r
 249               currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].\r
 250                  type);\r
 251             }\r
 252           }\r
 253           else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))\r
 254           {\r
 255 \r
 256             renderFeature(g, seq,\r
 257                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 258                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 259                           new Color( ( (Integer) av.featuresDisplayed.get(\r
 260                 sequenceFeatures[sfindex].type)).intValue()),\r
 261                           start, end, y1);\r
 262             renderFeature(g, seq,\r
 263                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 264                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 265                           new Color( ( (Integer) av.featuresDisplayed.get(\r
 266                 sequenceFeatures[sfindex].type)).intValue()),\r
 267                           start, end, y1);\r
 268 \r
 269           }\r
 270           else\r
 271             renderFeature(g, seq,\r
 272                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 273                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 274                           getColour(sequenceFeatures[sfindex].type),\r
 275                           start, end, y1);\r
 276 \r
 277 \r
 278         }\r
 279 \r
 280       }\r
 281 \r
 282         if(transparency!=1.0f && g!=null)\r
 283         {\r
 284           Graphics2D g2 = (Graphics2D) g;\r
 285           g2.setComposite(\r
 286               AlphaComposite.getInstance(\r
 287                   AlphaComposite.SRC_OVER, 1.0f));\r
 288         }\r
 289     }\r
 290 \r
 291 \r
 292     char s;\r
 293     int i;\r
 294     void renderFeature(Graphics g, SequenceI seq,\r
 295                        int fstart, int fend, Color featureColour, int start, int end,  int y1)\r
 296     {\r
 297 \r
 298       if (((fstart <= end) && (fend >= start)))\r
 299       {\r
 300         if (fstart < start)\r
 301         { // fix for if the feature we have starts before the sequence start,\r
 302           fstart = start; // but the feature end is still valid!!\r
 303         }\r
 304 \r
 305         if (fend >= end)\r
 306         {\r
 307           fend = end;\r
 308         }\r
 309           int pady = (y1 + av.charHeight) - av.charHeight / 5;\r
 310           for (i = fstart; i <= fend; i++)\r
 311           {\r
 312             s = seq.getCharAt(i);\r
 313 \r
 314             if (jalview.util.Comparison.isGap(s))\r
 315             {\r
 316               continue;\r
 317             }\r
 318 \r
 319             g.setColor(featureColour);\r
 320 \r
 321             g.fillRect( (i - start) * av.charWidth, y1, av.charWidth,av.charHeight);\r
 322 \r
 323             if(offscreenRender || !av.validCharWidth)\r
 324               continue;\r
 325 \r
 326             g.setColor(Color.white);\r
 327             charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
 328             g.drawString(String.valueOf(s),\r
 329                          charOffset + (av.charWidth * (i - start)),\r
 330                          pady);\r
 331 \r
 332           }\r
 333       }\r
 334     }\r
 335 \r
 336 \r
 337     boolean newFeatureAdded = false;\r
 338 \r
 339     public void featuresAdded()\r
 340     {\r
 341       findAllFeatures();\r
 342     }\r
 343 \r
 344    boolean findingFeatures = false;\r
 345    synchronized void findAllFeatures()\r
 346    {\r
 347       newFeatureAdded = false;\r
 348 \r
 349       if(findingFeatures)\r
 350       {\r
 351         newFeatureAdded = true;\r
 352         return;\r
 353       }\r
 354 \r
 355       findingFeatures = true;\r
 356       jalview.schemes.UserColourScheme ucs = new\r
 357           jalview.schemes.UserColourScheme();\r
 358 \r
 359       if(av.featuresDisplayed==null)\r
 360         av.featuresDisplayed = new Hashtable();\r
 361 \r
 362       av.featuresDisplayed.clear();\r
 363 \r
 364       Vector allfeatures = new Vector();\r
 365       for (int i = 0; i < av.alignment.getHeight(); i++)\r
 366       {\r
 367         SequenceFeature [] features\r
 368             = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
 369 \r
 370         if (features == null)\r
 371           continue;\r
 372 \r
 373         int index = 0;\r
 374         while (index < features.length)\r
 375         {\r
 376           if (!av.featuresDisplayed.containsKey(features[index].getType()))\r
 377           {\r
 378             if(!(features[index].begin == 0 && features[index].end ==0))\r
 379             {\r
 380               // If beginning and end are 0, the feature is for the whole sequence\r
 381               // and we don't want to render the feature in the normal way\r
 382 \r
 383               if (getColour(features[index].getType()) == null)\r
 384               {\r
 385                  featureColours.put(features[index].getType(),\r
 386                                    ucs.createColourFromName(features[index].\r
 387                     getType()));\r
 388               }\r
 389 \r
 390               av.featuresDisplayed.put(features[index].getType(),\r
 391                                        new Integer(getColour(features[index].\r
 392                   getType()).getRGB()));\r
 393               allfeatures.addElement(features[index].getType());\r
 394             }\r
 395           }\r
 396           index++;\r
 397         }\r
 398       }\r
 399 \r
 400       renderOrder = new String[allfeatures.size()];\r
 401       Enumeration en = allfeatures.elements();\r
 402       int i = allfeatures.size()-1;\r
 403       while(en.hasMoreElements())\r
 404       {\r
 405         renderOrder[i] = en.nextElement().toString();\r
 406         i--;\r
 407       }\r
 408 \r
 409       findingFeatures = false;\r
 410     }\r
 411 \r
 412     public Color getColour(String featureType)\r
 413     {\r
 414       Color colour = (Color)featureColours.get(featureType);\r
 415       return colour;\r
 416     }\r
 417 \r
 418 \r
 419     static String lastFeatureAdded;\r
 420     static String lastFeatureGroupAdded;\r
 421     static String lastDescriptionAdded;\r
 422 \r
 423     public boolean createNewFeatures(SequenceI[] sequences,\r
 424                                   SequenceFeature [] features)\r
 425     {\r
 426       return amendFeatures(sequences, features, true, null);\r
 427     }\r
 428 \r
 429     int featureIndex = 0;\r
 430     boolean amendFeatures(final SequenceI[] sequences,\r
 431                           final SequenceFeature[] features,\r
 432                           boolean newFeatures,\r
 433                           final AlignmentPanel ap)\r
 434     {\r
 435       JPanel bigPanel = new JPanel(new BorderLayout());\r
 436       final JComboBox name = new JComboBox();\r
 437       final JComboBox source = new JComboBox();\r
 438       final JTextArea description = new JTextArea(3,25);\r
 439       final JSpinner start = new JSpinner();\r
 440       final JSpinner end = new JSpinner();\r
 441       start.setPreferredSize(new Dimension(80,20));\r
 442       end.setPreferredSize(new Dimension(80,20));\r
 443       final JPanel colour = new JPanel();\r
 444       colour.setBorder(BorderFactory.createEtchedBorder());\r
 445       colour.setMaximumSize(new Dimension(40,10));\r
 446       colour.addMouseListener(new MouseAdapter()\r
 447           {\r
 448             public void mousePressed(MouseEvent evt)\r
 449             {\r
 450               colour.setBackground(\r
 451                   JColorChooser.showDialog(Desktop.desktop,\r
 452                                            "Select Feature Colour",\r
 453                                            colour.getBackground()));\r
 454             }\r
 455           });\r
 456 \r
 457       JPanel panel = new JPanel(new GridLayout(3, 2));\r
 458       panel.add(new JLabel("Sequence Feature Name: ",JLabel.RIGHT));\r
 459       panel.add(name);\r
 460       panel.add(new JLabel("Feature Group: ", JLabel.RIGHT));\r
 461       panel.add(source);\r
 462       panel.add(new JLabel("Feature Colour: ", JLabel.RIGHT));\r
 463       JPanel tmp = new JPanel();\r
 464       tmp.add(colour);\r
 465       colour.setPreferredSize(new Dimension(150,15));\r
 466       panel.add(tmp);\r
 467       name.setEditable(true);\r
 468       source.setEditable(true);\r
 469 \r
 470       bigPanel.add(panel, BorderLayout.NORTH);\r
 471       panel = new JPanel();\r
 472       panel.add(new JLabel("Description: ", JLabel.RIGHT));\r
 473       description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
 474       description.setLineWrap(true);\r
 475       panel.add(new JScrollPane(description));\r
 476 \r
 477       if(!newFeatures)\r
 478       {\r
 479         bigPanel.add(panel, BorderLayout.SOUTH);\r
 480 \r
 481         panel = new JPanel();\r
 482         panel.add(new JLabel(" Start:", JLabel.RIGHT));\r
 483         panel.add(start);\r
 484         panel.add(new JLabel("  End:", JLabel.RIGHT));\r
 485         panel.add(end);\r
 486         bigPanel.add(panel, BorderLayout.CENTER);\r
 487       }\r
 488       else\r
 489         bigPanel.add(panel, BorderLayout.CENTER);\r
 490 \r
 491       if (lastFeatureAdded == null)\r
 492         if (features[0].type != null)\r
 493           lastFeatureAdded = features[0].type;\r
 494         else\r
 495           lastFeatureAdded = "feature_1";\r
 496 \r
 497       if (lastFeatureGroupAdded == null)\r
 498         if (features[0].featureGroup != null)\r
 499           lastFeatureGroupAdded = features[0].featureGroup;\r
 500         else\r
 501           lastFeatureAdded = "Jalview";\r
 502 \r
 503 \r
 504       Enumeration en;\r
 505       if (featureGroups != null)\r
 506       {\r
 507         en = featureGroups.keys();\r
 508         while (en.hasMoreElements())\r
 509         {\r
 510           source.addItem(en.nextElement().toString());\r
 511         }\r
 512       }\r
 513 \r
 514       if (newFeatures)\r
 515       {\r
 516         if(av.featuresDisplayed != null)\r
 517         {\r
 518           en = av.featuresDisplayed.keys();\r
 519           while (en.hasMoreElements())\r
 520           {\r
 521             name.addItem(en.nextElement().toString());\r
 522           }\r
 523         }\r
 524 \r
 525         name.setSelectedItem(lastFeatureAdded);\r
 526         source.setSelectedItem(lastFeatureGroupAdded);\r
 527         description.setText(\r
 528             lastDescriptionAdded == null ?\r
 529             features[0].description : lastDescriptionAdded);\r
 530 \r
 531         if (getColour(lastFeatureAdded) != null)\r
 532         {\r
 533           colour.setBackground(getColour(lastFeatureAdded));\r
 534         }\r
 535         else\r
 536         {\r
 537           colour.setBackground(new Color(60, 160, 115));\r
 538         }\r
 539 \r
 540       }\r
 541       else if (!newFeatures)\r
 542       {\r
 543         featureIndex = 0;\r
 544         for(int f=0; f<features.length; f++)\r
 545         {\r
 546           name.addItem(features[f].getType().toString());\r
 547         }\r
 548 \r
 549         description.setText(features[0].getDescription());\r
 550         source.setSelectedItem(features[0].getFeatureGroup());\r
 551         start.setValue(new Integer(features[0].getBegin()));\r
 552         end.setValue(new Integer(features[0].getEnd()));\r
 553         colour.setBackground(\r
 554                 getColour(name.getSelectedItem().toString()));\r
 555         name.addItemListener(new ItemListener()\r
 556         {\r
 557           public void itemStateChanged(ItemEvent e)\r
 558           {\r
 559             int index = name.getSelectedIndex();\r
 560             if(index!=-1)\r
 561             {\r
 562               featureIndex = index;\r
 563               description.setText(features[index].getDescription());\r
 564               source.setSelectedItem(features[index].getFeatureGroup());\r
 565               start.setValue(new Integer(features[index].getBegin()));\r
 566               end.setValue(new Integer(features[index].getEnd()));\r
 567               colour.setBackground(\r
 568                   getColour(name.getSelectedItem().toString()));\r
 569 \r
 570               SearchResults highlight = new SearchResults();\r
 571               highlight.addResult(sequences[0],\r
 572                                   features[index].getBegin(),\r
 573                                   features[index].getEnd());\r
 574 \r
 575               ap.seqPanel.seqCanvas.highlightSearchResults(highlight);\r
 576 \r
 577             }\r
 578             Color col = getColour(name.getSelectedItem().toString());\r
 579             if (col == null)\r
 580               col = new\r
 581                   jalview.schemes.UserColourScheme()\r
 582                   .createColourFromName(name.getSelectedItem().toString());\r
 583 \r
 584             colour.setBackground(col);\r
 585           }\r
 586         });\r
 587 \r
 588       }\r
 589 \r
 590 \r
 591       Object [] options;\r
 592       if(!newFeatures)\r
 593         options = new Object[]{"Amend", "Delete", "Cancel"};\r
 594       else\r
 595         options = new Object[]{"OK", "Cancel"};\r
 596 \r
 597       String title = newFeatures ?  "Create New Sequence Feature(s)" :\r
 598                                     "Amend/Delete Features for "\r
 599                                     +sequences[0].getName();\r
 600 \r
 601       int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,\r
 602                                                    bigPanel,\r
 603                                                    title,\r
 604                                                    JOptionPane.YES_NO_CANCEL_OPTION,\r
 605                                                    JOptionPane.QUESTION_MESSAGE,\r
 606                                                    null,\r
 607                                                    options, "OK");\r
 608 \r
 609       jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();\r
 610 \r
 611       if (reply == JOptionPane.OK_OPTION\r
 612           && name.getSelectedItem() != null\r
 613           && source.getSelectedItem() != null)\r
 614       {\r
 615         //This ensures that the last sequence\r
 616         //is refreshed and new features are rendered\r
 617         lastSeq=null;\r
 618         lastFeatureAdded = name.getSelectedItem().toString();\r
 619         lastFeatureGroupAdded = source.getSelectedItem().toString();\r
 620         lastDescriptionAdded = description.getText().replaceAll("\n", " ");\r
 621       }\r
 622 \r
 623       if(!newFeatures)\r
 624       {\r
 625         SequenceFeature sf = features[featureIndex];\r
 626 \r
 627         if(reply==JOptionPane.NO_OPTION)\r
 628           sequences[0].getDatasetSequence().deleteFeature(sf);\r
 629         else if(reply==JOptionPane.YES_OPTION)\r
 630         {\r
 631           sf.type = lastFeatureAdded;\r
 632           sf.featureGroup = lastFeatureGroupAdded;\r
 633           sf.description = lastDescriptionAdded;\r
 634           setColour(sf.type, colour.getBackground());\r
 635           try{\r
 636             sf.begin = ((Integer)start.getValue()).intValue();\r
 637             sf.end = ((Integer)end.getValue()).intValue();\r
 638           }catch(NumberFormatException ex)\r
 639           {}\r
 640 \r
 641           ffile.parseDescriptionHTML(sf, false);\r
 642         }\r
 643       }\r
 644       else\r
 645       {\r
 646         if (reply == JOptionPane.OK_OPTION\r
 647             && name.getSelectedItem() != null\r
 648             && source.getSelectedItem() != null)\r
 649         {\r
 650           for (int i = 0; i < sequences.length; i++)\r
 651           {\r
 652             features[i].type = lastFeatureAdded;\r
 653             features[i].featureGroup = lastFeatureGroupAdded;\r
 654             features[i].description = lastDescriptionAdded;\r
 655             sequences[i].addSequenceFeature(features[i]);\r
 656             ffile.parseDescriptionHTML(features[i], false);\r
 657           }\r
 658 \r
 659           if (av.featuresDisplayed == null)\r
 660             av.featuresDisplayed = new Hashtable();\r
 661 \r
 662           if (featureGroups == null)\r
 663             featureGroups = new Hashtable();\r
 664 \r
 665           featureGroups.put(lastFeatureGroupAdded, new Boolean(true));\r
 666 \r
 667           Color col = colour.getBackground();\r
 668           setColour(lastFeatureAdded, colour.getBackground());\r
 669 \r
 670           av.featuresDisplayed.put(lastFeatureGroupAdded,\r
 671                                    new Integer(col.getRGB()));\r
 672 \r
 673           findAllFeatures();\r
 674 \r
 675           return true;\r
 676         }\r
 677         else\r
 678           return false;\r
 679       }\r
 680 \r
 681       if(name.getSelectedIndex()==-1)\r
 682         findAllFeatures();\r
 683 \r
 684 \r
 685       return true;\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 setTransparency(float value)\r
 694     {\r
 695       transparency = value;\r
 696     }\r
 697 \r
 698     public float getTransparency()\r
 699     {\r
 700       return transparency;\r
 701     }\r
 702 \r
 703     public void setFeaturePriority(Object [][] data)\r
 704     {\r
 705       // The feature table will display high priority\r
 706       // features at the top, but theses are the ones\r
 707       // we need to render last, so invert the data\r
 708       if(av.featuresDisplayed!=null)\r
 709         av.featuresDisplayed.clear();\r
 710       else\r
 711         av.featuresDisplayed = new Hashtable();\r
 712 \r
 713       renderOrder = new String[data.length];\r
 714 \r
 715       if (data.length > 0)\r
 716         for (int i = 0; i < data.length; i++)\r
 717         {\r
 718           String type = data[i][0].toString();\r
 719           setColour(type, (Color) data[i][1]);\r
 720           if ( ( (Boolean) data[i][2]).booleanValue())\r
 721           {\r
 722             av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));\r
 723           }\r
 724 \r
 725           renderOrder[data.length - i - 1] = type;\r
 726         }\r
 727 \r
 728     }\r
 729 \r
 730 \r
 731 \r
 732 \r
 733 }\r