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