src/jalview/gui/AlignFrame.java

   1 /********************\r
   2  * 2004 Jalview Reengineered\r
   3  * Barton Group\r
   4  * Dundee University\r
   5  *\r
   6  * AM Waterhouse\r
   7  *******************/\r
   8 \r
   9 \r
  10 \r
  11 \r
  12 package jalview.gui;\r
  13 \r
  14 import jalview.jbgui.GAlignFrame;\r
  15 import jalview.schemes.*;\r
  16 import jalview.datamodel.*;\r
  17 import jalview.analysis.*;\r
  18 import jalview.io.*;\r
  19 import jalview.ws.*;\r
  20 import java.awt.*;\r
  21 import java.awt.event.*;\r
  22 import java.awt.print.*;\r
  23 import javax.swing.*;\r
  24 import javax.swing.event.*;\r
  25 import java.util.*;\r
  26 import  java.awt.datatransfer.*;\r
  27 \r
  28 \r
  29 public class AlignFrame extends GAlignFrame\r
  30 {\r
  31   final AlignmentPanel alignPanel;\r
  32   final AlignViewport viewport;\r
  33   public AlignFrame(AlignmentI al)\r
  34   {\r
  35     viewport = new AlignViewport(al,true,true,false);\r
  36 \r
  37     String fontName = jalview.bin.Cache.getProperty("FONT_NAME");\r
  38     String fontStyle= jalview.bin.Cache.getProperty("FONT_STYLE");\r
  39     String fontSize = jalview.bin.Cache.getProperty("FONT_SIZE");\r
  40     if(fontName!=null && fontStyle!=null && fontSize!=null)\r
  41       viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );\r
  42 \r
  43 \r
  44     alignPanel = new AlignmentPanel(this, viewport);\r
  45     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
  46 \r
  47     // add conservation graph to alignment\r
  48     viewport.updateConservation();\r
  49     viewport.updateConsensus();\r
  50 \r
  51     alignPanel.annotationPanel.adjustPanelHeight();\r
  52     alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
  53     alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
  54 \r
  55 \r
  56     addInternalFrameListener(new InternalFrameAdapter()\r
  57    {\r
  58      public void internalFrameActivated(InternalFrameEvent evt)\r
  59      {\r
  60           javax.swing.SwingUtilities.invokeLater(new Runnable()\r
  61           {\r
  62             public void run()\r
  63             {      alignPanel.requestFocus();    }\r
  64           });\r
  65 \r
  66      }\r
  67    });\r
  68 \r
  69   }\r
  70 \r
  71   protected void saveAs_actionPerformed(ActionEvent e)\r
  72   {\r
  73     String suffix [] = null;\r
  74     if(e.getActionCommand().equals("FASTA"))\r
  75       suffix = new String[]{"fa", "fasta"};\r
  76     else if(e.getActionCommand().equals("MSF"))\r
  77       suffix = new String[]{"msf"};\r
  78     else if(e.getActionCommand().equals("CLUSTAL"))\r
  79       suffix = new String[]{"aln"};\r
  80     else if(e.getActionCommand().equals("BLC"))\r
  81       suffix = new String[]{"blc"};\r
  82     else if(e.getActionCommand().equals("PIR"))\r
  83       suffix = new String[]{"pir"};\r
  84     else if(e.getActionCommand().equals("PFAM"))\r
  85       suffix = new String[]{"pfam"};\r
  86 \r
  87     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")\r
  88         , suffix, e.getActionCommand()+" file");\r
  89     chooser.setFileView(new JalviewFileView());\r
  90     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
  91     chooser.setToolTipText("Save");\r
  92     int value = chooser.showSaveDialog(this);\r
  93     if(value == JalviewFileChooser.APPROVE_OPTION)\r
  94     {\r
  95       String choice =  chooser.getSelectedFile().getPath();\r
  96       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
  97       String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
  98       try{\r
  99         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
 100         out.println(output);\r
 101         out.close();\r
 102       }\r
 103       catch(Exception ex){}\r
 104     }\r
 105 \r
 106   }\r
 107 \r
 108   protected void outputText_actionPerformed(ActionEvent e)\r
 109   {\r
 110      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
 111      JInternalFrame frame = new JInternalFrame();\r
 112      cap.formatForOutput();\r
 113      frame.setContentPane(cap);\r
 114      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
 115      cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
 116   }\r
 117 \r
 118   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 119   {\r
 120     HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
 121     htmlOutput = null;\r
 122   }\r
 123 \r
 124   protected void createPNG_actionPerformed(ActionEvent e)\r
 125   {\r
 126     alignPanel.makePNG();\r
 127   }\r
 128 \r
 129   protected void epsFile_actionPerformed(ActionEvent e)\r
 130   {\r
 131     alignPanel.makeEPS();\r
 132   }\r
 133 \r
 134 \r
 135   public void printMenuItem_actionPerformed(ActionEvent e)\r
 136   {\r
 137     //Putting in a thread avoids Swing painting problems\r
 138     PrintThread thread = new PrintThread();\r
 139     thread.start();\r
 140   }\r
 141 \r
 142   class PrintThread extends Thread\r
 143   {\r
 144     public void run()\r
 145     {\r
 146       PrinterJob printJob = PrinterJob.getPrinterJob();\r
 147       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
 148       printJob.setPrintable(alignPanel, pf);\r
 149       if (printJob.printDialog())\r
 150       {\r
 151         try\r
 152         {\r
 153           printJob.print();\r
 154         }\r
 155         catch (Exception PrintException)\r
 156         {\r
 157           PrintException.printStackTrace();\r
 158         }\r
 159       }\r
 160     }\r
 161 \r
 162   }\r
 163 \r
 164 \r
 165 \r
 166 \r
 167   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 168   {\r
 169     try{\r
 170       this.setClosed(true);\r
 171     }catch(Exception ex){}\r
 172   }\r
 173 \r
 174   Stack historyList = new Stack();\r
 175   Stack redoList = new Stack();\r
 176   JMenuBar jMenuBar1 = new JMenuBar();\r
 177 \r
 178   void updateEditMenuBar()\r
 179   {\r
 180     if(historyList.size()>0)\r
 181      {\r
 182        undoMenuItem.setEnabled(true);\r
 183        Object [] history = (Object[])historyList.get(0);\r
 184        undoMenuItem.setText("Undo "+history[0]);\r
 185      }\r
 186     else\r
 187     {\r
 188       undoMenuItem.setEnabled(false);\r
 189       undoMenuItem.setText("Undo");\r
 190     }\r
 191 \r
 192     if(redoList.size()>0)\r
 193      {\r
 194        redoMenuItem.setEnabled(true);\r
 195        Object [] history = (Object[])redoList.get(0);\r
 196        redoMenuItem.setText("Redo "+history[0]);\r
 197      }\r
 198     else\r
 199     {\r
 200       redoMenuItem.setEnabled(false);\r
 201       redoMenuItem.setText("Redo");\r
 202     }\r
 203   }\r
 204 \r
 205   public void addHistoryItem(String type)\r
 206   {\r
 207     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 208     redoList.clear();\r
 209     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 210     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 211     {\r
 212       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 213                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 214     }\r
 215 \r
 216     historyList.add(0, new Object[]{type,  seq} );\r
 217     updateEditMenuBar();\r
 218   }\r
 219 \r
 220   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 221   {\r
 222     Object [] history = (Object[])historyList.remove(0);\r
 223     // add the redo state before continuing!!\r
 224     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 225     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
 226     {\r
 227       seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
 228                             viewport.getAlignment().getSequenceAt(i).\r
 229                             getSequence());\r
 230     }\r
 231     /////////\r
 232 \r
 233     redoList.add(0, new Object[] {history[0], seq});\r
 234 \r
 235       seq = (SequenceI[]) history[1];\r
 236       viewport.setAlignment( new Alignment(seq) );\r
 237       updateEditMenuBar();\r
 238       viewport.updateConsensus();\r
 239       alignPanel.RefreshPanels();\r
 240       alignPanel.RefreshPanels();\r
 241   }\r
 242 \r
 243   public void moveSelectedSequences(boolean up)\r
 244   {\r
 245     SequenceGroup sg = viewport.getSelectionGroup();\r
 246     if (sg == null)\r
 247       return;\r
 248 \r
 249     if (up)\r
 250     {\r
 251       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 252       {\r
 253         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 254         if (!sg.sequences.contains(seq))\r
 255           continue;\r
 256 \r
 257         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 258         if (sg.sequences.contains(temp))\r
 259           continue;\r
 260 \r
 261         viewport.alignment.getSequences().setElementAt(temp, i);\r
 262         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 263       }\r
 264     }\r
 265     else\r
 266     {\r
 267       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 268       {\r
 269         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 270         if (!sg.sequences.contains(seq))\r
 271           continue;\r
 272 \r
 273         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 274         if (sg.sequences.contains(temp))\r
 275           continue;\r
 276 \r
 277         viewport.alignment.getSequences().setElementAt(temp, i);\r
 278         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 279       }\r
 280     }\r
 281 \r
 282     alignPanel.RefreshPanels();\r
 283   }\r
 284 \r
 285 \r
 286 \r
 287   protected void copy_actionPerformed(ActionEvent e)\r
 288   {\r
 289    if(viewport.getSelectionGroup()==null)\r
 290      return;\r
 291 \r
 292    SequenceGroup sg = viewport.getSelectionGroup();\r
 293 \r
 294      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 295      StringBuffer buffer= new StringBuffer();\r
 296 \r
 297        for(int i=0; i<sg.getSize(); i++)\r
 298        {\r
 299          SequenceI seq = sg.getSequenceAt(i);\r
 300          buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
 301                         +seq.findPosition( sg.getEndRes() )+ "\t"\r
 302                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
 303        }\r
 304      c.setContents( new StringSelection( buffer.toString()) , null ) ;\r
 305 \r
 306   }\r
 307 \r
 308 \r
 309   protected void pasteNew_actionPerformed(ActionEvent e)\r
 310   {\r
 311     paste(true);\r
 312   }\r
 313 \r
 314   protected void pasteThis_actionPerformed(ActionEvent e)\r
 315   {\r
 316     addHistoryItem("Paste");\r
 317     paste(false);\r
 318   }\r
 319 \r
 320   void paste(boolean newAlignment)\r
 321   {\r
 322     try{\r
 323       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 324       Transferable contents = c.getContents(this);\r
 325       if (contents == null)\r
 326         return;\r
 327 \r
 328       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
 329       StringTokenizer st = new StringTokenizer(str);\r
 330       ArrayList seqs = new ArrayList();\r
 331       while (st.hasMoreElements())\r
 332       {\r
 333         String name = st.nextToken();\r
 334         int start = Integer.parseInt(st.nextToken());\r
 335         int end = Integer.parseInt(st.nextToken());\r
 336         Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
 337 \r
 338         if(!newAlignment)\r
 339           viewport.alignment.addSequence(sequence);\r
 340         else\r
 341           seqs.add(sequence);\r
 342       }\r
 343 \r
 344       if(newAlignment)\r
 345       {\r
 346         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 347         seqs.toArray(newSeqs);\r
 348         AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
 349         int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;\r
 350         if (newHeight > 500)\r
 351           newHeight = 500;\r
 352         Desktop.addInternalFrame(af, "Copied sequences", 700, 500);\r
 353       }\r
 354       else\r
 355       {\r
 356         viewport.setEndSeq(viewport.alignment.getHeight());\r
 357         viewport.alignment.getWidth();\r
 358         viewport.updateConservation();\r
 359         viewport.updateConsensus();\r
 360         alignPanel.RefreshPanels();\r
 361       }\r
 362 \r
 363     }catch(Exception ex){}// could be anything being pasted in here\r
 364 \r
 365   }\r
 366 \r
 367 \r
 368   protected void cut_actionPerformed(ActionEvent e)\r
 369   {\r
 370     copy_actionPerformed(null);\r
 371     delete_actionPerformed(null);\r
 372   }\r
 373 \r
 374   protected void delete_actionPerformed(ActionEvent e)\r
 375   {\r
 376     addHistoryItem("Delete");\r
 377     if (viewport.getSelectionGroup() == null)\r
 378       return;\r
 379 \r
 380      SequenceGroup sg = viewport.getSelectionGroup();\r
 381      for (int i=0;i < sg.sequences.size(); i++)\r
 382      {\r
 383        SequenceI seq = sg.getSequenceAt(i);\r
 384        int index = viewport.getAlignment().findIndex(seq);\r
 385        seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);\r
 386 \r
 387        if(seq.getSequence().length()<1)\r
 388           viewport.getAlignment().deleteSequence(seq);\r
 389       else\r
 390           viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 391      }\r
 392 \r
 393      viewport.setSelectionGroup(null);\r
 394      viewport.alignment.deleteGroup(sg);\r
 395      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());\r
 396      if(viewport.getAlignment().getHeight()<1)\r
 397      try\r
 398      {\r
 399        this.setClosed(true);\r
 400      }catch(Exception ex){}\r
 401    viewport.updateConservation();\r
 402    viewport.updateConsensus();\r
 403      alignPanel.RefreshPanels();\r
 404 \r
 405   }\r
 406 \r
 407 \r
 408 \r
 409   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 410   {\r
 411      Object [] history = (Object[])redoList.remove(0);\r
 412      SequenceI[] seq = (SequenceI[]) history[1];\r
 413      viewport.setAlignment( new Alignment(seq) );\r
 414      updateEditMenuBar();\r
 415      viewport.updateConsensus();\r
 416      alignPanel.RefreshPanels();\r
 417      alignPanel.RefreshPanels();\r
 418   }\r
 419 \r
 420 \r
 421   public void groupsMenuItem_actionPerformed(ActionEvent e)\r
 422   {\r
 423     GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
 424     JInternalFrame frame = new JInternalFrame();\r
 425     frame.setContentPane(geditor);\r
 426     Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
 427     frame.setResizable(false);\r
 428   }\r
 429 \r
 430   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 431   {\r
 432     viewport.alignment.deleteAllGroups();\r
 433     viewport.setSelectionGroup(null);\r
 434 \r
 435     alignPanel.RefreshPanels();\r
 436   }\r
 437 \r
 438 \r
 439 \r
 440   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 441   {\r
 442     SequenceGroup sg = new SequenceGroup();\r
 443     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 444       sg.addSequence( viewport.getAlignment().getSequenceAt(i));\r
 445     sg.setEndRes(viewport.alignment.getWidth());\r
 446     viewport.setSelectionGroup(sg);\r
 447     PaintRefresher.Refresh(null);\r
 448   }\r
 449 \r
 450   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 451   {\r
 452     viewport.setSelectionGroup(null);\r
 453     PaintRefresher.Refresh(null);\r
 454   }\r
 455 \r
 456   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 457   {\r
 458     SequenceGroup sg = viewport.getSelectionGroup();\r
 459     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 460       sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));\r
 461 \r
 462     PaintRefresher.Refresh(null);\r
 463   }\r
 464 \r
 465 \r
 466   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 467   {\r
 468     viewport.getColumnSelection().clear();\r
 469     repaint();\r
 470   }\r
 471 \r
 472   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 473   {\r
 474     addHistoryItem("delete columns");\r
 475     ColumnSelection colSel = viewport.getColumnSelection();\r
 476     if (colSel.size() > 0)\r
 477     {\r
 478       int min = colSel.getMin();\r
 479       viewport.getAlignment().trimLeft(min);\r
 480       colSel.compensateForEdit(0,min);\r
 481 \r
 482       if(viewport.getSelectionGroup()!=null)\r
 483         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 484 \r
 485       Vector groups = viewport.alignment.getGroups();\r
 486       for(int i=0; i<groups.size(); i++)\r
 487       {\r
 488         SequenceGroup sg = (SequenceGroup) groups.get(i);\r
 489         if(!sg.adjustForRemoveLeft(min))\r
 490           viewport.alignment.deleteGroup(sg);\r
 491       }\r
 492 \r
 493       alignPanel.RefreshPanels();\r
 494     }\r
 495   }\r
 496 \r
 497   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 498   {\r
 499     addHistoryItem("delete columns");\r
 500     ColumnSelection colSel = viewport.getColumnSelection();\r
 501     if (colSel.size() > 0)\r
 502     {\r
 503       int max = colSel.getMax();\r
 504       viewport.getAlignment().trimRight(max);\r
 505       if(viewport.getSelectionGroup()!=null)\r
 506         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 507 \r
 508       Vector groups = viewport.alignment.getGroups();\r
 509       for(int i=0; i<groups.size(); i++)\r
 510       {\r
 511         SequenceGroup sg = (SequenceGroup) groups.get(i);\r
 512         if(!sg.adjustForRemoveRight(max))\r
 513           viewport.alignment.deleteGroup(sg);\r
 514       }\r
 515 \r
 516 \r
 517 \r
 518       alignPanel.RefreshPanels();\r
 519     }\r
 520 \r
 521   }\r
 522 \r
 523   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 524   {\r
 525     addHistoryItem("delete gapped columns");\r
 526     viewport.getAlignment().removeGaps();\r
 527     viewport.updateConservation();\r
 528     viewport.updateConsensus();\r
 529     alignPanel.RefreshPanels();\r
 530   }\r
 531 \r
 532   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 533   {\r
 534     addHistoryItem("delete all gaps");\r
 535     SequenceI current;\r
 536     int jSize;\r
 537     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 538     {\r
 539       current = viewport.getAlignment().getSequenceAt(i);\r
 540       jSize = current.getLength();\r
 541       for (int j=0; j < jSize; j++)\r
 542         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 543         {\r
 544           current.deleteCharAt(j);\r
 545           j--;\r
 546           jSize--;\r
 547         }\r
 548     }\r
 549     viewport.updateConservation();\r
 550     viewport.updateConsensus();\r
 551     alignPanel.RefreshPanels();\r
 552   }\r
 553 \r
 554   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 555   {\r
 556     char thisChar = '-';\r
 557     char nextChar = '.';\r
 558     if(viewport.getGapCharacter()=='-')\r
 559     {\r
 560       thisChar = '.';\r
 561       nextChar = '-';\r
 562     }\r
 563     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 564     viewport.setGapCharacter(thisChar);\r
 565     alignPanel.RefreshPanels();\r
 566   }\r
 567 \r
 568   public void findMenuItem_actionPerformed(ActionEvent e)\r
 569   {\r
 570       JInternalFrame frame = new JInternalFrame();\r
 571       Finder finder = new Finder(viewport, alignPanel, frame);\r
 572       frame.setContentPane(finder);\r
 573      Desktop.addInternalFrame(frame, "Find", 340,110);\r
 574 \r
 575   }\r
 576 \r
 577 \r
 578   public void font_actionPerformed(ActionEvent e)\r
 579   {\r
 580    // JOptionPane op = new JOptionPane();\r
 581     JInternalFrame frame = new JInternalFrame();\r
 582     FontChooser fc = new FontChooser( alignPanel, frame );\r
 583     frame.setContentPane(fc);\r
 584     Desktop.addInternalFrame(frame, "Change Font", 480,100);\r
 585   }\r
 586 \r
 587   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 588   {\r
 589     viewport.setShowFullId( fullSeqId.isSelected() );\r
 590 \r
 591     alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );\r
 592     alignPanel.RefreshPanels();\r
 593   }\r
 594 \r
 595   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 596   {\r
 597       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 598       alignPanel.RefreshPanels();\r
 599   }\r
 600 \r
 601   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 602   {\r
 603     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 604     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
 605   }\r
 606 \r
 607 \r
 608   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 609   {\r
 610     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 611     alignPanel.RefreshPanels();\r
 612   }\r
 613 \r
 614   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 615   {\r
 616     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 617     alignPanel.RefreshPanels();\r
 618   }\r
 619 \r
 620 \r
 621   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 622   {\r
 623     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 624     alignPanel.RefreshPanels();\r
 625   }\r
 626 \r
 627   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
 628   {\r
 629     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 630     if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
 631     {\r
 632          AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);\r
 633          ((Alignment)viewport.alignment).featuresAdded = true;\r
 634     }\r
 635     alignPanel.RefreshPanels();\r
 636   }\r
 637 \r
 638   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 639   {\r
 640     alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );\r
 641   }\r
 642 \r
 643   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 644   {\r
 645     if (alignPanel.overviewPanel != null)\r
 646       return;\r
 647 \r
 648     JInternalFrame frame = new JInternalFrame();\r
 649     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 650    try{\r
 651      overview = new OverviewPanel(alignPanel, viewport);\r
 652      frame.setContentPane(overview);\r
 653     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 654                              frame.getWidth(), frame.getHeight());\r
 655     frame.pack();\r
 656     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 657     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 658       {\r
 659             alignPanel.setOverviewPanel(null);\r
 660       };\r
 661     });\r
 662     alignPanel.setOverviewPanel( overview );\r
 663 \r
 664   }catch(java.lang.OutOfMemoryError ex)\r
 665    {\r
 666      JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 667                                    +"\nTry reducing the font size.",\r
 668                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 669    }\r
 670 \r
 671 \r
 672   }\r
 673 \r
 674   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 675   {\r
 676     changeColour( null );\r
 677   }\r
 678 \r
 679 \r
 680   public void clustalColour_actionPerformed(ActionEvent e)\r
 681   {\r
 682     abovePIDThreshold.setSelected(false);\r
 683     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 684   }\r
 685 \r
 686   public void zappoColour_actionPerformed(ActionEvent e)\r
 687   {\r
 688     changeColour(new ZappoColourScheme());\r
 689   }\r
 690 \r
 691   public void taylorColour_actionPerformed(ActionEvent e)\r
 692   {\r
 693     changeColour(new TaylorColourScheme());\r
 694   }\r
 695 \r
 696 \r
 697   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 698   {\r
 699     changeColour( new HydrophobicColourScheme() );\r
 700   }\r
 701 \r
 702   public void helixColour_actionPerformed(ActionEvent e)\r
 703   {\r
 704     changeColour(new HelixColourScheme() );\r
 705   }\r
 706 \r
 707 \r
 708   public void strandColour_actionPerformed(ActionEvent e)\r
 709   {\r
 710     changeColour(new StrandColourScheme());\r
 711   }\r
 712 \r
 713 \r
 714   public void turnColour_actionPerformed(ActionEvent e)\r
 715   {\r
 716     changeColour(new TurnColourScheme());\r
 717   }\r
 718 \r
 719 \r
 720   public void buriedColour_actionPerformed(ActionEvent e)\r
 721   {\r
 722     changeColour(new BuriedColourScheme() );\r
 723   }\r
 724 \r
 725   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 726   {\r
 727     changeColour(new NucleotideColourScheme());\r
 728   }\r
 729 \r
 730 \r
 731   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 732   {\r
 733     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
 734   }\r
 735 \r
 736 \r
 737 \r
 738   void changeColour(ColourSchemeI cs)\r
 739   {\r
 740 \r
 741     if(viewport.getColourAppliesToAllGroups())\r
 742     {\r
 743       Vector groups = viewport.alignment.getGroups();\r
 744       for(int i=0; i<groups.size(); i++)\r
 745       {\r
 746         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 747         sg.cs = cs;\r
 748 \r
 749         if(abovePIDThreshold.isSelected())\r
 750           abovePIDThreshold_actionPerformed(null);\r
 751         else if( viewport.getConservationSelected() )\r
 752         {\r
 753           Conservation c = new Conservation("Group",\r
 754                                             ResidueProperties.propHash, 3,\r
 755                                             sg.sequences, sg.getStartRes(),\r
 756                                             sg.getEndRes());\r
 757           c.calculate();\r
 758           c.verdict(false, 100);\r
 759           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 760 \r
 761           sg.cs = ccs;\r
 762         }\r
 763 \r
 764       }\r
 765     }\r
 766 \r
 767 \r
 768     if ( viewport.getAbovePIDThreshold())\r
 769     {\r
 770       int threshold = 0;\r
 771       threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");\r
 772       Desktop.hideConservationSlider();\r
 773 \r
 774       if (cs instanceof ResidueColourScheme)\r
 775         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 776       else if (cs instanceof ScoreColourScheme)\r
 777         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 778 \r
 779       viewport.setGlobalColourScheme(cs);\r
 780 \r
 781     }\r
 782     else\r
 783     if (cs instanceof ResidueColourScheme)\r
 784       ( (ResidueColourScheme) cs).setThreshold(0);\r
 785     else if (cs instanceof ScoreColourScheme)\r
 786       ( (ScoreColourScheme) cs).setThreshold(0);\r
 787 \r
 788 \r
 789 \r
 790 \r
 791 if ( viewport.getConservationSelected() )\r
 792  {\r
 793    ConservationColourScheme ccs = null;\r
 794 \r
 795    Alignment al = (Alignment) viewport.alignment;\r
 796    Conservation c = new Conservation("All",\r
 797                                      ResidueProperties.propHash, 3,\r
 798                                      al.getSequences(), 0,\r
 799                                      al.getWidth());\r
 800 \r
 801    c.calculate();\r
 802    c.verdict(false, 100);\r
 803 \r
 804    ccs = new ConservationColourScheme(c, cs);\r
 805 \r
 806    int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,\r
 807        "Background");\r
 808 \r
 809    ccs.inc = threshold;\r
 810 \r
 811    viewport.setGlobalColourScheme(ccs);\r
 812 \r
 813   }\r
 814   else\r
 815        viewport.setGlobalColourScheme( cs );\r
 816 \r
 817     alignPanel.RefreshPanels();\r
 818   }\r
 819 \r
 820 \r
 821   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 822   {\r
 823     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 824     if(coloursChanging)\r
 825       return;\r
 826 \r
 827     coloursChanging = true;\r
 828 \r
 829     viewport.setAbovePIDThreshold(false);\r
 830     abovePIDThreshold.setSelected(false);\r
 831     Desktop.hidePIDSlider();\r
 832     if(!viewport.getConservationSelected())\r
 833       Desktop.hideConservationSlider();\r
 834 \r
 835    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 836    if(cs instanceof ConservationColourScheme )\r
 837      changeColour( ((ConservationColourScheme)cs).cs );\r
 838     else\r
 839       changeColour( cs );\r
 840 \r
 841     coloursChanging = false;\r
 842   }\r
 843 \r
 844   boolean coloursChanging = false;\r
 845   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 846   {\r
 847     if(coloursChanging)\r
 848       return;\r
 849 \r
 850     coloursChanging = true;\r
 851     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
 852 \r
 853     conservationMenuItem.setSelected(false);\r
 854     viewport.setConservationSelected(false);\r
 855     Desktop.hideConservationSlider();\r
 856 \r
 857     if(!viewport.getAbovePIDThreshold())\r
 858       Desktop.hidePIDSlider();\r
 859 \r
 860 \r
 861     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 862     if(cs instanceof ConservationColourScheme )\r
 863         changeColour( ((ConservationColourScheme)cs).cs );\r
 864     else\r
 865         changeColour( cs );\r
 866 \r
 867     coloursChanging = false;\r
 868   }\r
 869 \r
 870 \r
 871 \r
 872   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 873   {\r
 874     JInternalFrame frame = new JInternalFrame();\r
 875     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 876     frame.setContentPane(chooser);\r
 877     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 878     frame.setResizable(false);\r
 879     frame.setIconifiable(false);\r
 880     frame.setMaximizable(false);\r
 881   }\r
 882 \r
 883   public void PIDColour_actionPerformed(ActionEvent e)\r
 884   {\r
 885     changeColour( new PIDColourScheme() );\r
 886   }\r
 887 \r
 888 \r
 889   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 890   {\r
 891     changeColour(new Blosum62ColourScheme(viewport) );\r
 892   }\r
 893 \r
 894 \r
 895 \r
 896   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 897   {\r
 898     addHistoryItem("sort");\r
 899     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 900     alignPanel.RefreshPanels();\r
 901   }\r
 902 \r
 903   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 904   {\r
 905     addHistoryItem("sort");\r
 906     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 907     alignPanel.RefreshPanels();\r
 908   }\r
 909 \r
 910   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 911   {\r
 912     addHistoryItem("sort");\r
 913     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 914     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 915     alignPanel.RefreshPanels();\r
 916   }\r
 917 \r
 918   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 919   {\r
 920     addHistoryItem("sort");\r
 921     if(viewport.getCurrentTree()==null)\r
 922       return;\r
 923 \r
 924     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 925     alignPanel.RefreshPanels();\r
 926   }\r
 927 \r
 928   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 929   {\r
 930     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 931     JInternalFrame frame = new JInternalFrame();\r
 932     frame.setContentPane(sp);\r
 933     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);\r
 934     frame.setMaximizable(false);\r
 935     frame.setResizable(false);\r
 936 \r
 937   }\r
 938 \r
 939   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 940   {\r
 941     if(viewport.getSelectionGroup().getSize()<2)\r
 942       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 943     else\r
 944     {\r
 945       JInternalFrame frame = new JInternalFrame();\r
 946       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 947       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 948     }\r
 949   }\r
 950 \r
 951   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 952   {\r
 953 \r
 954     if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
 955        || viewport.getAlignment().getHeight()<4)\r
 956     {\r
 957       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
 958                                     +"at least 4 input sequences.",\r
 959                                     "Sequence selection insufficient",\r
 960                                     JOptionPane.WARNING_MESSAGE);\r
 961       return;\r
 962     }\r
 963 \r
 964     try{\r
 965       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 966       JInternalFrame frame = new JInternalFrame();\r
 967       frame.setContentPane(pcaPanel);\r
 968       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 969    }catch(java.lang.OutOfMemoryError ex)\r
 970    {\r
 971      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 972                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 973    }\r
 974 \r
 975 \r
 976   }\r
 977 \r
 978   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 979   {\r
 980     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 981   }\r
 982 \r
 983   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 984   {\r
 985     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 986   }\r
 987 \r
 988 \r
 989   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 990   {\r
 991     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 992   }\r
 993 \r
 994   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 995   {\r
 996     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 997   }\r
 998 \r
 999   void NewTreePanel(String type, String pwType, String title)\r
1000   {\r
1001     //are the sequences aligned?\r
1002     if(!viewport.alignment.isAligned())\r
1003     {\r
1004       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
1005                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
1006       return;\r
1007     }\r
1008 \r
1009     TreePanel tp=null;\r
1010    if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)\r
1011    {\r
1012      tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType,\r
1013                          0, viewport.alignment.getWidth());\r
1014    }\r
1015    else\r
1016    {\r
1017      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1018                          type, pwType,  0, viewport.alignment.getWidth());\r
1019    }\r
1020 \r
1021    Desktop.addInternalFrame(tp, title, 600, 500);\r
1022   }\r
1023 \r
1024 \r
1025 \r
1026 \r
1027   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
1028   {\r
1029     JInternalFrame frame = new JInternalFrame();\r
1030     ClustalThread ct = new ClustalThread(frame);\r
1031     Thread t = new Thread(ct);\r
1032     t.start();\r
1033     frame.setContentPane(ct);\r
1034      Desktop.addInternalFrame(frame, title, 300, 80);\r
1035 \r
1036   }\r
1037 \r
1038   class ClustalThread extends JPanel implements Runnable\r
1039   {\r
1040     Image [] image;\r
1041     int imageIndex = 0;\r
1042     boolean webServiceRunning = false;\r
1043     JInternalFrame frame;\r
1044     public ClustalThread(JInternalFrame frame)\r
1045     {\r
1046       this.frame = frame;\r
1047       image = new Image[9];\r
1048       for(int i=0; i<9; i++)\r
1049       {\r
1050         java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");\r
1051         if (url != null)\r
1052         {\r
1053           image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
1054           MediaTracker mt = new MediaTracker(this);\r
1055           mt.addImage(image[i], i);\r
1056           try{mt.waitForID(i);}\r
1057           catch(Exception ex){}\r
1058         }\r
1059       }\r
1060       DNATwirler twirler = new DNATwirler();\r
1061       twirler.start();\r
1062       webServiceRunning = true;\r
1063     }\r
1064 \r
1065     class DNATwirler extends Thread\r
1066     {\r
1067       public void run()\r
1068       {\r
1069         while(webServiceRunning)\r
1070         {\r
1071           try{\r
1072             Thread.sleep(100);\r
1073             imageIndex++;\r
1074             imageIndex %=9;\r
1075             repaint();\r
1076           }\r
1077           catch(Exception ex){}\r
1078         }\r
1079       }\r
1080     }\r
1081 \r
1082     // JBPNote\r
1083     // Should check to see if the server settings are valid\r
1084     // Need visual-delay indication here.\r
1085     public void run()\r
1086        {\r
1087          jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
1088          Vector sv = viewport.getAlignment().getSequences();\r
1089          SequenceI[] seqs = new SequenceI[sv.size()];\r
1090 \r
1091          int i = 0;\r
1092          do\r
1093          {\r
1094            seqs[i] = (SequenceI) sv.elementAt(i);\r
1095          }\r
1096          while (++i < sv.size());\r
1097 \r
1098          SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
1099 \r
1100          if (alignment != null)\r
1101          {\r
1102            AlignFrame af = new AlignFrame(new Alignment(alignment));\r
1103           af.clustalColour.setSelected(true);\r
1104           af.clustalColour_actionPerformed(null);\r
1105            Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),\r
1106                                     700, 500); // JBPNote - is there a new window geom. property ?\r
1107          }\r
1108          else\r
1109            JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",\r
1110                                          JOptionPane.WARNING_MESSAGE);\r
1111 \r
1112          webServiceRunning = false;\r
1113          try{\r
1114            frame.setClosed(true);\r
1115          }catch(Exception ex){}\r
1116        }\r
1117 \r
1118        public void paintComponent(Graphics g)\r
1119        {\r
1120          g.setColor(Color.white);\r
1121          g.fillRect(0,0,getWidth(), getHeight());\r
1122          if(image!=null)\r
1123          {\r
1124            g.drawImage(image[imageIndex],10,10,this);\r
1125          }\r
1126          g.setFont(new Font("Arial", Font.BOLD, 12));\r
1127          g.setColor(Color.black);\r
1128          g.drawString("Clustal Alignment Web Service running", 30,30);\r
1129        }\r
1130   }\r
1131   protected void jpred_actionPerformed(ActionEvent e)\r
1132 {\r
1133 \r
1134     JInternalFrame frame = new JInternalFrame();\r
1135     if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)\r
1136     {\r
1137       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1138       SequenceGroup seqs = viewport.getSelectionGroup();\r
1139       if (seqs.getSize() == 1 || !viewport.alignment.isAligned())\r
1140       {\r
1141         JPredClient ct = new JPredClient( (SequenceI)\r
1142                                          seqs.getSequenceAt(0));\r
1143       }\r
1144       else\r
1145       {\r
1146         int sz;\r
1147         SequenceI[] msa = new SequenceI[sz=seqs.getSize()];\r
1148         for (int i = 0; i < sz; i++)\r
1149         {\r
1150           msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1151         }\r
1152 \r
1153         JPredClient ct = new JPredClient(msa);\r
1154       }\r
1155 \r
1156     }\r
1157     else\r
1158     {\r
1159       Vector seqs = viewport.getAlignment().getSequences();\r
1160 \r
1161       if (seqs.size() == 1 || !viewport.alignment.isAligned())\r
1162       {\r
1163         JPredClient ct = new JPredClient( (SequenceI)\r
1164                                          seqs.elementAt(0));\r
1165       }\r
1166       else\r
1167       {\r
1168         SequenceI[] msa = new SequenceI[seqs.size()];\r
1169         for (int i = 0; i < seqs.size(); i++)\r
1170         {\r
1171           msa[i] = (SequenceI) seqs.elementAt(i);\r
1172         }\r
1173 \r
1174         JPredClient ct = new JPredClient(msa);\r
1175       }\r
1176 \r
1177     }\r
1178   }\r
1179 \r
1180     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
1181     // Pick the tree file\r
1182     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
1183         getProperty("LAST_DIRECTORY"));\r
1184     chooser.setFileView(new JalviewFileView());\r
1185     chooser.setDialogTitle("Select a newick-like tree file");\r
1186     chooser.setToolTipText("Load a tree file");\r
1187     int value = chooser.showOpenDialog(null);\r
1188     if (value == JalviewFileChooser.APPROVE_OPTION)\r
1189     {\r
1190       String choice = chooser.getSelectedFile().getPath();\r
1191       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1192       TreePanel treepanel = null;\r
1193       try\r
1194       {\r
1195         jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");\r
1196         fin.parse();\r
1197 \r
1198         if (fin.getTree() != null)\r
1199         {\r
1200           TreePanel tp = null;\r
1201           tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1202                              fin, "FromFile", choice);\r
1203           Desktop.addInternalFrame(tp, title, 600, 500);\r
1204         }\r
1205       }\r
1206       catch (Exception ex)\r
1207       {\r
1208         JOptionPane.showMessageDialog(Desktop.desktop,\r
1209                                       "Problem reading tree file",\r
1210                                       ex.getMessage(),\r
1211                                       JOptionPane.WARNING_MESSAGE);\r
1212         ex.printStackTrace();\r
1213       }\r
1214     }\r
1215   }\r
1216 \r
1217 }\r