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 static final int NEW_WINDOW_WIDTH = 700;\r
  34   public static final int NEW_WINDOW_HEIGHT = 500;\r
  35 \r
  36   public AlignFrame(AlignmentI al)\r
  37   {\r
  38     try{\r
  39       String ip = java.net.InetAddress.getLocalHost().getHostAddress();\r
  40       if( !ip.startsWith("10."))\r
  41         alignMenu.setVisible(false);\r
  42     }\r
  43     catch(java.net.UnknownHostException e){}\r
  44     viewport = new AlignViewport(al,true,true,false);\r
  45 \r
  46     String fontName = jalview.bin.Cache.getProperty("FONT_NAME");\r
  47     String fontStyle= jalview.bin.Cache.getProperty("FONT_STYLE");\r
  48     String fontSize = jalview.bin.Cache.getProperty("FONT_SIZE");\r
  49     if(fontName!=null && fontStyle!=null && fontSize!=null)\r
  50       viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );\r
  51 \r
  52     // add conservation graph to alignment\r
  53     viewport.updateConservation();\r
  54     viewport.updateConsensus();\r
  55 \r
  56 \r
  57     alignPanel = new AlignmentPanel(this, viewport);\r
  58 \r
  59     alignPanel.annotationPanel.adjustPanelHeight();\r
  60     alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
  61     alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
  62 \r
  63     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
  64 \r
  65 \r
  66     addInternalFrameListener(new InternalFrameAdapter()\r
  67    {\r
  68      public void internalFrameActivated(InternalFrameEvent evt)\r
  69      {\r
  70           javax.swing.SwingUtilities.invokeLater(new Runnable()\r
  71           {\r
  72             public void run()\r
  73             {      alignPanel.requestFocus();    }\r
  74           });\r
  75 \r
  76      }\r
  77    });\r
  78 \r
  79   }\r
  80 \r
  81   protected void saveAs_actionPerformed(ActionEvent e)\r
  82   {\r
  83     String suffix [] = null;\r
  84     if(e.getActionCommand().equals("FASTA"))\r
  85       suffix = new String[]{"fa", "fasta"};\r
  86     else if(e.getActionCommand().equals("MSF"))\r
  87       suffix = new String[]{"msf"};\r
  88     else if(e.getActionCommand().equals("CLUSTAL"))\r
  89       suffix = new String[]{"aln"};\r
  90     else if(e.getActionCommand().equals("BLC"))\r
  91       suffix = new String[]{"blc"};\r
  92     else if(e.getActionCommand().equals("PIR"))\r
  93       suffix = new String[]{"pir"};\r
  94     else if(e.getActionCommand().equals("PFAM"))\r
  95       suffix = new String[]{"pfam"};\r
  96 \r
  97 \r
  98     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")\r
  99         , suffix, e.getActionCommand()+" file");\r
 100     chooser.setFileView(new JalviewFileView());\r
 101     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
 102     chooser.setToolTipText("Save");\r
 103     int value = chooser.showSaveDialog(this);\r
 104     if(value == JalviewFileChooser.APPROVE_OPTION)\r
 105     {\r
 106       String choice =  chooser.getSelectedFile().getPath();\r
 107       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
 108       String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
 109       try{\r
 110         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
 111         out.println(output);\r
 112         out.close();\r
 113       }\r
 114       catch(Exception ex){}\r
 115     }\r
 116 \r
 117   }\r
 118 \r
 119   protected void outputText_actionPerformed(ActionEvent e)\r
 120   {\r
 121      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
 122      JInternalFrame frame = new JInternalFrame();\r
 123      cap.formatForOutput();\r
 124      frame.setContentPane(cap);\r
 125      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
 126      cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
 127   }\r
 128 \r
 129   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 130   {\r
 131     HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
 132     htmlOutput = null;\r
 133   }\r
 134 \r
 135   protected void createPNG_actionPerformed(ActionEvent e)\r
 136   {\r
 137     alignPanel.makePNG();\r
 138   }\r
 139 \r
 140   protected void epsFile_actionPerformed(ActionEvent e)\r
 141   {\r
 142     alignPanel.makeEPS();\r
 143   }\r
 144 \r
 145 \r
 146   public void printMenuItem_actionPerformed(ActionEvent e)\r
 147   {\r
 148     //Putting in a thread avoids Swing painting problems\r
 149     PrintThread thread = new PrintThread();\r
 150     thread.start();\r
 151   }\r
 152 \r
 153   class PrintThread extends Thread\r
 154   {\r
 155     public void run()\r
 156     {\r
 157       PrinterJob printJob = PrinterJob.getPrinterJob();\r
 158       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
 159       printJob.setPrintable(alignPanel, pf);\r
 160       if (printJob.printDialog())\r
 161       {\r
 162         try\r
 163         {\r
 164           printJob.print();\r
 165         }\r
 166         catch (Exception PrintException)\r
 167         {\r
 168           PrintException.printStackTrace();\r
 169         }\r
 170       }\r
 171     }\r
 172 \r
 173   }\r
 174 \r
 175 \r
 176 \r
 177 \r
 178   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 179   {\r
 180     try{\r
 181       this.setClosed(true);\r
 182     }catch(Exception ex){}\r
 183   }\r
 184 \r
 185   Stack historyList = new Stack();\r
 186   Stack redoList = new Stack();\r
 187   JMenuBar jMenuBar1 = new JMenuBar();\r
 188 \r
 189   void updateEditMenuBar()\r
 190   {\r
 191     if(historyList.size()>0)\r
 192      {\r
 193        undoMenuItem.setEnabled(true);\r
 194        Object [] history = (Object[])historyList.get(0);\r
 195        undoMenuItem.setText("Undo "+history[0]);\r
 196      }\r
 197     else\r
 198     {\r
 199       undoMenuItem.setEnabled(false);\r
 200       undoMenuItem.setText("Undo");\r
 201     }\r
 202 \r
 203     if(redoList.size()>0)\r
 204      {\r
 205        redoMenuItem.setEnabled(true);\r
 206        Object [] history = (Object[])redoList.get(0);\r
 207        redoMenuItem.setText("Redo "+history[0]);\r
 208      }\r
 209     else\r
 210     {\r
 211       redoMenuItem.setEnabled(false);\r
 212       redoMenuItem.setText("Redo");\r
 213     }\r
 214   }\r
 215 \r
 216   public void addHistoryItem(String type)\r
 217   {\r
 218     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 219     redoList.clear();\r
 220     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 221     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 222     {\r
 223       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 224                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 225     }\r
 226 \r
 227     historyList.add(0, new Object[]{type,  seq} );\r
 228     updateEditMenuBar();\r
 229   }\r
 230 \r
 231   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 232   {\r
 233     Object [] history = (Object[])historyList.remove(0);\r
 234     // add the redo state before continuing!!\r
 235     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 236     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
 237     {\r
 238       seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
 239                             viewport.getAlignment().getSequenceAt(i).\r
 240                             getSequence());\r
 241     }\r
 242     /////////\r
 243 \r
 244     redoList.add(0, new Object[] {history[0], seq});\r
 245 \r
 246       seq = (SequenceI[]) history[1];\r
 247       viewport.setAlignment( new Alignment(seq) );\r
 248       updateEditMenuBar();\r
 249       viewport.updateConsensus();\r
 250       alignPanel.repaint();\r
 251   }\r
 252 \r
 253   public void moveSelectedSequences(boolean up)\r
 254   {\r
 255     SequenceGroup sg = viewport.getSelectionGroup();\r
 256     if (sg == null)\r
 257       return;\r
 258 \r
 259     if (up)\r
 260     {\r
 261       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 262       {\r
 263         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 264         if (!sg.sequences.contains(seq))\r
 265           continue;\r
 266 \r
 267         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 268         if (sg.sequences.contains(temp))\r
 269           continue;\r
 270 \r
 271         viewport.alignment.getSequences().setElementAt(temp, i);\r
 272         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 273       }\r
 274     }\r
 275     else\r
 276     {\r
 277       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 278       {\r
 279         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 280         if (!sg.sequences.contains(seq))\r
 281           continue;\r
 282 \r
 283         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 284         if (sg.sequences.contains(temp))\r
 285           continue;\r
 286 \r
 287         viewport.alignment.getSequences().setElementAt(temp, i);\r
 288         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 289       }\r
 290     }\r
 291 \r
 292     alignPanel.repaint();\r
 293   }\r
 294 \r
 295 \r
 296 \r
 297   protected void copy_actionPerformed(ActionEvent e)\r
 298   {\r
 299    if(viewport.getSelectionGroup()==null)\r
 300      return;\r
 301 \r
 302    SequenceGroup sg = viewport.getSelectionGroup();\r
 303 \r
 304      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 305      StringBuffer buffer= new StringBuffer();\r
 306 \r
 307        for(int i=0; i<sg.getSize(); i++)\r
 308        {\r
 309          SequenceI seq = sg.getSequenceAt(i);\r
 310          buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
 311                         +seq.findPosition( sg.getEndRes() )+ "\t"\r
 312                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
 313        }\r
 314      c.setContents( new StringSelection( buffer.toString()) , null ) ;\r
 315 \r
 316   }\r
 317 \r
 318 \r
 319   protected void pasteNew_actionPerformed(ActionEvent e)\r
 320   {\r
 321     paste(true);\r
 322   }\r
 323 \r
 324   protected void pasteThis_actionPerformed(ActionEvent e)\r
 325   {\r
 326     addHistoryItem("Paste");\r
 327     paste(false);\r
 328   }\r
 329 \r
 330   void paste(boolean newAlignment)\r
 331   {\r
 332     try{\r
 333       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 334       Transferable contents = c.getContents(this);\r
 335       if (contents == null)\r
 336         return;\r
 337 \r
 338       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
 339       StringTokenizer st = new StringTokenizer(str);\r
 340       ArrayList seqs = new ArrayList();\r
 341       while (st.hasMoreElements())\r
 342       {\r
 343         String name = st.nextToken();\r
 344         int start = Integer.parseInt(st.nextToken());\r
 345         int end = Integer.parseInt(st.nextToken());\r
 346         Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
 347 \r
 348         if(!newAlignment)\r
 349           viewport.alignment.addSequence(sequence);\r
 350         else\r
 351           seqs.add(sequence);\r
 352       }\r
 353 \r
 354       if(newAlignment)\r
 355       {\r
 356         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 357         seqs.toArray(newSeqs);\r
 358         AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
 359         Desktop.addInternalFrame(af, "Copied sequences", NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
 360       }\r
 361       else\r
 362       {\r
 363         viewport.setEndSeq(viewport.alignment.getHeight());\r
 364         viewport.alignment.getWidth();\r
 365         viewport.updateConservation();\r
 366         viewport.updateConsensus();\r
 367         alignPanel.repaint();\r
 368       }\r
 369 \r
 370     }catch(Exception ex){}// could be anything being pasted in here\r
 371 \r
 372   }\r
 373 \r
 374 \r
 375   protected void cut_actionPerformed(ActionEvent e)\r
 376   {\r
 377     copy_actionPerformed(null);\r
 378     delete_actionPerformed(null);\r
 379   }\r
 380 \r
 381   protected void delete_actionPerformed(ActionEvent e)\r
 382   {\r
 383     addHistoryItem("Delete");\r
 384     if (viewport.getSelectionGroup() == null)\r
 385       return;\r
 386 \r
 387      SequenceGroup sg = viewport.getSelectionGroup();\r
 388      for (int i=0;i < sg.sequences.size(); i++)\r
 389      {\r
 390        SequenceI seq = sg.getSequenceAt(i);\r
 391        int index = viewport.getAlignment().findIndex(seq);\r
 392        seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);\r
 393 \r
 394        if(seq.getSequence().length()<1)\r
 395           viewport.getAlignment().deleteSequence(seq);\r
 396       else\r
 397           viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 398      }\r
 399 \r
 400      viewport.setSelectionGroup(null);\r
 401      viewport.alignment.deleteGroup(sg);\r
 402      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());\r
 403      if(viewport.getAlignment().getHeight()<1)\r
 404      try\r
 405      {\r
 406        this.setClosed(true);\r
 407      }catch(Exception ex){}\r
 408    viewport.updateConservation();\r
 409    viewport.updateConsensus();\r
 410      alignPanel.repaint();\r
 411 \r
 412   }\r
 413 \r
 414 \r
 415 \r
 416   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 417   {\r
 418      Object [] history = (Object[])redoList.remove(0);\r
 419      SequenceI[] seq = (SequenceI[]) history[1];\r
 420      viewport.setAlignment( new Alignment(seq) );\r
 421      updateEditMenuBar();\r
 422      viewport.updateConsensus();\r
 423      alignPanel.repaint();\r
 424      alignPanel.repaint();\r
 425   }\r
 426 \r
 427 \r
 428   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 429   {\r
 430     viewport.alignment.deleteAllGroups();\r
 431     viewport.setSelectionGroup(null);\r
 432 \r
 433     alignPanel.repaint();\r
 434   }\r
 435 \r
 436 \r
 437 \r
 438   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 439   {\r
 440     SequenceGroup sg = new SequenceGroup();\r
 441     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 442       sg.addSequence( viewport.getAlignment().getSequenceAt(i));\r
 443     sg.setEndRes(viewport.alignment.getWidth());\r
 444     viewport.setSelectionGroup(sg);\r
 445     PaintRefresher.Refresh(null);\r
 446   }\r
 447 \r
 448   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 449   {\r
 450     viewport.setSelectionGroup(null);\r
 451     PaintRefresher.Refresh(null);\r
 452   }\r
 453 \r
 454   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 455   {\r
 456     SequenceGroup sg = viewport.getSelectionGroup();\r
 457     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 458       sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));\r
 459 \r
 460     PaintRefresher.Refresh(null);\r
 461   }\r
 462 \r
 463 \r
 464   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 465   {\r
 466     viewport.getColumnSelection().clear();\r
 467     repaint();\r
 468   }\r
 469 \r
 470   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 471   {\r
 472     addHistoryItem("delete columns");\r
 473     ColumnSelection colSel = viewport.getColumnSelection();\r
 474     if (colSel.size() > 0)\r
 475     {\r
 476       int min = colSel.getMin();\r
 477       viewport.getAlignment().trimLeft(min);\r
 478       colSel.compensateForEdit(0,min);\r
 479 \r
 480       if(viewport.getSelectionGroup()!=null)\r
 481         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 482 \r
 483       Vector groups = viewport.alignment.getGroups();\r
 484       for(int i=0; i<groups.size(); i++)\r
 485       {\r
 486         SequenceGroup sg = (SequenceGroup) groups.get(i);\r
 487         if(!sg.adjustForRemoveLeft(min))\r
 488           viewport.alignment.deleteGroup(sg);\r
 489       }\r
 490 \r
 491       alignPanel.repaint();\r
 492     }\r
 493   }\r
 494 \r
 495   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 496   {\r
 497     addHistoryItem("delete columns");\r
 498     ColumnSelection colSel = viewport.getColumnSelection();\r
 499     if (colSel.size() > 0)\r
 500     {\r
 501       int max = colSel.getMax();\r
 502       viewport.getAlignment().trimRight(max);\r
 503       if(viewport.getSelectionGroup()!=null)\r
 504         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 505 \r
 506       Vector groups = viewport.alignment.getGroups();\r
 507       for(int i=0; i<groups.size(); i++)\r
 508       {\r
 509         SequenceGroup sg = (SequenceGroup) groups.get(i);\r
 510         if(!sg.adjustForRemoveRight(max))\r
 511           viewport.alignment.deleteGroup(sg);\r
 512       }\r
 513 \r
 514 \r
 515 \r
 516       alignPanel.repaint();\r
 517     }\r
 518 \r
 519   }\r
 520 \r
 521   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 522   {\r
 523     addHistoryItem("delete gapped columns");\r
 524     viewport.getAlignment().removeGaps();\r
 525     viewport.updateConservation();\r
 526     viewport.updateConsensus();\r
 527     alignPanel.repaint();\r
 528   }\r
 529 \r
 530   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 531   {\r
 532     addHistoryItem("delete all gaps");\r
 533     SequenceI current;\r
 534     int jSize;\r
 535     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 536     {\r
 537       current = viewport.getAlignment().getSequenceAt(i);\r
 538       jSize = current.getLength();\r
 539       for (int j=0; j < jSize; j++)\r
 540         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 541         {\r
 542           current.deleteCharAt(j);\r
 543           j--;\r
 544           jSize--;\r
 545         }\r
 546     }\r
 547     viewport.updateConservation();\r
 548     viewport.updateConsensus();\r
 549     alignPanel.repaint();\r
 550   }\r
 551 \r
 552   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 553   {\r
 554     char thisChar = '-';\r
 555     char nextChar = '.';\r
 556     if(viewport.getGapCharacter()=='-')\r
 557     {\r
 558       thisChar = '.';\r
 559       nextChar = '-';\r
 560     }\r
 561     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 562     viewport.setGapCharacter(thisChar);\r
 563     alignPanel.repaint();\r
 564   }\r
 565 \r
 566   public void findMenuItem_actionPerformed(ActionEvent e)\r
 567   {\r
 568     JInternalFrame frame = new JInternalFrame();\r
 569     Finder finder = new Finder(viewport, alignPanel, frame);\r
 570     frame.setContentPane(finder);\r
 571     Desktop.addInternalFrame(frame, "Find", 340,110, false);\r
 572     frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
 573 \r
 574   }\r
 575 \r
 576 \r
 577   public void font_actionPerformed(ActionEvent e)\r
 578   {\r
 579     JInternalFrame frame = new JInternalFrame();\r
 580     FontChooser fc = new FontChooser( alignPanel, frame );\r
 581     frame.setContentPane(fc);\r
 582     Desktop.addInternalFrame(frame, "Change Font", 480,100, false);\r
 583     frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
 584     if(alignPanel.getOverviewPanel()!=null)\r
 585       alignPanel.getOverviewPanel().updateOverviewImage();\r
 586   }\r
 587 \r
 588   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 589   {\r
 590     viewport.setShowFullId( fullSeqId.isSelected() );\r
 591 \r
 592     alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );\r
 593     alignPanel.repaint();\r
 594   }\r
 595 \r
 596   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 597   {\r
 598       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 599       alignPanel.repaint();\r
 600   }\r
 601 \r
 602   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 603   {\r
 604     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 605     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
 606     scaleAbove.setVisible( wrapMenuItem.isSelected() );\r
 607     scaleLeft.setVisible( wrapMenuItem.isSelected() );\r
 608     scaleRight.setVisible( wrapMenuItem.isSelected() );\r
 609     alignPanel.repaint();\r
 610   }\r
 611 \r
 612   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 613   {\r
 614     viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
 615     alignPanel.repaint();\r
 616   }\r
 617 \r
 618   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 619   {\r
 620     viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
 621     alignPanel.repaint();\r
 622   }\r
 623 \r
 624   protected void scaleRight_actionPerformed(ActionEvent e)\r
 625   {\r
 626     viewport.setScaleRightWrapped(scaleRight.isSelected());\r
 627     alignPanel.repaint();\r
 628   }\r
 629 \r
 630 \r
 631 \r
 632   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 633   {\r
 634     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 635     alignPanel.repaint();\r
 636   }\r
 637 \r
 638   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 639   {\r
 640     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 641     alignPanel.repaint();\r
 642   }\r
 643 \r
 644 \r
 645   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 646   {\r
 647     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 648     alignPanel.repaint();\r
 649   }\r
 650 \r
 651   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
 652   {\r
 653     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 654     if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
 655     {\r
 656          AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);\r
 657          ((Alignment)viewport.alignment).featuresAdded = true;\r
 658     }\r
 659     alignPanel.repaint();\r
 660   }\r
 661 \r
 662   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 663   {\r
 664     if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())\r
 665     {\r
 666       annotationPanelMenuItem.setSelected(false);\r
 667       return;\r
 668     }\r
 669     viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );\r
 670     alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );\r
 671   }\r
 672 \r
 673   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 674   {\r
 675     if (alignPanel.overviewPanel != null)\r
 676       return;\r
 677 \r
 678     JInternalFrame frame = new JInternalFrame();\r
 679     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 680      frame.setContentPane(overview);\r
 681     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 682                              frame.getWidth(), frame.getHeight());\r
 683     frame.pack();\r
 684     frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
 685     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 686     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 687       {\r
 688             alignPanel.setOverviewPanel(null);\r
 689       };\r
 690     });\r
 691 \r
 692     alignPanel.setOverviewPanel( overview );\r
 693 \r
 694 \r
 695   }\r
 696 \r
 697   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 698   {\r
 699     changeColour( null );\r
 700   }\r
 701 \r
 702 \r
 703   public void clustalColour_actionPerformed(ActionEvent e)\r
 704   {\r
 705     abovePIDThreshold.setSelected(false);\r
 706     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 707   }\r
 708 \r
 709   public void zappoColour_actionPerformed(ActionEvent e)\r
 710   {\r
 711     changeColour(new ZappoColourScheme());\r
 712   }\r
 713 \r
 714   public void taylorColour_actionPerformed(ActionEvent e)\r
 715   {\r
 716     changeColour(new TaylorColourScheme());\r
 717   }\r
 718 \r
 719 \r
 720   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 721   {\r
 722     changeColour( new HydrophobicColourScheme() );\r
 723   }\r
 724 \r
 725   public void helixColour_actionPerformed(ActionEvent e)\r
 726   {\r
 727     changeColour(new HelixColourScheme() );\r
 728   }\r
 729 \r
 730 \r
 731   public void strandColour_actionPerformed(ActionEvent e)\r
 732   {\r
 733     changeColour(new StrandColourScheme());\r
 734   }\r
 735 \r
 736 \r
 737   public void turnColour_actionPerformed(ActionEvent e)\r
 738   {\r
 739     changeColour(new TurnColourScheme());\r
 740   }\r
 741 \r
 742 \r
 743   public void buriedColour_actionPerformed(ActionEvent e)\r
 744   {\r
 745     changeColour(new BuriedColourScheme() );\r
 746   }\r
 747 \r
 748   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 749   {\r
 750     changeColour(new NucleotideColourScheme());\r
 751   }\r
 752 \r
 753 \r
 754   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 755   {\r
 756     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
 757   }\r
 758 \r
 759 \r
 760 \r
 761   void changeColour(ColourSchemeI cs)\r
 762   {\r
 763     int threshold = 0;\r
 764 \r
 765     if ( viewport.getAbovePIDThreshold() )\r
 766     {\r
 767       threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
 768 \r
 769       if (cs instanceof ResidueColourScheme)\r
 770         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 771       else if (cs instanceof ScoreColourScheme)\r
 772         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 773 \r
 774       viewport.setGlobalColourScheme(cs);\r
 775     }\r
 776     else if (cs instanceof ResidueColourScheme)\r
 777       ( (ResidueColourScheme) cs).setThreshold(0);\r
 778     else if (cs instanceof ScoreColourScheme)\r
 779       ( (ScoreColourScheme) cs).setThreshold(0);\r
 780 \r
 781 \r
 782 \r
 783     if (viewport.getConservationSelected())\r
 784     {\r
 785       ConservationColourScheme ccs = null;\r
 786 \r
 787       Alignment al = (Alignment) viewport.alignment;\r
 788       Conservation c = new Conservation("All",\r
 789                                         ResidueProperties.propHash, 3,\r
 790                                         al.getSequences(), 0,\r
 791                                         al.getWidth() - 1);\r
 792 \r
 793       c.calculate();\r
 794       c.verdict(false, viewport.ConsPercGaps);\r
 795 \r
 796       ccs = new ConservationColourScheme(c, cs);\r
 797 \r
 798       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 799       ccs.setConsensus( viewport.vconsensus );\r
 800       viewport.setGlobalColourScheme(ccs);\r
 801 \r
 802       SliderPanel.setConservationSlider(alignPanel, ccs, "Background");\r
 803 \r
 804     }\r
 805     else\r
 806     {\r
 807         // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 808         if (cs != null)\r
 809           cs.setConsensus(viewport.vconsensus);\r
 810         viewport.setGlobalColourScheme(cs);\r
 811     }\r
 812 \r
 813 \r
 814     if(viewport.getColourAppliesToAllGroups())\r
 815     {\r
 816       Vector groups = viewport.alignment.getGroups();\r
 817       for(int i=0; i<groups.size(); i++)\r
 818       {\r
 819         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 820 \r
 821         if (cs instanceof ClustalxColourScheme)\r
 822         {\r
 823           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
 824         }\r
 825         else\r
 826           try\r
 827           {\r
 828             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
 829           }\r
 830           catch (Exception ex)\r
 831           {\r
 832             ex.printStackTrace();\r
 833             sg.cs = cs;\r
 834           }\r
 835 \r
 836         if(viewport.getAbovePIDThreshold())\r
 837         {\r
 838           if (sg.cs instanceof ResidueColourScheme)\r
 839             ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
 840           else if (sg.cs instanceof ScoreColourScheme)\r
 841             ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
 842 \r
 843            sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );\r
 844         }\r
 845 \r
 846         if( viewport.getConservationSelected() )\r
 847         {\r
 848           Conservation c = new Conservation("Group",\r
 849                                             ResidueProperties.propHash, 3,\r
 850                                             sg.sequences, 0, viewport.alignment.getWidth()-1);\r
 851           c.calculate();\r
 852           c.verdict(false, viewport.ConsPercGaps);\r
 853           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 854 \r
 855           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 856           ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 857           sg.cs = ccs;\r
 858         }\r
 859         else\r
 860         {\r
 861           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 862           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 863         }\r
 864 \r
 865       }\r
 866     }\r
 867 \r
 868     if(alignPanel.getOverviewPanel()!=null)\r
 869       alignPanel.getOverviewPanel().updateOverviewImage();\r
 870     alignPanel.repaint();\r
 871   }\r
 872 \r
 873   protected void modifyPID_actionPerformed(ActionEvent e)\r
 874   {\r
 875       if(viewport.getAbovePIDThreshold())\r
 876       {\r
 877         SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
 878                                    "Background");\r
 879         SliderPanel.showPIDSlider();\r
 880       }\r
 881   }\r
 882 \r
 883   protected void modifyConservation_actionPerformed(ActionEvent e)\r
 884   {\r
 885     if(viewport.getConservationSelected())\r
 886     {\r
 887       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
 888                                         "Background");\r
 889       SliderPanel.showConservationSlider();\r
 890     }\r
 891   }\r
 892 \r
 893 \r
 894   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 895   {\r
 896     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 897 \r
 898     viewport.setAbovePIDThreshold(false);\r
 899     abovePIDThreshold.setSelected(false);\r
 900 \r
 901    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 902    if(cs instanceof ConservationColourScheme )\r
 903      changeColour( ((ConservationColourScheme)cs).cs );\r
 904     else\r
 905       changeColour( cs );\r
 906 \r
 907     modifyConservation_actionPerformed(null);\r
 908   }\r
 909 \r
 910   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 911   {\r
 912     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
 913 \r
 914     conservationMenuItem.setSelected(false);\r
 915     viewport.setConservationSelected(false);\r
 916 \r
 917     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 918 \r
 919     if(cs instanceof ConservationColourScheme )\r
 920         changeColour( ((ConservationColourScheme)cs).cs );\r
 921     else\r
 922         changeColour( cs );\r
 923 \r
 924     modifyPID_actionPerformed(null);\r
 925   }\r
 926 \r
 927 \r
 928 \r
 929   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 930   {\r
 931     JInternalFrame frame = new JInternalFrame();\r
 932     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 933     frame.setContentPane(chooser);\r
 934     Desktop.addInternalFrame(frame,"User defined colours", 450,540, false );\r
 935   }\r
 936 \r
 937   public void PIDColour_actionPerformed(ActionEvent e)\r
 938   {\r
 939     changeColour( new PIDColourScheme() );\r
 940   }\r
 941 \r
 942 \r
 943   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 944   {\r
 945     changeColour(new Blosum62ColourScheme() );\r
 946   }\r
 947 \r
 948 \r
 949 \r
 950   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 951   {\r
 952     addHistoryItem("sort");\r
 953     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 954     alignPanel.repaint();\r
 955   }\r
 956 \r
 957   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 958   {\r
 959     addHistoryItem("sort");\r
 960     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 961     alignPanel.repaint();\r
 962   }\r
 963 \r
 964   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 965   {\r
 966     addHistoryItem("sort");\r
 967     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 968     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 969     alignPanel.repaint();\r
 970   }\r
 971 \r
 972   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 973   {\r
 974     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 975     JInternalFrame frame = new JInternalFrame();\r
 976     frame.setContentPane(sp);\r
 977     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);\r
 978 \r
 979   }\r
 980 \r
 981   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 982   {\r
 983     if(viewport.getSelectionGroup().getSize()<2)\r
 984       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 985     else\r
 986     {\r
 987       JInternalFrame frame = new JInternalFrame();\r
 988       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 989       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 990     }\r
 991   }\r
 992 \r
 993   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 994   {\r
 995 \r
 996     if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
 997        || viewport.getAlignment().getHeight()<4)\r
 998     {\r
 999       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
1000                                     +"at least 4 input sequences.",\r
1001                                     "Sequence selection insufficient",\r
1002                                     JOptionPane.WARNING_MESSAGE);\r
1003       return;\r
1004     }\r
1005 \r
1006     try{\r
1007       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
1008       JInternalFrame frame = new JInternalFrame();\r
1009       frame.setContentPane(pcaPanel);\r
1010       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
1011    }catch(java.lang.OutOfMemoryError ex)\r
1012    {\r
1013      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
1014                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
1015    }\r
1016 \r
1017 \r
1018   }\r
1019 \r
1020   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1021   {\r
1022     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1023   }\r
1024 \r
1025   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1026   {\r
1027     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1028   }\r
1029 \r
1030 \r
1031   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1032   {\r
1033     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1034   }\r
1035 \r
1036   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1037   {\r
1038     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1039   }\r
1040 \r
1041   void NewTreePanel(String type, String pwType, String title)\r
1042   {\r
1043     //are the sequences aligned?\r
1044     if(!viewport.alignment.isAligned())\r
1045     {\r
1046       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
1047                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
1048       return;\r
1049     }\r
1050 \r
1051     final TreePanel tp;\r
1052     if (viewport.getSelectionGroup() != null &&\r
1053         viewport.getSelectionGroup().getSize() > 3)\r
1054     {\r
1055       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
1056                          pwType,\r
1057                          0, viewport.alignment.getWidth());\r
1058     }\r
1059     else\r
1060     {\r
1061       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1062                          type, pwType, 0, viewport.alignment.getWidth());\r
1063     }\r
1064 \r
1065    addTreeMenuItem(tp, title);\r
1066 \r
1067    Desktop.addInternalFrame(tp, title, 600, 500);\r
1068   }\r
1069 \r
1070   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1071   {\r
1072     final JMenuItem item = new JMenuItem(title);\r
1073     sortByTreeMenu.add(item);\r
1074     item.addActionListener(new java.awt.event.ActionListener()\r
1075     {\r
1076       public void actionPerformed(ActionEvent e)\r
1077       {\r
1078         addHistoryItem("sort");\r
1079         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1080         alignPanel.repaint();\r
1081       }\r
1082     });\r
1083 \r
1084     treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
1085     {\r
1086       public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
1087       {\r
1088         sortByTreeMenu.remove(item);\r
1089       };\r
1090     });\r
1091 \r
1092   }\r
1093 \r
1094 \r
1095   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
1096   {\r
1097      WebserviceInfo info = new WebserviceInfo("Clustal web service",\r
1098      "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"+\r
1099      " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."\r
1100     +" Nucleic Acids Research, submitted, June 1994.",\r
1101      450, 150);\r
1102 \r
1103     ClustalThread thread = new ClustalThread(info);\r
1104     thread.start();\r
1105   }\r
1106 \r
1107     class ClustalThread extends Thread\r
1108     {\r
1109       WebserviceInfo info;\r
1110       public ClustalThread(WebserviceInfo info)\r
1111       {this.info = info; }\r
1112 \r
1113       public void run()\r
1114       {\r
1115         info.setStatus(WebserviceInfo.STATE_RUNNING);\r
1116         jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
1117         Vector sv = viewport.getAlignment().getSequences();\r
1118         SequenceI[] seqs = new SequenceI[sv.size()];\r
1119 \r
1120         int i = 0;\r
1121         do\r
1122         {\r
1123           seqs[i] = (SequenceI) sv.elementAt(i);\r
1124         }\r
1125         while (++i < sv.size());\r
1126 \r
1127         SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
1128         if (alignment != null)\r
1129         {\r
1130           AlignFrame af = new AlignFrame(new Alignment(alignment));\r
1131           Desktop.addInternalFrame(af, title.concat(" - ClustalW Alignment"),\r
1132                                    NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
1133           af.clustalColour_actionPerformed(null);\r
1134           af.clustalColour.setSelected(true);\r
1135           info.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
1136         }\r
1137         else\r
1138         {\r
1139             info.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
1140             info.appendProgressText("Problem obtaining clustal alignment");\r
1141         }\r
1142       }\r
1143     }\r
1144 \r
1145   protected void jpred_actionPerformed(ActionEvent e)\r
1146 {\r
1147 \r
1148     if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)\r
1149     {\r
1150       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1151       SequenceGroup seqs = viewport.getSelectionGroup();\r
1152       if (seqs.getSize() == 1 || !viewport.alignment.isAligned())\r
1153       {\r
1154         JPredClient ct = new JPredClient( (SequenceI)seqs.getSequenceAt(0));\r
1155       }\r
1156       else\r
1157       {\r
1158         int sz;\r
1159         SequenceI[] msa = new SequenceI[sz=seqs.getSize()];\r
1160         for (int i = 0; i < sz; i++)\r
1161         {\r
1162           msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1163         }\r
1164 \r
1165         JPredClient ct = new JPredClient(msa);\r
1166       }\r
1167 \r
1168     }\r
1169     else\r
1170     {\r
1171       Vector seqs = viewport.getAlignment().getSequences();\r
1172 \r
1173       if (seqs.size() == 1 || !viewport.alignment.isAligned())\r
1174       {\r
1175         JPredClient ct = new JPredClient( (SequenceI)\r
1176                                          seqs.elementAt(0));\r
1177       }\r
1178       else\r
1179       {\r
1180         SequenceI[] msa = new SequenceI[seqs.size()];\r
1181         for (int i = 0; i < seqs.size(); i++)\r
1182         {\r
1183           msa[i] = (SequenceI) seqs.elementAt(i);\r
1184         }\r
1185 \r
1186         JPredClient ct = new JPredClient(msa);\r
1187       }\r
1188 \r
1189     }\r
1190   }\r
1191 \r
1192     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
1193     // Pick the tree file\r
1194     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
1195         getProperty("LAST_DIRECTORY"));\r
1196     chooser.setFileView(new JalviewFileView());\r
1197     chooser.setDialogTitle("Select a newick-like tree file");\r
1198     chooser.setToolTipText("Load a tree file");\r
1199     int value = chooser.showOpenDialog(null);\r
1200     if (value == JalviewFileChooser.APPROVE_OPTION)\r
1201     {\r
1202       String choice = chooser.getSelectedFile().getPath();\r
1203       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1204       TreePanel treepanel = null;\r
1205       try\r
1206       {\r
1207         jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");\r
1208         fin.parse();\r
1209 \r
1210         if (fin.getTree() != null)\r
1211         {\r
1212           TreePanel tp = null;\r
1213           tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1214                              fin, "FromFile", choice);\r
1215           Desktop.addInternalFrame(tp, title, 600, 500);\r
1216           addTreeMenuItem(tp, title);\r
1217         }\r
1218       }\r
1219       catch (Exception ex)\r
1220       {\r
1221         JOptionPane.showMessageDialog(Desktop.desktop,\r
1222                                       "Problem reading tree file",\r
1223                                       ex.getMessage(),\r
1224                                       JOptionPane.WARNING_MESSAGE);\r
1225         ex.printStackTrace();\r
1226       }\r
1227     }\r
1228   }\r
1229 \r
1230 }\r