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);\r
 583     frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
 584   }\r
 585 \r
 586   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 587   {\r
 588     viewport.setShowFullId( fullSeqId.isSelected() );\r
 589 \r
 590     alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );\r
 591     alignPanel.repaint();\r
 592   }\r
 593 \r
 594   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 595   {\r
 596       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 597       alignPanel.repaint();\r
 598   }\r
 599 \r
 600   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 601   {\r
 602     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 603     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
 604     scaleAbove.setVisible( wrapMenuItem.isSelected() );\r
 605     scaleLeft.setVisible( wrapMenuItem.isSelected() );\r
 606     scaleRight.setVisible( wrapMenuItem.isSelected() );\r
 607     alignPanel.repaint();\r
 608   }\r
 609 \r
 610   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 611   {\r
 612     viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
 613     alignPanel.repaint();\r
 614   }\r
 615 \r
 616   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 617   {\r
 618     viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
 619     alignPanel.repaint();\r
 620   }\r
 621 \r
 622   protected void scaleRight_actionPerformed(ActionEvent e)\r
 623   {\r
 624     viewport.setScaleRightWrapped(scaleRight.isSelected());\r
 625     alignPanel.repaint();\r
 626   }\r
 627 \r
 628 \r
 629 \r
 630   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 631   {\r
 632     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 633     alignPanel.repaint();\r
 634   }\r
 635 \r
 636   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 637   {\r
 638     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 639     alignPanel.repaint();\r
 640   }\r
 641 \r
 642 \r
 643   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 644   {\r
 645     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 646     alignPanel.repaint();\r
 647   }\r
 648 \r
 649   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
 650   {\r
 651     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 652     if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
 653     {\r
 654          AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);\r
 655          ((Alignment)viewport.alignment).featuresAdded = true;\r
 656     }\r
 657     alignPanel.repaint();\r
 658   }\r
 659 \r
 660   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 661   {\r
 662     if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())\r
 663     {\r
 664       annotationPanelMenuItem.setSelected(false);\r
 665       return;\r
 666     }\r
 667     viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );\r
 668     alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );\r
 669   }\r
 670 \r
 671   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 672   {\r
 673     if (alignPanel.overviewPanel != null)\r
 674       return;\r
 675 \r
 676     JInternalFrame frame = new JInternalFrame();\r
 677     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 678    try{\r
 679      overview = new OverviewPanel(alignPanel, viewport);\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.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 685     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 686       {\r
 687             alignPanel.setOverviewPanel(null);\r
 688       };\r
 689     });\r
 690     alignPanel.setOverviewPanel( overview );\r
 691 \r
 692   }catch(java.lang.OutOfMemoryError ex)\r
 693    {\r
 694      JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 695                                    +"\nTry reducing the font size.",\r
 696                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 697    }\r
 698 \r
 699 \r
 700   }\r
 701 \r
 702   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 703   {\r
 704     changeColour( null );\r
 705   }\r
 706 \r
 707 \r
 708   public void clustalColour_actionPerformed(ActionEvent e)\r
 709   {\r
 710     abovePIDThreshold.setSelected(false);\r
 711     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 712   }\r
 713 \r
 714   public void zappoColour_actionPerformed(ActionEvent e)\r
 715   {\r
 716     changeColour(new ZappoColourScheme());\r
 717   }\r
 718 \r
 719   public void taylorColour_actionPerformed(ActionEvent e)\r
 720   {\r
 721     changeColour(new TaylorColourScheme());\r
 722   }\r
 723 \r
 724 \r
 725   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 726   {\r
 727     changeColour( new HydrophobicColourScheme() );\r
 728   }\r
 729 \r
 730   public void helixColour_actionPerformed(ActionEvent e)\r
 731   {\r
 732     changeColour(new HelixColourScheme() );\r
 733   }\r
 734 \r
 735 \r
 736   public void strandColour_actionPerformed(ActionEvent e)\r
 737   {\r
 738     changeColour(new StrandColourScheme());\r
 739   }\r
 740 \r
 741 \r
 742   public void turnColour_actionPerformed(ActionEvent e)\r
 743   {\r
 744     changeColour(new TurnColourScheme());\r
 745   }\r
 746 \r
 747 \r
 748   public void buriedColour_actionPerformed(ActionEvent e)\r
 749   {\r
 750     changeColour(new BuriedColourScheme() );\r
 751   }\r
 752 \r
 753   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 754   {\r
 755     changeColour(new NucleotideColourScheme());\r
 756   }\r
 757 \r
 758 \r
 759   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 760   {\r
 761     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
 762   }\r
 763 \r
 764 \r
 765 \r
 766   void changeColour(ColourSchemeI cs)\r
 767   {\r
 768     int threshold = 0;\r
 769 \r
 770     if ( viewport.getAbovePIDThreshold() )\r
 771     {\r
 772       threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\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     else if (cs instanceof ResidueColourScheme)\r
 782       ( (ResidueColourScheme) cs).setThreshold(0);\r
 783     else if (cs instanceof ScoreColourScheme)\r
 784       ( (ScoreColourScheme) cs).setThreshold(0);\r
 785 \r
 786 \r
 787 \r
 788     if (viewport.getConservationSelected())\r
 789     {\r
 790       ConservationColourScheme ccs = null;\r
 791 \r
 792       Alignment al = (Alignment) viewport.alignment;\r
 793       Conservation c = new Conservation("All",\r
 794                                         ResidueProperties.propHash, 3,\r
 795                                         al.getSequences(), 0,\r
 796                                         al.getWidth() - 1);\r
 797 \r
 798       c.calculate();\r
 799       c.verdict(false, viewport.ConsPercGaps);\r
 800 \r
 801       ccs = new ConservationColourScheme(c, cs);\r
 802 \r
 803       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 804       ccs.setConsensus( viewport.vconsensus );\r
 805       viewport.setGlobalColourScheme(ccs);\r
 806 \r
 807       SliderPanel.setConservationSlider(alignPanel, ccs, "Background");\r
 808 \r
 809     }\r
 810     else\r
 811     {\r
 812         // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 813         if (cs != null)\r
 814           cs.setConsensus(viewport.vconsensus);\r
 815         viewport.setGlobalColourScheme(cs);\r
 816     }\r
 817 \r
 818 \r
 819     if(viewport.getColourAppliesToAllGroups())\r
 820     {\r
 821       Vector groups = viewport.alignment.getGroups();\r
 822       for(int i=0; i<groups.size(); i++)\r
 823       {\r
 824         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 825 \r
 826         if (cs instanceof ClustalxColourScheme)\r
 827         {\r
 828           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
 829         }\r
 830         else\r
 831           try\r
 832           {\r
 833             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
 834           }\r
 835           catch (Exception ex)\r
 836           {\r
 837             ex.printStackTrace();\r
 838             sg.cs = cs;\r
 839           }\r
 840 \r
 841         if(viewport.getAbovePIDThreshold())\r
 842         {\r
 843           if (sg.cs instanceof ResidueColourScheme)\r
 844             ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
 845           else if (sg.cs instanceof ScoreColourScheme)\r
 846             ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
 847 \r
 848            sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );\r
 849         }\r
 850 \r
 851         if( viewport.getConservationSelected() )\r
 852         {\r
 853           Conservation c = new Conservation("Group",\r
 854                                             ResidueProperties.propHash, 3,\r
 855                                             sg.sequences, 0, viewport.alignment.getWidth()-1);\r
 856           c.calculate();\r
 857           c.verdict(false, viewport.ConsPercGaps);\r
 858           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 859 \r
 860           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 861           ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 862           sg.cs = ccs;\r
 863         }\r
 864         else\r
 865         {\r
 866           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 867           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 868         }\r
 869 \r
 870       }\r
 871     }\r
 872 \r
 873 \r
 874 \r
 875     alignPanel.repaint();\r
 876   }\r
 877 \r
 878   protected void modifyPID_actionPerformed(ActionEvent e)\r
 879   {\r
 880       if(viewport.getAbovePIDThreshold())\r
 881       {\r
 882         SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
 883                                    "Background");\r
 884         SliderPanel.showPIDSlider();\r
 885       }\r
 886   }\r
 887 \r
 888   protected void modifyConservation_actionPerformed(ActionEvent e)\r
 889   {\r
 890     if(viewport.getConservationSelected())\r
 891     {\r
 892       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
 893                                         "Background");\r
 894       SliderPanel.showConservationSlider();\r
 895     }\r
 896   }\r
 897 \r
 898 \r
 899   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 900   {\r
 901     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 902 \r
 903     viewport.setAbovePIDThreshold(false);\r
 904     abovePIDThreshold.setSelected(false);\r
 905 \r
 906    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 907    if(cs instanceof ConservationColourScheme )\r
 908      changeColour( ((ConservationColourScheme)cs).cs );\r
 909     else\r
 910       changeColour( cs );\r
 911 \r
 912     modifyConservation_actionPerformed(null);\r
 913   }\r
 914 \r
 915   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 916   {\r
 917     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
 918 \r
 919     conservationMenuItem.setSelected(false);\r
 920     viewport.setConservationSelected(false);\r
 921 \r
 922     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 923 \r
 924     if(cs instanceof ConservationColourScheme )\r
 925         changeColour( ((ConservationColourScheme)cs).cs );\r
 926     else\r
 927         changeColour( cs );\r
 928 \r
 929     modifyPID_actionPerformed(null);\r
 930   }\r
 931 \r
 932 \r
 933 \r
 934   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 935   {\r
 936     JInternalFrame frame = new JInternalFrame();\r
 937     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 938     frame.setContentPane(chooser);\r
 939     Desktop.addInternalFrame(frame,"User defined colours", 450,540, false );\r
 940   }\r
 941 \r
 942   public void PIDColour_actionPerformed(ActionEvent e)\r
 943   {\r
 944     changeColour( new PIDColourScheme() );\r
 945   }\r
 946 \r
 947 \r
 948   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 949   {\r
 950     changeColour(new Blosum62ColourScheme() );\r
 951   }\r
 952 \r
 953 \r
 954 \r
 955   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 956   {\r
 957     addHistoryItem("sort");\r
 958     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 959     alignPanel.repaint();\r
 960   }\r
 961 \r
 962   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 963   {\r
 964     addHistoryItem("sort");\r
 965     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 966     alignPanel.repaint();\r
 967   }\r
 968 \r
 969   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 970   {\r
 971     addHistoryItem("sort");\r
 972     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 973     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 974     alignPanel.repaint();\r
 975   }\r
 976 \r
 977   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 978   {\r
 979     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 980     JInternalFrame frame = new JInternalFrame();\r
 981     frame.setContentPane(sp);\r
 982     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);\r
 983 \r
 984   }\r
 985 \r
 986   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 987   {\r
 988     if(viewport.getSelectionGroup().getSize()<2)\r
 989       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 990     else\r
 991     {\r
 992       JInternalFrame frame = new JInternalFrame();\r
 993       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 994       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 995     }\r
 996   }\r
 997 \r
 998   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 999   {\r
1000 \r
1001     if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
1002        || viewport.getAlignment().getHeight()<4)\r
1003     {\r
1004       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
1005                                     +"at least 4 input sequences.",\r
1006                                     "Sequence selection insufficient",\r
1007                                     JOptionPane.WARNING_MESSAGE);\r
1008       return;\r
1009     }\r
1010 \r
1011     try{\r
1012       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
1013       JInternalFrame frame = new JInternalFrame();\r
1014       frame.setContentPane(pcaPanel);\r
1015       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
1016    }catch(java.lang.OutOfMemoryError ex)\r
1017    {\r
1018      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
1019                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
1020    }\r
1021 \r
1022 \r
1023   }\r
1024 \r
1025   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1026   {\r
1027     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1028   }\r
1029 \r
1030   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1031   {\r
1032     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1033   }\r
1034 \r
1035 \r
1036   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1037   {\r
1038     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1039   }\r
1040 \r
1041   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1042   {\r
1043     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1044   }\r
1045 \r
1046   void NewTreePanel(String type, String pwType, String title)\r
1047   {\r
1048     //are the sequences aligned?\r
1049     if(!viewport.alignment.isAligned())\r
1050     {\r
1051       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
1052                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
1053       return;\r
1054     }\r
1055 \r
1056     final TreePanel tp;\r
1057     if (viewport.getSelectionGroup() != null &&\r
1058         viewport.getSelectionGroup().getSize() > 3)\r
1059     {\r
1060       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
1061                          pwType,\r
1062                          0, viewport.alignment.getWidth());\r
1063     }\r
1064     else\r
1065     {\r
1066       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1067                          type, pwType, 0, viewport.alignment.getWidth());\r
1068     }\r
1069 \r
1070    addTreeMenuItem(tp, title);\r
1071 \r
1072    Desktop.addInternalFrame(tp, title, 600, 500);\r
1073   }\r
1074 \r
1075   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1076   {\r
1077     final JMenuItem item = new JMenuItem(title);\r
1078     sortByTreeMenu.add(item);\r
1079     item.addActionListener(new java.awt.event.ActionListener()\r
1080     {\r
1081       public void actionPerformed(ActionEvent e)\r
1082       {\r
1083         addHistoryItem("sort");\r
1084         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1085         alignPanel.repaint();\r
1086       }\r
1087     });\r
1088 \r
1089     treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
1090     {\r
1091       public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
1092       {\r
1093         sortByTreeMenu.remove(item);\r
1094       };\r
1095     });\r
1096 \r
1097   }\r
1098 \r
1099 \r
1100   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
1101   {\r
1102      WebserviceInfo info = new WebserviceInfo("Clustal web service",\r
1103      "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"+\r
1104      " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."\r
1105     +" Nucleic Acids Research, submitted, June 1994.",\r
1106      450, 150);\r
1107 \r
1108     ClustalThread thread = new ClustalThread(info);\r
1109     thread.start();\r
1110   }\r
1111 \r
1112     class ClustalThread extends Thread\r
1113     {\r
1114       WebserviceInfo info;\r
1115       public ClustalThread(WebserviceInfo info)\r
1116       {this.info = info; }\r
1117 \r
1118       public void run()\r
1119       {\r
1120         info.setStatus(WebserviceInfo.STATE_RUNNING);\r
1121         jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
1122         Vector sv = viewport.getAlignment().getSequences();\r
1123         SequenceI[] seqs = new SequenceI[sv.size()];\r
1124 \r
1125         int i = 0;\r
1126         do\r
1127         {\r
1128           seqs[i] = (SequenceI) sv.elementAt(i);\r
1129         }\r
1130         while (++i < sv.size());\r
1131 \r
1132         SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
1133         if (alignment != null)\r
1134         {\r
1135           AlignFrame af = new AlignFrame(new Alignment(alignment));\r
1136           Desktop.addInternalFrame(af, title.concat(" - ClustalW Alignment"),\r
1137                                    NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
1138           af.clustalColour_actionPerformed(null);\r
1139           af.clustalColour.setSelected(true);\r
1140           info.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
1141         }\r
1142         else\r
1143         {\r
1144             info.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
1145             info.appendProgressText("Problem obtaining clustal alignment");\r
1146         }\r
1147       }\r
1148     }\r
1149 \r
1150   protected void jpred_actionPerformed(ActionEvent e)\r
1151 {\r
1152 \r
1153     if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)\r
1154     {\r
1155       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1156       SequenceGroup seqs = viewport.getSelectionGroup();\r
1157       if (seqs.getSize() == 1 || !viewport.alignment.isAligned())\r
1158       {\r
1159         JPredClient ct = new JPredClient( (SequenceI)seqs.getSequenceAt(0));\r
1160       }\r
1161       else\r
1162       {\r
1163         int sz;\r
1164         SequenceI[] msa = new SequenceI[sz=seqs.getSize()];\r
1165         for (int i = 0; i < sz; i++)\r
1166         {\r
1167           msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1168         }\r
1169 \r
1170         JPredClient ct = new JPredClient(msa);\r
1171       }\r
1172 \r
1173     }\r
1174     else\r
1175     {\r
1176       Vector seqs = viewport.getAlignment().getSequences();\r
1177 \r
1178       if (seqs.size() == 1 || !viewport.alignment.isAligned())\r
1179       {\r
1180         JPredClient ct = new JPredClient( (SequenceI)\r
1181                                          seqs.elementAt(0));\r
1182       }\r
1183       else\r
1184       {\r
1185         SequenceI[] msa = new SequenceI[seqs.size()];\r
1186         for (int i = 0; i < seqs.size(); i++)\r
1187         {\r
1188           msa[i] = (SequenceI) seqs.elementAt(i);\r
1189         }\r
1190 \r
1191         JPredClient ct = new JPredClient(msa);\r
1192       }\r
1193 \r
1194     }\r
1195   }\r
1196 \r
1197     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
1198     // Pick the tree file\r
1199     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
1200         getProperty("LAST_DIRECTORY"));\r
1201     chooser.setFileView(new JalviewFileView());\r
1202     chooser.setDialogTitle("Select a newick-like tree file");\r
1203     chooser.setToolTipText("Load a tree file");\r
1204     int value = chooser.showOpenDialog(null);\r
1205     if (value == JalviewFileChooser.APPROVE_OPTION)\r
1206     {\r
1207       String choice = chooser.getSelectedFile().getPath();\r
1208       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1209       TreePanel treepanel = null;\r
1210       try\r
1211       {\r
1212         jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");\r
1213         fin.parse();\r
1214 \r
1215         if (fin.getTree() != null)\r
1216         {\r
1217           TreePanel tp = null;\r
1218           tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1219                              fin, "FromFile", choice);\r
1220           Desktop.addInternalFrame(tp, title, 600, 500);\r
1221           addTreeMenuItem(tp, title);\r
1222         }\r
1223       }\r
1224       catch (Exception ex)\r
1225       {\r
1226         JOptionPane.showMessageDialog(Desktop.desktop,\r
1227                                       "Problem reading tree file",\r
1228                                       ex.getMessage(),\r
1229                                       JOptionPane.WARNING_MESSAGE);\r
1230         ex.printStackTrace();\r
1231       }\r
1232     }\r
1233   }\r
1234 \r
1235 }\r