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