src/jalview/gui/AlignFrame.java

   1 /********************\r
   2  * 2004 Jalview Reengineered\r
   3  * Barton Group\r
   4  * Dundee University\r
   5  *\r
   6  * AM Waterhouse\r
   7  *******************/\r
   8 \r
   9 \r
  10 \r
  11 \r
  12 package jalview.gui;\r
  13 \r
  14 import jalview.jbgui.GAlignFrame;\r
  15 import jalview.schemes.*;\r
  16 import jalview.datamodel.*;\r
  17 import jalview.analysis.*;\r
  18 import jalview.io.*;\r
  19 import jalview.ws.*;\r
  20 import java.awt.*;\r
  21 import java.awt.event.*;\r
  22 import java.awt.print.*;\r
  23 import javax.swing.*;\r
  24 import javax.swing.event.*;\r
  25 import java.util.*;\r
  26 import  java.awt.datatransfer.*;\r
  27 \r
  28 \r
  29 public class AlignFrame extends GAlignFrame\r
  30 {\r
  31   final AlignmentPanel alignPanel;\r
  32   final AlignViewport viewport;\r
  33   public AlignFrame(AlignmentI al)\r
  34   {\r
  35     viewport = new AlignViewport(al,true,true,false);\r
  36 \r
  37     String fontName = jalview.bin.Cache.getProperty("FONT_NAME");\r
  38     String fontStyle= jalview.bin.Cache.getProperty("FONT_STYLE");\r
  39     String fontSize = jalview.bin.Cache.getProperty("FONT_SIZE");\r
  40     if(fontName!=null && fontStyle!=null && fontSize!=null)\r
  41       viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );\r
  42 \r
  43 \r
  44     alignPanel = new AlignmentPanel(this, viewport);\r
  45     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
  46 \r
  47     // add conservation graph to alignment\r
  48     viewport.updateConservation();\r
  49     viewport.updateConsensus();\r
  50 \r
  51     alignPanel.annotationPanel.adjustPanelHeight();\r
  52     alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
  53     alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
  54 \r
  55 \r
  56     addInternalFrameListener(new InternalFrameAdapter()\r
  57    {\r
  58      public void internalFrameActivated(InternalFrameEvent evt)\r
  59      {\r
  60           javax.swing.SwingUtilities.invokeLater(new Runnable()\r
  61           {\r
  62             public void run()\r
  63             {      alignPanel.requestFocus();    }\r
  64           });\r
  65 \r
  66      }\r
  67    });\r
  68 \r
  69   }\r
  70 \r
  71   protected void saveAs_actionPerformed(ActionEvent e)\r
  72   {\r
  73     String suffix [] = null;\r
  74     if(e.getActionCommand().equals("FASTA"))\r
  75       suffix = new String[]{"fa", "fasta"};\r
  76     else if(e.getActionCommand().equals("MSF"))\r
  77       suffix = new String[]{"msf"};\r
  78     else if(e.getActionCommand().equals("CLUSTAL"))\r
  79       suffix = new String[]{"aln"};\r
  80     else if(e.getActionCommand().equals("BLC"))\r
  81       suffix = new String[]{"blc"};\r
  82     else if(e.getActionCommand().equals("PIR"))\r
  83       suffix = new String[]{"pir"};\r
  84     else if(e.getActionCommand().equals("PFAM"))\r
  85       suffix = new String[]{"pfam"};\r
  86 \r
  87     if(e.getActionCommand().equals("XML DUMP"))\r
  88     {\r
  89       XMLStore store = new XMLStore();\r
  90       store.store(viewport);\r
  91       return;\r
  92     }\r
  93 \r
  94     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")\r
  95         , suffix, e.getActionCommand()+" file");\r
  96     chooser.setFileView(new JalviewFileView());\r
  97     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
  98     chooser.setToolTipText("Save");\r
  99     int value = chooser.showSaveDialog(this);\r
 100     if(value == JalviewFileChooser.APPROVE_OPTION)\r
 101     {\r
 102       String choice =  chooser.getSelectedFile().getPath();\r
 103       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
 104       String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
 105       try{\r
 106         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
 107         out.println(output);\r
 108         out.close();\r
 109       }\r
 110       catch(Exception ex){}\r
 111     }\r
 112 \r
 113   }\r
 114 \r
 115   protected void outputText_actionPerformed(ActionEvent e)\r
 116   {\r
 117      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
 118      JInternalFrame frame = new JInternalFrame();\r
 119      cap.formatForOutput();\r
 120      frame.setContentPane(cap);\r
 121      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
 122      cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
 123   }\r
 124 \r
 125   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 126   {\r
 127     HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
 128     htmlOutput = null;\r
 129   }\r
 130 \r
 131   protected void createPNG_actionPerformed(ActionEvent e)\r
 132   {\r
 133     alignPanel.makePNG();\r
 134   }\r
 135 \r
 136   protected void epsFile_actionPerformed(ActionEvent e)\r
 137   {\r
 138     alignPanel.makeEPS();\r
 139   }\r
 140 \r
 141 \r
 142   public void printMenuItem_actionPerformed(ActionEvent e)\r
 143   {\r
 144     //Putting in a thread avoids Swing painting problems\r
 145     PrintThread thread = new PrintThread();\r
 146     thread.start();\r
 147   }\r
 148 \r
 149   class PrintThread extends Thread\r
 150   {\r
 151     public void run()\r
 152     {\r
 153       PrinterJob printJob = PrinterJob.getPrinterJob();\r
 154       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
 155       printJob.setPrintable(alignPanel, pf);\r
 156       if (printJob.printDialog())\r
 157       {\r
 158         try\r
 159         {\r
 160           printJob.print();\r
 161         }\r
 162         catch (Exception PrintException)\r
 163         {\r
 164           PrintException.printStackTrace();\r
 165         }\r
 166       }\r
 167     }\r
 168 \r
 169   }\r
 170 \r
 171 \r
 172 \r
 173 \r
 174   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 175   {\r
 176     try{\r
 177       this.setClosed(true);\r
 178     }catch(Exception ex){}\r
 179   }\r
 180 \r
 181   Stack historyList = new Stack();\r
 182   Stack redoList = new Stack();\r
 183   JMenuBar jMenuBar1 = new JMenuBar();\r
 184 \r
 185   void updateEditMenuBar()\r
 186   {\r
 187     if(historyList.size()>0)\r
 188      {\r
 189        undoMenuItem.setEnabled(true);\r
 190        Object [] history = (Object[])historyList.get(0);\r
 191        undoMenuItem.setText("Undo "+history[0]);\r
 192      }\r
 193     else\r
 194     {\r
 195       undoMenuItem.setEnabled(false);\r
 196       undoMenuItem.setText("Undo");\r
 197     }\r
 198 \r
 199     if(redoList.size()>0)\r
 200      {\r
 201        redoMenuItem.setEnabled(true);\r
 202        Object [] history = (Object[])redoList.get(0);\r
 203        redoMenuItem.setText("Redo "+history[0]);\r
 204      }\r
 205     else\r
 206     {\r
 207       redoMenuItem.setEnabled(false);\r
 208       redoMenuItem.setText("Redo");\r
 209     }\r
 210   }\r
 211 \r
 212   public void addHistoryItem(String type)\r
 213   {\r
 214     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 215     redoList.clear();\r
 216     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 217     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 218     {\r
 219       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 220                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 221     }\r
 222 \r
 223     historyList.add(0, new Object[]{type,  seq} );\r
 224     updateEditMenuBar();\r
 225   }\r
 226 \r
 227   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 228   {\r
 229     Object [] history = (Object[])historyList.remove(0);\r
 230     // add the redo state before continuing!!\r
 231     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 232     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
 233     {\r
 234       seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
 235                             viewport.getAlignment().getSequenceAt(i).\r
 236                             getSequence());\r
 237     }\r
 238     /////////\r
 239 \r
 240     redoList.add(0, new Object[] {history[0], seq});\r
 241 \r
 242       seq = (SequenceI[]) history[1];\r
 243       viewport.setAlignment( new Alignment(seq) );\r
 244       updateEditMenuBar();\r
 245       viewport.updateConsensus();\r
 246       alignPanel.RefreshPanels();\r
 247       alignPanel.RefreshPanels();\r
 248   }\r
 249 \r
 250   public void moveSelectedSequences(boolean up)\r
 251   {\r
 252     SequenceGroup sg = viewport.getSelectionGroup();\r
 253     if (sg == null)\r
 254       return;\r
 255 \r
 256     if (up)\r
 257     {\r
 258       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 259       {\r
 260         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 261         if (!sg.sequences.contains(seq))\r
 262           continue;\r
 263 \r
 264         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 265         if (sg.sequences.contains(temp))\r
 266           continue;\r
 267 \r
 268         viewport.alignment.getSequences().setElementAt(temp, i);\r
 269         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 270       }\r
 271     }\r
 272     else\r
 273     {\r
 274       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 275       {\r
 276         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 277         if (!sg.sequences.contains(seq))\r
 278           continue;\r
 279 \r
 280         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 281         if (sg.sequences.contains(temp))\r
 282           continue;\r
 283 \r
 284         viewport.alignment.getSequences().setElementAt(temp, i);\r
 285         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 286       }\r
 287     }\r
 288 \r
 289     alignPanel.RefreshPanels();\r
 290   }\r
 291 \r
 292 \r
 293 \r
 294   protected void copy_actionPerformed(ActionEvent e)\r
 295   {\r
 296    if(viewport.getSelectionGroup()==null)\r
 297      return;\r
 298 \r
 299    SequenceGroup sg = viewport.getSelectionGroup();\r
 300 \r
 301      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 302      StringBuffer buffer= new StringBuffer();\r
 303 \r
 304        for(int i=0; i<sg.getSize(); i++)\r
 305        {\r
 306          SequenceI seq = sg.getSequenceAt(i);\r
 307          buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
 308                         +seq.findPosition( sg.getEndRes() )+ "\t"\r
 309                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
 310        }\r
 311      c.setContents( new StringSelection( buffer.toString()) , null ) ;\r
 312 \r
 313   }\r
 314 \r
 315 \r
 316   protected void pasteNew_actionPerformed(ActionEvent e)\r
 317   {\r
 318     paste(true);\r
 319   }\r
 320 \r
 321   protected void pasteThis_actionPerformed(ActionEvent e)\r
 322   {\r
 323     addHistoryItem("Paste");\r
 324     paste(false);\r
 325   }\r
 326 \r
 327   void paste(boolean newAlignment)\r
 328   {\r
 329     try{\r
 330       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 331       Transferable contents = c.getContents(this);\r
 332       if (contents == null)\r
 333         return;\r
 334 \r
 335       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
 336       StringTokenizer st = new StringTokenizer(str);\r
 337       ArrayList seqs = new ArrayList();\r
 338       while (st.hasMoreElements())\r
 339       {\r
 340         String name = st.nextToken();\r
 341         int start = Integer.parseInt(st.nextToken());\r
 342         int end = Integer.parseInt(st.nextToken());\r
 343         Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
 344 \r
 345         if(!newAlignment)\r
 346           viewport.alignment.addSequence(sequence);\r
 347         else\r
 348           seqs.add(sequence);\r
 349       }\r
 350 \r
 351       if(newAlignment)\r
 352       {\r
 353         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 354         seqs.toArray(newSeqs);\r
 355         AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
 356         int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;\r
 357         if (newHeight > 500)\r
 358           newHeight = 500;\r
 359         Desktop.addInternalFrame(af, "Copied sequences", 700, 500);\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.RefreshPanels();\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.RefreshPanels();\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.RefreshPanels();\r
 424      alignPanel.RefreshPanels();\r
 425   }\r
 426 \r
 427 \r
 428   public void groupsMenuItem_actionPerformed(ActionEvent e)\r
 429   {\r
 430     GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
 431     JInternalFrame frame = new JInternalFrame();\r
 432     frame.setContentPane(geditor);\r
 433     Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
 434     frame.setResizable(false);\r
 435   }\r
 436 \r
 437   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 438   {\r
 439     viewport.alignment.deleteAllGroups();\r
 440     viewport.setSelectionGroup(null);\r
 441 \r
 442     alignPanel.RefreshPanels();\r
 443   }\r
 444 \r
 445 \r
 446 \r
 447   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 448   {\r
 449     SequenceGroup sg = new SequenceGroup();\r
 450     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 451       sg.addSequence( viewport.getAlignment().getSequenceAt(i));\r
 452     sg.setEndRes(viewport.alignment.getWidth());\r
 453     viewport.setSelectionGroup(sg);\r
 454     PaintRefresher.Refresh(null);\r
 455   }\r
 456 \r
 457   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 458   {\r
 459     viewport.setSelectionGroup(null);\r
 460     PaintRefresher.Refresh(null);\r
 461   }\r
 462 \r
 463   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 464   {\r
 465     SequenceGroup sg = viewport.getSelectionGroup();\r
 466     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 467       sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));\r
 468 \r
 469     PaintRefresher.Refresh(null);\r
 470   }\r
 471 \r
 472 \r
 473   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 474   {\r
 475     viewport.getColumnSelection().clear();\r
 476     repaint();\r
 477   }\r
 478 \r
 479   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 480   {\r
 481     addHistoryItem("delete columns");\r
 482     ColumnSelection colSel = viewport.getColumnSelection();\r
 483     if (colSel.size() > 0)\r
 484     {\r
 485       int min = colSel.getMin();\r
 486       viewport.getAlignment().trimLeft(min);\r
 487       colSel.compensateForEdit(0,min);\r
 488 \r
 489       if(viewport.getSelectionGroup()!=null)\r
 490         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 491 \r
 492       Vector groups = viewport.alignment.getGroups();\r
 493       for(int i=0; i<groups.size(); i++)\r
 494       {\r
 495         SequenceGroup sg = (SequenceGroup) groups.get(i);\r
 496         if(!sg.adjustForRemoveLeft(min))\r
 497           viewport.alignment.deleteGroup(sg);\r
 498       }\r
 499 \r
 500       alignPanel.RefreshPanels();\r
 501     }\r
 502   }\r
 503 \r
 504   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 505   {\r
 506     addHistoryItem("delete columns");\r
 507     ColumnSelection colSel = viewport.getColumnSelection();\r
 508     if (colSel.size() > 0)\r
 509     {\r
 510       int max = colSel.getMax();\r
 511       viewport.getAlignment().trimRight(max);\r
 512       if(viewport.getSelectionGroup()!=null)\r
 513         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 514 \r
 515       Vector groups = viewport.alignment.getGroups();\r
 516       for(int i=0; i<groups.size(); i++)\r
 517       {\r
 518         SequenceGroup sg = (SequenceGroup) groups.get(i);\r
 519         if(!sg.adjustForRemoveRight(max))\r
 520           viewport.alignment.deleteGroup(sg);\r
 521       }\r
 522 \r
 523 \r
 524 \r
 525       alignPanel.RefreshPanels();\r
 526     }\r
 527 \r
 528   }\r
 529 \r
 530   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 531   {\r
 532     addHistoryItem("delete gapped columns");\r
 533     viewport.getAlignment().removeGaps();\r
 534     viewport.updateConservation();\r
 535     viewport.updateConsensus();\r
 536     alignPanel.RefreshPanels();\r
 537   }\r
 538 \r
 539   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 540   {\r
 541     addHistoryItem("delete all gaps");\r
 542     SequenceI current;\r
 543     int jSize;\r
 544     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 545     {\r
 546       current = viewport.getAlignment().getSequenceAt(i);\r
 547       jSize = current.getLength();\r
 548       for (int j=0; j < jSize; j++)\r
 549         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 550         {\r
 551           current.deleteCharAt(j);\r
 552           j--;\r
 553           jSize--;\r
 554         }\r
 555     }\r
 556     viewport.updateConservation();\r
 557     viewport.updateConsensus();\r
 558     alignPanel.RefreshPanels();\r
 559   }\r
 560 \r
 561   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 562   {\r
 563     char thisChar = '-';\r
 564     char nextChar = '.';\r
 565     if(viewport.getGapCharacter()=='-')\r
 566     {\r
 567       thisChar = '.';\r
 568       nextChar = '-';\r
 569     }\r
 570     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 571     viewport.setGapCharacter(thisChar);\r
 572     alignPanel.RefreshPanels();\r
 573   }\r
 574 \r
 575   public void findMenuItem_actionPerformed(ActionEvent e)\r
 576   {\r
 577       JInternalFrame frame = new JInternalFrame();\r
 578       Finder finder = new Finder(viewport, alignPanel, frame);\r
 579       frame.setContentPane(finder);\r
 580      Desktop.addInternalFrame(frame, "Find", 340,110);\r
 581 \r
 582   }\r
 583 \r
 584 \r
 585   public void font_actionPerformed(ActionEvent e)\r
 586   {\r
 587     JInternalFrame frame = new JInternalFrame();\r
 588     FontChooser fc = new FontChooser( alignPanel, frame );\r
 589     frame.setContentPane(fc);\r
 590     Desktop.addInternalFrame(frame, "Change Font", 480,100);\r
 591   }\r
 592 \r
 593   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 594   {\r
 595     viewport.setShowFullId( fullSeqId.isSelected() );\r
 596 \r
 597     alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );\r
 598     alignPanel.RefreshPanels();\r
 599   }\r
 600 \r
 601   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 602   {\r
 603       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 604       alignPanel.RefreshPanels();\r
 605   }\r
 606 \r
 607   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 608   {\r
 609     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 610     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
 611   }\r
 612 \r
 613 \r
 614   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 615   {\r
 616     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 617     alignPanel.RefreshPanels();\r
 618   }\r
 619 \r
 620   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 621   {\r
 622     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 623     alignPanel.RefreshPanels();\r
 624   }\r
 625 \r
 626 \r
 627   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 628   {\r
 629     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 630     alignPanel.RefreshPanels();\r
 631   }\r
 632 \r
 633   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
 634   {\r
 635     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 636     if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
 637     {\r
 638          AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);\r
 639          ((Alignment)viewport.alignment).featuresAdded = true;\r
 640     }\r
 641     alignPanel.RefreshPanels();\r
 642   }\r
 643 \r
 644   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 645   {\r
 646     if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())\r
 647     {\r
 648       annotationPanelMenuItem.setSelected(false);\r
 649       return;\r
 650     }\r
 651     viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );\r
 652     alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );\r
 653   }\r
 654 \r
 655   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 656   {\r
 657     if (alignPanel.overviewPanel != null)\r
 658       return;\r
 659 \r
 660     JInternalFrame frame = new JInternalFrame();\r
 661     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 662    try{\r
 663      overview = new OverviewPanel(alignPanel, viewport);\r
 664      frame.setContentPane(overview);\r
 665     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 666                              frame.getWidth(), frame.getHeight());\r
 667     frame.pack();\r
 668     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 669     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 670       {\r
 671             alignPanel.setOverviewPanel(null);\r
 672       };\r
 673     });\r
 674     alignPanel.setOverviewPanel( overview );\r
 675 \r
 676   }catch(java.lang.OutOfMemoryError ex)\r
 677    {\r
 678      JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 679                                    +"\nTry reducing the font size.",\r
 680                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 681    }\r
 682 \r
 683 \r
 684   }\r
 685 \r
 686   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 687   {\r
 688     changeColour( null );\r
 689   }\r
 690 \r
 691 \r
 692   public void clustalColour_actionPerformed(ActionEvent e)\r
 693   {\r
 694     abovePIDThreshold.setSelected(false);\r
 695     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 696   }\r
 697 \r
 698   public void zappoColour_actionPerformed(ActionEvent e)\r
 699   {\r
 700     changeColour(new ZappoColourScheme());\r
 701   }\r
 702 \r
 703   public void taylorColour_actionPerformed(ActionEvent e)\r
 704   {\r
 705     changeColour(new TaylorColourScheme());\r
 706   }\r
 707 \r
 708 \r
 709   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 710   {\r
 711     changeColour( new HydrophobicColourScheme() );\r
 712   }\r
 713 \r
 714   public void helixColour_actionPerformed(ActionEvent e)\r
 715   {\r
 716     changeColour(new HelixColourScheme() );\r
 717   }\r
 718 \r
 719 \r
 720   public void strandColour_actionPerformed(ActionEvent e)\r
 721   {\r
 722     changeColour(new StrandColourScheme());\r
 723   }\r
 724 \r
 725 \r
 726   public void turnColour_actionPerformed(ActionEvent e)\r
 727   {\r
 728     changeColour(new TurnColourScheme());\r
 729   }\r
 730 \r
 731 \r
 732   public void buriedColour_actionPerformed(ActionEvent e)\r
 733   {\r
 734     changeColour(new BuriedColourScheme() );\r
 735   }\r
 736 \r
 737   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 738   {\r
 739     changeColour(new NucleotideColourScheme());\r
 740   }\r
 741 \r
 742 \r
 743   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 744   {\r
 745     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
 746   }\r
 747 \r
 748 \r
 749 \r
 750   void changeColour(ColourSchemeI cs)\r
 751   {\r
 752 \r
 753     if(viewport.getColourAppliesToAllGroups())\r
 754     {\r
 755       Vector groups = viewport.alignment.getGroups();\r
 756       for(int i=0; i<groups.size(); i++)\r
 757       {\r
 758         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 759         sg.cs = cs;\r
 760 \r
 761         if(abovePIDThreshold.isSelected())\r
 762           abovePIDThreshold_actionPerformed(null);\r
 763         else if( viewport.getConservationSelected() )\r
 764         {\r
 765           Conservation c = new Conservation("Group",\r
 766                                             ResidueProperties.propHash, 3,\r
 767                                             sg.sequences, sg.getStartRes(),\r
 768                                             sg.getEndRes());\r
 769           c.calculate();\r
 770           c.verdict(false, 100);\r
 771           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 772 \r
 773           sg.cs = ccs;\r
 774         }\r
 775 \r
 776       }\r
 777     }\r
 778 \r
 779 \r
 780     if ( viewport.getAbovePIDThreshold())\r
 781     {\r
 782       int threshold = 0;\r
 783       threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");\r
 784       Desktop.hideConservationSlider();\r
 785 \r
 786       if (cs instanceof ResidueColourScheme)\r
 787         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 788       else if (cs instanceof ScoreColourScheme)\r
 789         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 790 \r
 791       viewport.setGlobalColourScheme(cs);\r
 792 \r
 793     }\r
 794     else\r
 795     if (cs instanceof ResidueColourScheme)\r
 796       ( (ResidueColourScheme) cs).setThreshold(0);\r
 797     else if (cs instanceof ScoreColourScheme)\r
 798       ( (ScoreColourScheme) cs).setThreshold(0);\r
 799 \r
 800 \r
 801 \r
 802 \r
 803 if ( viewport.getConservationSelected() )\r
 804  {\r
 805    ConservationColourScheme ccs = null;\r
 806 \r
 807    Alignment al = (Alignment) viewport.alignment;\r
 808    Conservation c = new Conservation("All",\r
 809                                      ResidueProperties.propHash, 3,\r
 810                                      al.getSequences(), 0,\r
 811                                      al.getWidth());\r
 812 \r
 813    c.calculate();\r
 814    c.verdict(false, 100);\r
 815 \r
 816    ccs = new ConservationColourScheme(c, cs);\r
 817 \r
 818    int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,\r
 819        "Background");\r
 820 \r
 821    ccs.inc = threshold;\r
 822 \r
 823    viewport.setGlobalColourScheme(ccs);\r
 824 \r
 825   }\r
 826   else\r
 827        viewport.setGlobalColourScheme( cs );\r
 828 \r
 829     alignPanel.RefreshPanels();\r
 830   }\r
 831 \r
 832 \r
 833   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 834   {\r
 835     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 836     if(coloursChanging)\r
 837       return;\r
 838 \r
 839     coloursChanging = true;\r
 840 \r
 841     viewport.setAbovePIDThreshold(false);\r
 842     abovePIDThreshold.setSelected(false);\r
 843     Desktop.hidePIDSlider();\r
 844     if(!viewport.getConservationSelected())\r
 845       Desktop.hideConservationSlider();\r
 846 \r
 847    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 848    if(cs instanceof ConservationColourScheme )\r
 849      changeColour( ((ConservationColourScheme)cs).cs );\r
 850     else\r
 851       changeColour( cs );\r
 852 \r
 853     coloursChanging = false;\r
 854   }\r
 855 \r
 856   boolean coloursChanging = false;\r
 857   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 858   {\r
 859     if(coloursChanging)\r
 860       return;\r
 861 \r
 862     coloursChanging = true;\r
 863     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
 864 \r
 865     conservationMenuItem.setSelected(false);\r
 866     viewport.setConservationSelected(false);\r
 867     Desktop.hideConservationSlider();\r
 868 \r
 869     if(!viewport.getAbovePIDThreshold())\r
 870       Desktop.hidePIDSlider();\r
 871 \r
 872 \r
 873     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 874     if(cs instanceof ConservationColourScheme )\r
 875         changeColour( ((ConservationColourScheme)cs).cs );\r
 876     else\r
 877         changeColour( cs );\r
 878 \r
 879     coloursChanging = false;\r
 880   }\r
 881 \r
 882 \r
 883 \r
 884   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 885   {\r
 886     JInternalFrame frame = new JInternalFrame();\r
 887     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 888     frame.setContentPane(chooser);\r
 889     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 890     frame.setResizable(false);\r
 891     frame.setIconifiable(false);\r
 892     frame.setMaximizable(false);\r
 893   }\r
 894 \r
 895   public void PIDColour_actionPerformed(ActionEvent e)\r
 896   {\r
 897     changeColour( new PIDColourScheme() );\r
 898   }\r
 899 \r
 900 \r
 901   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 902   {\r
 903     changeColour(new Blosum62ColourScheme(viewport) );\r
 904   }\r
 905 \r
 906 \r
 907 \r
 908   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 909   {\r
 910     addHistoryItem("sort");\r
 911     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 912     alignPanel.RefreshPanels();\r
 913   }\r
 914 \r
 915   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 916   {\r
 917     addHistoryItem("sort");\r
 918     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 919     alignPanel.RefreshPanels();\r
 920   }\r
 921 \r
 922   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 923   {\r
 924     addHistoryItem("sort");\r
 925     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 926     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 927     alignPanel.RefreshPanels();\r
 928   }\r
 929 \r
 930   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 931   {\r
 932     addHistoryItem("sort");\r
 933     if(viewport.getCurrentTree()==null)\r
 934       return;\r
 935 \r
 936     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 937     alignPanel.RefreshPanels();\r
 938   }\r
 939 \r
 940   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 941   {\r
 942     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 943     JInternalFrame frame = new JInternalFrame();\r
 944     frame.setContentPane(sp);\r
 945     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);\r
 946     frame.setMaximizable(false);\r
 947     frame.setResizable(false);\r
 948 \r
 949   }\r
 950 \r
 951   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 952   {\r
 953     if(viewport.getSelectionGroup().getSize()<2)\r
 954       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 955     else\r
 956     {\r
 957       JInternalFrame frame = new JInternalFrame();\r
 958       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 959       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 960     }\r
 961   }\r
 962 \r
 963   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 964   {\r
 965 \r
 966     if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
 967        || viewport.getAlignment().getHeight()<4)\r
 968     {\r
 969       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
 970                                     +"at least 4 input sequences.",\r
 971                                     "Sequence selection insufficient",\r
 972                                     JOptionPane.WARNING_MESSAGE);\r
 973       return;\r
 974     }\r
 975 \r
 976     try{\r
 977       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 978       JInternalFrame frame = new JInternalFrame();\r
 979       frame.setContentPane(pcaPanel);\r
 980       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 981    }catch(java.lang.OutOfMemoryError ex)\r
 982    {\r
 983      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 984                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 985    }\r
 986 \r
 987 \r
 988   }\r
 989 \r
 990   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 991   {\r
 992     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 993   }\r
 994 \r
 995   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 996   {\r
 997     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 998   }\r
 999 \r
1000 \r
1001   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1002   {\r
1003     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1004   }\r
1005 \r
1006   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1007   {\r
1008     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1009   }\r
1010 \r
1011   void NewTreePanel(String type, String pwType, String title)\r
1012   {\r
1013     //are the sequences aligned?\r
1014     if(!viewport.alignment.isAligned())\r
1015     {\r
1016       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
1017                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
1018       return;\r
1019     }\r
1020 \r
1021     TreePanel tp=null;\r
1022    if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)\r
1023    {\r
1024      tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType,\r
1025                          0, viewport.alignment.getWidth());\r
1026    }\r
1027    else\r
1028    {\r
1029      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1030                          type, pwType,  0, viewport.alignment.getWidth());\r
1031    }\r
1032 \r
1033    Desktop.addInternalFrame(tp, title, 600, 500);\r
1034   }\r
1035 \r
1036 \r
1037 \r
1038 \r
1039   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
1040   {\r
1041     JInternalFrame frame = new JInternalFrame();\r
1042     ClustalThread ct = new ClustalThread(frame);\r
1043     Thread t = new Thread(ct);\r
1044     t.start();\r
1045     frame.setContentPane(ct);\r
1046      Desktop.addInternalFrame(frame, title, 300, 80);\r
1047 \r
1048   }\r
1049 \r
1050   class ClustalThread extends JPanel implements Runnable\r
1051   {\r
1052     Image [] image;\r
1053     int imageIndex = 0;\r
1054     boolean webServiceRunning = false;\r
1055     JInternalFrame frame;\r
1056     public ClustalThread(JInternalFrame frame)\r
1057     {\r
1058       this.frame = frame;\r
1059       image = new Image[9];\r
1060       for(int i=0; i<9; i++)\r
1061       {\r
1062         java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");\r
1063         if (url != null)\r
1064         {\r
1065           image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
1066           MediaTracker mt = new MediaTracker(this);\r
1067           mt.addImage(image[i], i);\r
1068           try{mt.waitForID(i);}\r
1069           catch(Exception ex){}\r
1070         }\r
1071       }\r
1072       DNATwirler twirler = new DNATwirler();\r
1073       twirler.start();\r
1074       webServiceRunning = true;\r
1075     }\r
1076 \r
1077     class DNATwirler extends Thread\r
1078     {\r
1079       public void run()\r
1080       {\r
1081         while(webServiceRunning)\r
1082         {\r
1083           try{\r
1084             Thread.sleep(100);\r
1085             imageIndex++;\r
1086             imageIndex %=9;\r
1087             repaint();\r
1088           }\r
1089           catch(Exception ex){}\r
1090         }\r
1091       }\r
1092     }\r
1093 \r
1094     // JBPNote\r
1095     // Should check to see if the server settings are valid\r
1096     // Need visual-delay indication here.\r
1097     public void run()\r
1098        {\r
1099          jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
1100          Vector sv = viewport.getAlignment().getSequences();\r
1101          SequenceI[] seqs = new SequenceI[sv.size()];\r
1102 \r
1103          int i = 0;\r
1104          do\r
1105          {\r
1106            seqs[i] = (SequenceI) sv.elementAt(i);\r
1107          }\r
1108          while (++i < sv.size());\r
1109 \r
1110          SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
1111 \r
1112          if (alignment != null)\r
1113          {\r
1114            AlignFrame af = new AlignFrame(new Alignment(alignment));\r
1115           af.clustalColour.setSelected(true);\r
1116           af.clustalColour_actionPerformed(null);\r
1117            Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),\r
1118                                     700, 500); // JBPNote - is there a new window geom. property ?\r
1119          }\r
1120          else\r
1121            JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",\r
1122                                          JOptionPane.WARNING_MESSAGE);\r
1123 \r
1124          webServiceRunning = false;\r
1125          try{\r
1126            frame.setClosed(true);\r
1127          }catch(Exception ex){}\r
1128        }\r
1129 \r
1130        public void paintComponent(Graphics g)\r
1131        {\r
1132          g.setColor(Color.white);\r
1133          g.fillRect(0,0,getWidth(), getHeight());\r
1134          if(image!=null)\r
1135          {\r
1136            g.drawImage(image[imageIndex],10,10,this);\r
1137          }\r
1138          g.setFont(new Font("Arial", Font.BOLD, 12));\r
1139          g.setColor(Color.black);\r
1140          g.drawString("Clustal Alignment Web Service running", 30,30);\r
1141        }\r
1142   }\r
1143   protected void jpred_actionPerformed(ActionEvent e)\r
1144 {\r
1145 \r
1146     JInternalFrame frame = new JInternalFrame();\r
1147     if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)\r
1148     {\r
1149       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1150       SequenceGroup seqs = viewport.getSelectionGroup();\r
1151       if (seqs.getSize() == 1 || !viewport.alignment.isAligned())\r
1152       {\r
1153         JPredClient ct = new JPredClient( (SequenceI)\r
1154                                          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         }\r
1217       }\r
1218       catch (Exception ex)\r
1219       {\r
1220         JOptionPane.showMessageDialog(Desktop.desktop,\r
1221                                       "Problem reading tree file",\r
1222                                       ex.getMessage(),\r
1223                                       JOptionPane.WARNING_MESSAGE);\r
1224         ex.printStackTrace();\r
1225       }\r
1226     }\r
1227   }\r
1228 \r
1229 }\r