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   public String currentFileFormat = "Jalview";\r
  36 \r
  37   public AlignFrame(AlignmentI al)\r
  38   {\r
  39     viewport = new AlignViewport(al);\r
  40 \r
  41     alignPanel = new AlignmentPanel(this, viewport);\r
  42     alignPanel.annotationPanel.adjustPanelHeight();\r
  43     alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
  44     alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
  45     alignPanel.setAnnotationVisible( viewport.getShowAnnotation() );\r
  46 \r
  47     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
  48 \r
  49     addInternalFrameListener(new InternalFrameAdapter()\r
  50    {\r
  51      public void internalFrameActivated(InternalFrameEvent evt)\r
  52      {\r
  53           javax.swing.SwingUtilities.invokeLater(new Runnable()\r
  54           {\r
  55             public void run()\r
  56             {      alignPanel.requestFocus();    }\r
  57           });\r
  58 \r
  59      }\r
  60    });\r
  61 \r
  62   }\r
  63 \r
  64   public void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
  65   {\r
  66     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")\r
  67         ,  new String[]{"fa, fasta, fastq", "aln",  "pfam", "msf", "pir","blc","jar"},\r
  68           new String[]{"FASTA", "CLUSTAL", "PFAM", "MSF", "PIR", "BLC", "Jalview"},\r
  69           currentFileFormat);\r
  70 \r
  71     chooser.setAcceptAllFileFilterUsed(false);\r
  72     chooser.setFileView(new JalviewFileView());\r
  73     chooser.setDialogTitle("Save Alignment to file");\r
  74     chooser.setToolTipText("Save");\r
  75     int value = chooser.showSaveDialog(this);\r
  76     if(value == JalviewFileChooser.APPROVE_OPTION)\r
  77     {\r
  78       currentFileFormat  = chooser.getSelectedFormat();\r
  79 \r
  80       if (currentFileFormat.equals("Jalview"))\r
  81       {\r
  82         String shortName = title.replace('/', '_');\r
  83         title = title.replace('\\', '_');\r
  84         String choice = chooser.getSelectedFile().getPath();\r
  85         Jalview2XML.SaveState(this, System.currentTimeMillis(), shortName,\r
  86                               choice);\r
  87         // USE Jalview2XML to save this file\r
  88         return;\r
  89       }\r
  90 \r
  91       String choice =  chooser.getSelectedFile().getPath();\r
  92       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
  93       String output = FormatAdapter.formatSequences(currentFileFormat, viewport.getAlignment().getSequences());\r
  94       try{\r
  95         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
  96         out.println(output);\r
  97         out.close();\r
  98       }\r
  99       catch(Exception ex){}\r
 100     }\r
 101 \r
 102   }\r
 103 \r
 104   protected void outputText_actionPerformed(ActionEvent e)\r
 105   {\r
 106      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
 107      JInternalFrame frame = new JInternalFrame();\r
 108      cap.formatForOutput();\r
 109      frame.setContentPane(cap);\r
 110      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
 111      cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
 112   }\r
 113 \r
 114   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 115   {\r
 116     HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
 117     htmlOutput = null;\r
 118   }\r
 119 \r
 120   protected void createPNG_actionPerformed(ActionEvent e)\r
 121   {\r
 122     alignPanel.makePNG();\r
 123   }\r
 124 \r
 125   protected void epsFile_actionPerformed(ActionEvent e)\r
 126   {\r
 127     alignPanel.makeEPS();\r
 128   }\r
 129 \r
 130 \r
 131   public void printMenuItem_actionPerformed(ActionEvent e)\r
 132   {\r
 133     //Putting in a thread avoids Swing painting problems\r
 134     PrintThread thread = new PrintThread();\r
 135     thread.start();\r
 136   }\r
 137 \r
 138   class PrintThread extends Thread\r
 139   {\r
 140     public void run()\r
 141     {\r
 142       PrinterJob printJob = PrinterJob.getPrinterJob();\r
 143       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
 144       printJob.setPrintable(alignPanel, pf);\r
 145       if (printJob.printDialog())\r
 146       {\r
 147         try\r
 148         {\r
 149           printJob.print();\r
 150         }\r
 151         catch (Exception PrintException)\r
 152         {\r
 153           PrintException.printStackTrace();\r
 154         }\r
 155       }\r
 156     }\r
 157 \r
 158   }\r
 159 \r
 160 \r
 161 \r
 162 \r
 163   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 164   {\r
 165     try{\r
 166       this.setClosed(true);\r
 167     }catch(Exception ex){}\r
 168   }\r
 169 \r
 170   Stack historyList = new Stack();\r
 171   Stack redoList = new Stack();\r
 172 \r
 173   void updateEditMenuBar()\r
 174   {\r
 175     if(historyList.size()>0)\r
 176      {\r
 177        undoMenuItem.setEnabled(true);\r
 178        Object [] history = (Object[])historyList.get(0);\r
 179        undoMenuItem.setText("Undo "+history[0]);\r
 180      }\r
 181     else\r
 182     {\r
 183       undoMenuItem.setEnabled(false);\r
 184       undoMenuItem.setText("Undo");\r
 185     }\r
 186 \r
 187     if(redoList.size()>0)\r
 188      {\r
 189        redoMenuItem.setEnabled(true);\r
 190        Object [] history = (Object[])redoList.get(0);\r
 191        redoMenuItem.setText("Redo "+history[0]);\r
 192      }\r
 193     else\r
 194     {\r
 195       redoMenuItem.setEnabled(false);\r
 196       redoMenuItem.setText("Redo");\r
 197     }\r
 198   }\r
 199 \r
 200   public void addHistoryItem(String type)\r
 201   {\r
 202     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 203     redoList.clear();\r
 204 \r
 205     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 206     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 207     {\r
 208       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 209                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 210     }\r
 211 \r
 212 \r
 213     historyList.add(0, new Object[]{type,  seq} );\r
 214     updateEditMenuBar();\r
 215   }\r
 216 \r
 217   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 218   {\r
 219     Object [] history = (Object[])historyList.remove(0);\r
 220     // add the redo state before continuing!!\r
 221     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 222     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
 223     {\r
 224       seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
 225                             viewport.getAlignment().getSequenceAt(i).\r
 226                             getSequence());\r
 227     }\r
 228     /////////\r
 229 \r
 230     redoList.add(0, new Object[] {history[0], seq});\r
 231 \r
 232       seq = (SequenceI[]) history[1];\r
 233       AlignmentAnnotation [] old = viewport.alignment.getAlignmentAnnotation();\r
 234       viewport.setAlignment( new Alignment(seq) );\r
 235       viewport.alignment.setGapCharacter( Preferences.gapSymbol );\r
 236       updateEditMenuBar();\r
 237       for(int i=0; i<old.length; i++)\r
 238         viewport.alignment.addAnnotation(old[i]);\r
 239       viewport.updateConsensus();\r
 240       viewport.updateConservation();\r
 241       alignPanel.repaint();\r
 242   }\r
 243 \r
 244   public void moveSelectedSequences(boolean up)\r
 245   {\r
 246     SequenceGroup sg = viewport.getSelectionGroup();\r
 247     if (sg == null)\r
 248       return;\r
 249 \r
 250     if (up)\r
 251     {\r
 252       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 253       {\r
 254         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 255         if (!sg.sequences.contains(seq))\r
 256           continue;\r
 257 \r
 258         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 259         if (sg.sequences.contains(temp))\r
 260           continue;\r
 261 \r
 262         viewport.alignment.getSequences().setElementAt(temp, i);\r
 263         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 264       }\r
 265     }\r
 266     else\r
 267     {\r
 268       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 269       {\r
 270         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 271         if (!sg.sequences.contains(seq))\r
 272           continue;\r
 273 \r
 274         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 275         if (sg.sequences.contains(temp))\r
 276           continue;\r
 277 \r
 278         viewport.alignment.getSequences().setElementAt(temp, i);\r
 279         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 280       }\r
 281     }\r
 282 \r
 283     alignPanel.repaint();\r
 284   }\r
 285 \r
 286 \r
 287 \r
 288   protected void copy_actionPerformed(ActionEvent e)\r
 289   {\r
 290    if(viewport.getSelectionGroup()==null)\r
 291      return;\r
 292 \r
 293    SequenceGroup sg = viewport.getSelectionGroup();\r
 294 \r
 295      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 296      StringBuffer buffer= new StringBuffer();\r
 297 \r
 298        for(int i=0; i<sg.getSize(); i++)\r
 299        {\r
 300          SequenceI seq = sg.getSequenceAt(i);\r
 301          buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
 302                         +seq.findPosition( sg.getEndRes() )+ "\t"\r
 303                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
 304        }\r
 305      c.setContents( new StringSelection( buffer.toString()) , null ) ;\r
 306 \r
 307   }\r
 308 \r
 309 \r
 310   protected void pasteNew_actionPerformed(ActionEvent e)\r
 311   {\r
 312     paste(true);\r
 313   }\r
 314 \r
 315   protected void pasteThis_actionPerformed(ActionEvent e)\r
 316   {\r
 317     addHistoryItem("Paste");\r
 318     paste(false);\r
 319   }\r
 320 \r
 321   void paste(boolean newAlignment)\r
 322   {\r
 323     try{\r
 324       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 325       Transferable contents = c.getContents(this);\r
 326       if (contents == null)\r
 327         return;\r
 328 \r
 329       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
 330       StringTokenizer st = new StringTokenizer(str);\r
 331       ArrayList seqs = new ArrayList();\r
 332       while (st.hasMoreElements())\r
 333       {\r
 334         String name = st.nextToken();\r
 335         int start = Integer.parseInt(st.nextToken());\r
 336         int end = Integer.parseInt(st.nextToken());\r
 337         Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
 338 \r
 339         if(!newAlignment)\r
 340           viewport.alignment.addSequence(sequence);\r
 341         else\r
 342           seqs.add(sequence);\r
 343       }\r
 344 \r
 345       if(newAlignment)\r
 346       {\r
 347         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 348         seqs.toArray(newSeqs);\r
 349         AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
 350         String newtitle = new String("Copied sequences");\r
 351         if( title.startsWith("Copied sequences"))\r
 352          newtitle = title;\r
 353        else\r
 354          newtitle = newtitle.concat("- from "+title);\r
 355 \r
 356         Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
 357       }\r
 358       else\r
 359       {\r
 360         viewport.setEndSeq(viewport.alignment.getHeight());\r
 361         viewport.alignment.getWidth();\r
 362         viewport.updateConservation();\r
 363         viewport.updateConsensus();\r
 364         alignPanel.repaint();\r
 365       }\r
 366 \r
 367     }catch(Exception ex){}// could be anything being pasted in here\r
 368 \r
 369   }\r
 370 \r
 371 \r
 372   protected void cut_actionPerformed(ActionEvent e)\r
 373   {\r
 374     copy_actionPerformed(null);\r
 375     delete_actionPerformed(null);\r
 376   }\r
 377 \r
 378   protected void delete_actionPerformed(ActionEvent e)\r
 379   {\r
 380     addHistoryItem("Delete");\r
 381     if (viewport.getSelectionGroup() == null)\r
 382       return;\r
 383 \r
 384      SequenceGroup sg = viewport.getSelectionGroup();\r
 385      for (int i=0;i < sg.sequences.size(); i++)\r
 386      {\r
 387        SequenceI seq = sg.getSequenceAt(i);\r
 388        int index = viewport.getAlignment().findIndex(seq);\r
 389        seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);\r
 390 \r
 391        if(seq.getSequence().length()<1)\r
 392           viewport.getAlignment().deleteSequence(seq);\r
 393       else\r
 394           viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 395      }\r
 396 \r
 397      viewport.setSelectionGroup(null);\r
 398      viewport.alignment.deleteGroup(sg);\r
 399      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());\r
 400      if(viewport.getAlignment().getHeight()<1)\r
 401      try\r
 402      {\r
 403        this.setClosed(true);\r
 404      }catch(Exception ex){}\r
 405    viewport.updateConservation();\r
 406    viewport.updateConsensus();\r
 407      alignPanel.repaint();\r
 408 \r
 409   }\r
 410 \r
 411 \r
 412 \r
 413   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 414   {\r
 415      Object [] history = (Object[])redoList.remove(0);\r
 416      SequenceI[] seq = (SequenceI[]) history[1];\r
 417      viewport.setAlignment( new Alignment(seq) );\r
 418      viewport.alignment.setGapCharacter( Preferences.gapSymbol );\r
 419      updateEditMenuBar();\r
 420      viewport.updateConsensus();\r
 421      alignPanel.repaint();\r
 422      alignPanel.repaint();\r
 423   }\r
 424 \r
 425 \r
 426   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 427   {\r
 428     viewport.alignment.deleteAllGroups();\r
 429     viewport.setSelectionGroup(null);\r
 430     alignPanel.repaint();\r
 431   }\r
 432 \r
 433 \r
 434 \r
 435   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 436   {\r
 437     SequenceGroup sg = new SequenceGroup();\r
 438     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 439       sg.addSequence( viewport.getAlignment().getSequenceAt(i));\r
 440     sg.setEndRes(viewport.alignment.getWidth());\r
 441     viewport.setSelectionGroup(sg);\r
 442     PaintRefresher.Refresh(null);\r
 443   }\r
 444 \r
 445   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 446   {\r
 447     viewport.setSelectionGroup(null);\r
 448     viewport.getColumnSelection().clear();\r
 449     viewport.setSelectionGroup(null);\r
 450     PaintRefresher.Refresh(null);\r
 451   }\r
 452 \r
 453   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 454   {\r
 455     SequenceGroup sg = viewport.getSelectionGroup();\r
 456     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 457       sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));\r
 458 \r
 459     PaintRefresher.Refresh(null);\r
 460   }\r
 461 \r
 462   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 463   {\r
 464     addHistoryItem("delete columns");\r
 465     ColumnSelection colSel = viewport.getColumnSelection();\r
 466     if (colSel.size() > 0)\r
 467     {\r
 468       int min = colSel.getMin();\r
 469       viewport.getAlignment().trimLeft(min);\r
 470       colSel.compensateForEdit(0,min);\r
 471 \r
 472       if(viewport.getSelectionGroup()!=null)\r
 473         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 474 \r
 475       Vector groups = viewport.alignment.getGroups();\r
 476       for(int i=0; i<groups.size(); i++)\r
 477       {\r
 478         SequenceGroup sg = (SequenceGroup) groups.get(i);\r
 479         if(!sg.adjustForRemoveLeft(min))\r
 480           viewport.alignment.deleteGroup(sg);\r
 481       }\r
 482 \r
 483       alignPanel.repaint();\r
 484     }\r
 485   }\r
 486 \r
 487   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 488   {\r
 489     addHistoryItem("delete columns");\r
 490     ColumnSelection colSel = viewport.getColumnSelection();\r
 491     if (colSel.size() > 0)\r
 492     {\r
 493       int max = colSel.getMax();\r
 494       viewport.getAlignment().trimRight(max);\r
 495       if(viewport.getSelectionGroup()!=null)\r
 496         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 497 \r
 498       Vector groups = viewport.alignment.getGroups();\r
 499       for(int i=0; i<groups.size(); i++)\r
 500       {\r
 501         SequenceGroup sg = (SequenceGroup) groups.get(i);\r
 502         if(!sg.adjustForRemoveRight(max))\r
 503           viewport.alignment.deleteGroup(sg);\r
 504       }\r
 505 \r
 506 \r
 507 \r
 508       alignPanel.repaint();\r
 509     }\r
 510 \r
 511   }\r
 512 \r
 513   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 514   {\r
 515     addHistoryItem("delete gapped columns");\r
 516     viewport.getAlignment().removeGaps();\r
 517     viewport.updateConservation();\r
 518     viewport.updateConsensus();\r
 519     alignPanel.repaint();\r
 520   }\r
 521 \r
 522   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 523   {\r
 524     addHistoryItem("delete all gaps");\r
 525     SequenceI current;\r
 526     int jSize;\r
 527     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 528     {\r
 529       current = viewport.getAlignment().getSequenceAt(i);\r
 530       jSize = current.getLength();\r
 531       for (int j=0; j < jSize; j++)\r
 532         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 533         {\r
 534           current.deleteCharAt(j);\r
 535           j--;\r
 536           jSize--;\r
 537         }\r
 538     }\r
 539     viewport.updateConservation();\r
 540     viewport.updateConsensus();\r
 541     alignPanel.repaint();\r
 542   }\r
 543 \r
 544 \r
 545   public void findMenuItem_actionPerformed(ActionEvent e)\r
 546   {\r
 547     JInternalFrame frame = new JInternalFrame();\r
 548     Finder finder = new Finder(viewport, alignPanel, frame);\r
 549     frame.setContentPane(finder);\r
 550     Desktop.addInternalFrame(frame, "Find", 340,110);\r
 551     frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
 552 \r
 553   }\r
 554 \r
 555 \r
 556   public void font_actionPerformed(ActionEvent e)\r
 557   {\r
 558     FontChooser fc = new FontChooser( alignPanel );\r
 559   }\r
 560 \r
 561   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 562   {\r
 563     viewport.setShowFullId( fullSeqId.isSelected() );\r
 564 \r
 565     alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );\r
 566     alignPanel.repaint();\r
 567   }\r
 568 \r
 569   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 570   {\r
 571       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 572       alignPanel.repaint();\r
 573   }\r
 574 \r
 575   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 576   {\r
 577     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 578     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
 579     scaleAbove.setVisible( wrapMenuItem.isSelected() );\r
 580     scaleLeft.setVisible( wrapMenuItem.isSelected() );\r
 581     scaleRight.setVisible( wrapMenuItem.isSelected() );\r
 582     alignPanel.repaint();\r
 583   }\r
 584 \r
 585   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 586   {\r
 587     viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
 588     alignPanel.repaint();\r
 589   }\r
 590 \r
 591   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 592   {\r
 593     viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
 594     alignPanel.repaint();\r
 595   }\r
 596 \r
 597   protected void scaleRight_actionPerformed(ActionEvent e)\r
 598   {\r
 599     viewport.setScaleRightWrapped(scaleRight.isSelected());\r
 600     alignPanel.repaint();\r
 601   }\r
 602 \r
 603 \r
 604 \r
 605   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 606   {\r
 607     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 608     alignPanel.repaint();\r
 609   }\r
 610 \r
 611   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 612   {\r
 613     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 614     alignPanel.repaint();\r
 615   }\r
 616 \r
 617 \r
 618   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 619   {\r
 620     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 621     alignPanel.repaint();\r
 622   }\r
 623 \r
 624   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
 625   {\r
 626     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 627     if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
 628     {\r
 629          SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment, alignPanel);\r
 630          ((Alignment)viewport.alignment).featuresAdded = true;\r
 631     }\r
 632     alignPanel.repaint();\r
 633   }\r
 634 \r
 635   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 636   {\r
 637     if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())\r
 638     {\r
 639       annotationPanelMenuItem.setSelected(false);\r
 640       return;\r
 641     }\r
 642     viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );\r
 643     alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );\r
 644   }\r
 645 \r
 646   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 647   {\r
 648     if (alignPanel.overviewPanel != null)\r
 649       return;\r
 650 \r
 651     JInternalFrame frame = new JInternalFrame();\r
 652     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 653      frame.setContentPane(overview);\r
 654     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 655                              frame.getWidth(), frame.getHeight());\r
 656     frame.pack();\r
 657     frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
 658     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 659     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 660       {\r
 661             alignPanel.setOverviewPanel(null);\r
 662       };\r
 663     });\r
 664 \r
 665     alignPanel.setOverviewPanel( overview );\r
 666 \r
 667 \r
 668   }\r
 669 \r
 670   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 671   {\r
 672     changeColour( null );\r
 673   }\r
 674 \r
 675 \r
 676   public void clustalColour_actionPerformed(ActionEvent e)\r
 677   {\r
 678     abovePIDThreshold.setSelected(false);\r
 679     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 680   }\r
 681 \r
 682   public void zappoColour_actionPerformed(ActionEvent e)\r
 683   {\r
 684     changeColour(new ZappoColourScheme());\r
 685   }\r
 686 \r
 687   public void taylorColour_actionPerformed(ActionEvent e)\r
 688   {\r
 689     changeColour(new TaylorColourScheme());\r
 690   }\r
 691 \r
 692 \r
 693   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 694   {\r
 695     changeColour( new HydrophobicColourScheme() );\r
 696   }\r
 697 \r
 698   public void helixColour_actionPerformed(ActionEvent e)\r
 699   {\r
 700     changeColour(new HelixColourScheme() );\r
 701   }\r
 702 \r
 703 \r
 704   public void strandColour_actionPerformed(ActionEvent e)\r
 705   {\r
 706     changeColour(new StrandColourScheme());\r
 707   }\r
 708 \r
 709 \r
 710   public void turnColour_actionPerformed(ActionEvent e)\r
 711   {\r
 712     changeColour(new TurnColourScheme());\r
 713   }\r
 714 \r
 715 \r
 716   public void buriedColour_actionPerformed(ActionEvent e)\r
 717   {\r
 718     changeColour(new BuriedColourScheme() );\r
 719   }\r
 720 \r
 721   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 722   {\r
 723     changeColour(new NucleotideColourScheme());\r
 724   }\r
 725 \r
 726 \r
 727   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 728   {\r
 729     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
 730   }\r
 731 \r
 732 \r
 733 \r
 734   void changeColour(ColourSchemeI cs)\r
 735   {\r
 736     int threshold = 0;\r
 737 \r
 738     if ( viewport.getAbovePIDThreshold() )\r
 739     {\r
 740       threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
 741 \r
 742       if (cs instanceof ResidueColourScheme)\r
 743         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 744       else if (cs instanceof ScoreColourScheme)\r
 745         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 746 \r
 747       viewport.setGlobalColourScheme(cs);\r
 748     }\r
 749     else if (cs instanceof ResidueColourScheme)\r
 750       ( (ResidueColourScheme) cs).setThreshold(0);\r
 751     else if (cs instanceof ScoreColourScheme)\r
 752       ( (ScoreColourScheme) cs).setThreshold(0);\r
 753 \r
 754 \r
 755 \r
 756     if (viewport.getConservationSelected())\r
 757     {\r
 758       ConservationColourScheme ccs = null;\r
 759 \r
 760       Alignment al = (Alignment) viewport.alignment;\r
 761       Conservation c = new Conservation("All",\r
 762                                         ResidueProperties.propHash, 3,\r
 763                                         al.getSequences(), 0,\r
 764                                         al.getWidth() - 1);\r
 765 \r
 766       c.calculate();\r
 767       c.verdict(false, viewport.ConsPercGaps);\r
 768 \r
 769       ccs = new ConservationColourScheme(c, cs);\r
 770 \r
 771       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 772       ccs.setConsensus( viewport.vconsensus );\r
 773       viewport.setGlobalColourScheme(ccs);\r
 774 \r
 775       SliderPanel.setConservationSlider(alignPanel, ccs, "Background");\r
 776 \r
 777     }\r
 778     else\r
 779     {\r
 780         // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 781         if (cs != null)\r
 782           cs.setConsensus(viewport.vconsensus);\r
 783         viewport.setGlobalColourScheme(cs);\r
 784     }\r
 785 \r
 786 \r
 787     if(viewport.getColourAppliesToAllGroups())\r
 788     {\r
 789       Vector groups = viewport.alignment.getGroups();\r
 790       for(int i=0; i<groups.size(); i++)\r
 791       {\r
 792         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 793 \r
 794         if (cs instanceof ClustalxColourScheme)\r
 795         {\r
 796           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
 797         }\r
 798         else if(cs!=null)\r
 799         {\r
 800           try{\r
 801             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
 802           }catch(Exception ex){ex.printStackTrace();}\r
 803         }\r
 804 \r
 805         if(viewport.getAbovePIDThreshold())\r
 806         {\r
 807           if (sg.cs instanceof ResidueColourScheme)\r
 808             ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
 809           else if (sg.cs instanceof ScoreColourScheme)\r
 810             ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
 811 \r
 812            sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );\r
 813         }\r
 814 \r
 815         if( viewport.getConservationSelected() )\r
 816         {\r
 817           Conservation c = new Conservation("Group",\r
 818                                             ResidueProperties.propHash, 3,\r
 819                                             sg.sequences, 0, viewport.alignment.getWidth()-1);\r
 820           c.calculate();\r
 821           c.verdict(false, viewport.ConsPercGaps);\r
 822           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 823 \r
 824           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 825           ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 826           sg.cs = ccs;\r
 827         }\r
 828         else if(cs!=null)\r
 829         {\r
 830           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 831           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 832         }\r
 833 \r
 834       }\r
 835     }\r
 836 \r
 837     if(alignPanel.getOverviewPanel()!=null)\r
 838       alignPanel.getOverviewPanel().updateOverviewImage();\r
 839     alignPanel.repaint();\r
 840   }\r
 841 \r
 842   protected void modifyPID_actionPerformed(ActionEvent e)\r
 843   {\r
 844       if(viewport.getAbovePIDThreshold())\r
 845       {\r
 846         SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
 847                                    "Background");\r
 848         SliderPanel.showPIDSlider();\r
 849       }\r
 850   }\r
 851 \r
 852   protected void modifyConservation_actionPerformed(ActionEvent e)\r
 853   {\r
 854     if(viewport.getConservationSelected())\r
 855     {\r
 856       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
 857                                         "Background");\r
 858       SliderPanel.showConservationSlider();\r
 859     }\r
 860   }\r
 861 \r
 862 \r
 863   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 864   {\r
 865     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 866 \r
 867     viewport.setAbovePIDThreshold(false);\r
 868     abovePIDThreshold.setSelected(false);\r
 869 \r
 870    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 871    if(cs instanceof ConservationColourScheme )\r
 872      changeColour( ((ConservationColourScheme)cs).cs );\r
 873     else\r
 874       changeColour( cs );\r
 875 \r
 876     modifyConservation_actionPerformed(null);\r
 877   }\r
 878 \r
 879   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 880   {\r
 881     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
 882 \r
 883     conservationMenuItem.setSelected(false);\r
 884     viewport.setConservationSelected(false);\r
 885 \r
 886     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 887 \r
 888     if(cs instanceof ConservationColourScheme )\r
 889         changeColour( ((ConservationColourScheme)cs).cs );\r
 890     else\r
 891         changeColour( cs );\r
 892 \r
 893     modifyPID_actionPerformed(null);\r
 894   }\r
 895 \r
 896 \r
 897 \r
 898   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 899   {\r
 900     UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);\r
 901   }\r
 902 \r
 903   public void PIDColour_actionPerformed(ActionEvent e)\r
 904   {\r
 905     changeColour( new PIDColourScheme() );\r
 906   }\r
 907 \r
 908 \r
 909   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 910   {\r
 911     changeColour(new Blosum62ColourScheme() );\r
 912   }\r
 913 \r
 914 \r
 915 \r
 916   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 917   {\r
 918     addHistoryItem("sort");\r
 919     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 920     alignPanel.repaint();\r
 921   }\r
 922 \r
 923   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 924   {\r
 925     addHistoryItem("sort");\r
 926     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 927     alignPanel.repaint();\r
 928   }\r
 929 \r
 930   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 931   {\r
 932     addHistoryItem("sort");\r
 933     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 934     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 935     alignPanel.repaint();\r
 936   }\r
 937 \r
 938   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 939   {\r
 940     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 941     JInternalFrame frame = new JInternalFrame();\r
 942     frame.setContentPane(sp);\r
 943     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);\r
 944 \r
 945   }\r
 946 \r
 947   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 948   {\r
 949     if(viewport.getSelectionGroup().getSize()<2)\r
 950       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 951     else\r
 952     {\r
 953       JInternalFrame frame = new JInternalFrame();\r
 954       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 955       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 956     }\r
 957   }\r
 958 \r
 959   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 960   {\r
 961 \r
 962     if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
 963        || viewport.getAlignment().getHeight()<4)\r
 964     {\r
 965       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
 966                                     +"at least 4 input sequences.",\r
 967                                     "Sequence selection insufficient",\r
 968                                     JOptionPane.WARNING_MESSAGE);\r
 969       return;\r
 970     }\r
 971 \r
 972     try{\r
 973       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 974       JInternalFrame frame = new JInternalFrame();\r
 975       frame.setContentPane(pcaPanel);\r
 976       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 977    }catch(java.lang.OutOfMemoryError ex)\r
 978    {\r
 979      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 980                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 981    }\r
 982 \r
 983 \r
 984   }\r
 985 \r
 986   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 987   {\r
 988     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 989   }\r
 990 \r
 991   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 992   {\r
 993     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 994   }\r
 995 \r
 996 \r
 997   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 998   {\r
 999     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1000   }\r
1001 \r
1002   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1003   {\r
1004     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1005   }\r
1006 \r
1007   void NewTreePanel(String type, String pwType, String title)\r
1008   {\r
1009     //are the sequences aligned?\r
1010     if(!viewport.alignment.isAligned())\r
1011     {\r
1012       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
1013                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
1014       return;\r
1015     }\r
1016 \r
1017     final TreePanel tp;\r
1018     if (viewport.getSelectionGroup() != null &&\r
1019         viewport.getSelectionGroup().getSize() > 3)\r
1020     {\r
1021       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
1022                          pwType,\r
1023                          0, viewport.alignment.getWidth());\r
1024     }\r
1025     else\r
1026     {\r
1027       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1028                          type, pwType, 0, viewport.alignment.getWidth());\r
1029     }\r
1030 \r
1031    addTreeMenuItem(tp, title);\r
1032 \r
1033    Desktop.addInternalFrame(tp, title, 600, 500);\r
1034   }\r
1035 \r
1036   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1037   {\r
1038     final JMenuItem item = new JMenuItem(title);\r
1039     sortByTreeMenu.add(item);\r
1040     item.addActionListener(new java.awt.event.ActionListener()\r
1041     {\r
1042       public void actionPerformed(ActionEvent e)\r
1043       {\r
1044         addHistoryItem("sort");\r
1045         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1046         alignPanel.repaint();\r
1047       }\r
1048     });\r
1049 \r
1050     treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
1051     {\r
1052       public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
1053       {\r
1054         sortByTreeMenu.remove(item);\r
1055       };\r
1056     });\r
1057 \r
1058   }\r
1059 \r
1060 \r
1061   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
1062   {\r
1063      WebserviceInfo info = new WebserviceInfo("Clustal web service",\r
1064      "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"+\r
1065      " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."\r
1066     +" Nucleic Acids Research, submitted, June 1994.",\r
1067      450, 150);\r
1068 \r
1069     ClustalThread thread = new ClustalThread(info);\r
1070     thread.start();\r
1071   }\r
1072 \r
1073     class ClustalThread extends Thread\r
1074     {\r
1075       WebserviceInfo info;\r
1076       public ClustalThread(WebserviceInfo info)\r
1077       {this.info = info; }\r
1078 \r
1079       public void run()\r
1080       {\r
1081         info.setStatus(WebserviceInfo.STATE_RUNNING);\r
1082         jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
1083         Vector sv = viewport.getAlignment().getSequences();\r
1084         SequenceI[] seqs = new SequenceI[sv.size()];\r
1085 \r
1086         int i = 0;\r
1087         do\r
1088         {\r
1089           seqs[i] = (SequenceI) sv.elementAt(i);\r
1090         }\r
1091         while (++i < sv.size());\r
1092 \r
1093         SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
1094         if (alignment != null)\r
1095         {\r
1096           AlignFrame af = new AlignFrame(new Alignment(alignment));\r
1097           Desktop.addInternalFrame(af, title.concat(" - ClustalW Alignment"),\r
1098                                    NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
1099           af.clustalColour_actionPerformed(null);\r
1100           af.clustalColour.setSelected(true);\r
1101           info.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
1102         }\r
1103         else\r
1104         {\r
1105             info.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
1106             info.appendProgressText("Problem obtaining clustal alignment");\r
1107         }\r
1108       }\r
1109     }\r
1110 \r
1111   protected void jpred_actionPerformed(ActionEvent e)\r
1112 {\r
1113 \r
1114     if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)\r
1115     {\r
1116       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1117       SequenceGroup seqs = viewport.getSelectionGroup();\r
1118       if (seqs.getSize() == 1 || !viewport.alignment.isAligned())\r
1119       {\r
1120         JPredClient ct = new JPredClient( (SequenceI)seqs.getSequenceAt(0));\r
1121       }\r
1122       else\r
1123       {\r
1124         int sz;\r
1125         SequenceI[] msa = new SequenceI[sz=seqs.getSize()];\r
1126         for (int i = 0; i < sz; i++)\r
1127         {\r
1128           msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1129         }\r
1130 \r
1131         JPredClient ct = new JPredClient(msa);\r
1132       }\r
1133 \r
1134     }\r
1135     else\r
1136     {\r
1137       Vector seqs = viewport.getAlignment().getSequences();\r
1138 \r
1139       if (seqs.size() == 1 || !viewport.alignment.isAligned())\r
1140       {\r
1141         JPredClient ct = new JPredClient( (SequenceI)\r
1142                                          seqs.elementAt(0));\r
1143       }\r
1144       else\r
1145       {\r
1146         SequenceI[] msa = new SequenceI[seqs.size()];\r
1147         for (int i = 0; i < seqs.size(); i++)\r
1148         {\r
1149           msa[i] = (SequenceI) seqs.elementAt(i);\r
1150         }\r
1151 \r
1152         JPredClient ct = new JPredClient(msa);\r
1153       }\r
1154 \r
1155     }\r
1156   }\r
1157   protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
1158   {\r
1159     // TODO:resolve which menu item was actually selected\r
1160     // Now, check we have enough sequences\r
1161       if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)\r
1162       {\r
1163         // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1164         SequenceGroup seqs = viewport.getSelectionGroup();\r
1165         int sz;\r
1166         SequenceI[] msa = new SequenceI[sz=seqs.getSize()];\r
1167         for (int i = 0; i < sz; i++)\r
1168         {\r
1169           msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1170         }\r
1171 \r
1172         MsaWSClient ct = new jalview.ws.MsaWSClient(msa);\r
1173       }\r
1174       else\r
1175       {\r
1176         Vector seqs = viewport.getAlignment().getSequences();\r
1177 \r
1178         if (seqs.size() > 1) {\r
1179           SequenceI[] msa = new SequenceI[seqs.size()];\r
1180           for (int i = 0; i < seqs.size(); i++)\r
1181           {\r
1182             msa[i] = (SequenceI) seqs.elementAt(i);\r
1183           }\r
1184 \r
1185           MsaWSClient ct = new MsaWSClient(msa);\r
1186         }\r
1187 \r
1188       }\r
1189     }\r
1190 \r
1191     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
1192     // Pick the tree file\r
1193     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
1194         getProperty("LAST_DIRECTORY"));\r
1195     chooser.setFileView(new JalviewFileView());\r
1196     chooser.setDialogTitle("Select a newick-like tree file");\r
1197     chooser.setToolTipText("Load a tree file");\r
1198     int value = chooser.showOpenDialog(null);\r
1199     if (value == JalviewFileChooser.APPROVE_OPTION)\r
1200     {\r
1201       String choice = chooser.getSelectedFile().getPath();\r
1202       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1203       try\r
1204       {\r
1205         jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");\r
1206         ShowNewickTree(fin, choice);\r
1207       }\r
1208       catch (Exception ex)\r
1209       {\r
1210         JOptionPane.showMessageDialog(Desktop.desktop,\r
1211                                       "Problem reading tree file",\r
1212                                       ex.getMessage(),\r
1213                                       JOptionPane.WARNING_MESSAGE);\r
1214         ex.printStackTrace();\r
1215       }\r
1216     }\r
1217   }\r
1218 \r
1219   public void ShowNewickTree(NewickFile nf, String title)\r
1220   {\r
1221     try{\r
1222       nf.parse();\r
1223       if (nf.getTree() != null)\r
1224       {\r
1225         TreePanel tp = new TreePanel(viewport,\r
1226                                      viewport.getAlignment().getSequences(),\r
1227                                      nf, "FromFile", title);\r
1228         Desktop.addInternalFrame(tp, title, 600, 500);\r
1229         addTreeMenuItem(tp, title);\r
1230         viewport.setCurrentTree(tp.getTree());\r
1231       }\r
1232      }catch(Exception ex){ex.printStackTrace();}\r
1233   }\r
1234 \r
1235 \r
1236 }\r