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