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     // add conservation graph to alignment\r
  44     viewport.updateConservation();\r
  45     viewport.updateConsensus();\r
  46 \r
  47 \r
  48     alignPanel = new AlignmentPanel(this, viewport);\r
  49 \r
  50     alignPanel.annotationPanel.adjustPanelHeight();\r
  51     alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
  52     alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
  53 \r
  54     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
  55 \r
  56 \r
  57     addInternalFrameListener(new InternalFrameAdapter()\r
  58    {\r
  59      public void internalFrameActivated(InternalFrameEvent evt)\r
  60      {\r
  61           javax.swing.SwingUtilities.invokeLater(new Runnable()\r
  62           {\r
  63             public void run()\r
  64             {      alignPanel.requestFocus();    }\r
  65           });\r
  66 \r
  67      }\r
  68    });\r
  69 \r
  70   }\r
  71 \r
  72   protected void saveAs_actionPerformed(ActionEvent e)\r
  73   {\r
  74     String suffix [] = null;\r
  75     if(e.getActionCommand().equals("FASTA"))\r
  76       suffix = new String[]{"fa", "fasta"};\r
  77     else if(e.getActionCommand().equals("MSF"))\r
  78       suffix = new String[]{"msf"};\r
  79     else if(e.getActionCommand().equals("CLUSTAL"))\r
  80       suffix = new String[]{"aln"};\r
  81     else if(e.getActionCommand().equals("BLC"))\r
  82       suffix = new String[]{"blc"};\r
  83     else if(e.getActionCommand().equals("PIR"))\r
  84       suffix = new String[]{"pir"};\r
  85     else if(e.getActionCommand().equals("PFAM"))\r
  86       suffix = new String[]{"pfam"};\r
  87 \r
  88 \r
  89     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")\r
  90         , suffix, e.getActionCommand()+" file");\r
  91     chooser.setFileView(new JalviewFileView());\r
  92     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
  93     chooser.setToolTipText("Save");\r
  94     int value = chooser.showSaveDialog(this);\r
  95     if(value == JalviewFileChooser.APPROVE_OPTION)\r
  96     {\r
  97       String choice =  chooser.getSelectedFile().getPath();\r
  98       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
  99       String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
 100       try{\r
 101         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
 102         out.println(output);\r
 103         out.close();\r
 104       }\r
 105       catch(Exception ex){}\r
 106     }\r
 107 \r
 108   }\r
 109 \r
 110   protected void outputText_actionPerformed(ActionEvent e)\r
 111   {\r
 112      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
 113      JInternalFrame frame = new JInternalFrame();\r
 114      cap.formatForOutput();\r
 115      frame.setContentPane(cap);\r
 116      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
 117      cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
 118   }\r
 119 \r
 120   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 121   {\r
 122     HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
 123     htmlOutput = null;\r
 124   }\r
 125 \r
 126   protected void createPNG_actionPerformed(ActionEvent e)\r
 127   {\r
 128     alignPanel.makePNG();\r
 129   }\r
 130 \r
 131   protected void epsFile_actionPerformed(ActionEvent e)\r
 132   {\r
 133     alignPanel.makeEPS();\r
 134   }\r
 135 \r
 136 \r
 137   public void printMenuItem_actionPerformed(ActionEvent e)\r
 138   {\r
 139     //Putting in a thread avoids Swing painting problems\r
 140     PrintThread thread = new PrintThread();\r
 141     thread.start();\r
 142   }\r
 143 \r
 144   class PrintThread extends Thread\r
 145   {\r
 146     public void run()\r
 147     {\r
 148       PrinterJob printJob = PrinterJob.getPrinterJob();\r
 149       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
 150       printJob.setPrintable(alignPanel, pf);\r
 151       if (printJob.printDialog())\r
 152       {\r
 153         try\r
 154         {\r
 155           printJob.print();\r
 156         }\r
 157         catch (Exception PrintException)\r
 158         {\r
 159           PrintException.printStackTrace();\r
 160         }\r
 161       }\r
 162     }\r
 163 \r
 164   }\r
 165 \r
 166 \r
 167 \r
 168 \r
 169   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 170   {\r
 171     try{\r
 172       this.setClosed(true);\r
 173     }catch(Exception ex){}\r
 174   }\r
 175 \r
 176   Stack historyList = new Stack();\r
 177   Stack redoList = new Stack();\r
 178   JMenuBar jMenuBar1 = new JMenuBar();\r
 179 \r
 180   void updateEditMenuBar()\r
 181   {\r
 182     if(historyList.size()>0)\r
 183      {\r
 184        undoMenuItem.setEnabled(true);\r
 185        Object [] history = (Object[])historyList.get(0);\r
 186        undoMenuItem.setText("Undo "+history[0]);\r
 187      }\r
 188     else\r
 189     {\r
 190       undoMenuItem.setEnabled(false);\r
 191       undoMenuItem.setText("Undo");\r
 192     }\r
 193 \r
 194     if(redoList.size()>0)\r
 195      {\r
 196        redoMenuItem.setEnabled(true);\r
 197        Object [] history = (Object[])redoList.get(0);\r
 198        redoMenuItem.setText("Redo "+history[0]);\r
 199      }\r
 200     else\r
 201     {\r
 202       redoMenuItem.setEnabled(false);\r
 203       redoMenuItem.setText("Redo");\r
 204     }\r
 205   }\r
 206 \r
 207   public void addHistoryItem(String type)\r
 208   {\r
 209     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 210     redoList.clear();\r
 211     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 212     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 213     {\r
 214       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 215                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 216     }\r
 217 \r
 218     historyList.add(0, new Object[]{type,  seq} );\r
 219     updateEditMenuBar();\r
 220   }\r
 221 \r
 222   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 223   {\r
 224     Object [] history = (Object[])historyList.remove(0);\r
 225     // add the redo state before continuing!!\r
 226     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 227     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
 228     {\r
 229       seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
 230                             viewport.getAlignment().getSequenceAt(i).\r
 231                             getSequence());\r
 232     }\r
 233     /////////\r
 234 \r
 235     redoList.add(0, new Object[] {history[0], seq});\r
 236 \r
 237       seq = (SequenceI[]) history[1];\r
 238       viewport.setAlignment( new Alignment(seq) );\r
 239       updateEditMenuBar();\r
 240       viewport.updateConsensus();\r
 241       alignPanel.RefreshPanels();\r
 242       alignPanel.RefreshPanels();\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.RefreshPanels();\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         int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;\r
 352         if (newHeight > 500)\r
 353           newHeight = 500;\r
 354         Desktop.addInternalFrame(af, "Copied sequences", 700, 500);\r
 355       }\r
 356       else\r
 357       {\r
 358         viewport.setEndSeq(viewport.alignment.getHeight());\r
 359         viewport.alignment.getWidth();\r
 360         viewport.updateConservation();\r
 361         viewport.updateConsensus();\r
 362         alignPanel.RefreshPanels();\r
 363       }\r
 364 \r
 365     }catch(Exception ex){}// could be anything being pasted in here\r
 366 \r
 367   }\r
 368 \r
 369 \r
 370   protected void cut_actionPerformed(ActionEvent e)\r
 371   {\r
 372     copy_actionPerformed(null);\r
 373     delete_actionPerformed(null);\r
 374   }\r
 375 \r
 376   protected void delete_actionPerformed(ActionEvent e)\r
 377   {\r
 378     addHistoryItem("Delete");\r
 379     if (viewport.getSelectionGroup() == null)\r
 380       return;\r
 381 \r
 382      SequenceGroup sg = viewport.getSelectionGroup();\r
 383      for (int i=0;i < sg.sequences.size(); i++)\r
 384      {\r
 385        SequenceI seq = sg.getSequenceAt(i);\r
 386        int index = viewport.getAlignment().findIndex(seq);\r
 387        seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);\r
 388 \r
 389        if(seq.getSequence().length()<1)\r
 390           viewport.getAlignment().deleteSequence(seq);\r
 391       else\r
 392           viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 393      }\r
 394 \r
 395      viewport.setSelectionGroup(null);\r
 396      viewport.alignment.deleteGroup(sg);\r
 397      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());\r
 398      if(viewport.getAlignment().getHeight()<1)\r
 399      try\r
 400      {\r
 401        this.setClosed(true);\r
 402      }catch(Exception ex){}\r
 403    viewport.updateConservation();\r
 404    viewport.updateConsensus();\r
 405      alignPanel.RefreshPanels();\r
 406 \r
 407   }\r
 408 \r
 409 \r
 410 \r
 411   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 412   {\r
 413      Object [] history = (Object[])redoList.remove(0);\r
 414      SequenceI[] seq = (SequenceI[]) history[1];\r
 415      viewport.setAlignment( new Alignment(seq) );\r
 416      updateEditMenuBar();\r
 417      viewport.updateConsensus();\r
 418      alignPanel.RefreshPanels();\r
 419      alignPanel.RefreshPanels();\r
 420   }\r
 421 \r
 422 \r
 423   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 424   {\r
 425     viewport.alignment.deleteAllGroups();\r
 426     viewport.setSelectionGroup(null);\r
 427 \r
 428     alignPanel.RefreshPanels();\r
 429   }\r
 430 \r
 431 \r
 432 \r
 433   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 434   {\r
 435     SequenceGroup sg = new SequenceGroup();\r
 436     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 437       sg.addSequence( viewport.getAlignment().getSequenceAt(i));\r
 438     sg.setEndRes(viewport.alignment.getWidth());\r
 439     viewport.setSelectionGroup(sg);\r
 440     PaintRefresher.Refresh(null);\r
 441   }\r
 442 \r
 443   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 444   {\r
 445     viewport.setSelectionGroup(null);\r
 446     PaintRefresher.Refresh(null);\r
 447   }\r
 448 \r
 449   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 450   {\r
 451     SequenceGroup sg = viewport.getSelectionGroup();\r
 452     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 453       sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));\r
 454 \r
 455     PaintRefresher.Refresh(null);\r
 456   }\r
 457 \r
 458 \r
 459   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 460   {\r
 461     viewport.getColumnSelection().clear();\r
 462     repaint();\r
 463   }\r
 464 \r
 465   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 466   {\r
 467     addHistoryItem("delete columns");\r
 468     ColumnSelection colSel = viewport.getColumnSelection();\r
 469     if (colSel.size() > 0)\r
 470     {\r
 471       int min = colSel.getMin();\r
 472       viewport.getAlignment().trimLeft(min);\r
 473       colSel.compensateForEdit(0,min);\r
 474 \r
 475       if(viewport.getSelectionGroup()!=null)\r
 476         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 477 \r
 478       Vector groups = viewport.alignment.getGroups();\r
 479       for(int i=0; i<groups.size(); i++)\r
 480       {\r
 481         SequenceGroup sg = (SequenceGroup) groups.get(i);\r
 482         if(!sg.adjustForRemoveLeft(min))\r
 483           viewport.alignment.deleteGroup(sg);\r
 484       }\r
 485 \r
 486       alignPanel.RefreshPanels();\r
 487     }\r
 488   }\r
 489 \r
 490   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 491   {\r
 492     addHistoryItem("delete columns");\r
 493     ColumnSelection colSel = viewport.getColumnSelection();\r
 494     if (colSel.size() > 0)\r
 495     {\r
 496       int max = colSel.getMax();\r
 497       viewport.getAlignment().trimRight(max);\r
 498       if(viewport.getSelectionGroup()!=null)\r
 499         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 500 \r
 501       Vector groups = viewport.alignment.getGroups();\r
 502       for(int i=0; i<groups.size(); i++)\r
 503       {\r
 504         SequenceGroup sg = (SequenceGroup) groups.get(i);\r
 505         if(!sg.adjustForRemoveRight(max))\r
 506           viewport.alignment.deleteGroup(sg);\r
 507       }\r
 508 \r
 509 \r
 510 \r
 511       alignPanel.RefreshPanels();\r
 512     }\r
 513 \r
 514   }\r
 515 \r
 516   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 517   {\r
 518     addHistoryItem("delete gapped columns");\r
 519     viewport.getAlignment().removeGaps();\r
 520     viewport.updateConservation();\r
 521     viewport.updateConsensus();\r
 522     alignPanel.RefreshPanels();\r
 523   }\r
 524 \r
 525   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 526   {\r
 527     addHistoryItem("delete all gaps");\r
 528     SequenceI current;\r
 529     int jSize;\r
 530     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 531     {\r
 532       current = viewport.getAlignment().getSequenceAt(i);\r
 533       jSize = current.getLength();\r
 534       for (int j=0; j < jSize; j++)\r
 535         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 536         {\r
 537           current.deleteCharAt(j);\r
 538           j--;\r
 539           jSize--;\r
 540         }\r
 541     }\r
 542     viewport.updateConservation();\r
 543     viewport.updateConsensus();\r
 544     alignPanel.RefreshPanels();\r
 545   }\r
 546 \r
 547   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 548   {\r
 549     char thisChar = '-';\r
 550     char nextChar = '.';\r
 551     if(viewport.getGapCharacter()=='-')\r
 552     {\r
 553       thisChar = '.';\r
 554       nextChar = '-';\r
 555     }\r
 556     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 557     viewport.setGapCharacter(thisChar);\r
 558     alignPanel.RefreshPanels();\r
 559   }\r
 560 \r
 561   public void findMenuItem_actionPerformed(ActionEvent e)\r
 562   {\r
 563       JInternalFrame frame = new JInternalFrame();\r
 564       Finder finder = new Finder(viewport, alignPanel, frame);\r
 565       frame.setContentPane(finder);\r
 566      Desktop.addInternalFrame(frame, "Find", 340,110);\r
 567 \r
 568   }\r
 569 \r
 570 \r
 571   public void font_actionPerformed(ActionEvent e)\r
 572   {\r
 573     JInternalFrame frame = new JInternalFrame();\r
 574     FontChooser fc = new FontChooser( alignPanel, frame );\r
 575     frame.setContentPane(fc);\r
 576     Desktop.addInternalFrame(frame, "Change Font", 480,100);\r
 577   }\r
 578 \r
 579   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 580   {\r
 581     viewport.setShowFullId( fullSeqId.isSelected() );\r
 582 \r
 583     alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );\r
 584     alignPanel.RefreshPanels();\r
 585   }\r
 586 \r
 587   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 588   {\r
 589       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 590       alignPanel.RefreshPanels();\r
 591   }\r
 592 \r
 593   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 594   {\r
 595     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 596     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
 597     scaleAbove.setVisible( wrapMenuItem.isSelected() );\r
 598     scaleLeft.setVisible( wrapMenuItem.isSelected() );\r
 599     scaleRight.setVisible( wrapMenuItem.isSelected() );\r
 600     alignPanel.RefreshPanels();\r
 601   }\r
 602 \r
 603   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 604   {\r
 605     viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
 606     alignPanel.repaint();\r
 607   }\r
 608 \r
 609   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 610   {\r
 611     viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
 612     alignPanel.repaint();\r
 613   }\r
 614 \r
 615   protected void scaleRight_actionPerformed(ActionEvent e)\r
 616   {\r
 617     viewport.setScaleRightWrapped(scaleRight.isSelected());\r
 618     alignPanel.repaint();\r
 619   }\r
 620 \r
 621 \r
 622 \r
 623   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 624   {\r
 625     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 626     alignPanel.RefreshPanels();\r
 627   }\r
 628 \r
 629   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 630   {\r
 631     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 632     alignPanel.RefreshPanels();\r
 633   }\r
 634 \r
 635 \r
 636   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 637   {\r
 638     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 639     alignPanel.RefreshPanels();\r
 640   }\r
 641 \r
 642   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
 643   {\r
 644     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 645     if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
 646     {\r
 647          AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);\r
 648          ((Alignment)viewport.alignment).featuresAdded = true;\r
 649     }\r
 650     alignPanel.RefreshPanels();\r
 651   }\r
 652 \r
 653   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 654   {\r
 655     if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())\r
 656     {\r
 657       annotationPanelMenuItem.setSelected(false);\r
 658       return;\r
 659     }\r
 660     viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );\r
 661     alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );\r
 662   }\r
 663 \r
 664   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 665   {\r
 666     if (alignPanel.overviewPanel != null)\r
 667       return;\r
 668 \r
 669     JInternalFrame frame = new JInternalFrame();\r
 670     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 671    try{\r
 672      overview = new OverviewPanel(alignPanel, viewport);\r
 673      frame.setContentPane(overview);\r
 674     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 675                              frame.getWidth(), frame.getHeight());\r
 676     frame.pack();\r
 677     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 678     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 679       {\r
 680             alignPanel.setOverviewPanel(null);\r
 681       };\r
 682     });\r
 683     alignPanel.setOverviewPanel( overview );\r
 684 \r
 685   }catch(java.lang.OutOfMemoryError ex)\r
 686    {\r
 687      JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 688                                    +"\nTry reducing the font size.",\r
 689                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 690    }\r
 691 \r
 692 \r
 693   }\r
 694 \r
 695   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 696   {\r
 697     changeColour( null );\r
 698   }\r
 699 \r
 700 \r
 701   public void clustalColour_actionPerformed(ActionEvent e)\r
 702   {\r
 703     abovePIDThreshold.setSelected(false);\r
 704     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 705   }\r
 706 \r
 707   public void zappoColour_actionPerformed(ActionEvent e)\r
 708   {\r
 709     changeColour(new ZappoColourScheme());\r
 710   }\r
 711 \r
 712   public void taylorColour_actionPerformed(ActionEvent e)\r
 713   {\r
 714     changeColour(new TaylorColourScheme());\r
 715   }\r
 716 \r
 717 \r
 718   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 719   {\r
 720     changeColour( new HydrophobicColourScheme() );\r
 721   }\r
 722 \r
 723   public void helixColour_actionPerformed(ActionEvent e)\r
 724   {\r
 725     changeColour(new HelixColourScheme() );\r
 726   }\r
 727 \r
 728 \r
 729   public void strandColour_actionPerformed(ActionEvent e)\r
 730   {\r
 731     changeColour(new StrandColourScheme());\r
 732   }\r
 733 \r
 734 \r
 735   public void turnColour_actionPerformed(ActionEvent e)\r
 736   {\r
 737     changeColour(new TurnColourScheme());\r
 738   }\r
 739 \r
 740 \r
 741   public void buriedColour_actionPerformed(ActionEvent e)\r
 742   {\r
 743     changeColour(new BuriedColourScheme() );\r
 744   }\r
 745 \r
 746   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 747   {\r
 748     changeColour(new NucleotideColourScheme());\r
 749   }\r
 750 \r
 751 \r
 752   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 753   {\r
 754     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
 755   }\r
 756 \r
 757 \r
 758 \r
 759   void changeColour(ColourSchemeI cs)\r
 760   {\r
 761 \r
 762     if(viewport.getColourAppliesToAllGroups())\r
 763     {\r
 764       Vector groups = viewport.alignment.getGroups();\r
 765       for(int i=0; i<groups.size(); i++)\r
 766       {\r
 767         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 768         sg.cs = cs;\r
 769 \r
 770         if(abovePIDThreshold.isSelected())\r
 771           abovePIDThreshold_actionPerformed(null);\r
 772         else if( viewport.getConservationSelected() )\r
 773         {\r
 774           Conservation c = new Conservation("Group",\r
 775                                             ResidueProperties.propHash, 3,\r
 776                                             sg.sequences, sg.getStartRes(),\r
 777                                             sg.getEndRes());\r
 778           c.calculate();\r
 779           c.verdict(false, 100);\r
 780           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 781 \r
 782           sg.cs = ccs;\r
 783         }\r
 784 \r
 785       }\r
 786     }\r
 787 \r
 788 \r
 789     if ( viewport.getAbovePIDThreshold())\r
 790     {\r
 791       int threshold = 0;\r
 792       threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");\r
 793       Desktop.hideConservationSlider();\r
 794 \r
 795       if (cs instanceof ResidueColourScheme)\r
 796         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 797       else if (cs instanceof ScoreColourScheme)\r
 798         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 799 \r
 800       viewport.setGlobalColourScheme(cs);\r
 801 \r
 802     }\r
 803     else\r
 804     if (cs instanceof ResidueColourScheme)\r
 805       ( (ResidueColourScheme) cs).setThreshold(0);\r
 806     else if (cs instanceof ScoreColourScheme)\r
 807       ( (ScoreColourScheme) cs).setThreshold(0);\r
 808 \r
 809 \r
 810 \r
 811 \r
 812 if ( viewport.getConservationSelected() )\r
 813  {\r
 814    ConservationColourScheme ccs = null;\r
 815 \r
 816    Alignment al = (Alignment) viewport.alignment;\r
 817    Conservation c = new Conservation("All",\r
 818                                      ResidueProperties.propHash, 3,\r
 819                                      al.getSequences(), 0,\r
 820                                      al.getWidth());\r
 821 \r
 822    c.calculate();\r
 823    c.verdict(false, 100);\r
 824 \r
 825    ccs = new ConservationColourScheme(c, cs);\r
 826 \r
 827    int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,\r
 828        "Background");\r
 829 \r
 830    ccs.inc = threshold;\r
 831 \r
 832    viewport.setGlobalColourScheme(ccs);\r
 833 \r
 834   }\r
 835   else\r
 836        viewport.setGlobalColourScheme( cs );\r
 837 \r
 838     alignPanel.RefreshPanels();\r
 839   }\r
 840 \r
 841 \r
 842   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 843   {\r
 844     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 845     if(coloursChanging)\r
 846       return;\r
 847 \r
 848     coloursChanging = true;\r
 849 \r
 850     viewport.setAbovePIDThreshold(false);\r
 851     abovePIDThreshold.setSelected(false);\r
 852     Desktop.hidePIDSlider();\r
 853     if(!viewport.getConservationSelected())\r
 854       Desktop.hideConservationSlider();\r
 855 \r
 856    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 857    if(cs instanceof ConservationColourScheme )\r
 858      changeColour( ((ConservationColourScheme)cs).cs );\r
 859     else\r
 860       changeColour( cs );\r
 861 \r
 862     coloursChanging = false;\r
 863   }\r
 864 \r
 865   boolean coloursChanging = false;\r
 866   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 867   {\r
 868     if(coloursChanging)\r
 869       return;\r
 870 \r
 871     coloursChanging = true;\r
 872     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
 873 \r
 874     conservationMenuItem.setSelected(false);\r
 875     viewport.setConservationSelected(false);\r
 876     Desktop.hideConservationSlider();\r
 877 \r
 878     if(!viewport.getAbovePIDThreshold())\r
 879       Desktop.hidePIDSlider();\r
 880 \r
 881 \r
 882     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 883     if(cs instanceof ConservationColourScheme )\r
 884         changeColour( ((ConservationColourScheme)cs).cs );\r
 885     else\r
 886         changeColour( cs );\r
 887 \r
 888     coloursChanging = false;\r
 889   }\r
 890 \r
 891 \r
 892 \r
 893   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 894   {\r
 895     JInternalFrame frame = new JInternalFrame();\r
 896     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 897     frame.setContentPane(chooser);\r
 898     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 899     frame.setResizable(false);\r
 900     frame.setIconifiable(false);\r
 901     frame.setMaximizable(false);\r
 902   }\r
 903 \r
 904   public void PIDColour_actionPerformed(ActionEvent e)\r
 905   {\r
 906     changeColour( new PIDColourScheme() );\r
 907   }\r
 908 \r
 909 \r
 910   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 911   {\r
 912     changeColour(new Blosum62ColourScheme(viewport) );\r
 913   }\r
 914 \r
 915 \r
 916 \r
 917   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 918   {\r
 919     addHistoryItem("sort");\r
 920     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 921     alignPanel.RefreshPanels();\r
 922   }\r
 923 \r
 924   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 925   {\r
 926     addHistoryItem("sort");\r
 927     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 928     alignPanel.RefreshPanels();\r
 929   }\r
 930 \r
 931   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 932   {\r
 933     addHistoryItem("sort");\r
 934     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 935     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 936     alignPanel.RefreshPanels();\r
 937   }\r
 938 \r
 939   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 940   {\r
 941     addHistoryItem("sort");\r
 942     if(viewport.getCurrentTree()==null)\r
 943       return;\r
 944 \r
 945     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 946     alignPanel.RefreshPanels();\r
 947   }\r
 948 \r
 949   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 950   {\r
 951     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 952     JInternalFrame frame = new JInternalFrame();\r
 953     frame.setContentPane(sp);\r
 954     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);\r
 955     frame.setMaximizable(false);\r
 956     frame.setResizable(false);\r
 957 \r
 958   }\r
 959 \r
 960   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 961   {\r
 962     if(viewport.getSelectionGroup().getSize()<2)\r
 963       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 964     else\r
 965     {\r
 966       JInternalFrame frame = new JInternalFrame();\r
 967       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 968       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 969     }\r
 970   }\r
 971 \r
 972   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 973   {\r
 974 \r
 975     if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
 976        || viewport.getAlignment().getHeight()<4)\r
 977     {\r
 978       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
 979                                     +"at least 4 input sequences.",\r
 980                                     "Sequence selection insufficient",\r
 981                                     JOptionPane.WARNING_MESSAGE);\r
 982       return;\r
 983     }\r
 984 \r
 985     try{\r
 986       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 987       JInternalFrame frame = new JInternalFrame();\r
 988       frame.setContentPane(pcaPanel);\r
 989       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 990    }catch(java.lang.OutOfMemoryError ex)\r
 991    {\r
 992      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 993                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 994    }\r
 995 \r
 996 \r
 997   }\r
 998 \r
 999   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1000   {\r
1001     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1002   }\r
1003 \r
1004   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1005   {\r
1006     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1007   }\r
1008 \r
1009 \r
1010   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1011   {\r
1012     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1013   }\r
1014 \r
1015   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1016   {\r
1017     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1018   }\r
1019 \r
1020   void NewTreePanel(String type, String pwType, String title)\r
1021   {\r
1022     //are the sequences aligned?\r
1023     if(!viewport.alignment.isAligned())\r
1024     {\r
1025       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
1026                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
1027       return;\r
1028     }\r
1029 \r
1030     TreePanel tp=null;\r
1031    if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)\r
1032    {\r
1033      tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType,\r
1034                          0, viewport.alignment.getWidth());\r
1035    }\r
1036    else\r
1037    {\r
1038      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1039                          type, pwType,  0, viewport.alignment.getWidth());\r
1040    }\r
1041 \r
1042    Desktop.addInternalFrame(tp, title, 600, 500);\r
1043   }\r
1044 \r
1045 \r
1046 \r
1047 \r
1048   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
1049   {\r
1050     JInternalFrame frame = new JInternalFrame();\r
1051     ClustalThread ct = new ClustalThread(frame);\r
1052     Thread t = new Thread(ct);\r
1053     t.start();\r
1054     frame.setContentPane(ct);\r
1055      Desktop.addInternalFrame(frame, title, 300, 80);\r
1056 \r
1057   }\r
1058 \r
1059   class ClustalThread extends JPanel implements Runnable\r
1060   {\r
1061     Image image;\r
1062     int angle = 0;\r
1063     boolean webServiceRunning = false;\r
1064     JInternalFrame frame;\r
1065     public ClustalThread(JInternalFrame frame)\r
1066     {\r
1067       this.frame = frame;\r
1068 \r
1069       java.net.URL url = getClass().getResource("/images/logo.gif");\r
1070       if (url != null)\r
1071       {\r
1072         image = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
1073         MediaTracker mt = new MediaTracker(this);\r
1074         mt.addImage(image, 0);\r
1075         try\r
1076         {\r
1077           mt.waitForID(0);\r
1078         }\r
1079         catch (Exception ex)\r
1080         {}\r
1081       }\r
1082 \r
1083       ImageSpinner spinner = new ImageSpinner();\r
1084       spinner.start();\r
1085       webServiceRunning = true;\r
1086     }\r
1087 \r
1088     class ImageSpinner extends Thread\r
1089     {\r
1090       public void run()\r
1091       {\r
1092         while(webServiceRunning)\r
1093         {\r
1094           try{\r
1095             Thread.sleep(10);\r
1096             angle+=1;\r
1097             angle %=360;\r
1098             repaint();\r
1099           }\r
1100           catch(Exception ex){}\r
1101         }\r
1102       }\r
1103     }\r
1104 \r
1105     // JBPNote\r
1106     // Should check to see if the server settings are valid\r
1107     // Need visual-delay indication here.\r
1108     public void run()\r
1109        {\r
1110          jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
1111          Vector sv = viewport.getAlignment().getSequences();\r
1112          SequenceI[] seqs = new SequenceI[sv.size()];\r
1113 \r
1114          int i = 0;\r
1115          do\r
1116          {\r
1117            seqs[i] = (SequenceI) sv.elementAt(i);\r
1118          }\r
1119          while (++i < sv.size());\r
1120 \r
1121          SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
1122 \r
1123          if (alignment != null)\r
1124          {\r
1125            AlignFrame af = new AlignFrame(new Alignment(alignment));\r
1126           af.clustalColour.setSelected(true);\r
1127           af.clustalColour_actionPerformed(null);\r
1128            Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),\r
1129                                     700, 500); // JBPNote - is there a new window geom. property ?\r
1130          }\r
1131          else\r
1132            JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",\r
1133                                          JOptionPane.WARNING_MESSAGE);\r
1134 \r
1135          webServiceRunning = false;\r
1136          try{\r
1137            frame.setClosed(true);\r
1138          }catch(Exception ex){}\r
1139        }\r
1140 \r
1141        public void paintComponent(Graphics g1)\r
1142        {\r
1143          Graphics2D g = (Graphics2D)g1;\r
1144          g.setColor(Color.white);\r
1145          g.fillRect(0,0,getWidth(), getHeight());\r
1146          if(image!=null)\r
1147          {\r
1148 \r
1149            g.rotate (Math.toRadians(angle), 28, 28);\r
1150 \r
1151            g.drawImage(image,10,10,this);\r
1152            g.rotate (-Math.toRadians(angle), 28, 28 );\r
1153          }\r
1154          g.setFont(new Font("Arial", Font.BOLD, 12));\r
1155          g.setColor(Color.black);\r
1156          g.drawString("Clustal Alignment Web Service running", 60,30);\r
1157        }\r
1158   }\r
1159   protected void jpred_actionPerformed(ActionEvent e)\r
1160 {\r
1161 \r
1162     JInternalFrame frame = new JInternalFrame();\r
1163     if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)\r
1164     {\r
1165       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1166       SequenceGroup seqs = viewport.getSelectionGroup();\r
1167       if (seqs.getSize() == 1 || !viewport.alignment.isAligned())\r
1168       {\r
1169         JPredClient ct = new JPredClient( (SequenceI)\r
1170                                          seqs.getSequenceAt(0));\r
1171       }\r
1172       else\r
1173       {\r
1174         int sz;\r
1175         SequenceI[] msa = new SequenceI[sz=seqs.getSize()];\r
1176         for (int i = 0; i < sz; i++)\r
1177         {\r
1178           msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1179         }\r
1180 \r
1181         JPredClient ct = new JPredClient(msa);\r
1182       }\r
1183 \r
1184     }\r
1185     else\r
1186     {\r
1187       Vector seqs = viewport.getAlignment().getSequences();\r
1188 \r
1189       if (seqs.size() == 1 || !viewport.alignment.isAligned())\r
1190       {\r
1191         JPredClient ct = new JPredClient( (SequenceI)\r
1192                                          seqs.elementAt(0));\r
1193       }\r
1194       else\r
1195       {\r
1196         SequenceI[] msa = new SequenceI[seqs.size()];\r
1197         for (int i = 0; i < seqs.size(); i++)\r
1198         {\r
1199           msa[i] = (SequenceI) seqs.elementAt(i);\r
1200         }\r
1201 \r
1202         JPredClient ct = new JPredClient(msa);\r
1203       }\r
1204 \r
1205     }\r
1206   }\r
1207 \r
1208     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
1209     // Pick the tree file\r
1210     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
1211         getProperty("LAST_DIRECTORY"));\r
1212     chooser.setFileView(new JalviewFileView());\r
1213     chooser.setDialogTitle("Select a newick-like tree file");\r
1214     chooser.setToolTipText("Load a tree file");\r
1215     int value = chooser.showOpenDialog(null);\r
1216     if (value == JalviewFileChooser.APPROVE_OPTION)\r
1217     {\r
1218       String choice = chooser.getSelectedFile().getPath();\r
1219       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1220       TreePanel treepanel = null;\r
1221       try\r
1222       {\r
1223         jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");\r
1224         fin.parse();\r
1225 \r
1226         if (fin.getTree() != null)\r
1227         {\r
1228           TreePanel tp = null;\r
1229           tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1230                              fin, "FromFile", choice);\r
1231           Desktop.addInternalFrame(tp, title, 600, 500);\r
1232         }\r
1233       }\r
1234       catch (Exception ex)\r
1235       {\r
1236         JOptionPane.showMessageDialog(Desktop.desktop,\r
1237                                       "Problem reading tree file",\r
1238                                       ex.getMessage(),\r
1239                                       JOptionPane.WARNING_MESSAGE);\r
1240         ex.printStackTrace();\r
1241       }\r
1242     }\r
1243   }\r
1244 \r
1245 }\r