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         alignMenu.setVisible(false);\r
  42     }\r
  43     catch(java.net.UnknownHostException e){}\r
  44     viewport = new AlignViewport(al,true,true,false);\r
  45 \r
  46     String fontName = jalview.bin.Cache.getProperty("FONT_NAME");\r
  47     String fontStyle= jalview.bin.Cache.getProperty("FONT_STYLE");\r
  48     String fontSize = jalview.bin.Cache.getProperty("FONT_SIZE");\r
  49     if(fontName!=null && fontStyle!=null && fontSize!=null)\r
  50       viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );\r
  51 \r
  52     // add conservation graph to alignment\r
  53     viewport.updateConservation();\r
  54     viewport.updateConsensus();\r
  55 \r
  56 \r
  57     alignPanel = new AlignmentPanel(this, viewport);\r
  58 \r
  59     alignPanel.annotationPanel.adjustPanelHeight();\r
  60     alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
  61     alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
  62 \r
  63     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
  64 \r
  65 \r
  66     addInternalFrameListener(new InternalFrameAdapter()\r
  67    {\r
  68      public void internalFrameActivated(InternalFrameEvent evt)\r
  69      {\r
  70           javax.swing.SwingUtilities.invokeLater(new Runnable()\r
  71           {\r
  72             public void run()\r
  73             {      alignPanel.requestFocus();    }\r
  74           });\r
  75 \r
  76      }\r
  77    });\r
  78 \r
  79   }\r
  80 \r
  81   protected void saveAs_actionPerformed(ActionEvent e)\r
  82   {\r
  83     String suffix [] = null;\r
  84     if(e.getActionCommand().equals("FASTA"))\r
  85       suffix = new String[]{"fa", "fasta"};\r
  86     else if(e.getActionCommand().equals("MSF"))\r
  87       suffix = new String[]{"msf"};\r
  88     else if(e.getActionCommand().equals("CLUSTAL"))\r
  89       suffix = new String[]{"aln"};\r
  90     else if(e.getActionCommand().equals("BLC"))\r
  91       suffix = new String[]{"blc"};\r
  92     else if(e.getActionCommand().equals("PIR"))\r
  93       suffix = new String[]{"pir"};\r
  94     else if(e.getActionCommand().equals("PFAM"))\r
  95       suffix = new String[]{"pfam"};\r
  96 \r
  97 \r
  98     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")\r
  99         , suffix, e.getActionCommand()+" file");\r
 100     chooser.setFileView(new JalviewFileView());\r
 101     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
 102     chooser.setToolTipText("Save");\r
 103     int value = chooser.showSaveDialog(this);\r
 104     if(value == JalviewFileChooser.APPROVE_OPTION)\r
 105     {\r
 106       String choice =  chooser.getSelectedFile().getPath();\r
 107       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
 108       String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
 109       try{\r
 110         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
 111         out.println(output);\r
 112         out.close();\r
 113       }\r
 114       catch(Exception ex){}\r
 115     }\r
 116 \r
 117   }\r
 118 \r
 119   protected void outputText_actionPerformed(ActionEvent e)\r
 120   {\r
 121      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
 122      JInternalFrame frame = new JInternalFrame();\r
 123      cap.formatForOutput();\r
 124      frame.setContentPane(cap);\r
 125      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
 126      cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
 127   }\r
 128 \r
 129   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 130   {\r
 131     HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
 132     htmlOutput = null;\r
 133   }\r
 134 \r
 135   protected void createPNG_actionPerformed(ActionEvent e)\r
 136   {\r
 137     alignPanel.makePNG();\r
 138   }\r
 139 \r
 140   protected void epsFile_actionPerformed(ActionEvent e)\r
 141   {\r
 142     alignPanel.makeEPS();\r
 143   }\r
 144 \r
 145 \r
 146   public void printMenuItem_actionPerformed(ActionEvent e)\r
 147   {\r
 148     //Putting in a thread avoids Swing painting problems\r
 149     PrintThread thread = new PrintThread();\r
 150     thread.start();\r
 151   }\r
 152 \r
 153   class PrintThread extends Thread\r
 154   {\r
 155     public void run()\r
 156     {\r
 157       PrinterJob printJob = PrinterJob.getPrinterJob();\r
 158       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
 159       printJob.setPrintable(alignPanel, pf);\r
 160       if (printJob.printDialog())\r
 161       {\r
 162         try\r
 163         {\r
 164           printJob.print();\r
 165         }\r
 166         catch (Exception PrintException)\r
 167         {\r
 168           PrintException.printStackTrace();\r
 169         }\r
 170       }\r
 171     }\r
 172 \r
 173   }\r
 174 \r
 175 \r
 176 \r
 177 \r
 178   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 179   {\r
 180     try{\r
 181       this.setClosed(true);\r
 182     }catch(Exception ex){}\r
 183   }\r
 184 \r
 185   Stack historyList = new Stack();\r
 186   Stack redoList = new Stack();\r
 187   JMenuBar jMenuBar1 = new JMenuBar();\r
 188 \r
 189   void updateEditMenuBar()\r
 190   {\r
 191     if(historyList.size()>0)\r
 192      {\r
 193        undoMenuItem.setEnabled(true);\r
 194        Object [] history = (Object[])historyList.get(0);\r
 195        undoMenuItem.setText("Undo "+history[0]);\r
 196      }\r
 197     else\r
 198     {\r
 199       undoMenuItem.setEnabled(false);\r
 200       undoMenuItem.setText("Undo");\r
 201     }\r
 202 \r
 203     if(redoList.size()>0)\r
 204      {\r
 205        redoMenuItem.setEnabled(true);\r
 206        Object [] history = (Object[])redoList.get(0);\r
 207        redoMenuItem.setText("Redo "+history[0]);\r
 208      }\r
 209     else\r
 210     {\r
 211       redoMenuItem.setEnabled(false);\r
 212       redoMenuItem.setText("Redo");\r
 213     }\r
 214   }\r
 215 \r
 216   public void addHistoryItem(String type)\r
 217   {\r
 218     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 219     redoList.clear();\r
 220     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 221     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 222     {\r
 223       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 224                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 225     }\r
 226 \r
 227     historyList.add(0, new Object[]{type,  seq} );\r
 228     updateEditMenuBar();\r
 229   }\r
 230 \r
 231   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 232   {\r
 233     Object [] history = (Object[])historyList.remove(0);\r
 234     // add the redo state before continuing!!\r
 235     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 236     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
 237     {\r
 238       seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
 239                             viewport.getAlignment().getSequenceAt(i).\r
 240                             getSequence());\r
 241     }\r
 242     /////////\r
 243 \r
 244     redoList.add(0, new Object[] {history[0], seq});\r
 245 \r
 246       seq = (SequenceI[]) history[1];\r
 247       viewport.setAlignment( new Alignment(seq) );\r
 248       updateEditMenuBar();\r
 249       viewport.updateConsensus();\r
 250       alignPanel.RefreshPanels();\r
 251       alignPanel.RefreshPanels();\r
 252   }\r
 253 \r
 254   public void moveSelectedSequences(boolean up)\r
 255   {\r
 256     SequenceGroup sg = viewport.getSelectionGroup();\r
 257     if (sg == null)\r
 258       return;\r
 259 \r
 260     if (up)\r
 261     {\r
 262       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 263       {\r
 264         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 265         if (!sg.sequences.contains(seq))\r
 266           continue;\r
 267 \r
 268         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 269         if (sg.sequences.contains(temp))\r
 270           continue;\r
 271 \r
 272         viewport.alignment.getSequences().setElementAt(temp, i);\r
 273         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 274       }\r
 275     }\r
 276     else\r
 277     {\r
 278       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 279       {\r
 280         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 281         if (!sg.sequences.contains(seq))\r
 282           continue;\r
 283 \r
 284         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 285         if (sg.sequences.contains(temp))\r
 286           continue;\r
 287 \r
 288         viewport.alignment.getSequences().setElementAt(temp, i);\r
 289         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 290       }\r
 291     }\r
 292 \r
 293     alignPanel.RefreshPanels();\r
 294   }\r
 295 \r
 296 \r
 297 \r
 298   protected void copy_actionPerformed(ActionEvent e)\r
 299   {\r
 300    if(viewport.getSelectionGroup()==null)\r
 301      return;\r
 302 \r
 303    SequenceGroup sg = viewport.getSelectionGroup();\r
 304 \r
 305      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 306      StringBuffer buffer= new StringBuffer();\r
 307 \r
 308        for(int i=0; i<sg.getSize(); i++)\r
 309        {\r
 310          SequenceI seq = sg.getSequenceAt(i);\r
 311          buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
 312                         +seq.findPosition( sg.getEndRes() )+ "\t"\r
 313                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
 314        }\r
 315      c.setContents( new StringSelection( buffer.toString()) , null ) ;\r
 316 \r
 317   }\r
 318 \r
 319 \r
 320   protected void pasteNew_actionPerformed(ActionEvent e)\r
 321   {\r
 322     paste(true);\r
 323   }\r
 324 \r
 325   protected void pasteThis_actionPerformed(ActionEvent e)\r
 326   {\r
 327     addHistoryItem("Paste");\r
 328     paste(false);\r
 329   }\r
 330 \r
 331   void paste(boolean newAlignment)\r
 332   {\r
 333     try{\r
 334       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 335       Transferable contents = c.getContents(this);\r
 336       if (contents == null)\r
 337         return;\r
 338 \r
 339       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
 340       StringTokenizer st = new StringTokenizer(str);\r
 341       ArrayList seqs = new ArrayList();\r
 342       while (st.hasMoreElements())\r
 343       {\r
 344         String name = st.nextToken();\r
 345         int start = Integer.parseInt(st.nextToken());\r
 346         int end = Integer.parseInt(st.nextToken());\r
 347         Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
 348 \r
 349         if(!newAlignment)\r
 350           viewport.alignment.addSequence(sequence);\r
 351         else\r
 352           seqs.add(sequence);\r
 353       }\r
 354 \r
 355       if(newAlignment)\r
 356       {\r
 357         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 358         seqs.toArray(newSeqs);\r
 359         AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
 360         Desktop.addInternalFrame(af, "Copied sequences", NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
 361       }\r
 362       else\r
 363       {\r
 364         viewport.setEndSeq(viewport.alignment.getHeight());\r
 365         viewport.alignment.getWidth();\r
 366         viewport.updateConservation();\r
 367         viewport.updateConsensus();\r
 368         alignPanel.RefreshPanels();\r
 369       }\r
 370 \r
 371     }catch(Exception ex){}// could be anything being pasted in here\r
 372 \r
 373   }\r
 374 \r
 375 \r
 376   protected void cut_actionPerformed(ActionEvent e)\r
 377   {\r
 378     copy_actionPerformed(null);\r
 379     delete_actionPerformed(null);\r
 380   }\r
 381 \r
 382   protected void delete_actionPerformed(ActionEvent e)\r
 383   {\r
 384     addHistoryItem("Delete");\r
 385     if (viewport.getSelectionGroup() == null)\r
 386       return;\r
 387 \r
 388      SequenceGroup sg = viewport.getSelectionGroup();\r
 389      for (int i=0;i < sg.sequences.size(); i++)\r
 390      {\r
 391        SequenceI seq = sg.getSequenceAt(i);\r
 392        int index = viewport.getAlignment().findIndex(seq);\r
 393        seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);\r
 394 \r
 395        if(seq.getSequence().length()<1)\r
 396           viewport.getAlignment().deleteSequence(seq);\r
 397       else\r
 398           viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 399      }\r
 400 \r
 401      viewport.setSelectionGroup(null);\r
 402      viewport.alignment.deleteGroup(sg);\r
 403      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());\r
 404      if(viewport.getAlignment().getHeight()<1)\r
 405      try\r
 406      {\r
 407        this.setClosed(true);\r
 408      }catch(Exception ex){}\r
 409    viewport.updateConservation();\r
 410    viewport.updateConsensus();\r
 411      alignPanel.RefreshPanels();\r
 412 \r
 413   }\r
 414 \r
 415 \r
 416 \r
 417   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 418   {\r
 419      Object [] history = (Object[])redoList.remove(0);\r
 420      SequenceI[] seq = (SequenceI[]) history[1];\r
 421      viewport.setAlignment( new Alignment(seq) );\r
 422      updateEditMenuBar();\r
 423      viewport.updateConsensus();\r
 424      alignPanel.RefreshPanels();\r
 425      alignPanel.RefreshPanels();\r
 426   }\r
 427 \r
 428 \r
 429   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 430   {\r
 431     viewport.alignment.deleteAllGroups();\r
 432     viewport.setSelectionGroup(null);\r
 433 \r
 434     alignPanel.RefreshPanels();\r
 435   }\r
 436 \r
 437 \r
 438 \r
 439   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 440   {\r
 441     SequenceGroup sg = new SequenceGroup();\r
 442     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 443       sg.addSequence( viewport.getAlignment().getSequenceAt(i));\r
 444     sg.setEndRes(viewport.alignment.getWidth());\r
 445     viewport.setSelectionGroup(sg);\r
 446     PaintRefresher.Refresh(null);\r
 447   }\r
 448 \r
 449   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 450   {\r
 451     viewport.setSelectionGroup(null);\r
 452     PaintRefresher.Refresh(null);\r
 453   }\r
 454 \r
 455   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 456   {\r
 457     SequenceGroup sg = viewport.getSelectionGroup();\r
 458     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 459       sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));\r
 460 \r
 461     PaintRefresher.Refresh(null);\r
 462   }\r
 463 \r
 464 \r
 465   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 466   {\r
 467     viewport.getColumnSelection().clear();\r
 468     repaint();\r
 469   }\r
 470 \r
 471   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 472   {\r
 473     addHistoryItem("delete columns");\r
 474     ColumnSelection colSel = viewport.getColumnSelection();\r
 475     if (colSel.size() > 0)\r
 476     {\r
 477       int min = colSel.getMin();\r
 478       viewport.getAlignment().trimLeft(min);\r
 479       colSel.compensateForEdit(0,min);\r
 480 \r
 481       if(viewport.getSelectionGroup()!=null)\r
 482         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 483 \r
 484       Vector groups = viewport.alignment.getGroups();\r
 485       for(int i=0; i<groups.size(); i++)\r
 486       {\r
 487         SequenceGroup sg = (SequenceGroup) groups.get(i);\r
 488         if(!sg.adjustForRemoveLeft(min))\r
 489           viewport.alignment.deleteGroup(sg);\r
 490       }\r
 491 \r
 492       alignPanel.RefreshPanels();\r
 493     }\r
 494   }\r
 495 \r
 496   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 497   {\r
 498     addHistoryItem("delete columns");\r
 499     ColumnSelection colSel = viewport.getColumnSelection();\r
 500     if (colSel.size() > 0)\r
 501     {\r
 502       int max = colSel.getMax();\r
 503       viewport.getAlignment().trimRight(max);\r
 504       if(viewport.getSelectionGroup()!=null)\r
 505         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 506 \r
 507       Vector groups = viewport.alignment.getGroups();\r
 508       for(int i=0; i<groups.size(); i++)\r
 509       {\r
 510         SequenceGroup sg = (SequenceGroup) groups.get(i);\r
 511         if(!sg.adjustForRemoveRight(max))\r
 512           viewport.alignment.deleteGroup(sg);\r
 513       }\r
 514 \r
 515 \r
 516 \r
 517       alignPanel.RefreshPanels();\r
 518     }\r
 519 \r
 520   }\r
 521 \r
 522   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 523   {\r
 524     addHistoryItem("delete gapped columns");\r
 525     viewport.getAlignment().removeGaps();\r
 526     viewport.updateConservation();\r
 527     viewport.updateConsensus();\r
 528     alignPanel.RefreshPanels();\r
 529   }\r
 530 \r
 531   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 532   {\r
 533     addHistoryItem("delete all gaps");\r
 534     SequenceI current;\r
 535     int jSize;\r
 536     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 537     {\r
 538       current = viewport.getAlignment().getSequenceAt(i);\r
 539       jSize = current.getLength();\r
 540       for (int j=0; j < jSize; j++)\r
 541         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 542         {\r
 543           current.deleteCharAt(j);\r
 544           j--;\r
 545           jSize--;\r
 546         }\r
 547     }\r
 548     viewport.updateConservation();\r
 549     viewport.updateConsensus();\r
 550     alignPanel.RefreshPanels();\r
 551   }\r
 552 \r
 553   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 554   {\r
 555     char thisChar = '-';\r
 556     char nextChar = '.';\r
 557     if(viewport.getGapCharacter()=='-')\r
 558     {\r
 559       thisChar = '.';\r
 560       nextChar = '-';\r
 561     }\r
 562     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 563     viewport.setGapCharacter(thisChar);\r
 564     alignPanel.RefreshPanels();\r
 565   }\r
 566 \r
 567   public void findMenuItem_actionPerformed(ActionEvent e)\r
 568   {\r
 569     JInternalFrame frame = new JInternalFrame();\r
 570     Finder finder = new Finder(viewport, alignPanel, frame);\r
 571     frame.setContentPane(finder);\r
 572     Desktop.addInternalFrame(frame, "Find", 340,110, false);\r
 573     frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
 574 \r
 575   }\r
 576 \r
 577 \r
 578   public void font_actionPerformed(ActionEvent e)\r
 579   {\r
 580     JInternalFrame frame = new JInternalFrame();\r
 581     FontChooser fc = new FontChooser( alignPanel, frame );\r
 582     frame.setContentPane(fc);\r
 583     Desktop.addInternalFrame(frame, "Change Font", 480,100);\r
 584   }\r
 585 \r
 586   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 587   {\r
 588     viewport.setShowFullId( fullSeqId.isSelected() );\r
 589 \r
 590     alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );\r
 591     alignPanel.RefreshPanels();\r
 592   }\r
 593 \r
 594   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 595   {\r
 596       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 597       alignPanel.RefreshPanels();\r
 598   }\r
 599 \r
 600   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 601   {\r
 602     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 603     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
 604     scaleAbove.setVisible( wrapMenuItem.isSelected() );\r
 605     scaleLeft.setVisible( wrapMenuItem.isSelected() );\r
 606     scaleRight.setVisible( wrapMenuItem.isSelected() );\r
 607     alignPanel.RefreshPanels();\r
 608   }\r
 609 \r
 610   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 611   {\r
 612     viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
 613     alignPanel.repaint();\r
 614   }\r
 615 \r
 616   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 617   {\r
 618     viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
 619     alignPanel.repaint();\r
 620   }\r
 621 \r
 622   protected void scaleRight_actionPerformed(ActionEvent e)\r
 623   {\r
 624     viewport.setScaleRightWrapped(scaleRight.isSelected());\r
 625     alignPanel.repaint();\r
 626   }\r
 627 \r
 628 \r
 629 \r
 630   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 631   {\r
 632     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 633     alignPanel.RefreshPanels();\r
 634   }\r
 635 \r
 636   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 637   {\r
 638     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 639     alignPanel.RefreshPanels();\r
 640   }\r
 641 \r
 642 \r
 643   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 644   {\r
 645     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 646     alignPanel.RefreshPanels();\r
 647   }\r
 648 \r
 649   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
 650   {\r
 651     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 652     if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
 653     {\r
 654          AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);\r
 655          ((Alignment)viewport.alignment).featuresAdded = true;\r
 656     }\r
 657     alignPanel.RefreshPanels();\r
 658   }\r
 659 \r
 660   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 661   {\r
 662     if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())\r
 663     {\r
 664       annotationPanelMenuItem.setSelected(false);\r
 665       return;\r
 666     }\r
 667     viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );\r
 668     alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );\r
 669   }\r
 670 \r
 671   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 672   {\r
 673     if (alignPanel.overviewPanel != null)\r
 674       return;\r
 675 \r
 676     JInternalFrame frame = new JInternalFrame();\r
 677     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 678    try{\r
 679      overview = new OverviewPanel(alignPanel, viewport);\r
 680      frame.setContentPane(overview);\r
 681     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 682                              frame.getWidth(), frame.getHeight());\r
 683     frame.pack();\r
 684     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 685     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 686       {\r
 687             alignPanel.setOverviewPanel(null);\r
 688       };\r
 689     });\r
 690     alignPanel.setOverviewPanel( overview );\r
 691 \r
 692   }catch(java.lang.OutOfMemoryError ex)\r
 693    {\r
 694      JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 695                                    +"\nTry reducing the font size.",\r
 696                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 697    }\r
 698 \r
 699 \r
 700   }\r
 701 \r
 702   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 703   {\r
 704     changeColour( null );\r
 705   }\r
 706 \r
 707 \r
 708   public void clustalColour_actionPerformed(ActionEvent e)\r
 709   {\r
 710     abovePIDThreshold.setSelected(false);\r
 711     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 712   }\r
 713 \r
 714   public void zappoColour_actionPerformed(ActionEvent e)\r
 715   {\r
 716     changeColour(new ZappoColourScheme());\r
 717   }\r
 718 \r
 719   public void taylorColour_actionPerformed(ActionEvent e)\r
 720   {\r
 721     changeColour(new TaylorColourScheme());\r
 722   }\r
 723 \r
 724 \r
 725   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 726   {\r
 727     changeColour( new HydrophobicColourScheme() );\r
 728   }\r
 729 \r
 730   public void helixColour_actionPerformed(ActionEvent e)\r
 731   {\r
 732     changeColour(new HelixColourScheme() );\r
 733   }\r
 734 \r
 735 \r
 736   public void strandColour_actionPerformed(ActionEvent e)\r
 737   {\r
 738     changeColour(new StrandColourScheme());\r
 739   }\r
 740 \r
 741 \r
 742   public void turnColour_actionPerformed(ActionEvent e)\r
 743   {\r
 744     changeColour(new TurnColourScheme());\r
 745   }\r
 746 \r
 747 \r
 748   public void buriedColour_actionPerformed(ActionEvent e)\r
 749   {\r
 750     changeColour(new BuriedColourScheme() );\r
 751   }\r
 752 \r
 753   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 754   {\r
 755     changeColour(new NucleotideColourScheme());\r
 756   }\r
 757 \r
 758 \r
 759   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 760   {\r
 761     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
 762   }\r
 763 \r
 764 \r
 765 \r
 766   void changeColour(ColourSchemeI cs)\r
 767   {\r
 768 \r
 769     if(viewport.getColourAppliesToAllGroups())\r
 770     {\r
 771       Vector groups = viewport.alignment.getGroups();\r
 772       for(int i=0; i<groups.size(); i++)\r
 773       {\r
 774         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 775         sg.cs = cs;\r
 776 \r
 777         if(abovePIDThreshold.isSelected())\r
 778           abovePIDThreshold_actionPerformed(null);\r
 779         else if( viewport.getConservationSelected() )\r
 780         {\r
 781           Conservation c = new Conservation("Group",\r
 782                                             ResidueProperties.propHash, 3,\r
 783                                             sg.sequences, sg.getStartRes(),\r
 784                                             sg.getEndRes());\r
 785           c.calculate();\r
 786           c.verdict(false, 100);\r
 787           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 788 \r
 789           sg.cs = ccs;\r
 790         }\r
 791 \r
 792       }\r
 793     }\r
 794 \r
 795 \r
 796     if ( viewport.getAbovePIDThreshold() )\r
 797     {\r
 798  //     int threshold = 0;\r
 799    //   threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");\r
 800       Desktop.hideConservationSlider();\r
 801 \r
 802  //     if (cs instanceof ResidueColourScheme)\r
 803  //       ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 804   //    else if (cs instanceof ScoreColourScheme)\r
 805    //     ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 806 \r
 807       viewport.setGlobalColourScheme(cs);\r
 808 \r
 809     }\r
 810     else\r
 811     if (cs instanceof ResidueColourScheme)\r
 812       ( (ResidueColourScheme) cs).setThreshold(0);\r
 813     else if (cs instanceof ScoreColourScheme)\r
 814       ( (ScoreColourScheme) cs).setThreshold(0);\r
 815 \r
 816 \r
 817 \r
 818 \r
 819 if ( viewport.getConservationSelected() )\r
 820  {\r
 821    ConservationColourScheme ccs = null;\r
 822 \r
 823    Alignment al = (Alignment) viewport.alignment;\r
 824    Conservation c = new Conservation("All",\r
 825                                      ResidueProperties.propHash, 3,\r
 826                                      al.getSequences(), 0,\r
 827                                      al.getWidth());\r
 828 \r
 829    c.calculate();\r
 830    c.verdict(false, 100);\r
 831 \r
 832    ccs = new ConservationColourScheme(c, cs);\r
 833 \r
 834  //  int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,    "Background");\r
 835 \r
 836  //  ccs.inc = threshold;\r
 837 \r
 838    viewport.setGlobalColourScheme(ccs);\r
 839 \r
 840   }\r
 841   else\r
 842        viewport.setGlobalColourScheme( cs );\r
 843 \r
 844     alignPanel.RefreshPanels();\r
 845   }\r
 846 \r
 847   protected void modifyPID_actionPerformed(ActionEvent e)\r
 848   {\r
 849     Desktop.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(), "Background");\r
 850   }\r
 851 \r
 852   protected void modifyConservation_actionPerformed(ActionEvent e)\r
 853   {\r
 854     Desktop.setConservationSliderSource(alignPanel, viewport.globalColourScheme,    "Background");\r
 855   }\r
 856 \r
 857 \r
 858   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 859   {\r
 860     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 861     if(coloursChanging)\r
 862       return;\r
 863 \r
 864     coloursChanging = true;\r
 865 \r
 866     viewport.setAbovePIDThreshold(false);\r
 867     abovePIDThreshold.setSelected(false);\r
 868     Desktop.hidePIDSlider();\r
 869     if(!viewport.getConservationSelected())\r
 870       Desktop.hideConservationSlider();\r
 871 \r
 872    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 873    if(cs instanceof ConservationColourScheme )\r
 874      changeColour( ((ConservationColourScheme)cs).cs );\r
 875     else\r
 876       changeColour( cs );\r
 877 \r
 878     coloursChanging = false;\r
 879   }\r
 880 \r
 881   boolean coloursChanging = false;\r
 882   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 883   {\r
 884     if(coloursChanging)\r
 885       return;\r
 886 \r
 887     coloursChanging = true;\r
 888     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
 889 \r
 890     conservationMenuItem.setSelected(false);\r
 891     viewport.setConservationSelected(false);\r
 892     Desktop.hideConservationSlider();\r
 893 \r
 894     if(!viewport.getAbovePIDThreshold())\r
 895       Desktop.hidePIDSlider();\r
 896 \r
 897 \r
 898     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 899     if(cs instanceof ConservationColourScheme )\r
 900         changeColour( ((ConservationColourScheme)cs).cs );\r
 901     else\r
 902         changeColour( cs );\r
 903 \r
 904     coloursChanging = false;\r
 905   }\r
 906 \r
 907 \r
 908 \r
 909   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 910   {\r
 911     JInternalFrame frame = new JInternalFrame();\r
 912     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 913     frame.setContentPane(chooser);\r
 914     Desktop.addInternalFrame(frame,"User defined colours", 450,540, false );\r
 915   }\r
 916 \r
 917   public void PIDColour_actionPerformed(ActionEvent e)\r
 918   {\r
 919     changeColour( new PIDColourScheme() );\r
 920   }\r
 921 \r
 922 \r
 923   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 924   {\r
 925     changeColour(new Blosum62ColourScheme(viewport) );\r
 926   }\r
 927 \r
 928 \r
 929 \r
 930   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 931   {\r
 932     addHistoryItem("sort");\r
 933     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 934     alignPanel.RefreshPanels();\r
 935   }\r
 936 \r
 937   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 938   {\r
 939     addHistoryItem("sort");\r
 940     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 941     alignPanel.RefreshPanels();\r
 942   }\r
 943 \r
 944   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 945   {\r
 946     addHistoryItem("sort");\r
 947     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 948     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 949     alignPanel.RefreshPanels();\r
 950   }\r
 951 \r
 952   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 953   {\r
 954     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 955     JInternalFrame frame = new JInternalFrame();\r
 956     frame.setContentPane(sp);\r
 957     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);\r
 958 \r
 959   }\r
 960 \r
 961   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 962   {\r
 963     if(viewport.getSelectionGroup().getSize()<2)\r
 964       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 965     else\r
 966     {\r
 967       JInternalFrame frame = new JInternalFrame();\r
 968       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 969       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 970     }\r
 971   }\r
 972 \r
 973   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 974   {\r
 975 \r
 976     if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
 977        || viewport.getAlignment().getHeight()<4)\r
 978     {\r
 979       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
 980                                     +"at least 4 input sequences.",\r
 981                                     "Sequence selection insufficient",\r
 982                                     JOptionPane.WARNING_MESSAGE);\r
 983       return;\r
 984     }\r
 985 \r
 986     try{\r
 987       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 988       JInternalFrame frame = new JInternalFrame();\r
 989       frame.setContentPane(pcaPanel);\r
 990       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 991    }catch(java.lang.OutOfMemoryError ex)\r
 992    {\r
 993      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 994                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 995    }\r
 996 \r
 997 \r
 998   }\r
 999 \r
1000   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1001   {\r
1002     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1003   }\r
1004 \r
1005   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1006   {\r
1007     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1008   }\r
1009 \r
1010 \r
1011   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1012   {\r
1013     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1014   }\r
1015 \r
1016   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1017   {\r
1018     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1019   }\r
1020 \r
1021   void NewTreePanel(String type, String pwType, String title)\r
1022   {\r
1023     //are the sequences aligned?\r
1024     if(!viewport.alignment.isAligned())\r
1025     {\r
1026       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
1027                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
1028       return;\r
1029     }\r
1030 \r
1031     final TreePanel tp;\r
1032     if (viewport.getSelectionGroup() != null &&\r
1033         viewport.getSelectionGroup().getSize() > 3)\r
1034     {\r
1035       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
1036                          pwType,\r
1037                          0, viewport.alignment.getWidth());\r
1038     }\r
1039     else\r
1040     {\r
1041       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1042                          type, pwType, 0, viewport.alignment.getWidth());\r
1043     }\r
1044 \r
1045    addTreeMenuItem(tp, title);\r
1046 \r
1047    Desktop.addInternalFrame(tp, title, 600, 500);\r
1048   }\r
1049 \r
1050   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1051   {\r
1052     final JMenuItem item = new JMenuItem(title);\r
1053     sortByTreeMenu.add(item);\r
1054     item.addActionListener(new java.awt.event.ActionListener()\r
1055     {\r
1056       public void actionPerformed(ActionEvent e)\r
1057       {\r
1058         addHistoryItem("sort");\r
1059         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1060         alignPanel.RefreshPanels();\r
1061       }\r
1062     });\r
1063 \r
1064     treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
1065     {\r
1066       public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
1067       {\r
1068         sortByTreeMenu.remove(item);\r
1069       };\r
1070     });\r
1071 \r
1072   }\r
1073 \r
1074 \r
1075   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
1076   {\r
1077     JInternalFrame frame = new JInternalFrame();\r
1078     ClustalThread ct = new ClustalThread(frame);\r
1079     Thread t = new Thread(ct);\r
1080     t.start();\r
1081     frame.setContentPane(ct);\r
1082      Desktop.addInternalFrame(frame, title, 320, 90);\r
1083 \r
1084   }\r
1085 \r
1086   class ClustalThread extends JPanel implements Runnable\r
1087   {\r
1088     Image image;\r
1089     int angle = 0;\r
1090     boolean webServiceRunning = false;\r
1091     JInternalFrame frame;\r
1092     public ClustalThread(JInternalFrame frame)\r
1093     {\r
1094       this.frame = frame;\r
1095 \r
1096       java.net.URL url = getClass().getResource("/images/logo.gif");\r
1097       if (url != null)\r
1098       {\r
1099         image = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
1100         MediaTracker mt = new MediaTracker(this);\r
1101         mt.addImage(image, 0);\r
1102         try\r
1103         {\r
1104           mt.waitForID(0);\r
1105         }\r
1106         catch (Exception ex)\r
1107         {}\r
1108       }\r
1109 \r
1110       ImageSpinner spinner = new ImageSpinner();\r
1111       spinner.start();\r
1112       webServiceRunning = true;\r
1113     }\r
1114 \r
1115     class ImageSpinner extends Thread\r
1116     {\r
1117       public void run()\r
1118       {\r
1119         while(webServiceRunning)\r
1120         {\r
1121           try{\r
1122             Thread.sleep(10);\r
1123             angle+=1;\r
1124             angle %=360;\r
1125             repaint();\r
1126           }\r
1127           catch(Exception ex){}\r
1128         }\r
1129       }\r
1130     }\r
1131 \r
1132     // JBPNote\r
1133     // Should check to see if the server settings are valid\r
1134     // Need visual-delay indication here.\r
1135     public void run()\r
1136        {\r
1137          jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
1138          Vector sv = viewport.getAlignment().getSequences();\r
1139          SequenceI[] seqs = new SequenceI[sv.size()];\r
1140 \r
1141          int i = 0;\r
1142          do\r
1143          {\r
1144            seqs[i] = (SequenceI) sv.elementAt(i);\r
1145          }\r
1146          while (++i < sv.size());\r
1147 \r
1148          SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
1149 \r
1150          if (alignment != null)\r
1151          {\r
1152            AlignFrame af = new AlignFrame(new Alignment(alignment));\r
1153            Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
1154            af.clustalColour_actionPerformed(null);\r
1155            af.clustalColour.setSelected(true);\r
1156          }\r
1157          else\r
1158            JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",\r
1159                                          JOptionPane.WARNING_MESSAGE);\r
1160 \r
1161          webServiceRunning = false;\r
1162          try{\r
1163            frame.setClosed(true);\r
1164          }catch(Exception ex){}\r
1165        }\r
1166 \r
1167        public void paintComponent(Graphics g1)\r
1168        {\r
1169          Graphics2D g = (Graphics2D)g1;\r
1170          g.setColor(Color.white);\r
1171          g.fillRect(0,0,getWidth(), getHeight());\r
1172          if(image!=null)\r
1173          {\r
1174 \r
1175            g.rotate (Math.toRadians(angle), 28, 28);\r
1176 \r
1177            g.drawImage(image,10,10,this);\r
1178            g.rotate (-Math.toRadians(angle), 28, 28 );\r
1179          }\r
1180          g.setFont(new Font("Arial", Font.BOLD, 12));\r
1181          g.setColor(Color.black);\r
1182          g.drawString("Clustal Alignment Web Service running", 60,30);\r
1183        }\r
1184   }\r
1185   protected void jpred_actionPerformed(ActionEvent e)\r
1186 {\r
1187 \r
1188     JInternalFrame frame = new JInternalFrame();\r
1189     if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)\r
1190     {\r
1191       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1192       SequenceGroup seqs = viewport.getSelectionGroup();\r
1193       if (seqs.getSize() == 1 || !viewport.alignment.isAligned())\r
1194       {\r
1195         JPredClient ct = new JPredClient( (SequenceI)\r
1196                                          seqs.getSequenceAt(0));\r
1197       }\r
1198       else\r
1199       {\r
1200         int sz;\r
1201         SequenceI[] msa = new SequenceI[sz=seqs.getSize()];\r
1202         for (int i = 0; i < sz; i++)\r
1203         {\r
1204           msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1205         }\r
1206 \r
1207         JPredClient ct = new JPredClient(msa);\r
1208       }\r
1209 \r
1210     }\r
1211     else\r
1212     {\r
1213       Vector seqs = viewport.getAlignment().getSequences();\r
1214 \r
1215       if (seqs.size() == 1 || !viewport.alignment.isAligned())\r
1216       {\r
1217         JPredClient ct = new JPredClient( (SequenceI)\r
1218                                          seqs.elementAt(0));\r
1219       }\r
1220       else\r
1221       {\r
1222         SequenceI[] msa = new SequenceI[seqs.size()];\r
1223         for (int i = 0; i < seqs.size(); i++)\r
1224         {\r
1225           msa[i] = (SequenceI) seqs.elementAt(i);\r
1226         }\r
1227 \r
1228         JPredClient ct = new JPredClient(msa);\r
1229       }\r
1230 \r
1231     }\r
1232   }\r
1233 \r
1234     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
1235     // Pick the tree file\r
1236     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
1237         getProperty("LAST_DIRECTORY"));\r
1238     chooser.setFileView(new JalviewFileView());\r
1239     chooser.setDialogTitle("Select a newick-like tree file");\r
1240     chooser.setToolTipText("Load a tree file");\r
1241     int value = chooser.showOpenDialog(null);\r
1242     if (value == JalviewFileChooser.APPROVE_OPTION)\r
1243     {\r
1244       String choice = chooser.getSelectedFile().getPath();\r
1245       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1246       TreePanel treepanel = null;\r
1247       try\r
1248       {\r
1249         jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");\r
1250         fin.parse();\r
1251 \r
1252         if (fin.getTree() != null)\r
1253         {\r
1254           TreePanel tp = null;\r
1255           tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1256                              fin, "FromFile", choice);\r
1257           Desktop.addInternalFrame(tp, title, 600, 500);\r
1258           addTreeMenuItem(tp, title);\r
1259         }\r
1260       }\r
1261       catch (Exception ex)\r
1262       {\r
1263         JOptionPane.showMessageDialog(Desktop.desktop,\r
1264                                       "Problem reading tree file",\r
1265                                       ex.getMessage(),\r
1266                                       JOptionPane.WARNING_MESSAGE);\r
1267         ex.printStackTrace();\r
1268       }\r
1269     }\r
1270   }\r
1271 \r
1272 }\r