src/jalview/gui/AlignFrame.java

   1 /********************\r
   2  * 2004 Jalview Reengineered\r
   3  * Barton Group\r
   4  * Dundee University\r
   5  *\r
   6  * AM Waterhouse\r
   7  *******************/\r
   8 \r
   9 \r
  10 \r
  11 \r
  12 package jalview.gui;\r
  13 \r
  14 import jalview.jbgui.GAlignFrame;\r
  15 import jalview.schemes.*;\r
  16 import jalview.datamodel.*;\r
  17 import jalview.analysis.*;\r
  18 import jalview.io.*;\r
  19 import jalview.ws.*;\r
  20 import java.awt.*;\r
  21 import java.awt.event.*;\r
  22 import java.awt.print.*;\r
  23 import javax.swing.*;\r
  24 import javax.swing.event.*;\r
  25 import java.util.*;\r
  26 import java.awt.datatransfer.*;\r
  27 \r
  28 \r
  29 public class AlignFrame extends GAlignFrame\r
  30 {\r
  31   final AlignmentPanel alignPanel;\r
  32   final AlignViewport viewport;\r
  33   public static final int NEW_WINDOW_WIDTH = 700;\r
  34   public static final int NEW_WINDOW_HEIGHT = 500;\r
  35   public String currentFileFormat = "Jalview";\r
  36 \r
  37   public AlignFrame(AlignmentI al)\r
  38   {\r
  39     viewport = new AlignViewport(al);\r
  40 \r
  41     alignPanel = new AlignmentPanel(this, viewport);\r
  42     alignPanel.annotationPanel.adjustPanelHeight();\r
  43     alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
  44     alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
  45     alignPanel.setAnnotationVisible( viewport.getShowAnnotation() );\r
  46 \r
  47     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
  48 \r
  49     addInternalFrameListener(new InternalFrameAdapter()\r
  50    {\r
  51      public void internalFrameActivated(InternalFrameEvent evt)\r
  52      {\r
  53           javax.swing.SwingUtilities.invokeLater(new Runnable()\r
  54           {\r
  55             public void run()\r
  56             {      alignPanel.requestFocus();    }\r
  57           });\r
  58 \r
  59      }\r
  60    });\r
  61 \r
  62   }\r
  63 \r
  64   public void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
  65   {\r
  66     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")\r
  67         ,  new String[]{"fa, fasta, fastq", "aln",  "pfam", "msf", "pir","blc","jar"},\r
  68           new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"},\r
  69           currentFileFormat);\r
  70 \r
  71     chooser.setAcceptAllFileFilterUsed(false);\r
  72     chooser.setFileView(new JalviewFileView());\r
  73     chooser.setDialogTitle("Save Alignment to file");\r
  74     chooser.setToolTipText("Save");\r
  75     int value = chooser.showSaveDialog(this);\r
  76     if(value == JalviewFileChooser.APPROVE_OPTION)\r
  77     {\r
  78       currentFileFormat  = chooser.getSelectedFormat();\r
  79 \r
  80       if (currentFileFormat.equals("Jalview"))\r
  81       {\r
  82         String shortName = title.replace('/', '_');\r
  83         title = title.replace('\\', '_');\r
  84         String choice = chooser.getSelectedFile().getPath();\r
  85         Jalview2XML.SaveState(this, System.currentTimeMillis(), shortName,\r
  86                               choice);\r
  87         // USE Jalview2XML to save this file\r
  88         return;\r
  89       }\r
  90 \r
  91       String choice =  chooser.getSelectedFile().getPath();\r
  92       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
  93       String output = FormatAdapter.formatSequences(currentFileFormat, viewport.getAlignment().getSequences());\r
  94       try{\r
  95         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
  96         out.println(output);\r
  97         out.close();\r
  98       }\r
  99       catch(Exception ex){}\r
 100     }\r
 101 \r
 102   }\r
 103 \r
 104   protected void outputText_actionPerformed(ActionEvent e)\r
 105   {\r
 106      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
 107      JInternalFrame frame = new JInternalFrame();\r
 108      cap.formatForOutput();\r
 109      frame.setContentPane(cap);\r
 110      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
 111      cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
 112   }\r
 113 \r
 114   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 115   {\r
 116     HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
 117     htmlOutput = null;\r
 118   }\r
 119 \r
 120   protected void createPNG_actionPerformed(ActionEvent e)\r
 121   {\r
 122     alignPanel.makePNG();\r
 123   }\r
 124 \r
 125   protected void epsFile_actionPerformed(ActionEvent e)\r
 126   {\r
 127     alignPanel.makeEPS();\r
 128   }\r
 129 \r
 130 \r
 131   public void printMenuItem_actionPerformed(ActionEvent e)\r
 132   {\r
 133     //Putting in a thread avoids Swing painting problems\r
 134     PrintThread thread = new PrintThread();\r
 135     thread.start();\r
 136   }\r
 137 \r
 138   class PrintThread extends Thread\r
 139   {\r
 140     public void run()\r
 141     {\r
 142       PrinterJob printJob = PrinterJob.getPrinterJob();\r
 143       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
 144       printJob.setPrintable(alignPanel, pf);\r
 145       if (printJob.printDialog())\r
 146       {\r
 147         try\r
 148         {\r
 149           printJob.print();\r
 150         }\r
 151         catch (Exception PrintException)\r
 152         {\r
 153           PrintException.printStackTrace();\r
 154         }\r
 155       }\r
 156     }\r
 157 \r
 158   }\r
 159 \r
 160 \r
 161 \r
 162 \r
 163   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 164   {\r
 165     try{\r
 166       this.setClosed(true);\r
 167     }catch(Exception ex){}\r
 168   }\r
 169 \r
 170   Stack historyList = new Stack();\r
 171   Stack redoList = new Stack();\r
 172 \r
 173   void updateEditMenuBar()\r
 174   {\r
 175     if(historyList.size()>0)\r
 176      {\r
 177        undoMenuItem.setEnabled(true);\r
 178        Object [] history = (Object[])historyList.get(0);\r
 179        undoMenuItem.setText("Undo "+history[0]);\r
 180      }\r
 181     else\r
 182     {\r
 183       undoMenuItem.setEnabled(false);\r
 184       undoMenuItem.setText("Undo");\r
 185     }\r
 186 \r
 187     if(redoList.size()>0)\r
 188      {\r
 189        redoMenuItem.setEnabled(true);\r
 190        Object [] history = (Object[])redoList.get(0);\r
 191        redoMenuItem.setText("Redo "+history[0]);\r
 192      }\r
 193     else\r
 194     {\r
 195       redoMenuItem.setEnabled(false);\r
 196       redoMenuItem.setText("Redo");\r
 197     }\r
 198   }\r
 199 \r
 200   public void addHistoryItem(String type)\r
 201   {\r
 202     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 203     redoList.clear();\r
 204 \r
 205     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 206     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 207     {\r
 208       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 209                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 210     }\r
 211 \r
 212 \r
 213     historyList.add(0, new Object[]{type,  seq} );\r
 214     updateEditMenuBar();\r
 215   }\r
 216 \r
 217   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 218   {\r
 219     Object [] history = (Object[])historyList.remove(0);\r
 220     // add the redo state before continuing!!\r
 221     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 222     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
 223     {\r
 224       seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
 225                             viewport.getAlignment().getSequenceAt(i).\r
 226                             getSequence());\r
 227     }\r
 228     /////////\r
 229 \r
 230     redoList.add(0, new Object[] {history[0], seq});\r
 231 \r
 232       seq = (SequenceI[]) history[1];\r
 233       AlignmentAnnotation [] old = viewport.alignment.getAlignmentAnnotation();\r
 234       viewport.setAlignment( new Alignment(seq) );\r
 235       viewport.alignment.setGapCharacter( Preferences.gapSymbol );\r
 236       updateEditMenuBar();\r
 237       for(int i=0; i<old.length; i++)\r
 238         viewport.alignment.addAnnotation(old[i]);\r
 239       viewport.updateConsensus();\r
 240       viewport.updateConservation();\r
 241       alignPanel.repaint();\r
 242   }\r
 243 \r
 244   public void moveSelectedSequences(boolean up)\r
 245   {\r
 246     SequenceGroup sg = viewport.getSelectionGroup();\r
 247     if (sg == null)\r
 248       return;\r
 249 \r
 250     if (up)\r
 251     {\r
 252       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 253       {\r
 254         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 255         if (!sg.sequences.contains(seq))\r
 256           continue;\r
 257 \r
 258         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 259         if (sg.sequences.contains(temp))\r
 260           continue;\r
 261 \r
 262         viewport.alignment.getSequences().setElementAt(temp, i);\r
 263         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 264       }\r
 265     }\r
 266     else\r
 267     {\r
 268       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 269       {\r
 270         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 271         if (!sg.sequences.contains(seq))\r
 272           continue;\r
 273 \r
 274         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 275         if (sg.sequences.contains(temp))\r
 276           continue;\r
 277 \r
 278         viewport.alignment.getSequences().setElementAt(temp, i);\r
 279         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 280       }\r
 281     }\r
 282 \r
 283     alignPanel.repaint();\r
 284   }\r
 285 \r
 286 \r
 287 \r
 288   protected void copy_actionPerformed(ActionEvent e)\r
 289   {\r
 290      if(viewport.getSelectionGroup()==null)\r
 291        return;\r
 292 \r
 293      SequenceGroup sg = viewport.getSelectionGroup();\r
 294 \r
 295      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 296      StringBuffer buffer= new StringBuffer();\r
 297 \r
 298      Hashtable orderedSeqs = new Hashtable();\r
 299      for(int i=0; i<sg.getSize(); i++)\r
 300      {\r
 301         SequenceI seq = sg.getSequenceAt(i);\r
 302         int index = viewport.alignment.findIndex(seq);\r
 303         orderedSeqs.put(index+"", seq);\r
 304      }\r
 305 \r
 306      int index=0;\r
 307      for(int i=0; i<sg.getSize(); i++)\r
 308      {\r
 309        SequenceI seq = null;\r
 310        while( seq == null )\r
 311        {\r
 312          if(orderedSeqs.containsKey(index+""))\r
 313          {\r
 314            seq = (SequenceI) orderedSeqs.get(index + "");\r
 315            index++;\r
 316            break;\r
 317          }\r
 318          else\r
 319            index++;\r
 320        }\r
 321 \r
 322          buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
 323                         +seq.findPosition( sg.getEndRes() )+ "\t"\r
 324                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
 325      }\r
 326      c.setContents( new StringSelection( buffer.toString()) , null ) ;\r
 327 \r
 328   }\r
 329 \r
 330 \r
 331   protected void pasteNew_actionPerformed(ActionEvent e)\r
 332   {\r
 333     paste(true);\r
 334   }\r
 335 \r
 336   protected void pasteThis_actionPerformed(ActionEvent e)\r
 337   {\r
 338     addHistoryItem("Paste");\r
 339     paste(false);\r
 340   }\r
 341 \r
 342   void paste(boolean newAlignment)\r
 343   {\r
 344     try{\r
 345       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 346       Transferable contents = c.getContents(this);\r
 347       if (contents == null)\r
 348         return;\r
 349 \r
 350       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
 351       StringTokenizer st = new StringTokenizer(str);\r
 352       ArrayList seqs = new ArrayList();\r
 353       while (st.hasMoreElements())\r
 354       {\r
 355         String name = st.nextToken();\r
 356         int start = Integer.parseInt(st.nextToken());\r
 357         int end = Integer.parseInt(st.nextToken());\r
 358         Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
 359 \r
 360         if(!newAlignment)\r
 361           viewport.alignment.addSequence(sequence);\r
 362         else\r
 363           seqs.add(sequence);\r
 364       }\r
 365 \r
 366       if(newAlignment)\r
 367       {\r
 368         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 369         seqs.toArray(newSeqs);\r
 370         AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
 371         String newtitle = new String("Copied sequences");\r
 372         if( title.startsWith("Copied sequences"))\r
 373          newtitle = title;\r
 374        else\r
 375          newtitle = newtitle.concat("- from "+title);\r
 376 \r
 377         Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
 378       }\r
 379       else\r
 380       {\r
 381         viewport.setEndSeq(viewport.alignment.getHeight());\r
 382         viewport.alignment.getWidth();\r
 383         viewport.updateConservation();\r
 384         viewport.updateConsensus();\r
 385         alignPanel.repaint();\r
 386       }\r
 387 \r
 388     }catch(Exception ex){}// could be anything being pasted in here\r
 389 \r
 390   }\r
 391 \r
 392 \r
 393   protected void cut_actionPerformed(ActionEvent e)\r
 394   {\r
 395     copy_actionPerformed(null);\r
 396     delete_actionPerformed(null);\r
 397   }\r
 398 \r
 399   protected void delete_actionPerformed(ActionEvent e)\r
 400   {\r
 401     addHistoryItem("Delete");\r
 402     if (viewport.getSelectionGroup() == null)\r
 403       return;\r
 404 \r
 405      SequenceGroup sg = viewport.getSelectionGroup();\r
 406      for (int i=0;i < sg.sequences.size(); i++)\r
 407      {\r
 408        SequenceI seq = sg.getSequenceAt(i);\r
 409        int index = viewport.getAlignment().findIndex(seq);\r
 410        seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);\r
 411 \r
 412        if(seq.getSequence().length()<1)\r
 413           viewport.getAlignment().deleteSequence(seq);\r
 414       else\r
 415           viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 416      }\r
 417 \r
 418      viewport.setSelectionGroup(null);\r
 419      viewport.alignment.deleteGroup(sg);\r
 420      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());\r
 421      if(viewport.getAlignment().getHeight()<1)\r
 422      try\r
 423      {\r
 424        this.setClosed(true);\r
 425      }catch(Exception ex){}\r
 426    viewport.updateConservation();\r
 427    viewport.updateConsensus();\r
 428      alignPanel.repaint();\r
 429 \r
 430   }\r
 431 \r
 432 \r
 433 \r
 434   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 435   {\r
 436      Object [] history = (Object[])redoList.remove(0);\r
 437      SequenceI[] seq = (SequenceI[]) history[1];\r
 438      viewport.setAlignment( new Alignment(seq) );\r
 439      viewport.alignment.setGapCharacter( Preferences.gapSymbol );\r
 440      updateEditMenuBar();\r
 441      viewport.updateConsensus();\r
 442      alignPanel.repaint();\r
 443      alignPanel.repaint();\r
 444   }\r
 445 \r
 446 \r
 447   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 448   {\r
 449     viewport.alignment.deleteAllGroups();\r
 450     viewport.setSelectionGroup(null);\r
 451     alignPanel.repaint();\r
 452   }\r
 453 \r
 454 \r
 455 \r
 456   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 457   {\r
 458     SequenceGroup sg = new SequenceGroup();\r
 459     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 460       sg.addSequence( viewport.getAlignment().getSequenceAt(i));\r
 461     sg.setEndRes(viewport.alignment.getWidth());\r
 462     viewport.setSelectionGroup(sg);\r
 463     PaintRefresher.Refresh(null);\r
 464   }\r
 465 \r
 466   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 467   {\r
 468     viewport.setSelectionGroup(null);\r
 469     viewport.getColumnSelection().clear();\r
 470     viewport.setSelectionGroup(null);\r
 471     PaintRefresher.Refresh(null);\r
 472   }\r
 473 \r
 474   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 475   {\r
 476     SequenceGroup sg = viewport.getSelectionGroup();\r
 477     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 478       sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));\r
 479 \r
 480     PaintRefresher.Refresh(null);\r
 481   }\r
 482 \r
 483   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 484   {\r
 485     addHistoryItem("delete columns");\r
 486     ColumnSelection colSel = viewport.getColumnSelection();\r
 487     if (colSel.size() > 0)\r
 488     {\r
 489       int min = colSel.getMin();\r
 490       viewport.getAlignment().trimLeft(min);\r
 491       colSel.compensateForEdit(0,min);\r
 492 \r
 493       if(viewport.getSelectionGroup()!=null)\r
 494         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 495 \r
 496       Vector groups = viewport.alignment.getGroups();\r
 497       for(int i=0; i<groups.size(); i++)\r
 498       {\r
 499         SequenceGroup sg = (SequenceGroup) groups.get(i);\r
 500         if(!sg.adjustForRemoveLeft(min))\r
 501           viewport.alignment.deleteGroup(sg);\r
 502       }\r
 503 \r
 504       alignPanel.repaint();\r
 505     }\r
 506   }\r
 507 \r
 508   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 509   {\r
 510     addHistoryItem("delete columns");\r
 511     ColumnSelection colSel = viewport.getColumnSelection();\r
 512     if (colSel.size() > 0)\r
 513     {\r
 514       int max = colSel.getMax();\r
 515       viewport.getAlignment().trimRight(max);\r
 516       if(viewport.getSelectionGroup()!=null)\r
 517         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 518 \r
 519       Vector groups = viewport.alignment.getGroups();\r
 520       for(int i=0; i<groups.size(); i++)\r
 521       {\r
 522         SequenceGroup sg = (SequenceGroup) groups.get(i);\r
 523         if(!sg.adjustForRemoveRight(max))\r
 524           viewport.alignment.deleteGroup(sg);\r
 525       }\r
 526 \r
 527 \r
 528 \r
 529       alignPanel.repaint();\r
 530     }\r
 531 \r
 532   }\r
 533 \r
 534   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 535   {\r
 536     addHistoryItem("delete gapped columns");\r
 537     viewport.getAlignment().removeGaps();\r
 538     viewport.updateConservation();\r
 539     viewport.updateConsensus();\r
 540     alignPanel.repaint();\r
 541   }\r
 542 \r
 543   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 544   {\r
 545     addHistoryItem("delete all gaps");\r
 546     SequenceI current;\r
 547     int jSize;\r
 548     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 549     {\r
 550       current = viewport.getAlignment().getSequenceAt(i);\r
 551       jSize = current.getLength();\r
 552       for (int j=0; j < jSize; j++)\r
 553         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 554         {\r
 555           current.deleteCharAt(j);\r
 556           j--;\r
 557           jSize--;\r
 558         }\r
 559     }\r
 560     viewport.updateConservation();\r
 561     viewport.updateConsensus();\r
 562     alignPanel.repaint();\r
 563   }\r
 564 \r
 565 \r
 566   public void findMenuItem_actionPerformed(ActionEvent e)\r
 567   {\r
 568     JInternalFrame frame = new JInternalFrame();\r
 569     Finder finder = new Finder(viewport, alignPanel, frame);\r
 570     frame.setContentPane(finder);\r
 571     Desktop.addInternalFrame(frame, "Find", 340,110);\r
 572     frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
 573 \r
 574   }\r
 575 \r
 576 \r
 577   public void font_actionPerformed(ActionEvent e)\r
 578   {\r
 579     FontChooser fc = new FontChooser( alignPanel );\r
 580   }\r
 581 \r
 582   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 583   {\r
 584     viewport.setShowFullId( fullSeqId.isSelected() );\r
 585 \r
 586     alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );\r
 587     alignPanel.repaint();\r
 588   }\r
 589 \r
 590   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 591   {\r
 592       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 593       alignPanel.repaint();\r
 594   }\r
 595 \r
 596   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 597   {\r
 598     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 599     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
 600     scaleAbove.setVisible( wrapMenuItem.isSelected() );\r
 601     scaleLeft.setVisible( wrapMenuItem.isSelected() );\r
 602     scaleRight.setVisible( wrapMenuItem.isSelected() );\r
 603     alignPanel.repaint();\r
 604   }\r
 605 \r
 606   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 607   {\r
 608     viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
 609     alignPanel.repaint();\r
 610   }\r
 611 \r
 612   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 613   {\r
 614     viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
 615     alignPanel.repaint();\r
 616   }\r
 617 \r
 618   protected void scaleRight_actionPerformed(ActionEvent e)\r
 619   {\r
 620     viewport.setScaleRightWrapped(scaleRight.isSelected());\r
 621     alignPanel.repaint();\r
 622   }\r
 623 \r
 624 \r
 625 \r
 626   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 627   {\r
 628     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 629     alignPanel.repaint();\r
 630   }\r
 631 \r
 632   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 633   {\r
 634     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 635     alignPanel.repaint();\r
 636   }\r
 637 \r
 638 \r
 639   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 640   {\r
 641     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 642     alignPanel.repaint();\r
 643   }\r
 644 \r
 645   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
 646   {\r
 647     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 648     if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
 649     {\r
 650          SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment, alignPanel);\r
 651          ((Alignment)viewport.alignment).featuresAdded = true;\r
 652     }\r
 653     alignPanel.repaint();\r
 654   }\r
 655 \r
 656   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 657   {\r
 658     if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())\r
 659     {\r
 660       annotationPanelMenuItem.setSelected(false);\r
 661       return;\r
 662     }\r
 663     viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );\r
 664     alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );\r
 665   }\r
 666 \r
 667   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 668   {\r
 669     if (alignPanel.overviewPanel != null)\r
 670       return;\r
 671 \r
 672     JInternalFrame frame = new JInternalFrame();\r
 673     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 674      frame.setContentPane(overview);\r
 675     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 676                              frame.getWidth(), frame.getHeight());\r
 677     frame.pack();\r
 678     frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
 679     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 680     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 681       {\r
 682             alignPanel.setOverviewPanel(null);\r
 683       };\r
 684     });\r
 685 \r
 686     alignPanel.setOverviewPanel( overview );\r
 687 \r
 688 \r
 689   }\r
 690 \r
 691   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 692   {\r
 693     changeColour( null );\r
 694   }\r
 695 \r
 696 \r
 697   public void clustalColour_actionPerformed(ActionEvent e)\r
 698   {\r
 699     abovePIDThreshold.setSelected(false);\r
 700     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 701   }\r
 702 \r
 703   public void zappoColour_actionPerformed(ActionEvent e)\r
 704   {\r
 705     changeColour(new ZappoColourScheme());\r
 706   }\r
 707 \r
 708   public void taylorColour_actionPerformed(ActionEvent e)\r
 709   {\r
 710     changeColour(new TaylorColourScheme());\r
 711   }\r
 712 \r
 713 \r
 714   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 715   {\r
 716     changeColour( new HydrophobicColourScheme() );\r
 717   }\r
 718 \r
 719   public void helixColour_actionPerformed(ActionEvent e)\r
 720   {\r
 721     changeColour(new HelixColourScheme() );\r
 722   }\r
 723 \r
 724 \r
 725   public void strandColour_actionPerformed(ActionEvent e)\r
 726   {\r
 727     changeColour(new StrandColourScheme());\r
 728   }\r
 729 \r
 730 \r
 731   public void turnColour_actionPerformed(ActionEvent e)\r
 732   {\r
 733     changeColour(new TurnColourScheme());\r
 734   }\r
 735 \r
 736 \r
 737   public void buriedColour_actionPerformed(ActionEvent e)\r
 738   {\r
 739     changeColour(new BuriedColourScheme() );\r
 740   }\r
 741 \r
 742   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 743   {\r
 744     changeColour(new NucleotideColourScheme());\r
 745   }\r
 746 \r
 747 \r
 748   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 749   {\r
 750     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
 751   }\r
 752 \r
 753 \r
 754 \r
 755   void changeColour(ColourSchemeI cs)\r
 756   {\r
 757     int threshold = 0;\r
 758 \r
 759     if ( viewport.getAbovePIDThreshold() )\r
 760     {\r
 761       threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
 762 \r
 763       if (cs instanceof ResidueColourScheme)\r
 764         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 765       else if (cs instanceof ScoreColourScheme)\r
 766         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 767 \r
 768       viewport.setGlobalColourScheme(cs);\r
 769     }\r
 770     else if (cs instanceof ResidueColourScheme)\r
 771       ( (ResidueColourScheme) cs).setThreshold(0);\r
 772     else if (cs instanceof ScoreColourScheme)\r
 773       ( (ScoreColourScheme) cs).setThreshold(0);\r
 774 \r
 775 \r
 776 \r
 777     if (viewport.getConservationSelected())\r
 778     {\r
 779       ConservationColourScheme ccs = null;\r
 780 \r
 781       Alignment al = (Alignment) viewport.alignment;\r
 782       Conservation c = new Conservation("All",\r
 783                                         ResidueProperties.propHash, 3,\r
 784                                         al.getSequences(), 0,\r
 785                                         al.getWidth() - 1);\r
 786 \r
 787       c.calculate();\r
 788       c.verdict(false, viewport.ConsPercGaps);\r
 789 \r
 790       ccs = new ConservationColourScheme(c, cs);\r
 791 \r
 792       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 793       ccs.setConsensus( viewport.vconsensus );\r
 794       viewport.setGlobalColourScheme(ccs);\r
 795 \r
 796       SliderPanel.setConservationSlider(alignPanel, ccs, "Background");\r
 797 \r
 798     }\r
 799     else\r
 800     {\r
 801         // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 802         if (cs != null)\r
 803           cs.setConsensus(viewport.vconsensus);\r
 804         viewport.setGlobalColourScheme(cs);\r
 805     }\r
 806 \r
 807 \r
 808     if(viewport.getColourAppliesToAllGroups())\r
 809     {\r
 810       Vector groups = viewport.alignment.getGroups();\r
 811       for(int i=0; i<groups.size(); i++)\r
 812       {\r
 813         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 814 \r
 815         if (cs instanceof ClustalxColourScheme)\r
 816         {\r
 817           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
 818         }\r
 819         else if(cs!=null)\r
 820         {\r
 821           try{\r
 822             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
 823           }catch(Exception ex){ex.printStackTrace();}\r
 824         }\r
 825 \r
 826         if(viewport.getAbovePIDThreshold())\r
 827         {\r
 828           if (sg.cs instanceof ResidueColourScheme)\r
 829             ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
 830           else if (sg.cs instanceof ScoreColourScheme)\r
 831             ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
 832 \r
 833            sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );\r
 834         }\r
 835 \r
 836         if( viewport.getConservationSelected() )\r
 837         {\r
 838           Conservation c = new Conservation("Group",\r
 839                                             ResidueProperties.propHash, 3,\r
 840                                             sg.sequences, 0, viewport.alignment.getWidth()-1);\r
 841           c.calculate();\r
 842           c.verdict(false, viewport.ConsPercGaps);\r
 843           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 844 \r
 845           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 846           ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 847           sg.cs = ccs;\r
 848         }\r
 849         else if(cs!=null)\r
 850         {\r
 851           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 852           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 853         }\r
 854 \r
 855       }\r
 856     }\r
 857 \r
 858     if(alignPanel.getOverviewPanel()!=null)\r
 859       alignPanel.getOverviewPanel().updateOverviewImage();\r
 860     alignPanel.repaint();\r
 861   }\r
 862 \r
 863   protected void modifyPID_actionPerformed(ActionEvent e)\r
 864   {\r
 865       if(viewport.getAbovePIDThreshold())\r
 866       {\r
 867         SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
 868                                    "Background");\r
 869         SliderPanel.showPIDSlider();\r
 870       }\r
 871   }\r
 872 \r
 873   protected void modifyConservation_actionPerformed(ActionEvent e)\r
 874   {\r
 875     if(viewport.getConservationSelected())\r
 876     {\r
 877       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
 878                                         "Background");\r
 879       SliderPanel.showConservationSlider();\r
 880     }\r
 881   }\r
 882 \r
 883 \r
 884   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 885   {\r
 886     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 887 \r
 888     viewport.setAbovePIDThreshold(false);\r
 889     abovePIDThreshold.setSelected(false);\r
 890 \r
 891    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 892    if(cs instanceof ConservationColourScheme )\r
 893      changeColour( ((ConservationColourScheme)cs).cs );\r
 894     else\r
 895       changeColour( cs );\r
 896 \r
 897     modifyConservation_actionPerformed(null);\r
 898   }\r
 899 \r
 900   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 901   {\r
 902     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
 903 \r
 904     conservationMenuItem.setSelected(false);\r
 905     viewport.setConservationSelected(false);\r
 906 \r
 907     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 908 \r
 909     if(cs instanceof ConservationColourScheme )\r
 910         changeColour( ((ConservationColourScheme)cs).cs );\r
 911     else\r
 912         changeColour( cs );\r
 913 \r
 914     modifyPID_actionPerformed(null);\r
 915   }\r
 916 \r
 917 \r
 918 \r
 919   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 920   {\r
 921     UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);\r
 922   }\r
 923 \r
 924   public void PIDColour_actionPerformed(ActionEvent e)\r
 925   {\r
 926     changeColour( new PIDColourScheme() );\r
 927   }\r
 928 \r
 929 \r
 930   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 931   {\r
 932     changeColour(new Blosum62ColourScheme() );\r
 933   }\r
 934 \r
 935 \r
 936 \r
 937   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 938   {\r
 939     addHistoryItem("sort");\r
 940     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 941     alignPanel.repaint();\r
 942   }\r
 943 \r
 944   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 945   {\r
 946     addHistoryItem("sort");\r
 947     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 948     alignPanel.repaint();\r
 949   }\r
 950 \r
 951   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 952   {\r
 953     addHistoryItem("sort");\r
 954     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 955     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 956     alignPanel.repaint();\r
 957   }\r
 958 \r
 959   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 960   {\r
 961     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 962     JInternalFrame frame = new JInternalFrame();\r
 963     frame.setContentPane(sp);\r
 964     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);\r
 965 \r
 966   }\r
 967 \r
 968   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 969   {\r
 970     if(viewport.getSelectionGroup().getSize()<2)\r
 971       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 972     else\r
 973     {\r
 974       JInternalFrame frame = new JInternalFrame();\r
 975       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 976       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 977     }\r
 978   }\r
 979 \r
 980   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 981   {\r
 982 \r
 983     if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
 984        || viewport.getAlignment().getHeight()<4)\r
 985     {\r
 986       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
 987                                     +"at least 4 input sequences.",\r
 988                                     "Sequence selection insufficient",\r
 989                                     JOptionPane.WARNING_MESSAGE);\r
 990       return;\r
 991     }\r
 992 \r
 993     try{\r
 994       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 995       JInternalFrame frame = new JInternalFrame();\r
 996       frame.setContentPane(pcaPanel);\r
 997       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 998    }catch(java.lang.OutOfMemoryError ex)\r
 999    {\r
1000      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
1001                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
1002    }\r
1003 \r
1004 \r
1005   }\r
1006 \r
1007   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1008   {\r
1009     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1010   }\r
1011 \r
1012   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1013   {\r
1014     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1015   }\r
1016 \r
1017 \r
1018   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1019   {\r
1020     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1021   }\r
1022 \r
1023   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1024   {\r
1025     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1026   }\r
1027 \r
1028   void NewTreePanel(String type, String pwType, String title)\r
1029   {\r
1030     //are the sequences aligned?\r
1031     if(!viewport.alignment.isAligned())\r
1032     {\r
1033       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
1034                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
1035       return;\r
1036     }\r
1037 \r
1038     final TreePanel tp;\r
1039     if (viewport.getSelectionGroup() != null &&\r
1040         viewport.getSelectionGroup().getSize() > 3)\r
1041     {\r
1042       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
1043                          pwType,\r
1044                          0, viewport.alignment.getWidth());\r
1045     }\r
1046     else\r
1047     {\r
1048       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1049                          type, pwType, 0, viewport.alignment.getWidth());\r
1050     }\r
1051 \r
1052    addTreeMenuItem(tp, title);\r
1053 \r
1054    Desktop.addInternalFrame(tp, title, 600, 500);\r
1055   }\r
1056 \r
1057   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1058   {\r
1059     final JMenuItem item = new JMenuItem(title);\r
1060     sortByTreeMenu.add(item);\r
1061     item.addActionListener(new java.awt.event.ActionListener()\r
1062     {\r
1063       public void actionPerformed(ActionEvent e)\r
1064       {\r
1065         addHistoryItem("sort");\r
1066         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1067         alignPanel.repaint();\r
1068       }\r
1069     });\r
1070 \r
1071     treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
1072     {\r
1073       public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
1074       {\r
1075         sortByTreeMenu.remove(item);\r
1076       };\r
1077     });\r
1078 \r
1079   }\r
1080 \r
1081 \r
1082   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
1083   {\r
1084      WebserviceInfo info = new WebserviceInfo("Clustal web service",\r
1085      "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"+\r
1086      " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."\r
1087     +" Nucleic Acids Research, submitted, June 1994.",\r
1088      450, 150);\r
1089 \r
1090     ClustalThread thread = new ClustalThread(info);\r
1091     thread.start();\r
1092   }\r
1093 \r
1094     class ClustalThread extends Thread\r
1095     {\r
1096       WebserviceInfo info;\r
1097       public ClustalThread(WebserviceInfo info)\r
1098       {this.info = info; }\r
1099 \r
1100       public void run()\r
1101       {\r
1102         info.setStatus(WebserviceInfo.STATE_RUNNING);\r
1103         jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
1104         Vector sv = viewport.getAlignment().getSequences();\r
1105         SequenceI[] seqs = new SequenceI[sv.size()];\r
1106 \r
1107         int i = 0;\r
1108         do\r
1109         {\r
1110           seqs[i] = (SequenceI) sv.elementAt(i);\r
1111         }\r
1112         while (++i < sv.size());\r
1113 \r
1114         SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
1115         if (alignment != null)\r
1116         {\r
1117           AlignFrame af = new AlignFrame(new Alignment(alignment));\r
1118           Desktop.addInternalFrame(af, title.concat(" - ClustalW Alignment"),\r
1119                                    NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
1120           af.clustalColour_actionPerformed(null);\r
1121           af.clustalColour.setSelected(true);\r
1122           info.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
1123         }\r
1124         else\r
1125         {\r
1126             info.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
1127             info.appendProgressText("Problem obtaining clustal alignment");\r
1128         }\r
1129       }\r
1130     }\r
1131 \r
1132   protected void jpred_actionPerformed(ActionEvent e)\r
1133 {\r
1134 \r
1135     if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)\r
1136     {\r
1137       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1138       SequenceGroup seqs = viewport.getSelectionGroup();\r
1139       if (seqs.getSize() == 1 || !viewport.alignment.isAligned())\r
1140       {\r
1141         JPredClient ct = new JPredClient( (SequenceI)seqs.getSequenceAt(0));\r
1142       }\r
1143       else\r
1144       {\r
1145         int sz;\r
1146         SequenceI[] msa = new SequenceI[sz=seqs.getSize()];\r
1147         for (int i = 0; i < sz; i++)\r
1148         {\r
1149           msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1150         }\r
1151 \r
1152         JPredClient ct = new JPredClient(msa);\r
1153       }\r
1154 \r
1155     }\r
1156     else\r
1157     {\r
1158       Vector seqs = viewport.getAlignment().getSequences();\r
1159 \r
1160       if (seqs.size() == 1 || !viewport.alignment.isAligned())\r
1161       {\r
1162         JPredClient ct = new JPredClient( (SequenceI)\r
1163                                          seqs.elementAt(0));\r
1164       }\r
1165       else\r
1166       {\r
1167         SequenceI[] msa = new SequenceI[seqs.size()];\r
1168         for (int i = 0; i < seqs.size(); i++)\r
1169         {\r
1170           msa[i] = (SequenceI) seqs.elementAt(i);\r
1171         }\r
1172 \r
1173         JPredClient ct = new JPredClient(msa);\r
1174       }\r
1175 \r
1176     }\r
1177   }\r
1178   protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
1179   {\r
1180     // TODO:resolve which menu item was actually selected\r
1181     // Now, check we have enough sequences\r
1182       if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)\r
1183       {\r
1184         // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1185         SequenceGroup seqs = viewport.getSelectionGroup();\r
1186         int sz;\r
1187         SequenceI[] msa = new SequenceI[sz=seqs.getSize()];\r
1188         for (int i = 0; i < sz; i++)\r
1189         {\r
1190           msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1191         }\r
1192 \r
1193         MsaWSClient ct = new jalview.ws.MsaWSClient(msa);\r
1194       }\r
1195       else\r
1196       {\r
1197         Vector seqs = viewport.getAlignment().getSequences();\r
1198 \r
1199         if (seqs.size() > 1) {\r
1200           SequenceI[] msa = new SequenceI[seqs.size()];\r
1201           for (int i = 0; i < seqs.size(); i++)\r
1202           {\r
1203             msa[i] = (SequenceI) seqs.elementAt(i);\r
1204           }\r
1205 \r
1206           MsaWSClient ct = new MsaWSClient(msa);\r
1207         }\r
1208 \r
1209       }\r
1210     }\r
1211 \r
1212     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
1213     // Pick the tree file\r
1214     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
1215         getProperty("LAST_DIRECTORY"));\r
1216     chooser.setFileView(new JalviewFileView());\r
1217     chooser.setDialogTitle("Select a newick-like tree file");\r
1218     chooser.setToolTipText("Load a tree file");\r
1219     int value = chooser.showOpenDialog(null);\r
1220     if (value == JalviewFileChooser.APPROVE_OPTION)\r
1221     {\r
1222       String choice = chooser.getSelectedFile().getPath();\r
1223       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1224       try\r
1225       {\r
1226         jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");\r
1227         ShowNewickTree(fin, choice);\r
1228       }\r
1229       catch (Exception ex)\r
1230       {\r
1231         JOptionPane.showMessageDialog(Desktop.desktop,\r
1232                                       "Problem reading tree file",\r
1233                                       ex.getMessage(),\r
1234                                       JOptionPane.WARNING_MESSAGE);\r
1235         ex.printStackTrace();\r
1236       }\r
1237     }\r
1238   }\r
1239 \r
1240   public void ShowNewickTree(NewickFile nf, String title)\r
1241   {\r
1242     try{\r
1243       nf.parse();\r
1244       if (nf.getTree() != null)\r
1245       {\r
1246         TreePanel tp = new TreePanel(viewport,\r
1247                                      viewport.getAlignment().getSequences(),\r
1248                                      nf, "FromFile", title);\r
1249         Desktop.addInternalFrame(tp, title, 600, 500);\r
1250         addTreeMenuItem(tp, title);\r
1251         viewport.setCurrentTree(tp.getTree());\r
1252       }\r
1253      }catch(Exception ex){ex.printStackTrace();}\r
1254   }\r
1255 \r
1256 \r
1257 }\r