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     super();\r
  36     viewport = new AlignViewport(al,true,true,false);\r
  37 \r
  38     String fontName = jalview.bin.Cache.getProperty("FONT_NAME");\r
  39     String fontStyle= jalview.bin.Cache.getProperty("FONT_STYLE");\r
  40     String fontSize = jalview.bin.Cache.getProperty("FONT_SIZE");\r
  41     if(fontName!=null && fontStyle!=null && fontSize!=null)\r
  42       viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );\r
  43 \r
  44 \r
  45 \r
  46     alignPanel = new AlignmentPanel(this, viewport);\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   protected void saveAs_actionPerformed(ActionEvent e)\r
  65   {\r
  66     String suffix = "";\r
  67     if(e.getActionCommand().equals("FASTA"))\r
  68       suffix = "fa";\r
  69     else if(e.getActionCommand().equals("MSF"))\r
  70       suffix = "msf";\r
  71     else if(e.getActionCommand().equals("CLUSTAL"))\r
  72       suffix = "aln";\r
  73     else if(e.getActionCommand().equals("BLC"))\r
  74       suffix = "blc";\r
  75     else if(e.getActionCommand().equals("PIR"))\r
  76       suffix = "pir";\r
  77     else if(e.getActionCommand().equals("PFAM"))\r
  78       suffix = "pfam";\r
  79 \r
  80     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")\r
  81         , new String[]{suffix}, e.getActionCommand()+" file");\r
  82     chooser.setFileView(new JalviewFileView());\r
  83     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
  84     chooser.setToolTipText("Save");\r
  85     int value = chooser.showSaveDialog(this);\r
  86     if(value == JalviewFileChooser.APPROVE_OPTION)\r
  87     {\r
  88       String choice =  chooser.getSelectedFile().getPath();\r
  89       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
  90       String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
  91       try{\r
  92         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
  93         out.println(output);\r
  94         out.close();\r
  95       }\r
  96       catch(Exception ex){}\r
  97     }\r
  98 \r
  99   }\r
 100 \r
 101   protected void outputText_actionPerformed(ActionEvent e)\r
 102   {\r
 103      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
 104      JInternalFrame frame = new JInternalFrame();\r
 105      cap.formatForOutput();\r
 106      frame.setContentPane(cap);\r
 107      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
 108      cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
 109   }\r
 110 \r
 111   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 112   {\r
 113     HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
 114     htmlOutput = null;\r
 115   }\r
 116 \r
 117   protected void createPNG_actionPerformed(ActionEvent e)\r
 118   {\r
 119     alignPanel.makePNG();\r
 120   }\r
 121 \r
 122   protected void epsFile_actionPerformed(ActionEvent e)\r
 123   {\r
 124     alignPanel.makeEPS();\r
 125   }\r
 126 \r
 127 \r
 128   public void printMenuItem_actionPerformed(ActionEvent e)\r
 129   {\r
 130     //Putting in a thread avoids Swing painting problems\r
 131     PrintThread thread = new PrintThread();\r
 132     thread.start();\r
 133   }\r
 134 \r
 135   class PrintThread extends Thread\r
 136   {\r
 137     public void run()\r
 138     {\r
 139       PrinterJob printJob = PrinterJob.getPrinterJob();\r
 140       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
 141       printJob.setPrintable(alignPanel, pf);\r
 142       if (printJob.printDialog())\r
 143       {\r
 144         try\r
 145         {\r
 146           printJob.print();\r
 147         }\r
 148         catch (Exception PrintException)\r
 149         {\r
 150           PrintException.printStackTrace();\r
 151         }\r
 152       }\r
 153     }\r
 154 \r
 155   }\r
 156 \r
 157 \r
 158 \r
 159 \r
 160   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 161   {\r
 162     try{\r
 163       this.setClosed(true);\r
 164     }catch(Exception ex){}\r
 165   }\r
 166 \r
 167   Stack historyList = new Stack();\r
 168   Stack redoList = new Stack();\r
 169   JMenuBar jMenuBar1 = new JMenuBar();\r
 170 \r
 171   void updateEditMenuBar()\r
 172   {\r
 173     if(historyList.size()>0)\r
 174      {\r
 175        undoMenuItem.setEnabled(true);\r
 176        Object [] history = (Object[])historyList.get(0);\r
 177        undoMenuItem.setText("Undo "+history[0]);\r
 178      }\r
 179     else\r
 180     {\r
 181       undoMenuItem.setEnabled(false);\r
 182       undoMenuItem.setText("Undo");\r
 183     }\r
 184 \r
 185     if(redoList.size()>0)\r
 186      {\r
 187        redoMenuItem.setEnabled(true);\r
 188        Object [] history = (Object[])redoList.get(0);\r
 189        redoMenuItem.setText("Redo "+history[0]);\r
 190      }\r
 191     else\r
 192     {\r
 193       redoMenuItem.setEnabled(false);\r
 194       redoMenuItem.setText("Redo");\r
 195     }\r
 196   }\r
 197 \r
 198   public void addHistoryItem(String type)\r
 199   {\r
 200     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 201     redoList.clear();\r
 202     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 203     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 204     {\r
 205       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 206                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 207     }\r
 208 \r
 209     historyList.add(0, new Object[]{type,  seq} );\r
 210     updateEditMenuBar();\r
 211   }\r
 212 \r
 213   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 214   {\r
 215     Object [] history = (Object[])historyList.remove(0);\r
 216     // add the redo state before continuing!!\r
 217     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 218     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
 219     {\r
 220       seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
 221                             viewport.getAlignment().getSequenceAt(i).\r
 222                             getSequence());\r
 223     }\r
 224     /////////\r
 225 \r
 226     redoList.add(0, new Object[] {history[0], seq});\r
 227 \r
 228       seq = (SequenceI[]) history[1];\r
 229       viewport.setAlignment( new Alignment(seq) );\r
 230       updateEditMenuBar();\r
 231       alignPanel.RefreshPanels();\r
 232   }\r
 233 \r
 234   public void moveSelectedSequences(boolean up)\r
 235   {\r
 236     SequenceGroup sg = viewport.getSelectionGroup();\r
 237     if (sg == null)\r
 238       return;\r
 239 \r
 240     if (up)\r
 241     {\r
 242       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 243       {\r
 244         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 245         if (!sg.sequences.contains(seq))\r
 246           continue;\r
 247 \r
 248         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 249         if (sg.sequences.contains(temp))\r
 250           continue;\r
 251 \r
 252         viewport.alignment.getSequences().setElementAt(temp, i);\r
 253         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 254       }\r
 255     }\r
 256     else\r
 257     {\r
 258       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 259       {\r
 260         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 261         if (!sg.sequences.contains(seq))\r
 262           continue;\r
 263 \r
 264         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 265         if (sg.sequences.contains(temp))\r
 266           continue;\r
 267 \r
 268         viewport.alignment.getSequences().setElementAt(temp, i);\r
 269         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 270       }\r
 271     }\r
 272 \r
 273     alignPanel.RefreshPanels();\r
 274   }\r
 275 \r
 276 \r
 277 \r
 278   protected void copy_actionPerformed(ActionEvent e)\r
 279   {\r
 280    if(viewport.getSelectionGroup()==null)\r
 281      return;\r
 282 \r
 283    SequenceGroup sg = viewport.getSelectionGroup();\r
 284 \r
 285      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 286      StringBuffer buffer= new StringBuffer();\r
 287 \r
 288        for(int i=0; i<sg.getSize(); i++)\r
 289        {\r
 290          SequenceI seq = sg.getSequenceAt(i);\r
 291          buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
 292                         +seq.findPosition( sg.getEndRes() )+ "\t"\r
 293                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
 294        }\r
 295      c.setContents( new StringSelection( buffer.toString()) , null ) ;\r
 296 \r
 297   }\r
 298 \r
 299 \r
 300   protected void pasteNew_actionPerformed(ActionEvent e)\r
 301   {\r
 302     paste(true);\r
 303   }\r
 304 \r
 305   protected void pasteThis_actionPerformed(ActionEvent e)\r
 306   {\r
 307     addHistoryItem("Paste");\r
 308     paste(false);\r
 309   }\r
 310 \r
 311   void paste(boolean newAlignment)\r
 312   {\r
 313     try{\r
 314       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 315       Transferable contents = c.getContents(this);\r
 316       if (contents == null)\r
 317         return;\r
 318 \r
 319       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
 320       StringTokenizer st = new StringTokenizer(str);\r
 321       ArrayList seqs = new ArrayList();\r
 322       while (st.hasMoreElements())\r
 323       {\r
 324         String name = st.nextToken();\r
 325         int start = Integer.parseInt(st.nextToken());\r
 326         int end = Integer.parseInt(st.nextToken());\r
 327         Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
 328 \r
 329         if(!newAlignment)\r
 330           viewport.alignment.addSequence(sequence);\r
 331         else\r
 332           seqs.add(sequence);\r
 333       }\r
 334 \r
 335       if(newAlignment)\r
 336       {\r
 337         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 338         seqs.toArray(newSeqs);\r
 339         AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
 340         int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;\r
 341         if (newHeight > 500)\r
 342           newHeight = 500;\r
 343         Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
 344       }\r
 345       else\r
 346       {\r
 347         viewport.setEndSeq(viewport.alignment.getHeight());\r
 348         viewport.alignment.getWidth();\r
 349         alignPanel.RefreshPanels();\r
 350       }\r
 351 \r
 352     }catch(Exception ex){}// could be anything being pasted in here\r
 353 \r
 354   }\r
 355 \r
 356 \r
 357   protected void cut_actionPerformed(ActionEvent e)\r
 358   {\r
 359     copy_actionPerformed(null);\r
 360     delete_actionPerformed(null);\r
 361   }\r
 362 \r
 363   protected void delete_actionPerformed(ActionEvent e)\r
 364   {\r
 365     addHistoryItem("Delete");\r
 366     if (viewport.getSelectionGroup() == null)\r
 367       return;\r
 368 \r
 369      SequenceGroup sg = viewport.getSelectionGroup();\r
 370      for (int i=0;i < sg.sequences.size(); i++)\r
 371      {\r
 372        SequenceI seq = sg.getSequenceAt(i);\r
 373        int index = viewport.getAlignment().findIndex(seq);\r
 374        seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);\r
 375 \r
 376        if(seq.getSequence().length()<1)\r
 377           viewport.getAlignment().deleteSequence(seq);\r
 378       else\r
 379           viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 380      }\r
 381 \r
 382      viewport.setSelectionGroup(null);\r
 383      viewport.alignment.deleteGroup(sg);\r
 384      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());\r
 385      if(viewport.getAlignment().getHeight()<1)\r
 386      try\r
 387      {\r
 388        this.setClosed(true);\r
 389      }catch(Exception ex){}\r
 390      alignPanel.RefreshPanels();\r
 391 \r
 392   }\r
 393 \r
 394 \r
 395 \r
 396   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 397   {\r
 398      Object [] history = (Object[])redoList.remove(0);\r
 399      SequenceI[] seq = (SequenceI[]) history[1];\r
 400      viewport.setAlignment( new Alignment(seq) );\r
 401      updateEditMenuBar();\r
 402      alignPanel.RefreshPanels();\r
 403   }\r
 404 \r
 405 \r
 406   public void groupsMenuItem_actionPerformed(ActionEvent e)\r
 407   {\r
 408     GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
 409     JInternalFrame frame = new JInternalFrame();\r
 410     frame.setContentPane(geditor);\r
 411     Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
 412     frame.setResizable(false);\r
 413   }\r
 414 \r
 415   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 416   {\r
 417     viewport.alignment.deleteAllGroups();\r
 418     viewport.setSelectionGroup(null);\r
 419 \r
 420     alignPanel.RefreshPanels();\r
 421   }\r
 422 \r
 423 \r
 424 \r
 425   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 426   {\r
 427     SequenceGroup sg = new SequenceGroup();\r
 428     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 429       sg.addSequence( viewport.getAlignment().getSequenceAt(i));\r
 430     sg.setEndRes(viewport.alignment.getWidth());\r
 431     viewport.setSelectionGroup(sg);\r
 432     PaintRefresher.Refresh(null);\r
 433   }\r
 434 \r
 435   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 436   {\r
 437     viewport.setSelectionGroup(null);\r
 438     PaintRefresher.Refresh(null);\r
 439   }\r
 440 \r
 441   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 442   {\r
 443     SequenceGroup sg = viewport.getSelectionGroup();\r
 444     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 445       sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));\r
 446 \r
 447     PaintRefresher.Refresh(null);\r
 448   }\r
 449 \r
 450 \r
 451   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 452   {\r
 453     viewport.getColumnSelection().clear();\r
 454     repaint();\r
 455   }\r
 456 \r
 457   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 458   {\r
 459     addHistoryItem("delete columns");\r
 460     ColumnSelection colSel = viewport.getColumnSelection();\r
 461     if (colSel.size() > 0)\r
 462     {\r
 463       int min = colSel.getMin();\r
 464       viewport.getAlignment().trimLeft(min);\r
 465       colSel.compensateForEdit(0,min);\r
 466       alignPanel.RefreshPanels();\r
 467     }\r
 468   }\r
 469 \r
 470   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 471   {\r
 472     addHistoryItem("delete columns");\r
 473     ColumnSelection colSel = viewport.getColumnSelection();\r
 474     if (colSel.size() > 0)\r
 475     {\r
 476       int max = colSel.getMax();\r
 477       if(max>1)\r
 478         viewport.getAlignment().trimRight(max);\r
 479 \r
 480       alignPanel.RefreshPanels();\r
 481     }\r
 482 \r
 483   }\r
 484 \r
 485   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 486   {\r
 487     addHistoryItem("delete gapped columns");\r
 488     viewport.getAlignment().removeGaps();\r
 489     alignPanel.RefreshPanels();\r
 490   }\r
 491 \r
 492   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 493   {\r
 494     addHistoryItem("delete all gaps");\r
 495     SequenceI current;\r
 496     int jSize;\r
 497     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 498     {\r
 499       current = viewport.getAlignment().getSequenceAt(i);\r
 500       jSize = current.getLength();\r
 501       for (int j=0; j < jSize; j++)\r
 502         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 503         {\r
 504           current.deleteCharAt(j);\r
 505           j--;\r
 506           jSize--;\r
 507         }\r
 508     }\r
 509 \r
 510     alignPanel.RefreshPanels();\r
 511   }\r
 512 \r
 513   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 514   {\r
 515     char thisChar = '-';\r
 516     char nextChar = '.';\r
 517     if(viewport.getGapCharacter()=='-')\r
 518     {\r
 519       thisChar = '.';\r
 520       nextChar = '-';\r
 521     }\r
 522     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 523     viewport.setGapCharacter(thisChar);\r
 524     alignPanel.RefreshPanels();\r
 525   }\r
 526 \r
 527   public void findMenuItem_actionPerformed(ActionEvent e)\r
 528   {\r
 529       JInternalFrame frame = new JInternalFrame();\r
 530       Finder finder = new Finder(viewport, alignPanel, frame);\r
 531       frame.setContentPane(finder);\r
 532      Desktop.addInternalFrame(frame, "Find", 340,110);\r
 533 \r
 534   }\r
 535 \r
 536 \r
 537   public void font_actionPerformed(ActionEvent e)\r
 538   {\r
 539    // JOptionPane op = new JOptionPane();\r
 540     JInternalFrame frame = new JInternalFrame();\r
 541     FontChooser fc = new FontChooser( alignPanel, frame );\r
 542     frame.setContentPane(fc);\r
 543     Desktop.addInternalFrame(frame, "Change Font", 480,100);\r
 544   }\r
 545 \r
 546   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 547   {\r
 548     viewport.setShowFullId( fullSeqId.isSelected() );\r
 549 \r
 550     alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );\r
 551     alignPanel.RefreshPanels();\r
 552   }\r
 553 \r
 554   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 555   {\r
 556       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 557       alignPanel.RefreshPanels();\r
 558   }\r
 559 \r
 560   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 561   {\r
 562     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 563     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
 564   }\r
 565 \r
 566 \r
 567   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 568   {\r
 569     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 570     alignPanel.RefreshPanels();\r
 571   }\r
 572 \r
 573   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 574   {\r
 575     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 576     alignPanel.RefreshPanels();\r
 577   }\r
 578 \r
 579 \r
 580   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 581   {\r
 582     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 583     alignPanel.RefreshPanels();\r
 584   }\r
 585 \r
 586   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
 587   {\r
 588     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 589     if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
 590     {\r
 591          AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);\r
 592          ((Alignment)viewport.alignment).featuresAdded = true;\r
 593     }\r
 594     alignPanel.RefreshPanels();\r
 595   }\r
 596 \r
 597   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 598   {\r
 599     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
 600   }\r
 601 \r
 602   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 603   {\r
 604     if (alignPanel.overviewPanel != null)\r
 605       return;\r
 606 \r
 607     JInternalFrame frame = new JInternalFrame();\r
 608     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 609    try{\r
 610      overview = new OverviewPanel(alignPanel, viewport);\r
 611      frame.setContentPane(overview);\r
 612     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 613                              frame.getWidth(), frame.getHeight());\r
 614     frame.pack();\r
 615     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 616     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 617       {\r
 618             alignPanel.setOverviewPanel(null);\r
 619       };\r
 620     });\r
 621     alignPanel.setOverviewPanel( overview );\r
 622 \r
 623   }catch(java.lang.OutOfMemoryError ex)\r
 624    {\r
 625      JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 626                                    +"\nTry reducing the font size.",\r
 627                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 628    }\r
 629 \r
 630 \r
 631   }\r
 632 \r
 633   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 634   {\r
 635     changeColour( null );\r
 636   }\r
 637 \r
 638 \r
 639   public void clustalColour_actionPerformed(ActionEvent e)\r
 640   {\r
 641     abovePIDThreshold.setSelected(false);\r
 642     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 643   }\r
 644 \r
 645   public void zappoColour_actionPerformed(ActionEvent e)\r
 646   {\r
 647     changeColour(new ZappoColourScheme());\r
 648   }\r
 649 \r
 650   public void taylorColour_actionPerformed(ActionEvent e)\r
 651   {\r
 652     changeColour(new TaylorColourScheme());\r
 653   }\r
 654 \r
 655 \r
 656   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 657   {\r
 658     changeColour( new HydrophobicColourScheme() );\r
 659   }\r
 660 \r
 661   public void helixColour_actionPerformed(ActionEvent e)\r
 662   {\r
 663     changeColour(new HelixColourScheme() );\r
 664   }\r
 665 \r
 666 \r
 667   public void strandColour_actionPerformed(ActionEvent e)\r
 668   {\r
 669     changeColour(new StrandColourScheme());\r
 670   }\r
 671 \r
 672 \r
 673   public void turnColour_actionPerformed(ActionEvent e)\r
 674   {\r
 675     changeColour(new TurnColourScheme());\r
 676   }\r
 677 \r
 678 \r
 679   public void buriedColour_actionPerformed(ActionEvent e)\r
 680   {\r
 681     changeColour(new BuriedColourScheme() );\r
 682   }\r
 683 \r
 684   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 685   {\r
 686     changeColour(new NucleotideColourScheme());\r
 687   }\r
 688 \r
 689 \r
 690   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 691   {\r
 692     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
 693   }\r
 694 \r
 695 \r
 696 \r
 697   void changeColour(ColourSchemeI cs)\r
 698   {\r
 699 \r
 700     if(viewport.getColourAppliesToAllGroups())\r
 701     {\r
 702       Vector groups = viewport.alignment.getGroups();\r
 703       for(int i=0; i<groups.size(); i++)\r
 704       {\r
 705         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 706         sg.cs = cs;\r
 707 \r
 708         if(abovePIDThreshold.isSelected())\r
 709           abovePIDThreshold_actionPerformed(null);\r
 710         else if( viewport.getConservationSelected() )\r
 711         {\r
 712           Conservation c = new Conservation("Group",\r
 713                                             ResidueProperties.propHash, 3,\r
 714                                             sg.sequences, sg.getStartRes(),\r
 715                                             sg.getEndRes());\r
 716           c.calculate();\r
 717           c.verdict(false, 100);\r
 718           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 719 \r
 720           sg.cs = ccs;\r
 721         }\r
 722 \r
 723       }\r
 724     }\r
 725 \r
 726 \r
 727     if ( viewport.getAbovePIDThreshold())\r
 728     {\r
 729       int threshold = 0;\r
 730       threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");\r
 731       Desktop.hideConservationSlider();\r
 732 \r
 733       if (cs instanceof ResidueColourScheme)\r
 734         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 735       else if (cs instanceof ScoreColourScheme)\r
 736         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 737 \r
 738       viewport.setGlobalColourScheme(cs);\r
 739 \r
 740     }\r
 741     else\r
 742     if (cs instanceof ResidueColourScheme)\r
 743       ( (ResidueColourScheme) cs).setThreshold(0);\r
 744     else if (cs instanceof ScoreColourScheme)\r
 745       ( (ScoreColourScheme) cs).setThreshold(0);\r
 746 \r
 747 \r
 748 \r
 749 \r
 750 if ( viewport.getConservationSelected() )\r
 751  {\r
 752    ConservationColourScheme ccs = null;\r
 753 \r
 754    Alignment al = (Alignment) viewport.alignment;\r
 755    Conservation c = new Conservation("All",\r
 756                                      ResidueProperties.propHash, 3,\r
 757                                      al.getSequences(), 0,\r
 758                                      al.getWidth());\r
 759 \r
 760    c.calculate();\r
 761    c.verdict(false, 100);\r
 762 \r
 763    ccs = new ConservationColourScheme(c, cs);\r
 764 \r
 765    int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,\r
 766        "Background");\r
 767 \r
 768    ccs.inc = threshold;\r
 769 \r
 770    viewport.setGlobalColourScheme(ccs);\r
 771 \r
 772   }\r
 773   else\r
 774        viewport.setGlobalColourScheme( cs );\r
 775 \r
 776     alignPanel.RefreshPanels();\r
 777   }\r
 778 \r
 779 \r
 780   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 781   {\r
 782     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 783 \r
 784     viewport.setAbovePIDThreshold(false);\r
 785     abovePIDThreshold.setSelected(false);\r
 786     Desktop.hidePIDSlider();\r
 787     if(!viewport.getConservationSelected())\r
 788       Desktop.hideConservationSlider();\r
 789 \r
 790    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 791    if(cs instanceof ConservationColourScheme )\r
 792      changeColour( ((ConservationColourScheme)cs).cs );\r
 793     else\r
 794       changeColour( cs );\r
 795   }\r
 796 \r
 797 \r
 798   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 799   {\r
 800     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
 801 \r
 802     conservationMenuItem.setSelected(false);\r
 803     viewport.setConservationSelected(false);\r
 804     Desktop.hideConservationSlider();\r
 805 \r
 806     if(!viewport.getAbovePIDThreshold())\r
 807       Desktop.hidePIDSlider();\r
 808 \r
 809 \r
 810     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 811     if(cs instanceof ConservationColourScheme )\r
 812         changeColour( ((ConservationColourScheme)cs).cs );\r
 813     else\r
 814         changeColour( cs );\r
 815 \r
 816   }\r
 817 \r
 818 \r
 819 \r
 820   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 821   {\r
 822     JInternalFrame frame = new JInternalFrame();\r
 823     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 824     frame.setContentPane(chooser);\r
 825     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 826     frame.setResizable(false);\r
 827     frame.setIconifiable(false);\r
 828     frame.setMaximizable(false);\r
 829   }\r
 830 \r
 831   public void PIDColour_actionPerformed(ActionEvent e)\r
 832   {\r
 833     changeColour( new PIDColourScheme() );\r
 834   }\r
 835 \r
 836 \r
 837   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 838   {\r
 839     changeColour(new Blosum62ColourScheme(viewport) );\r
 840   }\r
 841 \r
 842 \r
 843 \r
 844   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 845   {\r
 846     addHistoryItem("sort");\r
 847     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 848     alignPanel.RefreshPanels();\r
 849   }\r
 850 \r
 851   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 852   {\r
 853     addHistoryItem("sort");\r
 854     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 855     alignPanel.RefreshPanels();\r
 856   }\r
 857 \r
 858   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 859   {\r
 860     addHistoryItem("sort");\r
 861     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 862     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 863     alignPanel.RefreshPanels();\r
 864   }\r
 865 \r
 866   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 867   {\r
 868     addHistoryItem("sort");\r
 869     if(viewport.getCurrentTree()==null)\r
 870       return;\r
 871 \r
 872     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 873     alignPanel.RefreshPanels();\r
 874   }\r
 875 \r
 876   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 877   {\r
 878     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 879     JInternalFrame frame = new JInternalFrame();\r
 880     frame.setContentPane(sp);\r
 881     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);\r
 882     frame.setMaximizable(false);\r
 883     frame.setResizable(false);\r
 884 \r
 885   }\r
 886 \r
 887   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 888   {\r
 889     if(viewport.getSelectionGroup().getSize()<2)\r
 890       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 891     else\r
 892     {\r
 893       JInternalFrame frame = new JInternalFrame();\r
 894       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 895       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 896     }\r
 897   }\r
 898 \r
 899   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 900   {\r
 901 \r
 902     if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
 903        || viewport.getAlignment().getHeight()<4)\r
 904     {\r
 905       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
 906                                     +"at least 4 input sequences.",\r
 907                                     "Sequence selection insufficient",\r
 908                                     JOptionPane.WARNING_MESSAGE);\r
 909       return;\r
 910     }\r
 911 \r
 912     try{\r
 913       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 914       JInternalFrame frame = new JInternalFrame();\r
 915       frame.setContentPane(pcaPanel);\r
 916       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 917    }catch(java.lang.OutOfMemoryError ex)\r
 918    {\r
 919      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 920                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 921    }\r
 922 \r
 923 \r
 924   }\r
 925 \r
 926   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 927   {\r
 928     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 929   }\r
 930 \r
 931   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 932   {\r
 933     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 934   }\r
 935 \r
 936 \r
 937   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 938   {\r
 939     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 940   }\r
 941 \r
 942   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 943   {\r
 944     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 945   }\r
 946 \r
 947   void NewTreePanel(String type, String pwType, String title)\r
 948   {\r
 949     //are the sequences aligned?\r
 950     if(!viewport.alignment.isAligned())\r
 951     {\r
 952       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
 953                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
 954       return;\r
 955     }\r
 956 \r
 957     TreePanel tp=null;\r
 958    if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)\r
 959    {\r
 960      tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType,\r
 961                          0, viewport.alignment.getWidth());\r
 962    }\r
 963    else\r
 964    {\r
 965      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 966                          type, pwType,  0, viewport.alignment.getWidth());\r
 967    }\r
 968 \r
 969    Desktop.addInternalFrame(tp, title, 600, 500);\r
 970   }\r
 971 \r
 972 \r
 973 \r
 974 \r
 975   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 976   {\r
 977     JInternalFrame frame = new JInternalFrame();\r
 978     ClustalThread ct = new ClustalThread(frame);\r
 979     Thread t = new Thread(ct);\r
 980     t.start();\r
 981     frame.setContentPane(ct);\r
 982      Desktop.addInternalFrame(frame, title, 300, 80);\r
 983 \r
 984   }\r
 985 \r
 986   class ClustalThread extends JPanel implements Runnable\r
 987   {\r
 988     Image [] image;\r
 989     int imageIndex = 0;\r
 990     boolean webServiceRunning = false;\r
 991     JInternalFrame frame;\r
 992     public ClustalThread(JInternalFrame frame)\r
 993     {\r
 994       this.frame = frame;\r
 995       image = new Image[9];\r
 996       for(int i=0; i<9; i++)\r
 997       {\r
 998         java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");\r
 999         if (url != null)\r
1000         {\r
1001           image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
1002           MediaTracker mt = new MediaTracker(this);\r
1003           mt.addImage(image[i], i);\r
1004           try{mt.waitForID(i);}\r
1005           catch(Exception ex){}\r
1006         }\r
1007       }\r
1008       DNATwirler twirler = new DNATwirler();\r
1009       twirler.start();\r
1010       webServiceRunning = true;\r
1011     }\r
1012 \r
1013     class DNATwirler extends Thread\r
1014     {\r
1015       public void run()\r
1016       {\r
1017         while(webServiceRunning)\r
1018         {\r
1019           try{\r
1020             Thread.sleep(100);\r
1021             imageIndex++;\r
1022             imageIndex %=9;\r
1023             repaint();\r
1024           }\r
1025           catch(Exception ex){}\r
1026         }\r
1027       }\r
1028     }\r
1029 \r
1030     // JBPNote\r
1031     // Should check to see if the server settings are valid\r
1032     // Need visual-delay indication here.\r
1033     public void run()\r
1034        {\r
1035       /*   jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
1036          Vector sv = viewport.getAlignment().getSequences();\r
1037          SequenceI[] seqs = new SequenceI[sv.size()];\r
1038 \r
1039          int i = 0;\r
1040          do\r
1041          {\r
1042            seqs[i] = (SequenceI) sv.elementAt(i);\r
1043          }\r
1044          while (++i < sv.size());\r
1045 \r
1046          SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
1047 \r
1048          if (alignment != null)\r
1049          {\r
1050            AlignFrame af = new AlignFrame(new Alignment(alignment));\r
1051           af.clustalColour.setSelected(true);\r
1052           af.clustalColour_actionPerformed(null);\r
1053            Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),\r
1054                                     700, 500); // JBPNote - is there a new window geom. property ?\r
1055          }\r
1056          else\r
1057            JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",\r
1058                                          JOptionPane.WARNING_MESSAGE);\r
1059 \r
1060          webServiceRunning = false;\r
1061          try{\r
1062            frame.setClosed(true);\r
1063          }catch(Exception ex){}\r
1064        }\r
1065 \r
1066        public void paintComponent(Graphics g)\r
1067        {\r
1068          g.setColor(Color.white);\r
1069          g.fillRect(0,0,getWidth(), getHeight());\r
1070          if(image!=null)\r
1071          {\r
1072            g.drawImage(image[imageIndex],10,10,this);\r
1073          }\r
1074          g.setFont(new Font("Arial", Font.BOLD, 12));\r
1075          g.setColor(Color.black);\r
1076          g.drawString("Clustal Alignment Web Service running", 30,30);\r
1077        }\r
1078   }\r
1079   public void jpredMenuItem_actionPerformed(ActionEvent e)\r
1080     {\r
1081     //  JInternalFrame frame = new JInternalFrame();\r
1082 //      JPredClient ct = new JPredClient((SequenceI)\r
1083     ///                                   viewport.getAlignment().getSequences().elementAt(0));\r
1084     }\r
1085 \r
1086 */}}\r
1087   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
1088     // Pick the tree file\r
1089     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
1090         getProperty("LAST_DIRECTORY"));\r
1091     chooser.setFileView(new JalviewFileView());\r
1092     chooser.setDialogTitle("Select a newick-like tree file");\r
1093     chooser.setToolTipText("Load a tree file");\r
1094     int value = chooser.showOpenDialog(null);\r
1095     if (value == JalviewFileChooser.APPROVE_OPTION)\r
1096     {\r
1097       String choice = chooser.getSelectedFile().getPath();\r
1098       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1099       TreePanel treepanel = null;\r
1100       try\r
1101       {\r
1102         jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");\r
1103         fin.parse();\r
1104 \r
1105         if (fin.getTree() != null)\r
1106         {\r
1107           TreePanel tp = null;\r
1108           tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1109                              fin, "FromFile", choice);\r
1110           Desktop.addInternalFrame(tp, title, 600, 500);\r
1111         }\r
1112       }\r
1113       catch (Exception ex)\r
1114       {\r
1115         JOptionPane.showMessageDialog(Desktop.desktop,\r
1116                                       "Problem reading tree file",\r
1117                                       ex.getMessage(),\r
1118                                       JOptionPane.WARNING_MESSAGE);\r
1119         ex.printStackTrace();\r
1120       }\r
1121     }\r
1122   }\r
1123 \r
1124 }\r