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,true,false);\r
  37     alignPanel = new AlignmentPanel(this, viewport);\r
  38     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
  39     fontNameMenuItem.setText(viewport.getFont().getName());\r
  40     fontSizeMenuItem.setText(viewport.getFont().getSize()+"");\r
  41 \r
  42     addInternalFrameListener(new InternalFrameAdapter()\r
  43    {\r
  44      public void internalFrameActivated(InternalFrameEvent evt)\r
  45      {\r
  46           javax.swing.SwingUtilities.invokeLater(new Runnable()\r
  47           {\r
  48             public void run()\r
  49             {      alignPanel.requestFocus();    }\r
  50           });\r
  51 \r
  52      }\r
  53    });\r
  54 \r
  55   }\r
  56 \r
  57   protected void saveAs_actionPerformed(ActionEvent e)\r
  58   {\r
  59     JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
  60     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
  61     chooser.setToolTipText("Save");\r
  62     int value = chooser.showSaveDialog(this);\r
  63     if(value == JFileChooser.APPROVE_OPTION)\r
  64     {\r
  65       String choice =  chooser.getSelectedFile().getPath();\r
  66       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
  67       String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
  68       try{\r
  69         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
  70         out.println(output);\r
  71         out.close();\r
  72       }\r
  73       catch(Exception ex){}\r
  74     }\r
  75 \r
  76   }\r
  77 \r
  78   protected void outputText_actionPerformed(ActionEvent e)\r
  79   {\r
  80      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
  81      JInternalFrame frame = new JInternalFrame();\r
  82      cap.formatForOutput();\r
  83      frame.setContentPane(cap);\r
  84      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
  85      cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
  86   }\r
  87 \r
  88   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
  89   {\r
  90     HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
  91     htmlOutput = null;\r
  92   }\r
  93 \r
  94   protected void createJPG_actionPerformed(ActionEvent e)\r
  95   {\r
  96 \r
  97     int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight;\r
  98     int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth();\r
  99 \r
 100 \r
 101     if(!viewport.getWrapAlignment())\r
 102     {\r
 103       height = viewport.alignment.getHeight() * viewport.charHeight;\r
 104       width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth;\r
 105     }\r
 106 \r
 107     alignPanel.makeJPG( width, height);\r
 108   }\r
 109 \r
 110 \r
 111   public void printMenuItem_actionPerformed(ActionEvent e)\r
 112   {\r
 113     //Putting in a thread avoids Swing painting problems\r
 114     PrintThread thread = new PrintThread();\r
 115     thread.start();\r
 116   }\r
 117 \r
 118   class PrintThread extends Thread\r
 119   {\r
 120     public void run()\r
 121     {\r
 122       PrinterJob printJob = PrinterJob.getPrinterJob();\r
 123       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
 124       printJob.setPrintable(alignPanel, pf);\r
 125       if (printJob.printDialog())\r
 126       {\r
 127         try\r
 128         {\r
 129           printJob.print();\r
 130         }\r
 131         catch (Exception PrintException)\r
 132         {\r
 133           PrintException.printStackTrace();\r
 134         }\r
 135       }\r
 136     }\r
 137 \r
 138   }\r
 139 \r
 140 \r
 141 \r
 142 \r
 143   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 144   {\r
 145     try{\r
 146       this.setClosed(true);\r
 147     }catch(Exception ex){}\r
 148   }\r
 149 \r
 150   Stack historyList = new Stack();\r
 151   Stack redoList = new Stack();\r
 152 \r
 153   void updateEditMenuBar()\r
 154   {\r
 155     if(historyList.size()>0)\r
 156      {\r
 157        undoMenuItem.setEnabled(true);\r
 158        Object [] history = (Object[])historyList.get(0);\r
 159        undoMenuItem.setText("Undo "+history[0]);\r
 160      }\r
 161     else\r
 162     {\r
 163       undoMenuItem.setEnabled(false);\r
 164       undoMenuItem.setText("Undo");\r
 165     }\r
 166 \r
 167     if(redoList.size()>0)\r
 168      {\r
 169        redoMenuItem.setEnabled(true);\r
 170        Object [] history = (Object[])redoList.get(0);\r
 171        redoMenuItem.setText("Redo "+history[0]);\r
 172      }\r
 173     else\r
 174     {\r
 175       redoMenuItem.setEnabled(false);\r
 176       redoMenuItem.setText("Redo");\r
 177     }\r
 178   }\r
 179 \r
 180   public void addHistoryItem(String type)\r
 181   {\r
 182     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 183     redoList.clear();\r
 184     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 185     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 186     {\r
 187       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 188                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 189     }\r
 190 \r
 191     historyList.add(0, new Object[]{type,  seq} );\r
 192     updateEditMenuBar();\r
 193   }\r
 194 \r
 195   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 196   {\r
 197     Object [] history = (Object[])historyList.remove(0);\r
 198     // add the redo state before continuing!!\r
 199     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 200     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
 201     {\r
 202       seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
 203                             viewport.getAlignment().getSequenceAt(i).\r
 204                             getSequence());\r
 205     }\r
 206     /////////\r
 207 \r
 208     redoList.add(0, new Object[] {history[0], seq});\r
 209 \r
 210       seq = (SequenceI[]) history[1];\r
 211       viewport.setAlignment( new Alignment(seq) );\r
 212       updateEditMenuBar();\r
 213       alignPanel.RefreshPanels();\r
 214   }\r
 215 \r
 216   public void moveSelectedSequences(boolean up)\r
 217   {\r
 218     SequenceGroup sg = viewport.getRubberbandGroup();\r
 219     if (sg == null)\r
 220       return;\r
 221 \r
 222     if (up)\r
 223     {\r
 224       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 225       {\r
 226         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 227         if (!sg.sequences.contains(seq))\r
 228           continue;\r
 229 \r
 230         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 231         if (sg.sequences.contains(temp))\r
 232           continue;\r
 233 \r
 234         viewport.alignment.getSequences().setElementAt(temp, i);\r
 235         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 236       }\r
 237     }\r
 238     else\r
 239     {\r
 240       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 241       {\r
 242         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 243         if (!sg.sequences.contains(seq))\r
 244           continue;\r
 245 \r
 246         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 247         if (sg.sequences.contains(temp))\r
 248           continue;\r
 249 \r
 250         viewport.alignment.getSequences().setElementAt(temp, i);\r
 251         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 252       }\r
 253     }\r
 254 \r
 255     alignPanel.RefreshPanels();\r
 256   }\r
 257 \r
 258 \r
 259 \r
 260   protected void copy_actionPerformed(ActionEvent e)\r
 261   {\r
 262    if(viewport.getRubberbandGroup()==null)\r
 263      return;\r
 264 \r
 265    SequenceGroup sg = viewport.getRubberbandGroup();\r
 266 \r
 267      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 268      StringBuffer buffer= new StringBuffer();\r
 269 \r
 270        for(int i=0; i<sg.getSize(); i++)\r
 271        {\r
 272          SequenceI seq = sg.getSequenceAt(i);\r
 273          buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
 274                         +seq.findPosition( sg.getEndRes() )+ "\t"\r
 275                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
 276        }\r
 277      c.setContents( new StringSelection( buffer.toString()) , null ) ;\r
 278 \r
 279   }\r
 280 \r
 281 \r
 282   protected void pasteNew_actionPerformed(ActionEvent e)\r
 283   {\r
 284     paste(true);\r
 285   }\r
 286 \r
 287   protected void pasteThis_actionPerformed(ActionEvent e)\r
 288   {\r
 289     addHistoryItem("Paste");\r
 290     paste(false);\r
 291   }\r
 292 \r
 293   void paste(boolean newAlignment)\r
 294   {\r
 295     try{\r
 296       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 297       Transferable contents = c.getContents(this);\r
 298       if (contents == null)\r
 299         return;\r
 300 \r
 301       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
 302       StringTokenizer st = new StringTokenizer(str);\r
 303       ArrayList seqs = new ArrayList();\r
 304       while (st.hasMoreElements())\r
 305       {\r
 306         String name = st.nextToken();\r
 307         int start = Integer.parseInt(st.nextToken());\r
 308         int end = Integer.parseInt(st.nextToken());\r
 309         Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
 310 \r
 311         if(!newAlignment)\r
 312           viewport.alignment.addSequence(sequence);\r
 313         else\r
 314           seqs.add(sequence);\r
 315       }\r
 316 \r
 317       if(newAlignment)\r
 318       {\r
 319         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 320         seqs.toArray(newSeqs);\r
 321         AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
 322         int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;\r
 323         if (newHeight > 500)\r
 324           newHeight = 500;\r
 325         Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
 326       }\r
 327       else\r
 328       {\r
 329         viewport.setEndSeq(viewport.alignment.getHeight());\r
 330         viewport.alignment.getWidth();\r
 331         alignPanel.RefreshPanels();\r
 332       }\r
 333 \r
 334     }catch(Exception ex){}// could be anything being pasted in here\r
 335 \r
 336   }\r
 337 \r
 338 \r
 339   protected void cut_actionPerformed(ActionEvent e)\r
 340   {\r
 341     copy_actionPerformed(null);\r
 342     delete_actionPerformed(null);\r
 343   }\r
 344 \r
 345   protected void delete_actionPerformed(ActionEvent e)\r
 346   {\r
 347     addHistoryItem("Delete");\r
 348     if (viewport.getRubberbandGroup() == null)\r
 349       return;\r
 350 \r
 351      SequenceGroup sg = viewport.getRubberbandGroup();\r
 352      for (int i=0;i < sg.sequences.size(); i++)\r
 353              viewport.getAlignment().deleteSequence(sg.getSequenceAt(i));\r
 354 \r
 355      viewport.alignment.deleteGroup(sg);\r
 356      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());\r
 357      if(viewport.getAlignment().getHeight()<1)\r
 358      try\r
 359      {\r
 360        this.setClosed(true);\r
 361      }catch(Exception ex){}\r
 362      alignPanel.RefreshPanels();\r
 363 \r
 364   }\r
 365 \r
 366 \r
 367 \r
 368   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 369   {\r
 370      Object [] history = (Object[])redoList.remove(0);\r
 371      SequenceI[] seq = (SequenceI[]) history[1];\r
 372      viewport.setAlignment( new Alignment(seq) );\r
 373      updateEditMenuBar();\r
 374      alignPanel.RefreshPanels();\r
 375   }\r
 376 \r
 377 \r
 378   public void groupsMenuItem_actionPerformed(ActionEvent e)\r
 379   {\r
 380     GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
 381     JInternalFrame frame = new JInternalFrame();\r
 382     frame.setContentPane(geditor);\r
 383     Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
 384     frame.setResizable(false);\r
 385   }\r
 386 \r
 387   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 388   {\r
 389     viewport.alignment.deleteAllGroups();\r
 390     viewport.getSelection().clear();\r
 391 \r
 392     alignPanel.RefreshPanels();\r
 393   }\r
 394 \r
 395 \r
 396 \r
 397   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 398   {\r
 399     Selection sel = viewport.getSelection();\r
 400     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 401       sel.addElement( viewport.getAlignment().getSequenceAt(i));\r
 402     PaintRefresher.Refresh(null);\r
 403   }\r
 404 \r
 405   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 406   {\r
 407     viewport.setRubberbandGroup(null);\r
 408     viewport.getSelection().clear();\r
 409     PaintRefresher.Refresh(null);\r
 410   }\r
 411 \r
 412   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 413   {\r
 414     Selection sel = viewport.getSelection();\r
 415     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 416     {\r
 417       if (sel.contains(viewport.getAlignment().getSequenceAt(i)))\r
 418         sel.removeElement(viewport.getAlignment().getSequenceAt(i));\r
 419       else\r
 420         sel.addElement(viewport.getAlignment().getSequenceAt(i));\r
 421     }\r
 422     PaintRefresher.Refresh(null);\r
 423   }\r
 424 \r
 425 \r
 426   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 427   {\r
 428     viewport.getColumnSelection().clear();\r
 429     repaint();\r
 430   }\r
 431 \r
 432   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 433   {\r
 434     addHistoryItem("delete columns");\r
 435     ColumnSelection colSel = viewport.getColumnSelection();\r
 436     if (colSel.size() > 0)\r
 437     {\r
 438       int min = colSel.getMin();\r
 439       viewport.getAlignment().trimLeft(min);\r
 440       colSel.compensateForEdit(0,min);\r
 441       alignPanel.RefreshPanels();\r
 442     }\r
 443   }\r
 444 \r
 445   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 446   {\r
 447     addHistoryItem("delete columns");\r
 448     ColumnSelection colSel = viewport.getColumnSelection();\r
 449     if (colSel.size() > 0)\r
 450     {\r
 451       int max = colSel.getMax();\r
 452       if(max>1)\r
 453         viewport.getAlignment().trimRight(max);\r
 454 \r
 455       alignPanel.RefreshPanels();\r
 456     }\r
 457 \r
 458   }\r
 459 \r
 460   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 461   {\r
 462     addHistoryItem("delete gapped columns");\r
 463     viewport.getAlignment().removeGaps();\r
 464     alignPanel.RefreshPanels();\r
 465   }\r
 466 \r
 467   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 468   {\r
 469     addHistoryItem("delete all gaps");\r
 470     SequenceI current;\r
 471     int jSize;\r
 472     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 473     {\r
 474       current = viewport.getAlignment().getSequenceAt(i);\r
 475       jSize = current.getLength();\r
 476       for (int j=0; j < jSize; j++)\r
 477         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 478         {\r
 479           current.deleteCharAt(j);\r
 480           j--;\r
 481           jSize--;\r
 482         }\r
 483     }\r
 484 \r
 485     alignPanel.RefreshPanels();\r
 486   }\r
 487 \r
 488   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 489   {\r
 490     char thisChar = '-';\r
 491     char nextChar = '.';\r
 492     if(viewport.getGapCharacter()=='-')\r
 493     {\r
 494       thisChar = '.';\r
 495       nextChar = '-';\r
 496     }\r
 497     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 498     viewport.setGapCharacter(thisChar);\r
 499     alignPanel.RefreshPanels();\r
 500   }\r
 501 \r
 502   public void findMenuItem_actionPerformed(ActionEvent e)\r
 503   {\r
 504     JOptionPane op = new JOptionPane();\r
 505     JInternalFrame frame =  op.createInternalFrame(this, "Find");\r
 506     Finder finder = new Finder(viewport, alignPanel, frame);\r
 507     frame.setClosable(true);\r
 508     frame.setContentPane(finder);\r
 509     frame.setSize(340,110);\r
 510     frame.setVisible(true);\r
 511   }\r
 512 \r
 513 \r
 514 \r
 515   public void fontNameMenuItem_actionPerformed(ActionEvent e)\r
 516   {\r
 517     String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();\r
 518 \r
 519 \r
 520     String selection = JOptionPane.showInternalInputDialog(this,\r
 521                                 "Select font",\r
 522                                 "Font selection",\r
 523                                 JOptionPane.QUESTION_MESSAGE,\r
 524                                 null,fonts\r
 525                                 ,fontNameMenuItem.getText()).toString();\r
 526     if(selection!=null)\r
 527     {\r
 528        fontNameMenuItem.setText(selection);\r
 529        SetFont();\r
 530      }\r
 531 \r
 532   }\r
 533 \r
 534   public void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
 535   {\r
 536     String selection = JOptionPane.showInternalInputDialog(this,\r
 537                                 "Select font size",\r
 538                                 "Font size",\r
 539                                 JOptionPane.QUESTION_MESSAGE,\r
 540                                 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
 541                                 ,fontSizeMenuItem.getText()).toString();\r
 542     if(selection!=null)\r
 543      {\r
 544        fontSizeMenuItem.setText(selection);\r
 545        SetFont();\r
 546      }\r
 547   }\r
 548 \r
 549   public void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
 550   {\r
 551     String selection = JOptionPane.showInternalInputDialog(this,\r
 552                                 "Select font style",\r
 553                                 "Font style",\r
 554                                 JOptionPane.QUESTION_MESSAGE,\r
 555                                 null, new String[]{"plain", "bold", "italic"}\r
 556                                 ,fontStyleMenuItem.getText()).toString();\r
 557     if(selection!=null)\r
 558     {\r
 559       fontStyleMenuItem.setText(selection);\r
 560       SetFont();\r
 561     }\r
 562 \r
 563   }\r
 564 \r
 565   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 566   {\r
 567       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 568       alignPanel.RefreshPanels();\r
 569   }\r
 570 \r
 571   void SetFont()\r
 572   {\r
 573       int style = java.awt.Font.PLAIN;\r
 574       if(fontStyleMenuItem.getText().equals("bold"))\r
 575         style = java.awt.Font.BOLD;\r
 576       else if(fontStyleMenuItem.getText().equals("italic"))\r
 577         style = java.awt.Font.ITALIC;\r
 578 \r
 579       viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),\r
 580                                            style,\r
 581                                            Integer.parseInt(fontSizeMenuItem.getText())));\r
 582       alignPanel.RefreshPanels();\r
 583 \r
 584   }\r
 585 \r
 586   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 587   {\r
 588     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 589     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
 590   }\r
 591 \r
 592 \r
 593   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 594   {\r
 595     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 596     alignPanel.RefreshPanels();\r
 597   }\r
 598 \r
 599   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 600   {\r
 601     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 602     alignPanel.RefreshPanels();\r
 603   }\r
 604 \r
 605 \r
 606   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 607   {\r
 608     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 609     alignPanel.RefreshPanels();\r
 610   }\r
 611 \r
 612   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
 613   {\r
 614     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 615     if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
 616     {\r
 617          AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);\r
 618          ((Alignment)viewport.alignment).featuresAdded = true;\r
 619     }\r
 620     alignPanel.RefreshPanels();\r
 621   }\r
 622 \r
 623   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 624   {\r
 625     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
 626   }\r
 627 \r
 628   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 629   {\r
 630     if (alignPanel.overviewPanel != null)\r
 631       return;\r
 632 \r
 633     JInternalFrame frame = new JInternalFrame();\r
 634     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 635    try{\r
 636      overview = new OverviewPanel(alignPanel, viewport);\r
 637      frame.setContentPane(overview);\r
 638     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 639                              frame.getWidth(), frame.getHeight());\r
 640     frame.pack();\r
 641     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 642     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 643       {\r
 644             alignPanel.setOverviewPanel(null);\r
 645       };\r
 646     });\r
 647     alignPanel.setOverviewPanel( overview );\r
 648 \r
 649   }catch(java.lang.OutOfMemoryError ex)\r
 650    {\r
 651      JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 652                                    +"\nTry reducing the font size.",\r
 653                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 654    }\r
 655 \r
 656 \r
 657   }\r
 658 \r
 659   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 660   {\r
 661     changeColour( null );\r
 662   }\r
 663 \r
 664 \r
 665   public void clustalColour_actionPerformed(ActionEvent e)\r
 666   {\r
 667     abovePIDThreshold.setSelected(false);\r
 668     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 669   }\r
 670 \r
 671   public void zappoColour_actionPerformed(ActionEvent e)\r
 672   {\r
 673     changeColour(new ZappoColourScheme());\r
 674   }\r
 675 \r
 676   public void taylorColour_actionPerformed(ActionEvent e)\r
 677   {\r
 678     changeColour(new TaylorColourScheme());\r
 679   }\r
 680 \r
 681 \r
 682   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 683   {\r
 684     changeColour( new HydrophobicColourScheme() );\r
 685   }\r
 686 \r
 687   public void helixColour_actionPerformed(ActionEvent e)\r
 688   {\r
 689     changeColour(new HelixColourScheme() );\r
 690   }\r
 691 \r
 692 \r
 693   public void strandColour_actionPerformed(ActionEvent e)\r
 694   {\r
 695     changeColour(new StrandColourScheme());\r
 696   }\r
 697 \r
 698 \r
 699   public void turnColour_actionPerformed(ActionEvent e)\r
 700   {\r
 701     changeColour(new TurnColourScheme());\r
 702   }\r
 703 \r
 704 \r
 705   public void buriedColour_actionPerformed(ActionEvent e)\r
 706   {\r
 707     changeColour(new BuriedColourScheme() );\r
 708   }\r
 709 \r
 710   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 711   {\r
 712     changeColour(new NucleotideColourScheme());\r
 713   }\r
 714 \r
 715 \r
 716   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 717   {\r
 718     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
 719   }\r
 720 \r
 721 \r
 722 \r
 723   void changeColour(ColourSchemeI cs)\r
 724   {\r
 725 \r
 726     if(viewport.getColourAppliesToAllGroups())\r
 727     {\r
 728       Vector groups = viewport.alignment.getGroups();\r
 729       for(int i=0; i<groups.size(); i++)\r
 730       {\r
 731         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 732         sg.cs = cs;\r
 733 \r
 734         if(abovePIDThreshold.isSelected())\r
 735           abovePIDThreshold_actionPerformed(null);\r
 736         else if( viewport.getConservationSelected() )\r
 737         {\r
 738           Conservation c = new Conservation("Group",\r
 739                                             ResidueProperties.propHash, 3,\r
 740                                             sg.sequences, sg.getStartRes(),\r
 741                                             sg.getEndRes());\r
 742           c.calculate();\r
 743           c.verdict(false, 100);\r
 744           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 745 \r
 746           sg.cs = ccs;\r
 747         }\r
 748 \r
 749       }\r
 750     }\r
 751 \r
 752 \r
 753     if ( viewport.getAbovePIDThreshold())\r
 754     {\r
 755       int threshold = 0;\r
 756       threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");\r
 757       Desktop.hideConservationSlider();\r
 758 \r
 759       if (cs instanceof ResidueColourScheme)\r
 760         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 761       else if (cs instanceof ScoreColourScheme)\r
 762         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 763 \r
 764       viewport.setGlobalColourScheme(cs);\r
 765 \r
 766     }\r
 767     else\r
 768     if (cs instanceof ResidueColourScheme)\r
 769       ( (ResidueColourScheme) cs).setThreshold(0);\r
 770     else if (cs instanceof ScoreColourScheme)\r
 771       ( (ScoreColourScheme) cs).setThreshold(0);\r
 772 \r
 773 \r
 774 \r
 775 \r
 776 if ( viewport.getConservationSelected() )\r
 777  {\r
 778    ConservationColourScheme ccs = null;\r
 779 \r
 780    Alignment al = (Alignment) viewport.alignment;\r
 781    Conservation c = new Conservation("All",\r
 782                                      ResidueProperties.propHash, 3,\r
 783                                      al.getSequences(), 0,\r
 784                                      al.getWidth());\r
 785 \r
 786    c.calculate();\r
 787    c.verdict(false, 100);\r
 788 \r
 789    ccs = new ConservationColourScheme(c, cs);\r
 790 \r
 791    int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,\r
 792        "Background");\r
 793 \r
 794    ccs.inc = threshold;\r
 795 \r
 796    viewport.setGlobalColourScheme(ccs);\r
 797 \r
 798   }\r
 799   else\r
 800        viewport.setGlobalColourScheme( cs );\r
 801 \r
 802     alignPanel.RefreshPanels();\r
 803   }\r
 804 \r
 805 \r
 806   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 807   {\r
 808     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 809 \r
 810     viewport.setAbovePIDThreshold(false);\r
 811     abovePIDThreshold.setSelected(false);\r
 812     Desktop.hidePIDSlider();\r
 813     if(!viewport.getConservationSelected())\r
 814       Desktop.hideConservationSlider();\r
 815 \r
 816    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 817    if(cs instanceof ConservationColourScheme )\r
 818      changeColour( ((ConservationColourScheme)cs).cs );\r
 819     else\r
 820       changeColour( cs );\r
 821   }\r
 822 \r
 823 \r
 824   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 825   {\r
 826     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
 827 \r
 828     conservationMenuItem.setSelected(false);\r
 829     viewport.setConservationSelected(false);\r
 830     Desktop.hideConservationSlider();\r
 831 \r
 832     if(!viewport.getAbovePIDThreshold())\r
 833       Desktop.hidePIDSlider();\r
 834 \r
 835 \r
 836     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 837     if(cs instanceof ConservationColourScheme )\r
 838         changeColour( ((ConservationColourScheme)cs).cs );\r
 839     else\r
 840         changeColour( cs );\r
 841 \r
 842   }\r
 843 \r
 844 \r
 845 \r
 846   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 847   {\r
 848     JInternalFrame frame = new JInternalFrame();\r
 849     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 850     frame.setContentPane(chooser);\r
 851     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 852     frame.setResizable(false);\r
 853     frame.setIconifiable(false);\r
 854     frame.setMaximizable(false);\r
 855   }\r
 856 \r
 857   public void PIDColour_actionPerformed(ActionEvent e)\r
 858   {\r
 859     changeColour( new PIDColourScheme() );\r
 860   }\r
 861 \r
 862 \r
 863   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 864   {\r
 865     changeColour(new Blosum62ColourScheme(viewport) );\r
 866   }\r
 867 \r
 868 \r
 869 \r
 870   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 871   {\r
 872     addHistoryItem("sort");\r
 873     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 874     alignPanel.RefreshPanels();\r
 875   }\r
 876 \r
 877   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 878   {\r
 879     addHistoryItem("sort");\r
 880     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 881     alignPanel.RefreshPanels();\r
 882   }\r
 883 \r
 884   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 885   {\r
 886     addHistoryItem("sort");\r
 887     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 888     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 889     alignPanel.RefreshPanels();\r
 890   }\r
 891 \r
 892   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 893   {\r
 894     addHistoryItem("sort");\r
 895     if(viewport.getCurrentTree()==null)\r
 896       return;\r
 897 \r
 898     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 899     alignPanel.RefreshPanels();\r
 900   }\r
 901 \r
 902   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 903   {\r
 904     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 905     JInternalFrame frame = new JInternalFrame();\r
 906     frame.setContentPane(sp);\r
 907     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);\r
 908     frame.setMaximizable(false);\r
 909     frame.setResizable(false);\r
 910 \r
 911   }\r
 912 \r
 913   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 914   {\r
 915     if(viewport.getSelection().size()<2)\r
 916       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 917     else\r
 918     {\r
 919       JInternalFrame frame = new JInternalFrame();\r
 920       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 921       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 922     }\r
 923   }\r
 924 \r
 925   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 926   {\r
 927     if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)\r
 928        || viewport.getAlignment().getHeight()<4)\r
 929     {\r
 930       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
 931                                     +"at least 4 input sequences.",\r
 932                                     "Sequence selection insufficient",\r
 933                                     JOptionPane.WARNING_MESSAGE);\r
 934       return;\r
 935     }\r
 936 \r
 937     try{\r
 938       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 939       JInternalFrame frame = new JInternalFrame();\r
 940       frame.setContentPane(pcaPanel);\r
 941       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 942    }catch(java.lang.OutOfMemoryError ex)\r
 943    {\r
 944      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 945                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 946    }\r
 947 \r
 948 \r
 949   }\r
 950 \r
 951   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 952   {\r
 953     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 954   }\r
 955 \r
 956   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 957   {\r
 958     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 959   }\r
 960 \r
 961 \r
 962   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 963   {\r
 964     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 965   }\r
 966 \r
 967   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 968   {\r
 969     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 970   }\r
 971 \r
 972   void NewTreePanel(String type, String pwType, String title)\r
 973   {\r
 974     //are the sequences aligned?\r
 975     if(!viewport.alignment.isAligned())\r
 976     {\r
 977       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
 978                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
 979       return;\r
 980     }\r
 981 \r
 982     TreePanel tp=null;\r
 983    if (viewport.getSelection() != null && viewport.getSelection().size() > 3)\r
 984    {\r
 985      tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,\r
 986                          0, viewport.alignment.getWidth());\r
 987    }\r
 988    else\r
 989    {\r
 990      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 991                          type, pwType,  0, viewport.alignment.getWidth());\r
 992    }\r
 993 \r
 994    Desktop.addInternalFrame(tp, title, 600, 500);\r
 995   }\r
 996 \r
 997 \r
 998 \r
 999 \r
1000   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
1001   {\r
1002     JInternalFrame frame = new JInternalFrame();\r
1003     ClustalThread ct = new ClustalThread(frame);\r
1004     Thread t = new Thread(ct);\r
1005     t.start();\r
1006     frame.setContentPane(ct);\r
1007      Desktop.addInternalFrame(frame, title, 300, 80);\r
1008 \r
1009   }\r
1010 \r
1011   class ClustalThread extends JPanel implements Runnable\r
1012   {\r
1013     Image [] image;\r
1014     int imageIndex = 0;\r
1015     boolean webServiceRunning = false;\r
1016     JInternalFrame frame;\r
1017     public ClustalThread(JInternalFrame frame)\r
1018     {\r
1019       this.frame = frame;\r
1020       image = new Image[9];\r
1021       for(int i=0; i<9; i++)\r
1022       {\r
1023         java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");\r
1024         if (url != null)\r
1025         {\r
1026           image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
1027           MediaTracker mt = new MediaTracker(this);\r
1028           mt.addImage(image[i], i);\r
1029           try{mt.waitForID(i);}\r
1030           catch(Exception ex){}\r
1031         }\r
1032       }\r
1033       DNATwirler twirler = new DNATwirler();\r
1034       twirler.start();\r
1035       webServiceRunning = true;\r
1036     }\r
1037 \r
1038     class DNATwirler extends Thread\r
1039     {\r
1040       public void run()\r
1041       {\r
1042         while(webServiceRunning)\r
1043         {\r
1044           try{\r
1045             Thread.sleep(100);\r
1046             imageIndex++;\r
1047             imageIndex %=9;\r
1048             repaint();\r
1049           }\r
1050           catch(Exception ex){}\r
1051         }\r
1052       }\r
1053     }\r
1054 \r
1055     // JBPNote\r
1056     // Should check to see if the server settings are valid\r
1057     // Need visual-delay indication here.\r
1058     public void run()\r
1059        {\r
1060          jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
1061          Vector sv = viewport.getAlignment().getSequences();\r
1062          SequenceI[] seqs = new SequenceI[sv.size()];\r
1063 \r
1064          int i = 0;\r
1065          do\r
1066          {\r
1067            seqs[i] = (SequenceI) sv.elementAt(i);\r
1068          }\r
1069          while (++i < sv.size());\r
1070 \r
1071          SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
1072 \r
1073          if (alignment != null)\r
1074          {\r
1075            AlignFrame af = new AlignFrame(new Alignment(alignment));\r
1076           af.clustalColour.setSelected(true);\r
1077           af.clustalColour_actionPerformed(null);\r
1078            Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),\r
1079                                     700, 500); // JBPNote - is there a new window geom. property ?\r
1080          }\r
1081          else\r
1082            JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",\r
1083                                          JOptionPane.WARNING_MESSAGE);\r
1084 \r
1085          webServiceRunning = false;\r
1086          try{\r
1087            frame.setClosed(true);\r
1088          }catch(Exception ex){}\r
1089        }\r
1090 \r
1091        public void paintComponent(Graphics g)\r
1092        {\r
1093          g.setColor(Color.white);\r
1094          g.fillRect(0,0,getWidth(), getHeight());\r
1095          if(image!=null)\r
1096          {\r
1097            g.drawImage(image[imageIndex],10,10,this);\r
1098          }\r
1099          g.setFont(new Font("Arial", Font.BOLD, 12));\r
1100          g.setColor(Color.black);\r
1101          g.drawString("Clustal Alignment Web Service running", 30,30);\r
1102        }\r
1103   }\r
1104 }\r