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   ArrayList  historyList = new ArrayList();\r
 151   ArrayList redoList = new ArrayList();\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     paste(false);\r
 290   }\r
 291 \r
 292   void paste(boolean newAlignment)\r
 293   {\r
 294     try{\r
 295       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 296       Transferable contents = c.getContents(this);\r
 297       if (contents == null)\r
 298         return;\r
 299 \r
 300       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
 301       StringTokenizer st = new StringTokenizer(str);\r
 302       ArrayList seqs = new ArrayList();\r
 303       while (st.hasMoreElements())\r
 304       {\r
 305         String name = st.nextToken();\r
 306         int start = Integer.parseInt(st.nextToken());\r
 307         int end = Integer.parseInt(st.nextToken());\r
 308         Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
 309 \r
 310         if(!newAlignment)\r
 311           viewport.alignment.addSequence(sequence);\r
 312         else\r
 313           seqs.add(sequence);\r
 314       }\r
 315 \r
 316       if(newAlignment)\r
 317       {\r
 318         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 319         seqs.toArray(newSeqs);\r
 320         AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
 321         int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;\r
 322         if (newHeight > 500)\r
 323           newHeight = 500;\r
 324         Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
 325       }\r
 326       else\r
 327       {\r
 328         viewport.setEndSeq(viewport.alignment.getHeight());\r
 329         viewport.alignment.getWidth();\r
 330         alignPanel.RefreshPanels();\r
 331       }\r
 332 \r
 333     }catch(Exception ex){}// could be anything being pasted in here\r
 334 \r
 335   }\r
 336 \r
 337 \r
 338   protected void cut_actionPerformed(ActionEvent e)\r
 339   {\r
 340     copy_actionPerformed(null);\r
 341     delete_actionPerformed(null);\r
 342   }\r
 343 \r
 344   protected void delete_actionPerformed(ActionEvent e)\r
 345   {\r
 346     if (viewport.getRubberbandGroup() == null)\r
 347       return;\r
 348 \r
 349      SequenceGroup sg = viewport.getRubberbandGroup();\r
 350      for (int i=0;i < sg.sequences.size(); i++)\r
 351              viewport.getAlignment().deleteSequence(sg.getSequenceAt(i));\r
 352 \r
 353      viewport.alignment.deleteGroup(sg);\r
 354      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());\r
 355      if(viewport.getAlignment().getHeight()<1)\r
 356      try\r
 357      {\r
 358        this.setClosed(true);\r
 359      }catch(Exception ex){}\r
 360      alignPanel.RefreshPanels();\r
 361 \r
 362   }\r
 363 \r
 364 \r
 365 \r
 366   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 367   {\r
 368      Object [] history = (Object[])redoList.remove(0);\r
 369      SequenceI[] seq = (SequenceI[]) history[1];\r
 370      viewport.setAlignment( new Alignment(seq) );\r
 371      updateEditMenuBar();\r
 372      alignPanel.RefreshPanels();\r
 373   }\r
 374 \r
 375 \r
 376   public void groupsMenuItem_actionPerformed(ActionEvent e)\r
 377   {\r
 378     GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
 379     JInternalFrame frame = new JInternalFrame();\r
 380     frame.setContentPane(geditor);\r
 381     Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
 382     frame.setResizable(false);\r
 383   }\r
 384 \r
 385   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 386   {\r
 387     viewport.alignment.deleteAllGroups();\r
 388     viewport.getSelection().clear();\r
 389 \r
 390     alignPanel.RefreshPanels();\r
 391   }\r
 392 \r
 393 \r
 394 \r
 395   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 396   {\r
 397     Selection sel = viewport.getSelection();\r
 398     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 399       sel.addElement( viewport.getAlignment().getSequenceAt(i));\r
 400     PaintRefresher.Refresh(null);\r
 401   }\r
 402 \r
 403   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 404   {\r
 405     viewport.setRubberbandGroup(null);\r
 406     viewport.getSelection().clear();\r
 407     PaintRefresher.Refresh(null);\r
 408   }\r
 409 \r
 410   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 411   {\r
 412     Selection sel = viewport.getSelection();\r
 413     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 414     {\r
 415       if (sel.contains(viewport.getAlignment().getSequenceAt(i)))\r
 416         sel.removeElement(viewport.getAlignment().getSequenceAt(i));\r
 417       else\r
 418         sel.addElement(viewport.getAlignment().getSequenceAt(i));\r
 419     }\r
 420     PaintRefresher.Refresh(null);\r
 421   }\r
 422 \r
 423 \r
 424   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 425   {\r
 426     viewport.getColumnSelection().clear();\r
 427     repaint();\r
 428   }\r
 429 \r
 430   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 431   {\r
 432     addHistoryItem("delete columns");\r
 433     ColumnSelection colSel = viewport.getColumnSelection();\r
 434     if (colSel.size() > 0)\r
 435     {\r
 436       int min = colSel.getMin();\r
 437       viewport.getAlignment().trimLeft(min);\r
 438       colSel.compensateForEdit(0,min);\r
 439       alignPanel.RefreshPanels();\r
 440     }\r
 441   }\r
 442 \r
 443   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 444   {\r
 445     addHistoryItem("delete columns");\r
 446     ColumnSelection colSel = viewport.getColumnSelection();\r
 447     if (colSel.size() > 0)\r
 448     {\r
 449       int max = colSel.getMax();\r
 450       if(max>1)\r
 451         viewport.getAlignment().trimRight(max);\r
 452 \r
 453       alignPanel.RefreshPanels();\r
 454     }\r
 455 \r
 456   }\r
 457 \r
 458   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 459   {\r
 460     addHistoryItem("delete gapped columns");\r
 461     viewport.getAlignment().removeGaps();\r
 462     alignPanel.RefreshPanels();\r
 463   }\r
 464 \r
 465   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 466   {\r
 467     addHistoryItem("delete all gaps");\r
 468     SequenceI current;\r
 469     int jSize;\r
 470     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 471     {\r
 472       current = viewport.getAlignment().getSequenceAt(i);\r
 473       jSize = current.getLength();\r
 474       for (int j=0; j < jSize; j++)\r
 475         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 476         {\r
 477           current.deleteCharAt(j);\r
 478           j--;\r
 479           jSize--;\r
 480         }\r
 481     }\r
 482 \r
 483     alignPanel.RefreshPanels();\r
 484   }\r
 485 \r
 486   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 487   {\r
 488     char thisChar = '-';\r
 489     char nextChar = '.';\r
 490     if(viewport.getGapCharacter()=='-')\r
 491     {\r
 492       thisChar = '.';\r
 493       nextChar = '-';\r
 494     }\r
 495     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 496     viewport.setGapCharacter(thisChar);\r
 497     alignPanel.RefreshPanels();\r
 498   }\r
 499 \r
 500   public void findMenuItem_actionPerformed(ActionEvent e)\r
 501   {\r
 502     JOptionPane op = new JOptionPane();\r
 503     JInternalFrame frame =  op.createInternalFrame(this, "Find");\r
 504     Finder finder = new Finder(viewport, alignPanel, frame);\r
 505     frame.setClosable(true);\r
 506     frame.setContentPane(finder);\r
 507     frame.setSize(340,110);\r
 508     frame.setVisible(true);\r
 509   }\r
 510 \r
 511 \r
 512 \r
 513   public void fontNameMenuItem_actionPerformed(ActionEvent e)\r
 514   {\r
 515     String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();\r
 516 \r
 517 \r
 518     String selection = JOptionPane.showInternalInputDialog(this,\r
 519                                 "Select font",\r
 520                                 "Font selection",\r
 521                                 JOptionPane.QUESTION_MESSAGE,\r
 522                                 null,fonts\r
 523                                 ,fontNameMenuItem.getText()).toString();\r
 524     if(selection!=null)\r
 525     {\r
 526        fontNameMenuItem.setText(selection);\r
 527        SetFont();\r
 528      }\r
 529 \r
 530   }\r
 531 \r
 532   public void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
 533   {\r
 534     String selection = JOptionPane.showInternalInputDialog(this,\r
 535                                 "Select font size",\r
 536                                 "Font size",\r
 537                                 JOptionPane.QUESTION_MESSAGE,\r
 538                                 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
 539                                 ,fontSizeMenuItem.getText()).toString();\r
 540     if(selection!=null)\r
 541      {\r
 542        fontSizeMenuItem.setText(selection);\r
 543        SetFont();\r
 544      }\r
 545   }\r
 546 \r
 547   public void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
 548   {\r
 549     String selection = JOptionPane.showInternalInputDialog(this,\r
 550                                 "Select font style",\r
 551                                 "Font style",\r
 552                                 JOptionPane.QUESTION_MESSAGE,\r
 553                                 null, new String[]{"plain", "bold", "italic"}\r
 554                                 ,fontStyleMenuItem.getText()).toString();\r
 555     if(selection!=null)\r
 556     {\r
 557       fontStyleMenuItem.setText(selection);\r
 558       SetFont();\r
 559     }\r
 560 \r
 561   }\r
 562 \r
 563   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 564   {\r
 565       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 566       alignPanel.RefreshPanels();\r
 567   }\r
 568 \r
 569   void SetFont()\r
 570   {\r
 571       int style = java.awt.Font.PLAIN;\r
 572       if(fontStyleMenuItem.getText().equals("bold"))\r
 573         style = java.awt.Font.BOLD;\r
 574       else if(fontStyleMenuItem.getText().equals("italic"))\r
 575         style = java.awt.Font.ITALIC;\r
 576 \r
 577       viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),\r
 578                                            style,\r
 579                                            Integer.parseInt(fontSizeMenuItem.getText())));\r
 580       alignPanel.RefreshPanels();\r
 581 \r
 582   }\r
 583 \r
 584   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 585   {\r
 586     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 587     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
 588   }\r
 589 \r
 590 \r
 591   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 592   {\r
 593     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 594     alignPanel.RefreshPanels();\r
 595   }\r
 596 \r
 597   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 598   {\r
 599     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 600     alignPanel.RefreshPanels();\r
 601   }\r
 602 \r
 603 \r
 604   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 605   {\r
 606     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 607     alignPanel.RefreshPanels();\r
 608   }\r
 609 \r
 610   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
 611   {\r
 612     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 613     if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
 614     {\r
 615          AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);\r
 616          ((Alignment)viewport.alignment).featuresAdded = true;\r
 617     }\r
 618     alignPanel.RefreshPanels();\r
 619   }\r
 620 \r
 621   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 622   {\r
 623     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
 624   }\r
 625 \r
 626   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 627   {\r
 628     if (alignPanel.overviewPanel != null)\r
 629       return;\r
 630 \r
 631     JInternalFrame frame = new JInternalFrame();\r
 632     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 633    try{\r
 634      overview = new OverviewPanel(alignPanel, viewport);\r
 635      frame.setContentPane(overview);\r
 636     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 637                              frame.getWidth(), frame.getHeight());\r
 638     frame.pack();\r
 639     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 640     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 641       {\r
 642             alignPanel.setOverviewPanel(null);\r
 643       };\r
 644     });\r
 645     alignPanel.setOverviewPanel( overview );\r
 646 \r
 647   }catch(java.lang.OutOfMemoryError ex)\r
 648    {\r
 649      JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 650                                    +"\nTry reducing the font size.",\r
 651                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 652    }\r
 653 \r
 654 \r
 655   }\r
 656 \r
 657   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 658   {\r
 659     changeColour( null );\r
 660   }\r
 661 \r
 662 \r
 663   public void clustalColour_actionPerformed(ActionEvent e)\r
 664   {\r
 665     abovePIDThreshold.setSelected(false);\r
 666     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 667   }\r
 668 \r
 669   public void zappoColour_actionPerformed(ActionEvent e)\r
 670   {\r
 671     changeColour(new ZappoColourScheme());\r
 672   }\r
 673 \r
 674   public void taylorColour_actionPerformed(ActionEvent e)\r
 675   {\r
 676     changeColour(new TaylorColourScheme());\r
 677   }\r
 678 \r
 679 \r
 680   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 681   {\r
 682     changeColour( new HydrophobicColourScheme() );\r
 683   }\r
 684 \r
 685   public void helixColour_actionPerformed(ActionEvent e)\r
 686   {\r
 687     changeColour(new HelixColourScheme() );\r
 688   }\r
 689 \r
 690 \r
 691   public void strandColour_actionPerformed(ActionEvent e)\r
 692   {\r
 693     changeColour(new StrandColourScheme());\r
 694   }\r
 695 \r
 696 \r
 697   public void turnColour_actionPerformed(ActionEvent e)\r
 698   {\r
 699     changeColour(new TurnColourScheme());\r
 700   }\r
 701 \r
 702 \r
 703   public void buriedColour_actionPerformed(ActionEvent e)\r
 704   {\r
 705     changeColour(new BuriedColourScheme() );\r
 706   }\r
 707 \r
 708   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 709   {\r
 710     changeColour(new NucleotideColourScheme());\r
 711   }\r
 712 \r
 713 \r
 714   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 715   {\r
 716     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
 717   }\r
 718 \r
 719 \r
 720 \r
 721   void changeColour(ColourSchemeI cs)\r
 722   {\r
 723 \r
 724     if(viewport.getColourAppliesToAllGroups())\r
 725     {\r
 726       Vector groups = viewport.alignment.getGroups();\r
 727       for(int i=0; i<groups.size(); i++)\r
 728       {\r
 729         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 730         sg.cs = cs;\r
 731 \r
 732         if(abovePIDThreshold.isSelected())\r
 733           abovePIDThreshold_actionPerformed(null);\r
 734         else if( viewport.getConservationSelected() )\r
 735         {\r
 736           Conservation c = new Conservation("Group",\r
 737                                             ResidueProperties.propHash, 3,\r
 738                                             sg.sequences, sg.getStartRes(),\r
 739                                             sg.getEndRes());\r
 740           c.calculate();\r
 741           c.verdict(false, 100);\r
 742           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 743 \r
 744           sg.cs = ccs;\r
 745         }\r
 746 \r
 747       }\r
 748     }\r
 749 \r
 750 \r
 751     if ( viewport.getAbovePIDThreshold())\r
 752     {\r
 753       int threshold = 0;\r
 754       threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");\r
 755       Desktop.hideConservationSlider();\r
 756 \r
 757       if (cs instanceof ResidueColourScheme)\r
 758         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 759       else if (cs instanceof ScoreColourScheme)\r
 760         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 761 \r
 762       viewport.setGlobalColourScheme(cs);\r
 763 \r
 764     }\r
 765     else\r
 766     if (cs instanceof ResidueColourScheme)\r
 767       ( (ResidueColourScheme) cs).setThreshold(0);\r
 768     else if (cs instanceof ScoreColourScheme)\r
 769       ( (ScoreColourScheme) cs).setThreshold(0);\r
 770 \r
 771 \r
 772 \r
 773 \r
 774 if ( viewport.getConservationSelected() )\r
 775  {\r
 776    ConservationColourScheme ccs = null;\r
 777 \r
 778    Alignment al = (Alignment) viewport.alignment;\r
 779    Conservation c = new Conservation("All",\r
 780                                      ResidueProperties.propHash, 3,\r
 781                                      al.getSequences(), 0,\r
 782                                      al.getWidth());\r
 783 \r
 784    c.calculate();\r
 785    c.verdict(false, 100);\r
 786 \r
 787    ccs = new ConservationColourScheme(c, cs);\r
 788 \r
 789    int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,\r
 790        "Background");\r
 791 \r
 792    ccs.inc = threshold;\r
 793 \r
 794    viewport.setGlobalColourScheme(ccs);\r
 795 \r
 796   }\r
 797   else\r
 798        viewport.setGlobalColourScheme( cs );\r
 799 \r
 800     alignPanel.RefreshPanels();\r
 801   }\r
 802 \r
 803 \r
 804   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 805   {\r
 806     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 807 \r
 808     viewport.setAbovePIDThreshold(false);\r
 809     abovePIDThreshold.setSelected(false);\r
 810     Desktop.hidePIDSlider();\r
 811     if(!viewport.getConservationSelected())\r
 812       Desktop.hideConservationSlider();\r
 813 \r
 814    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 815    if(cs instanceof ConservationColourScheme )\r
 816      changeColour( ((ConservationColourScheme)cs).cs );\r
 817     else\r
 818       changeColour( cs );\r
 819   }\r
 820 \r
 821 \r
 822   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 823   {\r
 824     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
 825 \r
 826     conservationMenuItem.setSelected(false);\r
 827     viewport.setConservationSelected(false);\r
 828     Desktop.hideConservationSlider();\r
 829 \r
 830     if(!viewport.getAbovePIDThreshold())\r
 831       Desktop.hidePIDSlider();\r
 832 \r
 833 \r
 834     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 835     if(cs instanceof ConservationColourScheme )\r
 836         changeColour( ((ConservationColourScheme)cs).cs );\r
 837     else\r
 838         changeColour( cs );\r
 839 \r
 840   }\r
 841 \r
 842 \r
 843 \r
 844   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 845   {\r
 846     JInternalFrame frame = new JInternalFrame();\r
 847     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 848     frame.setContentPane(chooser);\r
 849     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 850     frame.setResizable(false);\r
 851     frame.setIconifiable(false);\r
 852     frame.setMaximizable(false);\r
 853   }\r
 854 \r
 855   public void PIDColour_actionPerformed(ActionEvent e)\r
 856   {\r
 857     changeColour( new PIDColourScheme() );\r
 858   }\r
 859 \r
 860 \r
 861   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 862   {\r
 863     changeColour(new Blosum62ColourScheme(viewport) );\r
 864   }\r
 865 \r
 866 \r
 867 \r
 868   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 869   {\r
 870     addHistoryItem("sort");\r
 871     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 872     alignPanel.RefreshPanels();\r
 873   }\r
 874 \r
 875   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 876   {\r
 877     addHistoryItem("sort");\r
 878     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 879     alignPanel.RefreshPanels();\r
 880   }\r
 881 \r
 882   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 883   {\r
 884     addHistoryItem("sort");\r
 885     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 886     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 887     alignPanel.RefreshPanels();\r
 888   }\r
 889 \r
 890   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 891   {\r
 892     addHistoryItem("sort");\r
 893     if(viewport.getCurrentTree()==null)\r
 894       return;\r
 895 \r
 896     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 897     alignPanel.RefreshPanels();\r
 898   }\r
 899 \r
 900   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 901   {\r
 902     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 903     JInternalFrame frame = new JInternalFrame();\r
 904     frame.setContentPane(sp);\r
 905     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);\r
 906     frame.setMaximizable(false);\r
 907     frame.setResizable(false);\r
 908 \r
 909   }\r
 910 \r
 911   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 912   {\r
 913     if(viewport.getSelection().size()<2)\r
 914       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 915     else\r
 916     {\r
 917       JInternalFrame frame = new JInternalFrame();\r
 918       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 919       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 920     }\r
 921   }\r
 922 \r
 923   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 924   {\r
 925     if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)\r
 926        || viewport.getAlignment().getHeight()<4)\r
 927     {\r
 928       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
 929                                     +"at least 4 input sequences.",\r
 930                                     "Sequence selection insufficient",\r
 931                                     JOptionPane.WARNING_MESSAGE);\r
 932       return;\r
 933     }\r
 934 \r
 935     try{\r
 936       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 937       JInternalFrame frame = new JInternalFrame();\r
 938       frame.setContentPane(pcaPanel);\r
 939       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 940    }catch(java.lang.OutOfMemoryError ex)\r
 941    {\r
 942      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 943                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 944    }\r
 945 \r
 946 \r
 947   }\r
 948 \r
 949   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 950   {\r
 951     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 952   }\r
 953 \r
 954   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 955   {\r
 956     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 957   }\r
 958 \r
 959 \r
 960   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 961   {\r
 962     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 963   }\r
 964 \r
 965   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 966   {\r
 967     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 968   }\r
 969 \r
 970   void NewTreePanel(String type, String pwType, String title)\r
 971   {\r
 972     //are the sequences aligned?\r
 973     if(!viewport.alignment.isAligned())\r
 974     {\r
 975       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
 976                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
 977       return;\r
 978     }\r
 979 \r
 980     TreePanel tp=null;\r
 981    if (viewport.getSelection() != null && viewport.getSelection().size() > 3)\r
 982    {\r
 983      tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,\r
 984                          0, viewport.alignment.getWidth());\r
 985    }\r
 986    else\r
 987    {\r
 988      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 989                          type, pwType,  0, viewport.alignment.getWidth());\r
 990    }\r
 991 \r
 992    Desktop.addInternalFrame(tp, title, 600, 500);\r
 993   }\r
 994 \r
 995 \r
 996 \r
 997 \r
 998   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 999   {\r
1000     JInternalFrame frame = new JInternalFrame();\r
1001     ClustalThread ct = new ClustalThread(frame);\r
1002     Thread t = new Thread(ct);\r
1003     t.start();\r
1004     frame.setContentPane(ct);\r
1005      Desktop.addInternalFrame(frame, title, 300, 80);\r
1006 \r
1007   }\r
1008 \r
1009   class ClustalThread extends JPanel implements Runnable\r
1010   {\r
1011     Image [] image;\r
1012     int imageIndex = 0;\r
1013     boolean webServiceRunning = false;\r
1014     JInternalFrame frame;\r
1015     public ClustalThread(JInternalFrame frame)\r
1016     {\r
1017       this.frame = frame;\r
1018       image = new Image[9];\r
1019       for(int i=0; i<9; i++)\r
1020       {\r
1021         java.net.URL url = getClass().getResource("/dna" + (i+1) + ".gif");\r
1022         if (url != null)\r
1023         {\r
1024           image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
1025           MediaTracker mt = new MediaTracker(this);\r
1026           mt.addImage(image[i], i);\r
1027           try{mt.waitForID(i);}\r
1028           catch(Exception ex){}\r
1029         }\r
1030       }\r
1031       DNATwirler twirler = new DNATwirler();\r
1032       twirler.start();\r
1033       webServiceRunning = true;\r
1034     }\r
1035 \r
1036     class DNATwirler extends Thread\r
1037     {\r
1038       public void run()\r
1039       {\r
1040         while(webServiceRunning)\r
1041         {\r
1042           try{\r
1043             Thread.sleep(100);\r
1044             imageIndex++;\r
1045             imageIndex %=9;\r
1046             repaint();\r
1047           }\r
1048           catch(Exception ex){}\r
1049         }\r
1050       }\r
1051     }\r
1052 \r
1053     // JBPNote\r
1054     // Should check to see if the server settings are valid\r
1055     // Need visual-delay indication here.\r
1056     public void run()\r
1057        {\r
1058          jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
1059          Vector sv = viewport.getAlignment().getSequences();\r
1060          SequenceI[] seqs = new SequenceI[sv.size()];\r
1061 \r
1062          int i = 0;\r
1063          do\r
1064          {\r
1065            seqs[i] = (SequenceI) sv.elementAt(i);\r
1066          }\r
1067          while (++i < sv.size());\r
1068 \r
1069          SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
1070 \r
1071          if (alignment != null)\r
1072          {\r
1073            AlignFrame af = new AlignFrame(new Alignment(alignment));\r
1074           af.clustalColour.setSelected(true);\r
1075           af.clustalColour_actionPerformed(null);\r
1076            Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),\r
1077                                     700, 500); // JBPNote - is there a new window geom. property ?\r
1078          }\r
1079          else\r
1080            JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",\r
1081                                          JOptionPane.WARNING_MESSAGE);\r
1082 \r
1083          webServiceRunning = false;\r
1084          try{\r
1085            frame.setClosed(true);\r
1086          }catch(Exception ex){}\r
1087        }\r
1088 \r
1089        public void paintComponent(Graphics g)\r
1090        {\r
1091          g.setColor(Color.white);\r
1092          g.fillRect(0,0,getWidth(), getHeight());\r
1093          if(image!=null)\r
1094          {\r
1095            g.drawImage(image[imageIndex],10,10,this);\r
1096          }\r
1097          g.setFont(new Font("Arial", Font.BOLD, 12));\r
1098          g.setColor(Color.black);\r
1099          g.drawString("Clustal Alignment Web Service running", 30,30);\r
1100        }\r
1101   }\r
1102 }\r