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