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 MCview.*;\r
  21 import java.awt.*;\r
  22 import java.awt.event.*;\r
  23 import java.awt.print.*;\r
  24 import javax.swing.*;\r
  25 import javax.swing.event.*;\r
  26 import java.util.*;\r
  27 import jalview.datamodel.SequenceI;\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 \r
  43   protected void saveAs_actionPerformed(ActionEvent e)\r
  44   {\r
  45     JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);\r
  46     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
  47     chooser.setToolTipText("Save");\r
  48     int value = chooser.showSaveDialog(this);\r
  49     if(value == JFileChooser.APPROVE_OPTION)\r
  50     {\r
  51       String choice =  chooser.getSelectedFile().getPath();\r
  52       jalview.bin.Cache.LAST_DIRECTORY = choice;\r
  53       String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
  54       try{\r
  55         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
  56         out.println(output);\r
  57         out.close();\r
  58       }\r
  59       catch(Exception ex){}\r
  60     }\r
  61 \r
  62   }\r
  63 \r
  64   protected void outputText_actionPerformed(ActionEvent e)\r
  65   {\r
  66      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
  67      JInternalFrame frame = new JInternalFrame();\r
  68      cap.formatForOutput();\r
  69      frame.setContentPane(cap);\r
  70      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
  71      cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
  72   }\r
  73 \r
  74   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
  75   {\r
  76     HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
  77     htmlOutput = null;\r
  78   }\r
  79 \r
  80   public void printMenuItem_actionPerformed(ActionEvent e)\r
  81   {\r
  82     //Putting in a thread avoids Swing painting problems\r
  83     PrintThread thread = new PrintThread();\r
  84     thread.start();\r
  85   }\r
  86 \r
  87   class PrintThread extends Thread\r
  88   {\r
  89     public void run()\r
  90     {\r
  91       PrinterJob printJob = PrinterJob.getPrinterJob();\r
  92       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
  93       printJob.setPrintable(alignPanel, pf);\r
  94       if (printJob.printDialog())\r
  95       {\r
  96         try\r
  97         {\r
  98           printJob.print();\r
  99         }\r
 100         catch (Exception PrintException)\r
 101         {\r
 102           PrintException.printStackTrace();\r
 103         }\r
 104       }\r
 105     }\r
 106 \r
 107   }\r
 108 \r
 109 \r
 110 \r
 111 \r
 112   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 113   {\r
 114     try{\r
 115       this.setClosed(true);\r
 116     }catch(Exception ex){}\r
 117   }\r
 118 \r
 119   ArrayList  historyList = new ArrayList();\r
 120   ArrayList redoList = new ArrayList();\r
 121 \r
 122   void updateEditMenuBar()\r
 123   {\r
 124     if(historyList.size()>0)\r
 125      {\r
 126        undoMenuItem.setEnabled(true);\r
 127        Object [] history = (Object[])historyList.get(0);\r
 128        undoMenuItem.setText("Undo "+history[0]);\r
 129      }\r
 130     else\r
 131     {\r
 132       undoMenuItem.setEnabled(false);\r
 133       undoMenuItem.setText("Undo");\r
 134     }\r
 135 \r
 136     if(redoList.size()>0)\r
 137      {\r
 138        redoMenuItem.setEnabled(true);\r
 139        Object [] history = (Object[])redoList.get(0);\r
 140        redoMenuItem.setText("Redo "+history[0]);\r
 141      }\r
 142     else\r
 143     {\r
 144       redoMenuItem.setEnabled(false);\r
 145       redoMenuItem.setText("Redo");\r
 146     }\r
 147   }\r
 148 \r
 149   public void addHistoryItem(String type)\r
 150   {\r
 151     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 152     redoList.clear();\r
 153     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 154     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 155     {\r
 156       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 157                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 158     }\r
 159 \r
 160     historyList.add(0, new Object[]{type,  seq} );\r
 161     updateEditMenuBar();\r
 162   }\r
 163 \r
 164   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 165   {\r
 166     Object [] history = (Object[])historyList.remove(0);\r
 167     // add the redo state before continuing!!\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).\r
 173                             getSequence());\r
 174     }\r
 175     /////////\r
 176 \r
 177     redoList.add(0, new Object[] {history[0], seq});\r
 178 \r
 179       seq = (SequenceI[]) history[1];\r
 180       viewport.setAlignment( new Alignment(seq) );\r
 181       updateEditMenuBar();\r
 182       alignPanel.RefreshPanels();\r
 183   }\r
 184 \r
 185 \r
 186   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 187   {\r
 188      Object [] history = (Object[])redoList.remove(0);\r
 189      SequenceI[] seq = (SequenceI[]) history[1];\r
 190      viewport.setAlignment( new Alignment(seq) );\r
 191      updateEditMenuBar();\r
 192      alignPanel.RefreshPanels();\r
 193   }\r
 194 \r
 195 \r
 196   public void groupsMenuItem_actionPerformed(ActionEvent e)\r
 197   {\r
 198     GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
 199     JInternalFrame frame = new JInternalFrame();\r
 200     frame.setContentPane(geditor);\r
 201     Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
 202     frame.setResizable(false);\r
 203   }\r
 204 \r
 205   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 206   {\r
 207     viewport.alignment.deleteAllGroups();\r
 208     alignPanel.RefreshPanels();\r
 209   }\r
 210 \r
 211 \r
 212 \r
 213   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 214   {\r
 215     Selection sel = viewport.getSelection();\r
 216     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 217       sel.addElement( viewport.getAlignment().getSequenceAt(i));\r
 218     PaintRefresher.Refresh(null);\r
 219   }\r
 220 \r
 221   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 222   {\r
 223     viewport.getSelection().clear();\r
 224     PaintRefresher.Refresh(null);\r
 225   }\r
 226 \r
 227   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 228   {\r
 229     Selection sel = viewport.getSelection();\r
 230     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 231     {\r
 232       if (sel.contains(viewport.getAlignment().getSequenceAt(i)))\r
 233         sel.removeElement(viewport.getAlignment().getSequenceAt(i));\r
 234       else\r
 235         sel.addElement(viewport.getAlignment().getSequenceAt(i));\r
 236     }\r
 237     PaintRefresher.Refresh(null);\r
 238   }\r
 239 \r
 240 \r
 241   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 242   {\r
 243     viewport.getColumnSelection().clear();\r
 244     repaint();\r
 245   }\r
 246 \r
 247   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 248   {\r
 249     addHistoryItem("delete columns");\r
 250     ColumnSelection colSel = viewport.getColumnSelection();\r
 251     if (colSel.size() > 0)\r
 252     {\r
 253       int min = colSel.getMin();\r
 254       viewport.getAlignment().trimLeft(min);\r
 255       colSel.compensateForEdit(0,min);\r
 256       alignPanel.RefreshPanels();\r
 257     }\r
 258   }\r
 259 \r
 260   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 261   {\r
 262     addHistoryItem("delete columns");\r
 263     ColumnSelection colSel = viewport.getColumnSelection();\r
 264     if (colSel.size() > 0)\r
 265     {\r
 266       int max = colSel.getMax();\r
 267       if(max>1)\r
 268         viewport.getAlignment().trimRight(max);\r
 269 \r
 270       alignPanel.RefreshPanels();\r
 271     }\r
 272 \r
 273   }\r
 274 \r
 275   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 276   {\r
 277     addHistoryItem("delete gapped columns");\r
 278     viewport.getAlignment().removeGaps();\r
 279     alignPanel.RefreshPanels();\r
 280   }\r
 281 \r
 282   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 283   {\r
 284     addHistoryItem("delete all gaps");\r
 285     SequenceI current;\r
 286     int jSize;\r
 287     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 288     {\r
 289       current = viewport.getAlignment().getSequenceAt(i);\r
 290       jSize = current.getLength();\r
 291       for (int j=0; j < jSize; j++)\r
 292         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 293         {\r
 294           current.deleteCharAt(j);\r
 295           j--;\r
 296           jSize--;\r
 297         }\r
 298     }\r
 299 \r
 300     alignPanel.RefreshPanels();\r
 301   }\r
 302 \r
 303   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 304   {\r
 305     char thisChar = '-';\r
 306     char nextChar = '.';\r
 307     if(viewport.getGapCharacter()=='-')\r
 308     {\r
 309       thisChar = '.';\r
 310       nextChar = '-';\r
 311     }\r
 312     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 313     viewport.setGapCharacter(thisChar);\r
 314     alignPanel.RefreshPanels();\r
 315   }\r
 316 \r
 317   public void findMenuItem_actionPerformed(ActionEvent e)\r
 318   {\r
 319     JOptionPane op = new JOptionPane();\r
 320     JInternalFrame frame =  op.createInternalFrame(this, "Find");\r
 321     Finder finder = new Finder(viewport, alignPanel, frame);\r
 322     frame.setClosable(true);\r
 323     frame.setContentPane(finder);\r
 324     frame.setSize(340,110);\r
 325     frame.setVisible(true);\r
 326   }\r
 327 \r
 328 \r
 329 \r
 330   public void fontNameMenuItem_actionPerformed(ActionEvent e)\r
 331   {\r
 332     String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();\r
 333 \r
 334 \r
 335     String selection = JOptionPane.showInternalInputDialog(this,\r
 336                                 "Select font",\r
 337                                 "Font selection",\r
 338                                 JOptionPane.QUESTION_MESSAGE,\r
 339                                 null,fonts\r
 340                                 ,fontNameMenuItem.getText()).toString();\r
 341     if(selection!=null)\r
 342     {\r
 343        fontNameMenuItem.setText(selection);\r
 344        SetFont();\r
 345      }\r
 346 \r
 347   }\r
 348 \r
 349   public void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
 350   {\r
 351     String selection = JOptionPane.showInternalInputDialog(this,\r
 352                                 "Select font size",\r
 353                                 "Font size",\r
 354                                 JOptionPane.QUESTION_MESSAGE,\r
 355                                 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
 356                                 ,fontSizeMenuItem.getText()).toString();\r
 357     if(selection!=null)\r
 358      {\r
 359        fontSizeMenuItem.setText(selection);\r
 360        SetFont();\r
 361      }\r
 362   }\r
 363 \r
 364   public void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
 365   {\r
 366     String selection = JOptionPane.showInternalInputDialog(this,\r
 367                                 "Select font style",\r
 368                                 "Font style",\r
 369                                 JOptionPane.QUESTION_MESSAGE,\r
 370                                 null, new String[]{"plain", "bold", "italic"}\r
 371                                 ,fontStyleMenuItem.getText()).toString();\r
 372     if(selection!=null)\r
 373     {\r
 374       fontStyleMenuItem.setText(selection);\r
 375       SetFont();\r
 376     }\r
 377 \r
 378   }\r
 379 \r
 380   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 381   {\r
 382       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 383       alignPanel.RefreshPanels();\r
 384   }\r
 385 \r
 386   void SetFont()\r
 387   {\r
 388       int style = java.awt.Font.PLAIN;\r
 389       if(fontStyleMenuItem.getText().equals("bold"))\r
 390         style = java.awt.Font.BOLD;\r
 391       else if(fontStyleMenuItem.getText().equals("italic"))\r
 392         style = java.awt.Font.ITALIC;\r
 393 \r
 394       viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),\r
 395                                            style,\r
 396                                            Integer.parseInt(fontSizeMenuItem.getText())));\r
 397       alignPanel.RefreshPanels();\r
 398 \r
 399   }\r
 400 \r
 401   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 402   {\r
 403     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 404     alignPanel.RefreshPanels();\r
 405   }\r
 406 \r
 407 \r
 408   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 409   {\r
 410     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 411     alignPanel.RefreshPanels();\r
 412   }\r
 413 \r
 414   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 415   {\r
 416     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 417     alignPanel.RefreshPanels();\r
 418   }\r
 419 \r
 420 \r
 421   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 422   {\r
 423     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 424     alignPanel.RefreshPanels();\r
 425   }\r
 426 \r
 427   public void secondaryStructure_actionPerformed(ActionEvent evt)\r
 428   {\r
 429     alignPanel.setSecondaryStructureVisible(secondaryStructure.isSelected());\r
 430   }\r
 431 \r
 432   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 433   {\r
 434     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
 435   }\r
 436 \r
 437   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 438   {\r
 439     if (alignPanel.overviewPanel != null)\r
 440       return;\r
 441 \r
 442     JInternalFrame frame = new JInternalFrame();\r
 443     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 444    try{\r
 445      overview = new OverviewPanel(alignPanel, viewport);\r
 446      frame.setContentPane(overview);\r
 447     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 448                              frame.getWidth(), frame.getHeight());\r
 449     frame.pack();\r
 450     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 451     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 452       {\r
 453             alignPanel.setOverviewPanel(null);\r
 454       };\r
 455     });\r
 456     alignPanel.setOverviewPanel( overview );\r
 457 \r
 458   }catch(java.lang.OutOfMemoryError ex)\r
 459    {\r
 460      JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 461                                    +"\nTry reducing the font size.",\r
 462                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 463    }\r
 464 \r
 465 \r
 466   }\r
 467 \r
 468   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 469   {\r
 470     viewport.setGlobalColourScheme( null );\r
 471     changeColour();\r
 472   }\r
 473 \r
 474 \r
 475   public void Colour_actionPerformed(ActionEvent e)\r
 476   {\r
 477     viewport.setGlobalColourScheme(new ClustalxColourScheme( ));\r
 478     conservationMenuItem.setSelected(false);\r
 479     abovePIDThreshold.setSelected(false);\r
 480     changeColour();\r
 481   }\r
 482 \r
 483   public void zappoColour_actionPerformed(ActionEvent e)\r
 484   {\r
 485     viewport.setGlobalColourScheme(new ZappoColourScheme() );\r
 486     changeColour();\r
 487   }\r
 488 \r
 489   public void taylorColour_actionPerformed(ActionEvent e)\r
 490   {\r
 491     viewport.setGlobalColourScheme(new TaylorColourScheme() );\r
 492     changeColour();\r
 493   }\r
 494 \r
 495 \r
 496   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 497   {\r
 498     viewport.setGlobalColourScheme( new HydrophobicColourScheme() );\r
 499     changeColour();\r
 500   }\r
 501 \r
 502   public void helixColour_actionPerformed(ActionEvent e)\r
 503   {\r
 504     viewport.setGlobalColourScheme( new HelixColourScheme()  );\r
 505     changeColour();\r
 506   }\r
 507 \r
 508 \r
 509   public void strandColour_actionPerformed(ActionEvent e)\r
 510   {\r
 511     viewport.setGlobalColourScheme(new StrandColourScheme() );\r
 512     changeColour();\r
 513   }\r
 514 \r
 515 \r
 516   public void turnColour_actionPerformed(ActionEvent e)\r
 517   {\r
 518     viewport.setGlobalColourScheme(new TurnColourScheme() );\r
 519     changeColour();\r
 520   }\r
 521 \r
 522 \r
 523   public void buriedColour_actionPerformed(ActionEvent e)\r
 524   {\r
 525     viewport.setGlobalColourScheme( new BuriedColourScheme() );\r
 526     changeColour();\r
 527   }\r
 528 \r
 529   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 530   {\r
 531     viewport.setGlobalColourScheme( new NucleotideColourScheme() );\r
 532     changeColour();\r
 533   }\r
 534 \r
 535 \r
 536   void changeColour()\r
 537   {\r
 538     if(abovePIDThreshold.isSelected())\r
 539       abovePIDThreshold_actionPerformed(null);\r
 540     else if(conservationMenuItem.isSelected())\r
 541       conservationMenuItem_actionPerformed(null);\r
 542 \r
 543 \r
 544      alignPanel.RefreshPanels();\r
 545   }\r
 546 \r
 547   void addConservationOrPIDColour()\r
 548   {\r
 549     int x=0, y=0, threshold = 70;\r
 550 \r
 551     if(sliderFrame!=null)\r
 552        try\r
 553        {\r
 554          x = sliderFrame.getX();\r
 555          y = sliderFrame.getY();\r
 556          SliderPanel sp = (SliderPanel) sliderFrame.getContentPane();\r
 557          threshold = sp.getValue();\r
 558          sliderFrame.setClosed(true);\r
 559        }\r
 560        catch (Exception ex)\r
 561        {    ex.printStackTrace();   }\r
 562 \r
 563      ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
 564 \r
 565      ConservationColourScheme ccs = null;\r
 566      if (oldCs instanceof ConservationColourScheme)\r
 567        ccs = (ConservationColourScheme) oldCs;\r
 568 \r
 569      if(conservationMenuItem.isSelected())\r
 570      {\r
 571        Alignment al = (Alignment)viewport.alignment;\r
 572        Conservation c = new Conservation("All",\r
 573                             ResidueProperties.propHash, 3, al.getSequences(), 0,\r
 574                             al.getWidth() );\r
 575 \r
 576        c.calculate();\r
 577        c.verdict(false, 100);\r
 578 \r
 579        if(ccs!=null)\r
 580          ccs = new ConservationColourScheme(c, ccs.cs);\r
 581        else\r
 582          ccs = new ConservationColourScheme(c, oldCs);\r
 583 \r
 584         viewport.setGlobalColourScheme( ccs );\r
 585 \r
 586      }\r
 587      else if(oldCs instanceof ConservationColourScheme)\r
 588      {\r
 589        oldCs = ccs.cs;\r
 590        viewport.setGlobalColourScheme( oldCs );\r
 591      }\r
 592 \r
 593 \r
 594      if( conservationMenuItem.isSelected() || abovePIDThreshold.isSelected() )\r
 595      {\r
 596        sliderFrame = new JInternalFrame();\r
 597        sliderFrame.setMaximizable(false);\r
 598        sliderFrame.setResizable(false);\r
 599 \r
 600        SliderPanel sp = null;\r
 601        if (conservationMenuItem.isSelected())\r
 602        {\r
 603         if(threshold > 50)\r
 604           threshold = 30;\r
 605         sp = new SliderPanel(alignPanel, threshold, true,ccs);\r
 606         Desktop.addInternalFrame(sliderFrame, "Conservation Colour Increment  (Global colour)", 400, 90);\r
 607         threshold = 0;\r
 608        }\r
 609        else if (abovePIDThreshold.isSelected())\r
 610        {\r
 611          sp = new SliderPanel(alignPanel, threshold, false, oldCs);\r
 612          sp.cs = oldCs;\r
 613          Desktop.addInternalFrame(sliderFrame, "Percentage Identity Threshold (Global colour)", 400, 90);\r
 614        }\r
 615 \r
 616        sliderFrame.setContentPane(sp);\r
 617        if(x!=0 && y!=0)\r
 618                sliderFrame.setLocation(x,y);\r
 619 \r
 620      }\r
 621      else\r
 622        threshold = 0;\r
 623 \r
 624 \r
 625      if (oldCs instanceof ResidueColourScheme)\r
 626      {\r
 627        ResidueColourScheme rcs = (ResidueColourScheme) oldCs;\r
 628        rcs.setThreshold(threshold);\r
 629      }\r
 630      else if (oldCs instanceof ScoreColourScheme)\r
 631      {\r
 632        ScoreColourScheme scs = (ScoreColourScheme) oldCs;\r
 633        scs.setThreshold(threshold);\r
 634      }\r
 635 \r
 636 \r
 637   }\r
 638 \r
 639   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 640   {\r
 641    if(abovePIDThreshold.isSelected())\r
 642     abovePIDThreshold.setSelected(false);\r
 643 \r
 644    viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 645 \r
 646    addConservationOrPIDColour();\r
 647   }\r
 648 \r
 649   JInternalFrame sliderFrame;\r
 650   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 651   {\r
 652       if(conservationMenuItem.isSelected())\r
 653         conservationMenuItem.setSelected(false);\r
 654 \r
 655       addConservationOrPIDColour();\r
 656   }\r
 657 \r
 658 \r
 659 \r
 660   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 661   {\r
 662     JInternalFrame frame = new JInternalFrame();\r
 663     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 664     frame.setContentPane(chooser);\r
 665     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 666     frame.setResizable(false);\r
 667     frame.setIconifiable(false);\r
 668     frame.setMaximizable(false);\r
 669   }\r
 670 \r
 671   public void PIDColour_actionPerformed(ActionEvent e)\r
 672   {\r
 673     viewport.setGlobalColourScheme( new PIDColourScheme() );\r
 674     alignPanel.setColourScheme( );\r
 675   }\r
 676 \r
 677 \r
 678   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 679   {\r
 680     viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport)  );\r
 681     alignPanel.setColourScheme();\r
 682   }\r
 683 \r
 684 \r
 685 \r
 686   protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
 687   {\r
 688     ColourKey colourKey = new ColourKey( viewport.getGlobalColourScheme() );\r
 689     Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);\r
 690   }\r
 691 \r
 692 \r
 693   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 694   {\r
 695     addHistoryItem("sort");\r
 696     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 697     alignPanel.RefreshPanels();\r
 698   }\r
 699 \r
 700   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 701   {\r
 702     addHistoryItem("sort");\r
 703     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 704     alignPanel.RefreshPanels();\r
 705   }\r
 706 \r
 707   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 708   {\r
 709     addHistoryItem("sort");\r
 710     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 711     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 712     alignPanel.RefreshPanels();\r
 713   }\r
 714 \r
 715   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 716   {\r
 717     addHistoryItem("sort");\r
 718     if(viewport.getCurrentTree()==null)\r
 719       return;\r
 720 \r
 721     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 722     alignPanel.RefreshPanels();\r
 723   }\r
 724 \r
 725   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 726   {\r
 727     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 728     JInternalFrame frame = new JInternalFrame();\r
 729     frame.setContentPane(sp);\r
 730     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);\r
 731     frame.setMaximizable(false);\r
 732     frame.setResizable(false);\r
 733 \r
 734   }\r
 735 \r
 736   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 737   {\r
 738     if(viewport.getSelection().size()<2)\r
 739       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 740     else\r
 741     {\r
 742       JInternalFrame frame = new JInternalFrame();\r
 743       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 744       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 745     }\r
 746   }\r
 747 \r
 748   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 749   {\r
 750     if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)\r
 751        || viewport.getAlignment().getHeight()<4)\r
 752     {\r
 753       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
 754                                     +"at least 4 input sequences.",\r
 755                                     "Sequence selection insufficient",\r
 756                                     JOptionPane.WARNING_MESSAGE);\r
 757       return;\r
 758     }\r
 759 \r
 760     try{\r
 761       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 762       JInternalFrame frame = new JInternalFrame();\r
 763       frame.setContentPane(pcaPanel);\r
 764       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 765    }catch(java.lang.OutOfMemoryError ex)\r
 766    {\r
 767      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 768                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 769    }\r
 770 \r
 771 \r
 772   }\r
 773 \r
 774   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 775   {\r
 776     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 777   }\r
 778 \r
 779   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 780   {\r
 781     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 782   }\r
 783 \r
 784 \r
 785   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 786   {\r
 787     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 788   }\r
 789 \r
 790   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 791   {\r
 792     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 793   }\r
 794 \r
 795   void NewTreePanel(String type, String pwType, String title)\r
 796   {\r
 797     JInternalFrame frame = new javax.swing.JInternalFrame();\r
 798     TreePanel tp=null;\r
 799    if (viewport.getSelection() != null && viewport.getSelection().size() > 3)\r
 800    {\r
 801      tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,\r
 802                          viewport.getStartRes(), viewport.getEndRes());\r
 803    }\r
 804    else\r
 805    {\r
 806      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 807                          type, pwType, viewport.getStartRes(),\r
 808                          viewport.getEndRes());\r
 809    }\r
 810 \r
 811    frame.setContentPane(tp);\r
 812    Desktop.addInternalFrame(frame, title, 600, 500);\r
 813   }\r
 814 \r
 815 \r
 816 \r
 817 \r
 818   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 819   {\r
 820     JInternalFrame frame = new JInternalFrame();\r
 821     ClustalThread ct = new ClustalThread(frame);\r
 822     Thread t = new Thread(ct);\r
 823     t.start();\r
 824     frame.setContentPane(ct);\r
 825      Desktop.addInternalFrame(frame, title, 300, 80);\r
 826 \r
 827   }\r
 828 \r
 829   class ClustalThread extends JPanel implements Runnable\r
 830   {\r
 831     Image [] image;\r
 832     int imageIndex = 0;\r
 833     boolean webServiceRunning = false;\r
 834     JInternalFrame frame;\r
 835     public ClustalThread(JInternalFrame frame)\r
 836     {\r
 837       this.frame = frame;\r
 838       image = new Image[9];\r
 839       for(int i=0; i<9; i++)\r
 840       {\r
 841         java.net.URL url = getClass().getResource("/dna" + (i+1) + ".gif");\r
 842         if (url != null)\r
 843         {\r
 844           image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
 845           MediaTracker mt = new MediaTracker(this);\r
 846           mt.addImage(image[i], i);\r
 847           try{mt.waitForID(i);}\r
 848           catch(Exception ex){}\r
 849         }\r
 850       }\r
 851       DNATwirler twirler = new DNATwirler();\r
 852       twirler.start();\r
 853       webServiceRunning = true;\r
 854     }\r
 855 \r
 856     class DNATwirler extends Thread\r
 857     {\r
 858       public void run()\r
 859       {\r
 860         while(webServiceRunning)\r
 861         {\r
 862           try{\r
 863             Thread.sleep(100);\r
 864             imageIndex++;\r
 865             imageIndex %=9;\r
 866             repaint();\r
 867           }\r
 868           catch(Exception ex){}\r
 869         }\r
 870       }\r
 871     }\r
 872 \r
 873     // JBPNote\r
 874     // Should check to see if the server settings are valid\r
 875     // Need visual-delay indication here.\r
 876     public void run()\r
 877        {\r
 878          jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
 879          Vector sv = viewport.getAlignment().getSequences();\r
 880          SequenceI[] seqs = new SequenceI[sv.size()];\r
 881 \r
 882          int i = 0;\r
 883          do\r
 884          {\r
 885            seqs[i] = (SequenceI) sv.elementAt(i);\r
 886          }\r
 887          while (++i < sv.size());\r
 888 \r
 889          SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
 890 \r
 891          if (alignment != null)\r
 892          {\r
 893            AlignFrame af = new AlignFrame(new Alignment(alignment));\r
 894            Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),\r
 895                                     700, 500); // JBPNote - is there a new window geom. property ?\r
 896          }\r
 897          else\r
 898            JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",\r
 899                                          JOptionPane.WARNING_MESSAGE);\r
 900 \r
 901          webServiceRunning = false;\r
 902          try{\r
 903            frame.setClosed(true);\r
 904          }catch(Exception ex){}\r
 905        }\r
 906 \r
 907        public void paintComponent(Graphics g)\r
 908        {\r
 909          g.setColor(Color.white);\r
 910          g.fillRect(0,0,getWidth(), getHeight());\r
 911          if(image!=null)\r
 912          {\r
 913            g.drawImage(image[imageIndex],10,10,this);\r
 914          }\r
 915          g.setFont(new Font("Arial", Font.BOLD, 12));\r
 916          g.setColor(Color.black);\r
 917          g.drawString("Clustal Alignment Web Service running", 30,30);\r
 918        }\r
 919 \r
 920 \r
 921   }\r
 922 \r
 923 \r
 924   public void pdbTest_actionPerformed(ActionEvent e)\r
 925   {\r
 926    String reply =\r
 927        JOptionPane.showInternalInputDialog(this, "Enter pdb code",\r
 928                                            "PDB test viewer", JOptionPane.QUESTION_MESSAGE);\r
 929 \r
 930    String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";\r
 931    if (reply.length()>1)\r
 932      url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id="+reply;\r
 933 \r
 934    try\r
 935    {\r
 936      PDBfile pdb = new PDBfile(url,\r
 937                                "URL");\r
 938     Sequence seq = (Sequence)viewport.getAlignment().getSequenceAt(0);\r
 939     seq.setPDBfile(pdb);\r
 940      ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).isVisible = true;\r
 941      ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).sequence = seq;\r
 942   // ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).colourBySequence();\r
 943 \r
 944      rotCanvas rc = new rotCanvas(pdb);\r
 945      JInternalFrame frame = new JInternalFrame();\r
 946      frame.setContentPane(rc);\r
 947      Desktop.addInternalFrame(frame, url, 400,400);\r
 948    }\r
 949    catch (Exception ex)\r
 950    {\r
 951      ex.printStackTrace();\r
 952    }\r
 953 \r
 954   }\r
 955 \r
 956 \r
 957   public void doKeyPressed(KeyEvent evt)\r
 958   {\r
 959 \r
 960     System.out.println(evt.getKeyChar());\r
 961     if(evt.isControlDown() && evt.getKeyChar()=='f')\r
 962       findMenuItem_actionPerformed(null);\r
 963 \r
 964   }\r
 965 \r
 966 \r
 967 }\r