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 \r
 206   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 207   {\r
 208     Selection sel = viewport.getSelection();\r
 209     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 210       sel.addElement( viewport.getAlignment().getSequenceAt(i));\r
 211     PaintRefresher.Refresh(null);\r
 212   }\r
 213 \r
 214   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 215   {\r
 216     viewport.getSelection().clear();\r
 217     PaintRefresher.Refresh(null);\r
 218   }\r
 219 \r
 220   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 221   {\r
 222     Selection sel = viewport.getSelection();\r
 223     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 224     {\r
 225       if (sel.contains(viewport.getAlignment().getSequenceAt(i)))\r
 226         sel.removeElement(viewport.getAlignment().getSequenceAt(i));\r
 227       else\r
 228         sel.addElement(viewport.getAlignment().getSequenceAt(i));\r
 229     }\r
 230     PaintRefresher.Refresh(null);\r
 231   }\r
 232 \r
 233 \r
 234   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 235   {\r
 236     viewport.getColumnSelection().clear();\r
 237     repaint();\r
 238   }\r
 239 \r
 240   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 241   {\r
 242     addHistoryItem("delete columns");\r
 243     ColumnSelection colSel = viewport.getColumnSelection();\r
 244     if (colSel.size() > 0)\r
 245     {\r
 246       int min = colSel.getMin();\r
 247       viewport.getAlignment().trimLeft(min);\r
 248       colSel.compensateForEdit(0,min);\r
 249       alignPanel.RefreshPanels();\r
 250     }\r
 251   }\r
 252 \r
 253   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 254   {\r
 255     addHistoryItem("delete columns");\r
 256     ColumnSelection colSel = viewport.getColumnSelection();\r
 257     if (colSel.size() > 0)\r
 258     {\r
 259       int max = colSel.getMax();\r
 260       if(max>1)\r
 261         viewport.getAlignment().trimRight(max);\r
 262 \r
 263       alignPanel.RefreshPanels();\r
 264     }\r
 265 \r
 266   }\r
 267 \r
 268   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 269   {\r
 270     addHistoryItem("delete gapped columns");\r
 271     viewport.getAlignment().removeGaps();\r
 272     alignPanel.RefreshPanels();\r
 273   }\r
 274 \r
 275   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 276   {\r
 277     addHistoryItem("delete all gaps");\r
 278     SequenceI current;\r
 279     int jSize;\r
 280     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 281     {\r
 282       current = viewport.getAlignment().getSequenceAt(i);\r
 283       jSize = current.getLength();\r
 284       for (int j=0; j < jSize; j++)\r
 285         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 286         {\r
 287           current.deleteCharAt(j);\r
 288           j--;\r
 289           jSize--;\r
 290         }\r
 291     }\r
 292 \r
 293     alignPanel.RefreshPanels();\r
 294   }\r
 295 \r
 296   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 297   {\r
 298     char thisChar = '-';\r
 299     char nextChar = '.';\r
 300     if(viewport.getGapCharacter()=='-')\r
 301     {\r
 302       thisChar = '.';\r
 303       nextChar = '-';\r
 304     }\r
 305     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 306     viewport.setGapCharacter(thisChar);\r
 307     alignPanel.RefreshPanels();\r
 308   }\r
 309 \r
 310   public void findMenuItem_actionPerformed(ActionEvent e)\r
 311   {\r
 312     JOptionPane op = new JOptionPane();\r
 313     JInternalFrame frame =  op.createInternalFrame(this, "Find");\r
 314     Finder finder = new Finder(viewport, alignPanel, frame);\r
 315     frame.setContentPane(finder);\r
 316     frame.setSize(300,110);\r
 317     frame.setVisible(true);\r
 318   }\r
 319 \r
 320 \r
 321 \r
 322   public void fontNameMenuItem_actionPerformed(ActionEvent e)\r
 323   {\r
 324     String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();\r
 325 \r
 326 \r
 327     String selection = JOptionPane.showInternalInputDialog(this,\r
 328                                 "Select font",\r
 329                                 "Font selection",\r
 330                                 JOptionPane.QUESTION_MESSAGE,\r
 331                                 null,fonts\r
 332                                 ,fontNameMenuItem.getText()).toString();\r
 333     if(selection!=null)\r
 334     {\r
 335        fontNameMenuItem.setText(selection);\r
 336        SetFont();\r
 337      }\r
 338 \r
 339   }\r
 340 \r
 341   public void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
 342   {\r
 343     String selection = JOptionPane.showInternalInputDialog(this,\r
 344                                 "Select font size",\r
 345                                 "Font size",\r
 346                                 JOptionPane.QUESTION_MESSAGE,\r
 347                                 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
 348                                 ,fontSizeMenuItem.getText()).toString();\r
 349     if(selection!=null)\r
 350      {\r
 351        fontSizeMenuItem.setText(selection);\r
 352        SetFont();\r
 353      }\r
 354   }\r
 355 \r
 356   public void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
 357   {\r
 358     String selection = JOptionPane.showInternalInputDialog(this,\r
 359                                 "Select font style",\r
 360                                 "Font style",\r
 361                                 JOptionPane.QUESTION_MESSAGE,\r
 362                                 null, new String[]{"plain", "bold", "italic"}\r
 363                                 ,fontStyleMenuItem.getText()).toString();\r
 364     if(selection!=null)\r
 365     {\r
 366       fontStyleMenuItem.setText(selection);\r
 367       SetFont();\r
 368     }\r
 369 \r
 370   }\r
 371 \r
 372   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 373   {\r
 374       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 375       alignPanel.RefreshPanels();\r
 376   }\r
 377 \r
 378   void SetFont()\r
 379   {\r
 380       int style = java.awt.Font.PLAIN;\r
 381       if(fontStyleMenuItem.getText().equals("bold"))\r
 382         style = java.awt.Font.BOLD;\r
 383       else if(fontStyleMenuItem.getText().equals("italic"))\r
 384         style = java.awt.Font.ITALIC;\r
 385 \r
 386       viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),\r
 387                                            style,\r
 388                                            Integer.parseInt(fontSizeMenuItem.getText())));\r
 389       alignPanel.RefreshPanels();\r
 390 \r
 391   }\r
 392 \r
 393   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 394   {\r
 395     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 396     alignPanel.RefreshPanels();\r
 397   }\r
 398 \r
 399 \r
 400   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 401   {\r
 402     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 403     alignPanel.RefreshPanels();\r
 404   }\r
 405 \r
 406   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 407   {\r
 408     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 409     alignPanel.RefreshPanels();\r
 410   }\r
 411 \r
 412 \r
 413   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 414   {\r
 415     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 416     alignPanel.RefreshPanels();\r
 417   }\r
 418 \r
 419 \r
 420   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 421   {\r
 422     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
 423   }\r
 424 \r
 425   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 426   {\r
 427 \r
 428     JInternalFrame frame = new JInternalFrame();\r
 429     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 430    try{\r
 431      overview = new OverviewPanel(alignPanel, viewport);\r
 432      frame.setContentPane(overview);\r
 433     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 434                              frame.getWidth(), frame.getHeight());\r
 435     frame.pack();\r
 436     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 437     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 438       {\r
 439             alignPanel.setOverviewPanel(null);\r
 440       };\r
 441     });\r
 442     alignPanel.setOverviewPanel( overview );\r
 443 \r
 444   }catch(java.lang.OutOfMemoryError ex)\r
 445    {\r
 446      JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 447                                    +"\nTry reducing the font size.",\r
 448                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 449    }\r
 450 \r
 451 \r
 452   }\r
 453 \r
 454   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 455   {\r
 456     viewport.setGlobalColourScheme( null );\r
 457     changeColour();\r
 458   }\r
 459 \r
 460 \r
 461   public void Colour_actionPerformed(ActionEvent e)\r
 462   {\r
 463     viewport.setGlobalColourScheme(new ClustalxColourScheme( ));\r
 464     conservationMenuItem.setSelected(false);\r
 465     abovePIDThreshold.setSelected(false);\r
 466     changeColour();\r
 467   }\r
 468 \r
 469   public void zappoColour_actionPerformed(ActionEvent e)\r
 470   {\r
 471     viewport.setGlobalColourScheme(new ZappoColourScheme() );\r
 472     changeColour();\r
 473   }\r
 474 \r
 475   public void taylorColour_actionPerformed(ActionEvent e)\r
 476   {\r
 477     viewport.setGlobalColourScheme(new TaylorColourScheme() );\r
 478     changeColour();\r
 479   }\r
 480 \r
 481 \r
 482   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 483   {\r
 484     viewport.setGlobalColourScheme( new HydrophobicColourScheme() );\r
 485     changeColour();\r
 486   }\r
 487 \r
 488   public void helixColour_actionPerformed(ActionEvent e)\r
 489   {\r
 490     viewport.setGlobalColourScheme( new HelixColourScheme()  );\r
 491     changeColour();\r
 492   }\r
 493 \r
 494 \r
 495   public void strandColour_actionPerformed(ActionEvent e)\r
 496   {\r
 497     viewport.setGlobalColourScheme(new StrandColourScheme() );\r
 498     changeColour();\r
 499   }\r
 500 \r
 501 \r
 502   public void turnColour_actionPerformed(ActionEvent e)\r
 503   {\r
 504     viewport.setGlobalColourScheme(new TurnColourScheme() );\r
 505     changeColour();\r
 506   }\r
 507 \r
 508 \r
 509   public void buriedColour_actionPerformed(ActionEvent e)\r
 510   {\r
 511     viewport.setGlobalColourScheme( new BuriedColourScheme() );\r
 512     changeColour();\r
 513   }\r
 514 \r
 515   void changeColour()\r
 516   {\r
 517     if(abovePIDThreshold.isSelected())\r
 518       abovePIDThreshold_actionPerformed(null);\r
 519     else if(conservationMenuItem.isSelected())\r
 520       conservationMenuItem_actionPerformed(null);\r
 521 \r
 522      alignPanel.seqPanel.seqCanvas.paintFlag = true;\r
 523      alignPanel.repaint();\r
 524   }\r
 525 \r
 526   void addConservationOrPIDColour()\r
 527   {\r
 528     int x=0, y=0, threshold = 70;\r
 529 \r
 530     if(sliderFrame!=null)\r
 531        try\r
 532        {\r
 533          x = sliderFrame.getX();\r
 534          y = sliderFrame.getY();\r
 535          SliderPanel sp = (SliderPanel) sliderFrame.getContentPane();\r
 536          threshold = sp.getValue();\r
 537          sliderFrame.setClosed(true);\r
 538        }\r
 539        catch (Exception ex)\r
 540        {    ex.printStackTrace();   }\r
 541 \r
 542      ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
 543 \r
 544      ConservationColourScheme ccs = null;\r
 545      if (oldCs instanceof ConservationColourScheme)\r
 546        ccs = (ConservationColourScheme) oldCs;\r
 547 \r
 548      if(conservationMenuItem.isSelected())\r
 549      {\r
 550        Alignment al = (Alignment)viewport.alignment;\r
 551        Conservation c = new Conservation("All",\r
 552                             ResidueProperties.propHash, 3, al.getSequences(), 0,\r
 553                             al.getWidth() );\r
 554 \r
 555        c.calculate();\r
 556        c.verdict(false, 100);\r
 557 \r
 558        if(ccs!=null)\r
 559          ccs = new ConservationColourScheme(c, ccs.cs);\r
 560        else\r
 561          ccs = new ConservationColourScheme(c, oldCs);\r
 562 \r
 563         viewport.setGlobalColourScheme( ccs );\r
 564 \r
 565      }\r
 566      else if(oldCs instanceof ConservationColourScheme)\r
 567      {\r
 568        oldCs = ccs.cs;\r
 569        viewport.setGlobalColourScheme( oldCs );\r
 570      }\r
 571 \r
 572 \r
 573      if( conservationMenuItem.isSelected() || abovePIDThreshold.isSelected() )\r
 574      {\r
 575        sliderFrame = new JInternalFrame();\r
 576        sliderFrame.setMaximizable(false);\r
 577        sliderFrame.setResizable(false);\r
 578 \r
 579        SliderPanel sp = null;\r
 580        if (conservationMenuItem.isSelected())\r
 581        {\r
 582         if(threshold > 50)\r
 583           threshold = 30;\r
 584         sp = new SliderPanel(alignPanel, threshold, true,ccs);\r
 585         Desktop.addInternalFrame(sliderFrame, "Conservation Colour Increment  (Global colour)", 400, 90);\r
 586         threshold = 0;\r
 587        }\r
 588        else if (abovePIDThreshold.isSelected())\r
 589        {\r
 590          sp = new SliderPanel(alignPanel, threshold, false, oldCs);\r
 591          sp.cs = oldCs;\r
 592          Desktop.addInternalFrame(sliderFrame, "Percentage Identity Threshold (Global colour)", 400, 90);\r
 593        }\r
 594 \r
 595        sliderFrame.setContentPane(sp);\r
 596        if(x!=0 && y!=0)\r
 597                sliderFrame.setLocation(x,y);\r
 598 \r
 599      }\r
 600      else\r
 601        threshold = 0;\r
 602 \r
 603 \r
 604      if (oldCs instanceof ResidueColourScheme)\r
 605      {\r
 606        ResidueColourScheme rcs = (ResidueColourScheme) oldCs;\r
 607        rcs.setThreshold(threshold);\r
 608      }\r
 609      else if (oldCs instanceof ScoreColourScheme)\r
 610      {\r
 611        ScoreColourScheme scs = (ScoreColourScheme) oldCs;\r
 612        scs.setThreshold(threshold);\r
 613      }\r
 614 \r
 615      alignPanel.seqPanel.seqCanvas.paintFlag = true;\r
 616      alignPanel.repaint();\r
 617 \r
 618   }\r
 619 \r
 620   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 621   {\r
 622    if(abovePIDThreshold.isSelected())\r
 623     abovePIDThreshold.setSelected(false);\r
 624 \r
 625    viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 626 \r
 627    addConservationOrPIDColour();\r
 628   }\r
 629 \r
 630   JInternalFrame sliderFrame;\r
 631   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 632   {\r
 633       if(conservationMenuItem.isSelected())\r
 634         conservationMenuItem.setSelected(false);\r
 635 \r
 636       addConservationOrPIDColour();\r
 637   }\r
 638 \r
 639 \r
 640 \r
 641   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 642   {\r
 643     JInternalFrame frame = new JInternalFrame();\r
 644     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 645     frame.setContentPane(chooser);\r
 646     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 647     frame.setResizable(false);\r
 648     frame.setIconifiable(false);\r
 649     frame.setMaximizable(false);\r
 650   }\r
 651 \r
 652   public void PIDColour_actionPerformed(ActionEvent e)\r
 653   {\r
 654     viewport.setGlobalColourScheme( new PIDColourScheme() );\r
 655     alignPanel.setColourScheme( );\r
 656   }\r
 657 \r
 658 \r
 659   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 660   {\r
 661     viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport)  );\r
 662     alignPanel.setColourScheme();\r
 663   }\r
 664 \r
 665 \r
 666 \r
 667   protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
 668   {\r
 669     ColourKey colourKey = new ColourKey( viewport.getGlobalColourScheme() );\r
 670     Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);\r
 671   }\r
 672 \r
 673 \r
 674   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 675   {\r
 676     addHistoryItem("sort");\r
 677     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 678     alignPanel.RefreshPanels();\r
 679   }\r
 680 \r
 681   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 682   {\r
 683     addHistoryItem("sort");\r
 684     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 685     alignPanel.RefreshPanels();\r
 686   }\r
 687 \r
 688   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 689   {\r
 690     addHistoryItem("sort");\r
 691     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 692     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 693     alignPanel.RefreshPanels();\r
 694   }\r
 695 \r
 696   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 697   {\r
 698     addHistoryItem("sort");\r
 699     if(viewport.getCurrentTree()==null)\r
 700       return;\r
 701 \r
 702     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 703     alignPanel.RefreshPanels();\r
 704   }\r
 705 \r
 706   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 707   {\r
 708     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 709     JInternalFrame frame = new JInternalFrame();\r
 710     frame.setContentPane(sp);\r
 711     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);\r
 712     frame.setMaximizable(false);\r
 713     frame.setResizable(false);\r
 714 \r
 715   }\r
 716 \r
 717   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 718   {\r
 719     if(viewport.getSelection().size()<2)\r
 720       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 721     else\r
 722     {\r
 723       JInternalFrame frame = new JInternalFrame();\r
 724       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 725       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 726     }\r
 727   }\r
 728 \r
 729   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 730   {\r
 731     if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)\r
 732        || viewport.getAlignment().getHeight()<4)\r
 733     {\r
 734       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
 735                                     +"at least 4 input sequences.",\r
 736                                     "Sequence selection insufficient",\r
 737                                     JOptionPane.WARNING_MESSAGE);\r
 738       return;\r
 739     }\r
 740 \r
 741     try{\r
 742       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 743       JInternalFrame frame = new JInternalFrame();\r
 744       frame.setContentPane(pcaPanel);\r
 745       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 746    }catch(java.lang.OutOfMemoryError ex)\r
 747    {\r
 748      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 749                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 750    }\r
 751 \r
 752 \r
 753   }\r
 754 \r
 755   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 756   {\r
 757     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 758   }\r
 759 \r
 760   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 761   {\r
 762     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 763   }\r
 764 \r
 765 \r
 766   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 767   {\r
 768     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 769   }\r
 770 \r
 771   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 772   {\r
 773     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 774   }\r
 775 \r
 776   void NewTreePanel(String type, String pwType, String title)\r
 777   {\r
 778     JInternalFrame frame = new javax.swing.JInternalFrame();\r
 779     TreePanel tp=null;\r
 780    if (viewport.getSelection() != null && viewport.getSelection().size() > 3)\r
 781    {\r
 782      tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,\r
 783                          viewport.getStartRes(), viewport.getEndRes());\r
 784    }\r
 785    else\r
 786    {\r
 787      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 788                          type, pwType, viewport.getStartRes(),\r
 789                          viewport.getEndRes());\r
 790    }\r
 791 \r
 792    frame.setContentPane(tp);\r
 793    Desktop.addInternalFrame(frame, title, 600, 500);\r
 794   }\r
 795 \r
 796 \r
 797 \r
 798   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 799   {\r
 800     // JBPNote\r
 801     // Should check to see if the server settings are valid\r
 802     // Need visual-delay indication here.\r
 803     Jemboss jemboss = new Jemboss();\r
 804 \r
 805     Vector sv = viewport.getAlignment().getSequences();\r
 806     SequenceI[] seqs = new SequenceI[sv.size()];\r
 807 \r
 808     int i=0;\r
 809     do\r
 810     {\r
 811       seqs[i] = (SequenceI) sv.elementAt(i);\r
 812     } while (++i<sv.size());\r
 813 \r
 814     SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
 815 \r
 816     if (alignment != null)\r
 817     {\r
 818       AlignFrame af = new AlignFrame(new Alignment(alignment));\r
 819       Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"), \r
 820                                700, 500); // JBPNote - is there a new window geom. property ?\r
 821     }\r
 822   }\r
 823 \r
 824   public void pdbTest_actionPerformed(ActionEvent e)\r
 825   {\r
 826    String reply = \r
 827        JOptionPane.showInternalInputDialog(this, "Enter pdb code", \r
 828                                            "PDB test viewer", JOptionPane.QUESTION_MESSAGE);\r
 829 \r
 830    String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";\r
 831    if (reply.length()>1)\r
 832      url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id="+reply;\r
 833 \r
 834    try\r
 835    {\r
 836      PDBfile pdb = new PDBfile(url,\r
 837                                "URL");\r
 838     Sequence seq = (Sequence)viewport.getAlignment().getSequenceAt(0);\r
 839     seq.setPDBfile(pdb);\r
 840      ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).isVisible = true;\r
 841      ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).sequence = seq;\r
 842   // ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).colourBySequence();\r
 843 \r
 844      rotCanvas rc = new rotCanvas(pdb);\r
 845      JInternalFrame frame = new JInternalFrame();\r
 846      frame.setContentPane(rc);\r
 847      Desktop.addInternalFrame(frame, url, 400,400);\r
 848    }\r
 849    catch (Exception ex)\r
 850    {\r
 851      ex.printStackTrace();\r
 852    }\r
 853 \r
 854   }\r
 855 \r
 856 \r
 857   public void doKeyPressed(KeyEvent evt)\r
 858   {\r
 859 \r
 860     System.out.println(evt.getKeyChar());\r
 861     if(evt.isControlDown() && evt.getKeyChar()=='f')\r
 862       findMenuItem_actionPerformed(null);\r
 863 \r
 864   }\r
 865 \r
 866 \r
 867 }\r