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