src/jalview/gui/AlignFrame.java

   1 /********************\r
   2  * 2004 Jalview Reengineered\r
   3  * Barton Group\r
   4  * Dundee University\r
   5  *\r
   6  * AM Waterhouse\r
   7  *******************/\r
   8 \r
   9 \r
  10 \r
  11 \r
  12 package jalview.gui;\r
  13 \r
  14 import jalview.jbgui.GAlignFrame;\r
  15 import jalview.schemes.*;\r
  16 import jalview.datamodel.*;\r
  17 import jalview.analysis.*;\r
  18 import jalview.io.*;\r
  19 import jalview.ws.*;\r
  20 import java.awt.*;\r
  21 import java.awt.event.*;\r
  22 import java.awt.print.*;\r
  23 import javax.swing.*;\r
  24 import javax.swing.event.*;\r
  25 import java.util.*;\r
  26 import jalview.datamodel.SequenceI;\r
  27 \r
  28 public class AlignFrame extends GAlignFrame\r
  29 {\r
  30   final AlignmentPanel alignPanel;\r
  31   final AlignViewport viewport;\r
  32   public AlignFrame(AlignmentI al)\r
  33   {\r
  34     super();\r
  35 \r
  36     AlignmentUtil.addUniprotFeatures(al);\r
  37 \r
  38     viewport = new AlignViewport(al,true,true,true,false);\r
  39     alignPanel = new AlignmentPanel(this, viewport);\r
  40     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
  41     fontNameMenuItem.setText(viewport.getFont().getName());\r
  42     fontSizeMenuItem.setText(viewport.getFont().getSize()+"");\r
  43   }\r
  44 \r
  45   protected void saveAs_actionPerformed(ActionEvent e)\r
  46   {\r
  47     JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);\r
  48     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
  49     chooser.setToolTipText("Save");\r
  50     int value = chooser.showSaveDialog(this);\r
  51     if(value == JFileChooser.APPROVE_OPTION)\r
  52     {\r
  53       String choice =  chooser.getSelectedFile().getPath();\r
  54       jalview.bin.Cache.LAST_DIRECTORY = choice;\r
  55       String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
  56       try{\r
  57         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
  58         out.println(output);\r
  59         out.close();\r
  60       }\r
  61       catch(Exception ex){}\r
  62     }\r
  63 \r
  64   }\r
  65 \r
  66   protected void outputText_actionPerformed(ActionEvent e)\r
  67   {\r
  68      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
  69      JInternalFrame frame = new JInternalFrame();\r
  70      cap.formatForOutput();\r
  71      frame.setContentPane(cap);\r
  72      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
  73      cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
  74   }\r
  75 \r
  76   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
  77   {\r
  78     HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
  79     htmlOutput = null;\r
  80   }\r
  81 \r
  82   public void printMenuItem_actionPerformed(ActionEvent e)\r
  83   {\r
  84     //Putting in a thread avoids Swing painting problems\r
  85     PrintThread thread = new PrintThread();\r
  86     thread.start();\r
  87   }\r
  88 \r
  89   class PrintThread extends Thread\r
  90   {\r
  91     public void run()\r
  92     {\r
  93       PrinterJob printJob = PrinterJob.getPrinterJob();\r
  94       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
  95       printJob.setPrintable(alignPanel, pf);\r
  96       if (printJob.printDialog())\r
  97       {\r
  98         try\r
  99         {\r
 100           printJob.print();\r
 101         }\r
 102         catch (Exception PrintException)\r
 103         {\r
 104           PrintException.printStackTrace();\r
 105         }\r
 106       }\r
 107     }\r
 108 \r
 109   }\r
 110 \r
 111 \r
 112 \r
 113 \r
 114   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 115   {\r
 116     try{\r
 117       this.setClosed(true);\r
 118     }catch(Exception ex){}\r
 119   }\r
 120 \r
 121   ArrayList  historyList = new ArrayList();\r
 122   ArrayList redoList = new ArrayList();\r
 123 \r
 124   void updateEditMenuBar()\r
 125   {\r
 126     if(historyList.size()>0)\r
 127      {\r
 128        undoMenuItem.setEnabled(true);\r
 129        Object [] history = (Object[])historyList.get(0);\r
 130        undoMenuItem.setText("Undo "+history[0]);\r
 131      }\r
 132     else\r
 133     {\r
 134       undoMenuItem.setEnabled(false);\r
 135       undoMenuItem.setText("Undo");\r
 136     }\r
 137 \r
 138     if(redoList.size()>0)\r
 139      {\r
 140        redoMenuItem.setEnabled(true);\r
 141        Object [] history = (Object[])redoList.get(0);\r
 142        redoMenuItem.setText("Redo "+history[0]);\r
 143      }\r
 144     else\r
 145     {\r
 146       redoMenuItem.setEnabled(false);\r
 147       redoMenuItem.setText("Redo");\r
 148     }\r
 149   }\r
 150 \r
 151   public void addHistoryItem(String type)\r
 152   {\r
 153     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 154     redoList.clear();\r
 155     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 156     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 157     {\r
 158       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 159                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 160     }\r
 161 \r
 162     historyList.add(0, new Object[]{type,  seq} );\r
 163     updateEditMenuBar();\r
 164   }\r
 165 \r
 166   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 167   {\r
 168     Object [] history = (Object[])historyList.remove(0);\r
 169     // add the redo state before continuing!!\r
 170     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 171     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
 172     {\r
 173       seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
 174                             viewport.getAlignment().getSequenceAt(i).\r
 175                             getSequence());\r
 176     }\r
 177     /////////\r
 178 \r
 179     redoList.add(0, new Object[] {history[0], seq});\r
 180 \r
 181       seq = (SequenceI[]) history[1];\r
 182       viewport.setAlignment( new Alignment(seq) );\r
 183       updateEditMenuBar();\r
 184       alignPanel.RefreshPanels();\r
 185   }\r
 186 \r
 187 \r
 188   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 189   {\r
 190      Object [] history = (Object[])redoList.remove(0);\r
 191      SequenceI[] seq = (SequenceI[]) history[1];\r
 192      viewport.setAlignment( new Alignment(seq) );\r
 193      updateEditMenuBar();\r
 194      alignPanel.RefreshPanels();\r
 195   }\r
 196 \r
 197 \r
 198   public void groupsMenuItem_actionPerformed(ActionEvent e)\r
 199   {\r
 200     GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
 201     JInternalFrame frame = new JInternalFrame();\r
 202     frame.setContentPane(geditor);\r
 203     Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
 204     frame.setResizable(false);\r
 205   }\r
 206 \r
 207   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 208   {\r
 209     viewport.alignment.deleteAllGroups();\r
 210     viewport.getSelection().clear();\r
 211 \r
 212     alignPanel.RefreshPanels();\r
 213   }\r
 214 \r
 215 \r
 216 \r
 217   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 218   {\r
 219     Selection sel = viewport.getSelection();\r
 220     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 221       sel.addElement( viewport.getAlignment().getSequenceAt(i));\r
 222     PaintRefresher.Refresh(null);\r
 223   }\r
 224 \r
 225   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 226   {\r
 227     viewport.setRubberbandGroup(null);\r
 228     viewport.getSelection().clear();\r
 229     PaintRefresher.Refresh(null);\r
 230   }\r
 231 \r
 232   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 233   {\r
 234     Selection sel = viewport.getSelection();\r
 235     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 236     {\r
 237       if (sel.contains(viewport.getAlignment().getSequenceAt(i)))\r
 238         sel.removeElement(viewport.getAlignment().getSequenceAt(i));\r
 239       else\r
 240         sel.addElement(viewport.getAlignment().getSequenceAt(i));\r
 241     }\r
 242     PaintRefresher.Refresh(null);\r
 243   }\r
 244 \r
 245 \r
 246   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 247   {\r
 248     viewport.getColumnSelection().clear();\r
 249     repaint();\r
 250   }\r
 251 \r
 252   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 253   {\r
 254     addHistoryItem("delete columns");\r
 255     ColumnSelection colSel = viewport.getColumnSelection();\r
 256     if (colSel.size() > 0)\r
 257     {\r
 258       int min = colSel.getMin();\r
 259       viewport.getAlignment().trimLeft(min);\r
 260       colSel.compensateForEdit(0,min);\r
 261       alignPanel.RefreshPanels();\r
 262     }\r
 263   }\r
 264 \r
 265   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 266   {\r
 267     addHistoryItem("delete columns");\r
 268     ColumnSelection colSel = viewport.getColumnSelection();\r
 269     if (colSel.size() > 0)\r
 270     {\r
 271       int max = colSel.getMax();\r
 272       if(max>1)\r
 273         viewport.getAlignment().trimRight(max);\r
 274 \r
 275       alignPanel.RefreshPanels();\r
 276     }\r
 277 \r
 278   }\r
 279 \r
 280   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 281   {\r
 282     addHistoryItem("delete gapped columns");\r
 283     viewport.getAlignment().removeGaps();\r
 284     alignPanel.RefreshPanels();\r
 285   }\r
 286 \r
 287   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 288   {\r
 289     addHistoryItem("delete all gaps");\r
 290     SequenceI current;\r
 291     int jSize;\r
 292     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 293     {\r
 294       current = viewport.getAlignment().getSequenceAt(i);\r
 295       jSize = current.getLength();\r
 296       for (int j=0; j < jSize; j++)\r
 297         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 298         {\r
 299           current.deleteCharAt(j);\r
 300           j--;\r
 301           jSize--;\r
 302         }\r
 303     }\r
 304 \r
 305     alignPanel.RefreshPanels();\r
 306   }\r
 307 \r
 308   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 309   {\r
 310     char thisChar = '-';\r
 311     char nextChar = '.';\r
 312     if(viewport.getGapCharacter()=='-')\r
 313     {\r
 314       thisChar = '.';\r
 315       nextChar = '-';\r
 316     }\r
 317     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 318     viewport.setGapCharacter(thisChar);\r
 319     alignPanel.RefreshPanels();\r
 320   }\r
 321 \r
 322   public void findMenuItem_actionPerformed(ActionEvent e)\r
 323   {\r
 324     JOptionPane op = new JOptionPane();\r
 325     JInternalFrame frame =  op.createInternalFrame(this, "Find");\r
 326     Finder finder = new Finder(viewport, alignPanel, frame);\r
 327     frame.setClosable(true);\r
 328     frame.setContentPane(finder);\r
 329     frame.setSize(340,110);\r
 330     frame.setVisible(true);\r
 331   }\r
 332 \r
 333 \r
 334 \r
 335   public void fontNameMenuItem_actionPerformed(ActionEvent e)\r
 336   {\r
 337     String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();\r
 338 \r
 339 \r
 340     String selection = JOptionPane.showInternalInputDialog(this,\r
 341                                 "Select font",\r
 342                                 "Font selection",\r
 343                                 JOptionPane.QUESTION_MESSAGE,\r
 344                                 null,fonts\r
 345                                 ,fontNameMenuItem.getText()).toString();\r
 346     if(selection!=null)\r
 347     {\r
 348        fontNameMenuItem.setText(selection);\r
 349        SetFont();\r
 350      }\r
 351 \r
 352   }\r
 353 \r
 354   public void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
 355   {\r
 356     String selection = JOptionPane.showInternalInputDialog(this,\r
 357                                 "Select font size",\r
 358                                 "Font size",\r
 359                                 JOptionPane.QUESTION_MESSAGE,\r
 360                                 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
 361                                 ,fontSizeMenuItem.getText()).toString();\r
 362     if(selection!=null)\r
 363      {\r
 364        fontSizeMenuItem.setText(selection);\r
 365        SetFont();\r
 366      }\r
 367   }\r
 368 \r
 369   public void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
 370   {\r
 371     String selection = JOptionPane.showInternalInputDialog(this,\r
 372                                 "Select font style",\r
 373                                 "Font style",\r
 374                                 JOptionPane.QUESTION_MESSAGE,\r
 375                                 null, new String[]{"plain", "bold", "italic"}\r
 376                                 ,fontStyleMenuItem.getText()).toString();\r
 377     if(selection!=null)\r
 378     {\r
 379       fontStyleMenuItem.setText(selection);\r
 380       SetFont();\r
 381     }\r
 382 \r
 383   }\r
 384 \r
 385   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 386   {\r
 387       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 388       alignPanel.RefreshPanels();\r
 389   }\r
 390 \r
 391   void SetFont()\r
 392   {\r
 393       int style = java.awt.Font.PLAIN;\r
 394       if(fontStyleMenuItem.getText().equals("bold"))\r
 395         style = java.awt.Font.BOLD;\r
 396       else if(fontStyleMenuItem.getText().equals("italic"))\r
 397         style = java.awt.Font.ITALIC;\r
 398 \r
 399       viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),\r
 400                                            style,\r
 401                                            Integer.parseInt(fontSizeMenuItem.getText())));\r
 402       alignPanel.RefreshPanels();\r
 403 \r
 404   }\r
 405 \r
 406   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 407   {\r
 408     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 409     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
 410   }\r
 411 \r
 412 \r
 413   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 414   {\r
 415     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 416     alignPanel.RefreshPanels();\r
 417   }\r
 418 \r
 419   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 420   {\r
 421     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 422     alignPanel.RefreshPanels();\r
 423   }\r
 424 \r
 425 \r
 426   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 427   {\r
 428     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 429     alignPanel.RefreshPanels();\r
 430   }\r
 431 \r
 432   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
 433   {\r
 434     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 435     alignPanel.RefreshPanels();\r
 436   }\r
 437 \r
 438   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 439   {\r
 440     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
 441   }\r
 442 \r
 443   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 444   {\r
 445     if (alignPanel.overviewPanel != null)\r
 446       return;\r
 447 \r
 448     JInternalFrame frame = new JInternalFrame();\r
 449     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 450    try{\r
 451      overview = new OverviewPanel(alignPanel, viewport);\r
 452      frame.setContentPane(overview);\r
 453     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 454                              frame.getWidth(), frame.getHeight());\r
 455     frame.pack();\r
 456     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 457     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 458       {\r
 459             alignPanel.setOverviewPanel(null);\r
 460       };\r
 461     });\r
 462     alignPanel.setOverviewPanel( overview );\r
 463 \r
 464   }catch(java.lang.OutOfMemoryError ex)\r
 465    {\r
 466      JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 467                                    +"\nTry reducing the font size.",\r
 468                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 469    }\r
 470 \r
 471 \r
 472   }\r
 473 \r
 474   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 475   {\r
 476     viewport.setGlobalColourScheme( null );\r
 477     changeColour();\r
 478   }\r
 479 \r
 480 \r
 481   public void clustalColour_actionPerformed(ActionEvent e)\r
 482   {\r
 483     viewport.setGlobalColourScheme(\r
 484       new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 485     abovePIDThreshold.setSelected(false);\r
 486     changeColour();\r
 487   }\r
 488 \r
 489   public void zappoColour_actionPerformed(ActionEvent e)\r
 490   {\r
 491     viewport.setGlobalColourScheme(new ZappoColourScheme() );\r
 492     changeColour();\r
 493   }\r
 494 \r
 495   public void taylorColour_actionPerformed(ActionEvent e)\r
 496   {\r
 497     viewport.setGlobalColourScheme(new TaylorColourScheme() );\r
 498     changeColour();\r
 499   }\r
 500 \r
 501 \r
 502   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 503   {\r
 504     viewport.setGlobalColourScheme( new HydrophobicColourScheme() );\r
 505     changeColour();\r
 506   }\r
 507 \r
 508   public void helixColour_actionPerformed(ActionEvent e)\r
 509   {\r
 510     viewport.setGlobalColourScheme( new HelixColourScheme()  );\r
 511     changeColour();\r
 512   }\r
 513 \r
 514 \r
 515   public void strandColour_actionPerformed(ActionEvent e)\r
 516   {\r
 517     viewport.setGlobalColourScheme(new StrandColourScheme() );\r
 518     changeColour();\r
 519   }\r
 520 \r
 521 \r
 522   public void turnColour_actionPerformed(ActionEvent e)\r
 523   {\r
 524     viewport.setGlobalColourScheme(new TurnColourScheme() );\r
 525     changeColour();\r
 526   }\r
 527 \r
 528 \r
 529   public void buriedColour_actionPerformed(ActionEvent e)\r
 530   {\r
 531     viewport.setGlobalColourScheme( new BuriedColourScheme() );\r
 532     changeColour();\r
 533   }\r
 534 \r
 535   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 536   {\r
 537     viewport.setGlobalColourScheme( new NucleotideColourScheme() );\r
 538     changeColour();\r
 539   }\r
 540 \r
 541 \r
 542   void changeColour()\r
 543   {\r
 544     if(abovePIDThreshold.isSelected())\r
 545       abovePIDThreshold_actionPerformed(null);\r
 546     else if(conservationMenuItem.isSelected())\r
 547       conservationMenuItem_actionPerformed(null);\r
 548 \r
 549     alignPanel.RefreshPanels();\r
 550   }\r
 551 \r
 552 \r
 553   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 554   {\r
 555    if(abovePIDThreshold.isSelected())\r
 556    {\r
 557      abovePIDThreshold.setSelected(false);\r
 558      Desktop.hidePIDSlider();\r
 559    }\r
 560 \r
 561    viewport.setConservationSelected(conservationMenuItem.isSelected());\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,\r
 574                                            al.getSequences(), 0,\r
 575                                            al.getWidth());\r
 576 \r
 577          c.calculate();\r
 578          c.verdict(false, 100);\r
 579 \r
 580          if (ccs != null)\r
 581            ccs = new ConservationColourScheme(c, ccs.cs);\r
 582          else\r
 583            ccs = new ConservationColourScheme(c, oldCs);\r
 584 \r
 585 \r
 586          int threshold = Desktop.setConservationSliderSource(alignPanel, ccs, "Background");\r
 587 \r
 588          ccs.inc = threshold;\r
 589 \r
 590          if (ccs.cs instanceof ResidueColourScheme)\r
 591            ((ResidueColourScheme) ccs.cs).setThreshold(0);\r
 592          else if (ccs.cs instanceof ScoreColourScheme)\r
 593            ((ScoreColourScheme)ccs.cs).setThreshold(0);\r
 594 \r
 595          viewport.setGlobalColourScheme(ccs);\r
 596 \r
 597 \r
 598        }\r
 599        else if (oldCs instanceof ConservationColourScheme)\r
 600        {\r
 601          /// ie, if we remove ConservationColourScheme from backgroundColour\r
 602          oldCs = ccs.cs;\r
 603          viewport.setGlobalColourScheme(oldCs);\r
 604          Desktop.hideConservationSlider();\r
 605        }\r
 606 \r
 607        if(e!=null)\r
 608          alignPanel.RefreshPanels();\r
 609   }\r
 610 \r
 611 \r
 612   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 613   {\r
 614       if(conservationMenuItem.isSelected())\r
 615         conservationMenuItem.setSelected(false);\r
 616 \r
 617       ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
 618       int threshold = 0;\r
 619       if (oldCs instanceof ConservationColourScheme)\r
 620      {\r
 621        ConservationColourScheme ccs = (ConservationColourScheme) oldCs;\r
 622        oldCs = ccs.cs;\r
 623      }\r
 624 \r
 625      if(abovePIDThreshold.isSelected())\r
 626      {\r
 627        threshold = Desktop.setPIDSliderSource(alignPanel, oldCs, "Background");\r
 628        Desktop.hideConservationSlider();\r
 629      }\r
 630      else\r
 631        Desktop.hidePIDSlider();\r
 632 \r
 633       if (oldCs instanceof ResidueColourScheme)\r
 634           ((ResidueColourScheme) oldCs).setThreshold(threshold);\r
 635       else if (oldCs instanceof ScoreColourScheme)\r
 636           ((ScoreColourScheme)oldCs).setThreshold(threshold);\r
 637 \r
 638     viewport.setGlobalColourScheme(oldCs);\r
 639      if(e!=null)\r
 640         alignPanel.RefreshPanels();\r
 641   }\r
 642 \r
 643 \r
 644 \r
 645   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 646   {\r
 647     JInternalFrame frame = new JInternalFrame();\r
 648     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 649     frame.setContentPane(chooser);\r
 650     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 651     frame.setResizable(false);\r
 652     frame.setIconifiable(false);\r
 653     frame.setMaximizable(false);\r
 654   }\r
 655 \r
 656   public void PIDColour_actionPerformed(ActionEvent e)\r
 657   {\r
 658     viewport.setGlobalColourScheme( new PIDColourScheme() );\r
 659     alignPanel.setColourScheme( );\r
 660   }\r
 661 \r
 662 \r
 663   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 664   {\r
 665     viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport)  );\r
 666     changeColour();\r
 667   }\r
 668 \r
 669 \r
 670 \r
 671   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 672   {\r
 673     addHistoryItem("sort");\r
 674     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 675     alignPanel.RefreshPanels();\r
 676   }\r
 677 \r
 678   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 679   {\r
 680     addHistoryItem("sort");\r
 681     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 682     alignPanel.RefreshPanels();\r
 683   }\r
 684 \r
 685   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 686   {\r
 687     addHistoryItem("sort");\r
 688     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 689     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 690     alignPanel.RefreshPanels();\r
 691   }\r
 692 \r
 693   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 694   {\r
 695     addHistoryItem("sort");\r
 696     if(viewport.getCurrentTree()==null)\r
 697       return;\r
 698 \r
 699     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 700     alignPanel.RefreshPanels();\r
 701   }\r
 702 \r
 703   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 704   {\r
 705     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 706     JInternalFrame frame = new JInternalFrame();\r
 707     frame.setContentPane(sp);\r
 708     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);\r
 709     frame.setMaximizable(false);\r
 710     frame.setResizable(false);\r
 711 \r
 712   }\r
 713 \r
 714   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 715   {\r
 716     if(viewport.getSelection().size()<2)\r
 717       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 718     else\r
 719     {\r
 720       JInternalFrame frame = new JInternalFrame();\r
 721       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 722       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 723     }\r
 724   }\r
 725 \r
 726   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 727   {\r
 728     if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)\r
 729        || viewport.getAlignment().getHeight()<4)\r
 730     {\r
 731       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
 732                                     +"at least 4 input sequences.",\r
 733                                     "Sequence selection insufficient",\r
 734                                     JOptionPane.WARNING_MESSAGE);\r
 735       return;\r
 736     }\r
 737 \r
 738     try{\r
 739       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 740       JInternalFrame frame = new JInternalFrame();\r
 741       frame.setContentPane(pcaPanel);\r
 742       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 743    }catch(java.lang.OutOfMemoryError ex)\r
 744    {\r
 745      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 746                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 747    }\r
 748 \r
 749 \r
 750   }\r
 751 \r
 752   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 753   {\r
 754     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 755   }\r
 756 \r
 757   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 758   {\r
 759     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 760   }\r
 761 \r
 762 \r
 763   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 764   {\r
 765     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 766   }\r
 767 \r
 768   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 769   {\r
 770     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 771   }\r
 772 \r
 773   void NewTreePanel(String type, String pwType, String title)\r
 774   {\r
 775     JInternalFrame frame = new javax.swing.JInternalFrame();\r
 776     TreePanel tp=null;\r
 777    if (viewport.getSelection() != null && viewport.getSelection().size() > 3)\r
 778    {\r
 779      tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,\r
 780                          viewport.getStartRes(), viewport.getEndRes());\r
 781    }\r
 782    else\r
 783    {\r
 784      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 785                          type, pwType, viewport.getStartRes(),\r
 786                          viewport.getEndRes());\r
 787    }\r
 788 \r
 789    frame.setContentPane(tp);\r
 790    Desktop.addInternalFrame(frame, title, 600, 500);\r
 791   }\r
 792 \r
 793 \r
 794 \r
 795 \r
 796   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 797   {\r
 798     JInternalFrame frame = new JInternalFrame();\r
 799     ClustalThread ct = new ClustalThread(frame);\r
 800     Thread t = new Thread(ct);\r
 801     t.start();\r
 802     frame.setContentPane(ct);\r
 803      Desktop.addInternalFrame(frame, title, 300, 80);\r
 804 \r
 805   }\r
 806 \r
 807   class ClustalThread extends JPanel implements Runnable\r
 808   {\r
 809     Image [] image;\r
 810     int imageIndex = 0;\r
 811     boolean webServiceRunning = false;\r
 812     JInternalFrame frame;\r
 813     public ClustalThread(JInternalFrame frame)\r
 814     {\r
 815       this.frame = frame;\r
 816       image = new Image[9];\r
 817       for(int i=0; i<9; i++)\r
 818       {\r
 819         java.net.URL url = getClass().getResource("/dna" + (i+1) + ".gif");\r
 820         if (url != null)\r
 821         {\r
 822           image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
 823           MediaTracker mt = new MediaTracker(this);\r
 824           mt.addImage(image[i], i);\r
 825           try{mt.waitForID(i);}\r
 826           catch(Exception ex){}\r
 827         }\r
 828       }\r
 829       DNATwirler twirler = new DNATwirler();\r
 830       twirler.start();\r
 831       webServiceRunning = true;\r
 832     }\r
 833 \r
 834     class DNATwirler extends Thread\r
 835     {\r
 836       public void run()\r
 837       {\r
 838         while(webServiceRunning)\r
 839         {\r
 840           try{\r
 841             Thread.sleep(100);\r
 842             imageIndex++;\r
 843             imageIndex %=9;\r
 844             repaint();\r
 845           }\r
 846           catch(Exception ex){}\r
 847         }\r
 848       }\r
 849     }\r
 850 \r
 851     // JBPNote\r
 852     // Should check to see if the server settings are valid\r
 853     // Need visual-delay indication here.\r
 854     public void run()\r
 855        {\r
 856          jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
 857          Vector sv = viewport.getAlignment().getSequences();\r
 858          SequenceI[] seqs = new SequenceI[sv.size()];\r
 859 \r
 860          int i = 0;\r
 861          do\r
 862          {\r
 863            seqs[i] = (SequenceI) sv.elementAt(i);\r
 864          }\r
 865          while (++i < sv.size());\r
 866 \r
 867          SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
 868 \r
 869          if (alignment != null)\r
 870          {\r
 871            AlignFrame af = new AlignFrame(new Alignment(alignment));\r
 872           af.clustalColour.setSelected(true);\r
 873           af.clustalColour_actionPerformed(null);\r
 874            Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),\r
 875                                     700, 500); // JBPNote - is there a new window geom. property ?\r
 876          }\r
 877          else\r
 878            JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",\r
 879                                          JOptionPane.WARNING_MESSAGE);\r
 880 \r
 881          webServiceRunning = false;\r
 882          try{\r
 883            frame.setClosed(true);\r
 884          }catch(Exception ex){}\r
 885        }\r
 886 \r
 887        public void paintComponent(Graphics g)\r
 888        {\r
 889          g.setColor(Color.white);\r
 890          g.fillRect(0,0,getWidth(), getHeight());\r
 891          if(image!=null)\r
 892          {\r
 893            g.drawImage(image[imageIndex],10,10,this);\r
 894          }\r
 895          g.setFont(new Font("Arial", Font.BOLD, 12));\r
 896          g.setColor(Color.black);\r
 897          g.drawString("Clustal Alignment Web Service running", 30,30);\r
 898        }\r
 899   }\r
 900 \r
 901 \r
 902   public void doKeyPressed(KeyEvent evt)\r
 903   {\r
 904     if(evt.isControlDown() && evt.getKeyChar()=='f')\r
 905       findMenuItem_actionPerformed(null);\r
 906   }\r
 907 \r
 908 \r
 909 }\r