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 MCview.*;\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 java.util.*;\r
  25 \r
  26 public class AlignFrame extends GAlignFrame\r
  27 {\r
  28   final AlignmentPanel alignPanel;\r
  29   final AlignViewport viewport;\r
  30   public AlignFrame(AlignmentI al)\r
  31   {\r
  32     super();\r
  33     viewport = new AlignViewport(al,true,true,true,false);\r
  34     alignPanel = new AlignmentPanel(this, viewport);\r
  35     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
  36     fontNameMenuItem.setText(viewport.getFont().getName());\r
  37     fontSizeMenuItem.setText(viewport.getFont().getSize()+"");\r
  38   }\r
  39 \r
  40   protected void saveAs_actionPerformed(ActionEvent e)\r
  41   {\r
  42     JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);\r
  43     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
  44     chooser.setToolTipText("Save");\r
  45     int value = chooser.showSaveDialog(this);\r
  46     if(value == JFileChooser.APPROVE_OPTION)\r
  47     {\r
  48       String choice =  chooser.getSelectedFile().getPath();\r
  49       jalview.bin.Cache.LAST_DIRECTORY = choice;\r
  50       String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
  51       try{\r
  52         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
  53         out.println(output);\r
  54         out.close();\r
  55       }\r
  56       catch(Exception ex){}\r
  57     }\r
  58 \r
  59   }\r
  60 \r
  61   protected void outputText_actionPerformed(ActionEvent e)\r
  62   {\r
  63      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
  64      JInternalFrame frame = new JInternalFrame();\r
  65      cap.formatForOutput();\r
  66      frame.setContentPane(cap);\r
  67      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
  68      cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
  69   }\r
  70 \r
  71   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
  72   {\r
  73     HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
  74     htmlOutput = null;\r
  75   }\r
  76 \r
  77   public void printMenuItem_actionPerformed(ActionEvent e)\r
  78   {\r
  79     //Putting in a thread avoids Swing painting problems\r
  80     PrintThread thread = new PrintThread();\r
  81     thread.start();\r
  82   }\r
  83 \r
  84   class PrintThread extends Thread\r
  85   {\r
  86     public void run()\r
  87     {\r
  88       PrinterJob printJob = PrinterJob.getPrinterJob();\r
  89       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
  90       printJob.setPrintable(alignPanel, pf);\r
  91       if (printJob.printDialog())\r
  92       {\r
  93         try\r
  94         {\r
  95           printJob.print();\r
  96         }\r
  97         catch (Exception PrintException)\r
  98         {\r
  99           PrintException.printStackTrace();\r
 100         }\r
 101       }\r
 102     }\r
 103 \r
 104   }\r
 105 \r
 106 \r
 107 \r
 108 \r
 109   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 110   {\r
 111     try{\r
 112       this.setClosed(true);\r
 113     }catch(Exception ex){}\r
 114   }\r
 115 \r
 116   ArrayList  historyList = new ArrayList();\r
 117   ArrayList redoList = new ArrayList();\r
 118 \r
 119   void updateEditMenuBar()\r
 120   {\r
 121     if(historyList.size()>0)\r
 122      {\r
 123        undoMenuItem.setEnabled(true);\r
 124        Object [] history = (Object[])historyList.get(0);\r
 125        undoMenuItem.setText("Undo "+history[0]);\r
 126      }\r
 127     else\r
 128     {\r
 129       undoMenuItem.setEnabled(false);\r
 130       undoMenuItem.setText("Undo");\r
 131     }\r
 132 \r
 133     if(redoList.size()>0)\r
 134      {\r
 135        redoMenuItem.setEnabled(true);\r
 136        Object [] history = (Object[])redoList.get(0);\r
 137        redoMenuItem.setText("Redo "+history[0]);\r
 138      }\r
 139     else\r
 140     {\r
 141       redoMenuItem.setEnabled(false);\r
 142       redoMenuItem.setText("Redo");\r
 143     }\r
 144   }\r
 145 \r
 146   public void addHistoryItem(String type)\r
 147   {\r
 148     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 149     redoList.clear();\r
 150     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 151     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 152     {\r
 153       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 154                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 155     }\r
 156 \r
 157     historyList.add(0, new Object[]{type,  seq} );\r
 158     updateEditMenuBar();\r
 159   }\r
 160 \r
 161   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 162   {\r
 163     Object [] history = (Object[])historyList.remove(0);\r
 164     // add the redo state before continuing!!\r
 165     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 166     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
 167     {\r
 168       seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
 169                             viewport.getAlignment().getSequenceAt(i).\r
 170                             getSequence());\r
 171     }\r
 172     /////////\r
 173 \r
 174     redoList.add(0, new Object[] {history[0], seq});\r
 175 \r
 176       seq = (SequenceI[]) history[1];\r
 177       viewport.setAlignment( new Alignment(seq) );\r
 178       updateEditMenuBar();\r
 179       alignPanel.RefreshPanels();\r
 180   }\r
 181 \r
 182 \r
 183   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 184   {\r
 185      Object [] history = (Object[])redoList.remove(0);\r
 186      SequenceI[] seq = (SequenceI[]) history[1];\r
 187      viewport.setAlignment( new Alignment(seq) );\r
 188      updateEditMenuBar();\r
 189      alignPanel.RefreshPanels();\r
 190   }\r
 191 \r
 192   protected void modifyAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 193   {\r
 194     viewport.groupDefiningMode = !modifyAlignmentMenuItem.isSelected();\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   public void groupEditingMenuItem_actionPerformed(ActionEvent e)\r
 208   {\r
 209     viewport.setGroupEdit( groupEditingMenuItem.isSelected() );\r
 210   }\r
 211 \r
 212   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 213   {\r
 214     Selection sel = viewport.getSelection();\r
 215     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 216       sel.addElement( viewport.getAlignment().getSequenceAt(i));\r
 217     PaintRefresher.Refresh(null);\r
 218   }\r
 219 \r
 220   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 221   {\r
 222     viewport.getSelection().clear();\r
 223     PaintRefresher.Refresh(null);\r
 224   }\r
 225 \r
 226   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 227   {\r
 228     Selection sel = viewport.getSelection();\r
 229     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 230     {\r
 231       if (sel.contains(viewport.getAlignment().getSequenceAt(i)))\r
 232         sel.removeElement(viewport.getAlignment().getSequenceAt(i));\r
 233       else\r
 234         sel.addElement(viewport.getAlignment().getSequenceAt(i));\r
 235     }\r
 236     PaintRefresher.Refresh(null);\r
 237   }\r
 238 \r
 239 \r
 240   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 241   {\r
 242     viewport.getColumnSelection().clear();\r
 243     repaint();\r
 244   }\r
 245 \r
 246   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 247   {\r
 248     addHistoryItem("delete columns");\r
 249     ColumnSelection colSel = viewport.getColumnSelection();\r
 250     if (colSel.size() > 0)\r
 251     {\r
 252       int min = colSel.getMin();\r
 253       viewport.getAlignment().trimLeft(min);\r
 254       colSel.compensateForEdit(0,min);\r
 255       alignPanel.RefreshPanels();\r
 256     }\r
 257   }\r
 258 \r
 259   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 260   {\r
 261     addHistoryItem("delete columns");\r
 262     ColumnSelection colSel = viewport.getColumnSelection();\r
 263     if (colSel.size() > 0)\r
 264     {\r
 265       int max = colSel.getMax();\r
 266       if(max>1)\r
 267         viewport.getAlignment().trimRight(max);\r
 268 \r
 269       alignPanel.RefreshPanels();\r
 270     }\r
 271 \r
 272   }\r
 273 \r
 274   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 275   {\r
 276     addHistoryItem("delete gapped columns");\r
 277     viewport.getAlignment().removeGaps();\r
 278     alignPanel.RefreshPanels();\r
 279   }\r
 280 \r
 281   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 282   {\r
 283     addHistoryItem("delete all gaps");\r
 284     SequenceI current;\r
 285     int jSize;\r
 286     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 287     {\r
 288       current = viewport.getAlignment().getSequenceAt(i);\r
 289       jSize = current.getLength();\r
 290       for (int j=0; j < jSize; j++)\r
 291         if (current.getCharAt(j)=='-' || current.getCharAt(j)=='.' || current.getCharAt(j)==' ')\r
 292         {\r
 293           current.deleteCharAt(j);\r
 294           j--;\r
 295           jSize--;\r
 296         }\r
 297     }\r
 298 \r
 299     alignPanel.RefreshPanels();\r
 300   }\r
 301 \r
 302   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 303   {\r
 304     char thisChar = '-';\r
 305     char nextChar = '.';\r
 306     if(viewport.getGapCharacter()=='-')\r
 307     {\r
 308       thisChar = '.';\r
 309       nextChar = '-';\r
 310     }\r
 311     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 312     viewport.setGapCharacter(thisChar);\r
 313     alignPanel.RefreshPanels();\r
 314   }\r
 315 \r
 316   public void findMenuItem_actionPerformed(ActionEvent e)\r
 317   {\r
 318     JOptionPane op = new JOptionPane();\r
 319     JInternalFrame frame =  op.createInternalFrame(this, "Find");\r
 320     Finder finder = new Finder(viewport, alignPanel, frame);\r
 321     frame.setContentPane(finder);\r
 322     frame.setSize(300,110);\r
 323     frame.setVisible(true);\r
 324   }\r
 325 \r
 326 \r
 327 \r
 328   public void fontNameMenuItem_actionPerformed(ActionEvent e)\r
 329   {\r
 330     String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();\r
 331 \r
 332 \r
 333     String selection = JOptionPane.showInternalInputDialog(this,\r
 334                                 "Select font",\r
 335                                 "Font selection",\r
 336                                 JOptionPane.QUESTION_MESSAGE,\r
 337                                 null,fonts\r
 338                                 ,fontNameMenuItem.getText()).toString();\r
 339     if(selection!=null)\r
 340     {\r
 341        fontNameMenuItem.setText(selection);\r
 342        SetFont();\r
 343      }\r
 344 \r
 345   }\r
 346 \r
 347   public void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
 348   {\r
 349     String selection = JOptionPane.showInternalInputDialog(this,\r
 350                                 "Select font size",\r
 351                                 "Font size",\r
 352                                 JOptionPane.QUESTION_MESSAGE,\r
 353                                 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
 354                                 ,fontSizeMenuItem.getText()).toString();\r
 355     if(selection!=null)\r
 356      {\r
 357        fontSizeMenuItem.setText(selection);\r
 358        SetFont();\r
 359      }\r
 360   }\r
 361 \r
 362   public void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
 363   {\r
 364     String selection = JOptionPane.showInternalInputDialog(this,\r
 365                                 "Select font style",\r
 366                                 "Font style",\r
 367                                 JOptionPane.QUESTION_MESSAGE,\r
 368                                 null, new String[]{"plain", "bold", "italic"}\r
 369                                 ,fontStyleMenuItem.getText()).toString();\r
 370     if(selection!=null)\r
 371     {\r
 372       fontStyleMenuItem.setText(selection);\r
 373       SetFont();\r
 374     }\r
 375 \r
 376   }\r
 377 \r
 378   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 379   {\r
 380       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 381       alignPanel.RefreshPanels();\r
 382   }\r
 383 \r
 384   void SetFont()\r
 385   {\r
 386       int style = java.awt.Font.PLAIN;\r
 387       if(fontStyleMenuItem.getText().equals("bold"))\r
 388         style = java.awt.Font.BOLD;\r
 389       else if(fontStyleMenuItem.getText().equals("italic"))\r
 390         style = java.awt.Font.ITALIC;\r
 391 \r
 392       viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),\r
 393                                            style,\r
 394                                            Integer.parseInt(fontSizeMenuItem.getText())));\r
 395       alignPanel.RefreshPanels();\r
 396 \r
 397   }\r
 398 \r
 399   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 400   {\r
 401     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 402     alignPanel.RefreshPanels();\r
 403   }\r
 404 \r
 405 \r
 406   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 407   {\r
 408     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 409     alignPanel.RefreshPanels();\r
 410   }\r
 411 \r
 412   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 413   {\r
 414     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 415     alignPanel.RefreshPanels();\r
 416   }\r
 417 \r
 418 \r
 419   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 420   {\r
 421     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 422     alignPanel.RefreshPanels();\r
 423   }\r
 424 \r
 425 \r
 426   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 427   {\r
 428     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
 429   }\r
 430 \r
 431   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 432   {\r
 433 \r
 434     JInternalFrame frame = new JInternalFrame();\r
 435     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 436    try{\r
 437      overview = new OverviewPanel(alignPanel, viewport);\r
 438      frame.setContentPane(overview);\r
 439     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 440                              frame.getWidth(), frame.getHeight());\r
 441     frame.pack();\r
 442     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 443     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 444       {\r
 445             alignPanel.setOverviewPanel(null);\r
 446       };\r
 447     });\r
 448     alignPanel.setOverviewPanel( overview );\r
 449 \r
 450   }catch(java.lang.OutOfMemoryError ex)\r
 451    {\r
 452      JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 453                                    +"\nTry reducing the font size.",\r
 454                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 455    }\r
 456 \r
 457 \r
 458   }\r
 459 \r
 460   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 461   {\r
 462     viewport.setGlobalColourScheme( null );\r
 463     alignPanel.setColourScheme();\r
 464   }\r
 465 \r
 466 \r
 467   public void clustalColour_actionPerformed(ActionEvent e)\r
 468   {\r
 469    // alignPanel.setColourScheme( new ClustalxColourScheme() );\r
 470   }\r
 471 \r
 472   public void zappoColour_actionPerformed(ActionEvent e)\r
 473   {\r
 474     viewport.setGlobalColourScheme(new ZappoColourScheme() );\r
 475     alignPanel.setColourScheme(  );\r
 476   }\r
 477 \r
 478   public void taylorColour_actionPerformed(ActionEvent e)\r
 479   {\r
 480     viewport.setGlobalColourScheme(new TaylorColourScheme() );\r
 481     alignPanel.setColourScheme(  );\r
 482   }\r
 483 \r
 484 \r
 485   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 486   {\r
 487     viewport.setGlobalColourScheme( new HydrophobicColourScheme() );\r
 488     alignPanel.setColourScheme( );\r
 489   }\r
 490 \r
 491   public void helixColour_actionPerformed(ActionEvent e)\r
 492   {\r
 493     viewport.setGlobalColourScheme( new HelixColourScheme()  );\r
 494     alignPanel.setColourScheme();\r
 495   }\r
 496 \r
 497 \r
 498   public void strandColour_actionPerformed(ActionEvent e)\r
 499   {\r
 500     viewport.setGlobalColourScheme(new StrandColourScheme() );\r
 501     alignPanel.setColourScheme(  );\r
 502   }\r
 503 \r
 504 \r
 505   public void turnColour_actionPerformed(ActionEvent e)\r
 506   {\r
 507     viewport.setGlobalColourScheme(new TurnColourScheme() );\r
 508     alignPanel.setColourScheme(  );\r
 509   }\r
 510 \r
 511 \r
 512   public void buriedColour_actionPerformed(ActionEvent e)\r
 513   {\r
 514     viewport.setGlobalColourScheme( new BuriedColourScheme() );\r
 515     alignPanel.setColourScheme( );\r
 516   }\r
 517 \r
 518 \r
 519   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 520   {\r
 521     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 522     conservationColourIncMenuItem.setEnabled( conservationMenuItem.isSelected() );\r
 523     alignPanel.setColourScheme();\r
 524   }\r
 525 \r
 526   public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
 527  {\r
 528    ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);\r
 529    JInternalFrame frame = new JInternalFrame();\r
 530    frame.setContentPane(cip);\r
 531    Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);\r
 532    frame.setMaximizable(false);\r
 533  }\r
 534 \r
 535 \r
 536   public void abovePIDColour_actionPerformed(ActionEvent e)\r
 537   {\r
 538     viewport.setGlobalColourScheme(new PIDColourScheme());\r
 539     alignPanel.setColourScheme( );\r
 540   }\r
 541 \r
 542 \r
 543   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 544   {\r
 545     JInternalFrame frame = new JInternalFrame();\r
 546     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 547     frame.setContentPane(chooser);\r
 548     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 549     frame.setResizable(false);\r
 550     frame.setIconifiable(false);\r
 551     frame.setMaximizable(false);\r
 552   }\r
 553 \r
 554   public void PIDColour_actionPerformed(ActionEvent e)\r
 555   {\r
 556     viewport.setGlobalColourScheme(new PIDColourScheme() );\r
 557     alignPanel.setColourScheme( );\r
 558   }\r
 559 \r
 560 \r
 561   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 562   {\r
 563     viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport)  );\r
 564     alignPanel.setColourScheme();\r
 565   }\r
 566 \r
 567 \r
 568 \r
 569   protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
 570   {\r
 571     ColourKey colourKey = new ColourKey( viewport.getGlobalColourScheme() );\r
 572     Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);\r
 573   }\r
 574 \r
 575 \r
 576   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 577   {\r
 578     addHistoryItem("sort");\r
 579     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 580     alignPanel.RefreshPanels();\r
 581   }\r
 582 \r
 583   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 584   {\r
 585     addHistoryItem("sort");\r
 586     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 587     alignPanel.RefreshPanels();\r
 588   }\r
 589 \r
 590   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 591   {\r
 592     addHistoryItem("sort");\r
 593     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 594     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 595     alignPanel.RefreshPanels();\r
 596   }\r
 597 \r
 598   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 599   {\r
 600     addHistoryItem("sort");\r
 601     if(viewport.getCurrentTree()==null)\r
 602       return;\r
 603 \r
 604     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 605     alignPanel.RefreshPanels();\r
 606   }\r
 607 \r
 608   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 609   {\r
 610 \r
 611   }\r
 612 \r
 613   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 614   {\r
 615     if(viewport.getSelection().size()<2)\r
 616       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 617     else\r
 618     {\r
 619       JInternalFrame frame = new JInternalFrame();\r
 620       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 621       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 622     }\r
 623   }\r
 624 \r
 625   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 626   {\r
 627     if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)\r
 628        || viewport.getAlignment().getHeight()<4)\r
 629     {\r
 630       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
 631                                     +"at least 4 input sequences.",\r
 632                                     "Sequence selection insufficient",\r
 633                                     JOptionPane.WARNING_MESSAGE);\r
 634       return;\r
 635     }\r
 636 \r
 637     try{\r
 638       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 639       JInternalFrame frame = new JInternalFrame();\r
 640       frame.setContentPane(pcaPanel);\r
 641       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 642    }catch(java.lang.OutOfMemoryError ex)\r
 643    {\r
 644      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 645                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 646    }\r
 647 \r
 648 \r
 649   }\r
 650 \r
 651   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 652   {\r
 653     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 654   }\r
 655 \r
 656   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 657   {\r
 658     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 659   }\r
 660 \r
 661 \r
 662   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 663   {\r
 664     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 665   }\r
 666 \r
 667   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 668   {\r
 669     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 670   }\r
 671 \r
 672   void NewTreePanel(String type, String pwType, String title)\r
 673   {\r
 674     JInternalFrame frame = new javax.swing.JInternalFrame();\r
 675     TreePanel tp=null;\r
 676    if (viewport.getSelection() != null && viewport.getSelection().size() > 3)\r
 677    {\r
 678      tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,\r
 679                          viewport.getStartRes(), viewport.getEndRes());\r
 680    }\r
 681    else\r
 682    {\r
 683      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 684                          type, pwType, viewport.getStartRes(),\r
 685                          viewport.getEndRes());\r
 686    }\r
 687 \r
 688    frame.setContentPane(tp);\r
 689    Desktop.addInternalFrame(frame, title, 600, 500);\r
 690   }\r
 691 \r
 692 \r
 693 \r
 694   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 695   {\r
 696     JOptionPane.showInternalMessageDialog(this, "Jalview is currently being reengineered"\r
 697                                   +"\nwithin the Barton Group, Dundee University."\r
 698                                   +"\nThis will be available as a web service 2005",\r
 699                                   "Web service", JOptionPane.INFORMATION_MESSAGE);\r
 700   }\r
 701 \r
 702   public void pdbTest_actionPerformed(ActionEvent e)\r
 703   {\r
 704    String reply = JOptionPane.showInternalInputDialog(this, "Enter pdb code", "PDB test viewer", JOptionPane.QUESTION_MESSAGE);\r
 705 \r
 706    String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";\r
 707    if (reply.length()>1)\r
 708      url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id="+reply;\r
 709 \r
 710    try\r
 711    {\r
 712      PDBfile pdb = new PDBfile(url,\r
 713                                "URL");\r
 714     Sequence seq = (Sequence)viewport.getAlignment().getSequenceAt(0);\r
 715     seq.setPDBfile(pdb);\r
 716      ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).isVisible = true;\r
 717      ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).sequence = seq;\r
 718   // ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).colourBySequence();\r
 719 \r
 720      rotCanvas rc = new rotCanvas(pdb);\r
 721      JInternalFrame frame = new JInternalFrame();\r
 722      frame.setContentPane(rc);\r
 723      Desktop.addInternalFrame(frame, url, 400,400);\r
 724    }\r
 725    catch (Exception ex)\r
 726    {\r
 727      ex.printStackTrace();\r
 728    }\r
 729 \r
 730   }\r
 731 \r
 732 \r
 733   public void doKeyPressed(KeyEvent evt)\r
 734   {\r
 735 \r
 736     System.out.println(evt.getKeyChar());\r
 737     if(evt.isControlDown() && evt.getKeyChar()=='f')\r
 738       findMenuItem_actionPerformed(null);\r
 739 \r
 740   }\r
 741 \r
 742 \r
 743 }\r