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 java.awt.event.*;\r
  20 import java.awt.*;\r
  21 import javax.swing.*;\r
  22 import java.util.*;\r
  23 \r
  24 public class AlignFrame extends GAlignFrame\r
  25 {\r
  26   final AlignmentPanel alignPanel;\r
  27   final AlignViewport viewport;\r
  28   public AlignFrame(AlignmentI al)\r
  29   {\r
  30     super();\r
  31     viewport = new AlignViewport(al,true,true,true,false);\r
  32     alignPanel = new AlignmentPanel(this, viewport);\r
  33     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
  34     fontNameMenuItem.setText(viewport.getFont().getName());\r
  35     fontSizeMenuItem.setText(viewport.getFont().getSize()+"");\r
  36   }\r
  37 \r
  38   protected void saveAs_actionPerformed(ActionEvent e)\r
  39   {\r
  40     JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);\r
  41     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
  42     chooser.setToolTipText("Save");\r
  43     int value = chooser.showSaveDialog(this);\r
  44     if(value == JFileChooser.APPROVE_OPTION)\r
  45     {\r
  46       String choice =  chooser.getSelectedFile().getPath();\r
  47       jalview.bin.Cache.LAST_DIRECTORY = choice;\r
  48       String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
  49       try{\r
  50         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
  51         out.println(output);\r
  52         out.close();\r
  53       }\r
  54       catch(Exception ex){}\r
  55     }\r
  56 \r
  57   }\r
  58 \r
  59   protected void outputText_actionPerformed(ActionEvent e)\r
  60   {\r
  61      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
  62      JInternalFrame frame = new JInternalFrame();\r
  63      cap.formatForOutput();\r
  64      frame.setContentPane(cap);\r
  65      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
  66      cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
  67   }\r
  68 \r
  69   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
  70   {\r
  71     HTMLOutput htmlOutput = new HTMLOutput(viewport.getAlignment(), alignPanel.seqPanel.getColourScheme());\r
  72     htmlOutput = null;\r
  73   }\r
  74 \r
  75   public void saveAsPostscriptMenuItem_actionPerformed(ActionEvent e)\r
  76   {\r
  77 \r
  78   }\r
  79 \r
  80   public void closeMenuItem_actionPerformed(ActionEvent e)\r
  81   {\r
  82     try{\r
  83       this.setClosed(true);\r
  84     }catch(Exception ex){}\r
  85   }\r
  86 \r
  87   ArrayList  historyList = new ArrayList();\r
  88   ArrayList redoList = new ArrayList();\r
  89 \r
  90   void updateEditMenuBar()\r
  91   {\r
  92     if(historyList.size()>0)\r
  93      {\r
  94        undoMenuItem.setEnabled(true);\r
  95        Object [] history = (Object[])historyList.get(0);\r
  96        undoMenuItem.setText("Undo "+history[0]);\r
  97      }\r
  98     else\r
  99     {\r
 100       undoMenuItem.setEnabled(false);\r
 101       undoMenuItem.setText("Undo");\r
 102     }\r
 103 \r
 104     if(redoList.size()>0)\r
 105      {\r
 106        redoMenuItem.setEnabled(true);\r
 107        Object [] history = (Object[])redoList.get(0);\r
 108        redoMenuItem.setText("Redo "+history[0]);\r
 109      }\r
 110     else\r
 111     {\r
 112       redoMenuItem.setEnabled(false);\r
 113       redoMenuItem.setText("Redo");\r
 114     }\r
 115   }\r
 116 \r
 117   public void addHistoryItem(String type)\r
 118   {\r
 119     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 120     redoList.clear();\r
 121     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 122     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 123     {\r
 124       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 125                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 126     }\r
 127 \r
 128     historyList.add(0, new Object[]{type,  seq} );\r
 129     updateEditMenuBar();\r
 130   }\r
 131 \r
 132   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 133   {\r
 134     Object [] history = (Object[])historyList.remove(0);\r
 135     // add the redo state before continuing!!\r
 136     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 137     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
 138     {\r
 139       seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
 140                             viewport.getAlignment().getSequenceAt(i).\r
 141                             getSequence());\r
 142     }\r
 143     /////////\r
 144 \r
 145     redoList.add(0, new Object[] {history[0], seq});\r
 146 \r
 147       seq = (SequenceI[]) history[1];\r
 148       viewport.setAlignment( new Alignment(seq) );\r
 149       updateEditMenuBar();\r
 150       alignPanel.RefreshPanels();\r
 151   }\r
 152 \r
 153 \r
 154   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 155   {\r
 156      Object [] history = (Object[])redoList.remove(0);\r
 157      SequenceI[] seq = (SequenceI[]) history[1];\r
 158      viewport.setAlignment( new Alignment(seq) );\r
 159      updateEditMenuBar();\r
 160      alignPanel.RefreshPanels();\r
 161   }\r
 162 \r
 163 \r
 164 \r
 165   public void groupsMenuItem_actionPerformed(ActionEvent e)\r
 166   {\r
 167     GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
 168     JInternalFrame frame = new JInternalFrame();\r
 169     frame.setContentPane(geditor);\r
 170     Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
 171     frame.setResizable(false);\r
 172   }\r
 173 \r
 174   public void groupEditingMenuItem_actionPerformed(ActionEvent e)\r
 175   {\r
 176     viewport.setGroupEdit( groupEditingMenuItem.isSelected() );\r
 177   }\r
 178 \r
 179   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 180   {\r
 181     Selection sel = viewport.getSelection();\r
 182     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 183       sel.addElement( viewport.getAlignment().getSequenceAt(i));\r
 184     PaintRefresher.Refresh(null);\r
 185   }\r
 186 \r
 187   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 188   {\r
 189     viewport.getSelection().clear();\r
 190     PaintRefresher.Refresh(null);\r
 191   }\r
 192 \r
 193   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 194   {\r
 195     Selection sel = viewport.getSelection();\r
 196     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 197     {\r
 198       if (sel.contains(viewport.getAlignment().getSequenceAt(i)))\r
 199         sel.removeElement(viewport.getAlignment().getSequenceAt(i));\r
 200       else\r
 201         sel.addElement(viewport.getAlignment().getSequenceAt(i));\r
 202     }\r
 203     PaintRefresher.Refresh(null);\r
 204   }\r
 205 \r
 206   public void deleteSelectedMenuItem_actionPerformed(ActionEvent e)\r
 207   {\r
 208     addHistoryItem("delete selection");\r
 209 \r
 210     for (int i=0;i < viewport.getSelection().size(); i++)\r
 211             viewport.getAlignment().deleteSequence(viewport.getSelection().sequenceAt(i));\r
 212 \r
 213     viewport.getSelection().clear();\r
 214     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());\r
 215     alignPanel.RefreshPanels();\r
 216   }\r
 217 \r
 218   public void moveSelectedMenuItem_actionPerformed(ActionEvent e)\r
 219   {\r
 220     copySelectedMenuItem_actionPerformed(null);\r
 221     deleteSelectedMenuItem_actionPerformed(null);\r
 222     alignPanel.repaint();\r
 223   }\r
 224 \r
 225   public void copySelectedMenuItem_actionPerformed(ActionEvent e)\r
 226   {\r
 227     if(viewport.getSelection().size()==0)\r
 228       return;\r
 229 \r
 230    SequenceI[] s = new Sequence[viewport.getSelection().size()];\r
 231    for (int i=0; i < viewport.getSelection().size(); i++) {\r
 232      s[i] = new Sequence(viewport.getSelection().sequenceAt(i));\r
 233     }\r
 234     AlignFrame af = new AlignFrame(new Alignment(s));\r
 235     int newHeight = s.length * af.viewport.getCharHeight() + 200;\r
 236     if(newHeight>500)\r
 237       newHeight=500;\r
 238     Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);\r
 239   }\r
 240 \r
 241   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 242   {\r
 243     viewport.getColumnSelection().clear();\r
 244     repaint();\r
 245   }\r
 246 \r
 247   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 248   {\r
 249     addHistoryItem("delete columns");\r
 250     ColumnSelection colSel = viewport.getColumnSelection();\r
 251     if (colSel.size() > 0)\r
 252     {\r
 253       int min = colSel.getMin();\r
 254       viewport.getAlignment().trimLeft(min);\r
 255       colSel.compensateForEdit(0,min);\r
 256       alignPanel.RefreshPanels();\r
 257     }\r
 258   }\r
 259 \r
 260   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 261   {\r
 262     addHistoryItem("delete columns");\r
 263     ColumnSelection colSel = viewport.getColumnSelection();\r
 264     if (colSel.size() > 0)\r
 265     {\r
 266       int max = colSel.getMax();\r
 267       if(max>1)\r
 268         viewport.getAlignment().trimRight(max);\r
 269 \r
 270       alignPanel.RefreshPanels();\r
 271     }\r
 272 \r
 273   }\r
 274 \r
 275   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 276   {\r
 277     addHistoryItem("delete gapped columns");\r
 278     viewport.getAlignment().removeGaps();\r
 279     alignPanel.RefreshPanels();\r
 280   }\r
 281 \r
 282   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 283   {\r
 284     addHistoryItem("delete all gaps");\r
 285     SequenceI current;\r
 286     int jSize;\r
 287     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 288     {\r
 289       current = viewport.getAlignment().getSequenceAt(i);\r
 290       jSize = current.getLength();\r
 291       for (int j=0; j < jSize; j++)\r
 292         if (current.getCharAt(j)=='-' || current.getCharAt(j)=='.' || current.getCharAt(j)==' ')\r
 293         {\r
 294           current.deleteCharAt(j);\r
 295           j--;\r
 296           jSize--;\r
 297         }\r
 298     }\r
 299 \r
 300     alignPanel.RefreshPanels();\r
 301   }\r
 302 \r
 303   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 304   {\r
 305     String thisChar = "-";\r
 306     String nextChar = ".";\r
 307     if(viewport.getGapCharacter().equals("-"))\r
 308     {\r
 309       thisChar = ".";\r
 310       nextChar = "-";\r
 311     }\r
 312     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 313     viewport.setGapCharacter(thisChar);\r
 314   }\r
 315 \r
 316 \r
 317   public void fontNameMenuItem_actionPerformed(ActionEvent e)\r
 318   {\r
 319     String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();\r
 320 \r
 321 \r
 322     String selection = JOptionPane.showInputDialog(this,\r
 323                                 "Select font",\r
 324                                 "Font selection",\r
 325                                 JOptionPane.QUESTION_MESSAGE,\r
 326                                 null,fonts\r
 327                                 ,fontNameMenuItem.getText()).toString();\r
 328     if(selection!=null)\r
 329     {\r
 330        fontNameMenuItem.setText(selection);\r
 331        SetFont();\r
 332      }\r
 333 \r
 334   }\r
 335 \r
 336   public void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
 337   {\r
 338     String selection = JOptionPane.showInputDialog(this,\r
 339                                 "Select font size",\r
 340                                 "Font size",\r
 341                                 JOptionPane.QUESTION_MESSAGE,\r
 342                                 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
 343                                 ,fontSizeMenuItem.getText()).toString();\r
 344     if(selection!=null)\r
 345      {\r
 346        fontSizeMenuItem.setText(selection);\r
 347        SetFont();\r
 348      }\r
 349   }\r
 350 \r
 351   public void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
 352   {\r
 353     String selection = JOptionPane.showInputDialog(this,\r
 354                                 "Select font style",\r
 355                                 "Font style",\r
 356                                 JOptionPane.QUESTION_MESSAGE,\r
 357                                 null, new String[]{"plain", "bold", "italic"}\r
 358                                 ,fontStyleMenuItem.getText()).toString();\r
 359     if(selection!=null)\r
 360     {\r
 361       fontStyleMenuItem.setText(selection);\r
 362       SetFont();\r
 363     }\r
 364 \r
 365   }\r
 366 \r
 367   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 368   {\r
 369     viewport.setColourText( colourTextMenuItem.isSelected() );\r
 370     alignPanel.RefreshPanels();\r
 371   }\r
 372 \r
 373   void SetFont()\r
 374   {\r
 375       int style = java.awt.Font.PLAIN;\r
 376       if(fontStyleMenuItem.getText().equals("bold"))\r
 377         style = java.awt.Font.BOLD;\r
 378       else if(fontStyleMenuItem.getText().equals("italic"))\r
 379         style = java.awt.Font.ITALIC;\r
 380 \r
 381       viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),\r
 382                                            style,\r
 383                                            Integer.parseInt(fontSizeMenuItem.getText())));\r
 384       alignPanel.RefreshPanels();\r
 385 \r
 386   }\r
 387 \r
 388   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 389   {\r
 390     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 391     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
 392   }\r
 393 \r
 394 \r
 395   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 396   {\r
 397     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 398     alignPanel.RefreshPanels();\r
 399   }\r
 400 \r
 401   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 402   {\r
 403     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 404     alignPanel.RefreshPanels();\r
 405   }\r
 406 \r
 407 \r
 408   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 409   {\r
 410     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
 411   }\r
 412 \r
 413   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 414   {\r
 415 \r
 416     JInternalFrame frame = new JInternalFrame();\r
 417     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 418    try{\r
 419      overview = new OverviewPanel(alignPanel, viewport);\r
 420      frame.setContentPane(overview);\r
 421     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 422                              frame.getWidth(), frame.getHeight());\r
 423     frame.pack();\r
 424     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 425     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 426       {\r
 427             alignPanel.setOverviewPanel(null);\r
 428       };\r
 429     });\r
 430     alignPanel.setOverviewPanel( overview );\r
 431 \r
 432   }catch(java.lang.OutOfMemoryError ex)\r
 433    {\r
 434      JOptionPane.showMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 435                                    +"\nTry reducing the font size.",\r
 436                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 437    }\r
 438 \r
 439 \r
 440   }\r
 441 \r
 442   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 443   {\r
 444     alignPanel.setColourScheme(null, false);\r
 445   }\r
 446 \r
 447 \r
 448   public void clustalColour_actionPerformed(ActionEvent e)\r
 449   {\r
 450    // alignPanel.setColourScheme( new ClustalxColourScheme() );\r
 451   }\r
 452 \r
 453   public void zappoColour_actionPerformed(ActionEvent e)\r
 454   {\r
 455     alignPanel.setColourScheme( new ZappoColourScheme(), conservationMenuItem.isSelected() );\r
 456   }\r
 457 \r
 458   public void taylorColour_actionPerformed(ActionEvent e)\r
 459   {\r
 460     alignPanel.setColourScheme( new TaylorColourScheme(),conservationMenuItem.isSelected() );\r
 461   }\r
 462 \r
 463 \r
 464   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 465   {\r
 466     alignPanel.setColourScheme( new HydrophobicColourScheme(),conservationMenuItem.isSelected() );\r
 467   }\r
 468 \r
 469   public void helixColour_actionPerformed(ActionEvent e)\r
 470   {\r
 471     alignPanel.setColourScheme( new HelixColourScheme(),conservationMenuItem.isSelected() );\r
 472   }\r
 473 \r
 474 \r
 475   public void strandColour_actionPerformed(ActionEvent e)\r
 476   {\r
 477     alignPanel.setColourScheme( new StrandColourScheme() ,conservationMenuItem.isSelected() );\r
 478   }\r
 479 \r
 480 \r
 481   public void turnColour_actionPerformed(ActionEvent e)\r
 482   {\r
 483     alignPanel.setColourScheme( new TurnColourScheme() ,conservationMenuItem.isSelected() );\r
 484   }\r
 485 \r
 486 \r
 487   public void buriedColour_actionPerformed(ActionEvent e)\r
 488   {\r
 489     alignPanel.setColourScheme( new BuriedColourScheme() ,conservationMenuItem.isSelected() );\r
 490   }\r
 491 \r
 492 \r
 493   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 494   {\r
 495     alignPanel.setColourScheme ( alignPanel.seqPanel.getColourScheme(),conservationMenuItem.isSelected() );\r
 496     conservationColourIncMenuItem.setEnabled( conservationMenuItem.isSelected() );\r
 497   }\r
 498 \r
 499 \r
 500 \r
 501   public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
 502  {\r
 503    ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);\r
 504    JInternalFrame frame = new JInternalFrame();\r
 505    frame.setContentPane(cip);\r
 506    Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);\r
 507    frame.setMaximizable(false);\r
 508  }\r
 509 \r
 510 \r
 511   public void abovePIDColour_actionPerformed(ActionEvent e)\r
 512   {\r
 513     alignPanel.setColourScheme( new PIDColourScheme() ,conservationMenuItem.isSelected() );\r
 514   }\r
 515 \r
 516 \r
 517   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 518   {\r
 519     JInternalFrame frame = new JInternalFrame();\r
 520     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel.seqPanel );\r
 521     frame.setContentPane(chooser);\r
 522     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 523     frame.setResizable(false);\r
 524     frame.setIconifiable(false);\r
 525     frame.setMaximizable(false);\r
 526   }\r
 527 \r
 528   public void PIDColour_actionPerformed(ActionEvent e)\r
 529   {\r
 530     alignPanel.setColourScheme( new PIDColourScheme(),conservationMenuItem.isSelected() );\r
 531   }\r
 532 \r
 533 \r
 534   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 535   {\r
 536     alignPanel.setColourScheme( new Blosum62ColourScheme(viewport) ,conservationMenuItem.isSelected() );\r
 537   }\r
 538 \r
 539 \r
 540 \r
 541   protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
 542   {\r
 543     ColourKey colourKey = new ColourKey( alignPanel.seqPanel.getColourScheme() );\r
 544     Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);\r
 545   }\r
 546 \r
 547 \r
 548   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 549   {\r
 550     addHistoryItem("sort");\r
 551     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 552     alignPanel.RefreshPanels();\r
 553   }\r
 554 \r
 555   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 556   {\r
 557     addHistoryItem("sort");\r
 558     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 559     alignPanel.RefreshPanels();\r
 560   }\r
 561 \r
 562   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 563   {\r
 564     addHistoryItem("sort");\r
 565     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 566     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 567     alignPanel.RefreshPanels();\r
 568   }\r
 569 \r
 570   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 571   {\r
 572     addHistoryItem("sort");\r
 573     if(viewport.getCurrentTree()==null)\r
 574       return;\r
 575 \r
 576     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 577     alignPanel.RefreshPanels();\r
 578   }\r
 579 \r
 580   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 581   {\r
 582 \r
 583   }\r
 584 \r
 585   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 586   {\r
 587     if(viewport.getSelection().size()<2)\r
 588       JOptionPane.showMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 589     else\r
 590     {\r
 591       JInternalFrame frame = new JInternalFrame();\r
 592       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 593       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 594     }\r
 595   }\r
 596 \r
 597   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 598   {\r
 599     if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)\r
 600        || viewport.getAlignment().getHeight()<4)\r
 601     {\r
 602       JOptionPane.showMessageDialog(this, "Principal component analysis must take\n"\r
 603                                     +"at least 4 input sequences.",\r
 604                                     "Sequence selection insufficient",\r
 605                                     JOptionPane.WARNING_MESSAGE);\r
 606       return;\r
 607     }\r
 608 \r
 609     try{\r
 610       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 611       JInternalFrame frame = new JInternalFrame();\r
 612       frame.setContentPane(pcaPanel);\r
 613       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 614    }catch(java.lang.OutOfMemoryError ex)\r
 615    {\r
 616      JOptionPane.showMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 617                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 618    }\r
 619 \r
 620 \r
 621   }\r
 622 \r
 623   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 624   {\r
 625     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 626   }\r
 627 \r
 628   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 629   {\r
 630     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 631   }\r
 632 \r
 633 \r
 634   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 635   {\r
 636     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 637   }\r
 638 \r
 639   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 640   {\r
 641     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 642   }\r
 643 \r
 644   void NewTreePanel(String type, String pwType, String title)\r
 645   {\r
 646     JInternalFrame frame = new javax.swing.JInternalFrame();\r
 647     TreePanel tp=null;\r
 648    if (viewport.getSelection() != null && viewport.getSelection().size() > 3)\r
 649    {\r
 650      tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,\r
 651                          viewport.getStartRes(), viewport.getEndRes());\r
 652    }\r
 653    else\r
 654    {\r
 655      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 656                          type, pwType, viewport.getStartRes(),\r
 657                          viewport.getEndRes());\r
 658    }\r
 659 \r
 660    frame.setContentPane(tp);\r
 661    Desktop.addInternalFrame(frame, title, 600, 500);\r
 662   }\r
 663 \r
 664 \r
 665 \r
 666   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 667   {\r
 668     JOptionPane.showMessageDialog(this, "Jalview is currently being reengineered"\r
 669                                   +"\nwithin the Barton Group, Dundee University."\r
 670                                   +"\nThis will be available as a web service 2005",\r
 671                                   "Web service", JOptionPane.INFORMATION_MESSAGE);\r
 672   }\r
 673 \r
 674 }\r