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.getAlignment(), alignPanel.seqPanel.getColourScheme());\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     //  printJob.\r
  90       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
  91       printJob.setPrintable(alignPanel, pf);\r
  92       if (printJob.printDialog())\r
  93       {\r
  94         try\r
  95         {\r
  96           printJob.print();\r
  97         }\r
  98         catch (Exception PrintException)\r
  99         {\r
 100           PrintException.printStackTrace();\r
 101         }\r
 102       }\r
 103     }\r
 104 \r
 105   }\r
 106 \r
 107 \r
 108 \r
 109 \r
 110   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 111   {\r
 112     try{\r
 113       this.setClosed(true);\r
 114     }catch(Exception ex){}\r
 115   }\r
 116 \r
 117   ArrayList  historyList = new ArrayList();\r
 118   ArrayList redoList = new ArrayList();\r
 119 \r
 120   void updateEditMenuBar()\r
 121   {\r
 122     if(historyList.size()>0)\r
 123      {\r
 124        undoMenuItem.setEnabled(true);\r
 125        Object [] history = (Object[])historyList.get(0);\r
 126        undoMenuItem.setText("Undo "+history[0]);\r
 127      }\r
 128     else\r
 129     {\r
 130       undoMenuItem.setEnabled(false);\r
 131       undoMenuItem.setText("Undo");\r
 132     }\r
 133 \r
 134     if(redoList.size()>0)\r
 135      {\r
 136        redoMenuItem.setEnabled(true);\r
 137        Object [] history = (Object[])redoList.get(0);\r
 138        redoMenuItem.setText("Redo "+history[0]);\r
 139      }\r
 140     else\r
 141     {\r
 142       redoMenuItem.setEnabled(false);\r
 143       redoMenuItem.setText("Redo");\r
 144     }\r
 145   }\r
 146 \r
 147   public void addHistoryItem(String type)\r
 148   {\r
 149     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 150     redoList.clear();\r
 151     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 152     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 153     {\r
 154       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 155                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 156     }\r
 157 \r
 158     historyList.add(0, new Object[]{type,  seq} );\r
 159     updateEditMenuBar();\r
 160   }\r
 161 \r
 162   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 163   {\r
 164     Object [] history = (Object[])historyList.remove(0);\r
 165     // add the redo state before continuing!!\r
 166     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 167     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
 168     {\r
 169       seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
 170                             viewport.getAlignment().getSequenceAt(i).\r
 171                             getSequence());\r
 172     }\r
 173     /////////\r
 174 \r
 175     redoList.add(0, new Object[] {history[0], seq});\r
 176 \r
 177       seq = (SequenceI[]) history[1];\r
 178       viewport.setAlignment( new Alignment(seq) );\r
 179       updateEditMenuBar();\r
 180       alignPanel.RefreshPanels();\r
 181   }\r
 182 \r
 183 \r
 184   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 185   {\r
 186      Object [] history = (Object[])redoList.remove(0);\r
 187      SequenceI[] seq = (SequenceI[]) history[1];\r
 188      viewport.setAlignment( new Alignment(seq) );\r
 189      updateEditMenuBar();\r
 190      alignPanel.RefreshPanels();\r
 191   }\r
 192 \r
 193 \r
 194 \r
 195   public void groupsMenuItem_actionPerformed(ActionEvent e)\r
 196   {\r
 197     GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
 198     JInternalFrame frame = new JInternalFrame();\r
 199     frame.setContentPane(geditor);\r
 200     Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
 201     frame.setResizable(false);\r
 202   }\r
 203 \r
 204   public void groupEditingMenuItem_actionPerformed(ActionEvent e)\r
 205   {\r
 206     viewport.setGroupEdit( groupEditingMenuItem.isSelected() );\r
 207   }\r
 208 \r
 209   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 210   {\r
 211     Selection sel = viewport.getSelection();\r
 212     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 213       sel.addElement( viewport.getAlignment().getSequenceAt(i));\r
 214     PaintRefresher.Refresh(null);\r
 215   }\r
 216 \r
 217   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 218   {\r
 219     viewport.getSelection().clear();\r
 220     PaintRefresher.Refresh(null);\r
 221   }\r
 222 \r
 223   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 224   {\r
 225     Selection sel = viewport.getSelection();\r
 226     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 227     {\r
 228       if (sel.contains(viewport.getAlignment().getSequenceAt(i)))\r
 229         sel.removeElement(viewport.getAlignment().getSequenceAt(i));\r
 230       else\r
 231         sel.addElement(viewport.getAlignment().getSequenceAt(i));\r
 232     }\r
 233     PaintRefresher.Refresh(null);\r
 234   }\r
 235 \r
 236   public void deleteSelectedMenuItem_actionPerformed(ActionEvent e)\r
 237   {\r
 238     addHistoryItem("delete selection");\r
 239 \r
 240     for (int i=0;i < viewport.getSelection().size(); i++)\r
 241             viewport.getAlignment().deleteSequence(viewport.getSelection().sequenceAt(i));\r
 242 \r
 243     viewport.getSelection().clear();\r
 244     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());\r
 245     alignPanel.RefreshPanels();\r
 246   }\r
 247 \r
 248   public void moveSelectedMenuItem_actionPerformed(ActionEvent e)\r
 249   {\r
 250     copySelectedMenuItem_actionPerformed(null);\r
 251     deleteSelectedMenuItem_actionPerformed(null);\r
 252     alignPanel.repaint();\r
 253   }\r
 254 \r
 255   public void copySelectedMenuItem_actionPerformed(ActionEvent e)\r
 256   {\r
 257     if(viewport.getSelection().size()==0)\r
 258       return;\r
 259 \r
 260    SequenceI[] s = new Sequence[viewport.getSelection().size()];\r
 261    for (int i=0; i < viewport.getSelection().size(); i++) {\r
 262      s[i] = new Sequence(viewport.getSelection().sequenceAt(i));\r
 263     }\r
 264     AlignFrame af = new AlignFrame(new Alignment(s));\r
 265     int newHeight = s.length * af.viewport.getCharHeight() + 200;\r
 266     if(newHeight>500)\r
 267       newHeight=500;\r
 268     Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);\r
 269   }\r
 270 \r
 271   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 272   {\r
 273     viewport.getColumnSelection().clear();\r
 274     repaint();\r
 275   }\r
 276 \r
 277   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 278   {\r
 279     addHistoryItem("delete columns");\r
 280     ColumnSelection colSel = viewport.getColumnSelection();\r
 281     if (colSel.size() > 0)\r
 282     {\r
 283       int min = colSel.getMin();\r
 284       viewport.getAlignment().trimLeft(min);\r
 285       colSel.compensateForEdit(0,min);\r
 286       alignPanel.RefreshPanels();\r
 287     }\r
 288   }\r
 289 \r
 290   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 291   {\r
 292     addHistoryItem("delete columns");\r
 293     ColumnSelection colSel = viewport.getColumnSelection();\r
 294     if (colSel.size() > 0)\r
 295     {\r
 296       int max = colSel.getMax();\r
 297       if(max>1)\r
 298         viewport.getAlignment().trimRight(max);\r
 299 \r
 300       alignPanel.RefreshPanels();\r
 301     }\r
 302 \r
 303   }\r
 304 \r
 305   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 306   {\r
 307     addHistoryItem("delete gapped columns");\r
 308     viewport.getAlignment().removeGaps();\r
 309     alignPanel.RefreshPanels();\r
 310   }\r
 311 \r
 312   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 313   {\r
 314     addHistoryItem("delete all gaps");\r
 315     SequenceI current;\r
 316     int jSize;\r
 317     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 318     {\r
 319       current = viewport.getAlignment().getSequenceAt(i);\r
 320       jSize = current.getLength();\r
 321       for (int j=0; j < jSize; j++)\r
 322         if (current.getCharAt(j)=='-' || current.getCharAt(j)=='.' || current.getCharAt(j)==' ')\r
 323         {\r
 324           current.deleteCharAt(j);\r
 325           j--;\r
 326           jSize--;\r
 327         }\r
 328     }\r
 329 \r
 330     alignPanel.RefreshPanels();\r
 331   }\r
 332 \r
 333   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 334   {\r
 335     String thisChar = "-";\r
 336     String nextChar = ".";\r
 337     if(viewport.getGapCharacter().equals("-"))\r
 338     {\r
 339       thisChar = ".";\r
 340       nextChar = "-";\r
 341     }\r
 342     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 343     viewport.setGapCharacter(thisChar);\r
 344   }\r
 345 \r
 346 \r
 347   public void fontNameMenuItem_actionPerformed(ActionEvent e)\r
 348   {\r
 349     String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();\r
 350 \r
 351 \r
 352     String selection = JOptionPane.showInputDialog(this,\r
 353                                 "Select font",\r
 354                                 "Font selection",\r
 355                                 JOptionPane.QUESTION_MESSAGE,\r
 356                                 null,fonts\r
 357                                 ,fontNameMenuItem.getText()).toString();\r
 358     if(selection!=null)\r
 359     {\r
 360        fontNameMenuItem.setText(selection);\r
 361        SetFont();\r
 362      }\r
 363 \r
 364   }\r
 365 \r
 366   public void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
 367   {\r
 368     String selection = JOptionPane.showInputDialog(this,\r
 369                                 "Select font size",\r
 370                                 "Font size",\r
 371                                 JOptionPane.QUESTION_MESSAGE,\r
 372                                 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
 373                                 ,fontSizeMenuItem.getText()).toString();\r
 374     if(selection!=null)\r
 375      {\r
 376        fontSizeMenuItem.setText(selection);\r
 377        SetFont();\r
 378      }\r
 379   }\r
 380 \r
 381   public void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
 382   {\r
 383     String selection = JOptionPane.showInputDialog(this,\r
 384                                 "Select font style",\r
 385                                 "Font style",\r
 386                                 JOptionPane.QUESTION_MESSAGE,\r
 387                                 null, new String[]{"plain", "bold", "italic"}\r
 388                                 ,fontStyleMenuItem.getText()).toString();\r
 389     if(selection!=null)\r
 390     {\r
 391       fontStyleMenuItem.setText(selection);\r
 392       SetFont();\r
 393     }\r
 394 \r
 395   }\r
 396 \r
 397   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 398   {\r
 399       updateResidueView();\r
 400   }\r
 401 \r
 402   void SetFont()\r
 403   {\r
 404       int style = java.awt.Font.PLAIN;\r
 405       if(fontStyleMenuItem.getText().equals("bold"))\r
 406         style = java.awt.Font.BOLD;\r
 407       else if(fontStyleMenuItem.getText().equals("italic"))\r
 408         style = java.awt.Font.ITALIC;\r
 409 \r
 410       viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),\r
 411                                            style,\r
 412                                            Integer.parseInt(fontSizeMenuItem.getText())));\r
 413       alignPanel.RefreshPanels();\r
 414 \r
 415   }\r
 416 \r
 417   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 418   {\r
 419      updateResidueView();\r
 420   }\r
 421 \r
 422 \r
 423   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 424   {\r
 425      updateResidueView();\r
 426   }\r
 427 \r
 428   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 429   {\r
 430      updateResidueView();\r
 431   }\r
 432 \r
 433   void updateResidueView()\r
 434   {\r
 435     if (viewport.getSelection().size() == 0)\r
 436      {\r
 437        for (int i = 0; i < viewport.alignment.getGroups().size(); i++)\r
 438        {\r
 439          SequenceGroup sg = (SequenceGroup) viewport.alignment.getGroups().elementAt(i);\r
 440          sg.setDisplayBoxes( viewBoxesMenuItem.isSelected() );\r
 441          sg.setDisplayText( viewTextMenuItem.isSelected() );\r
 442          sg.setColourText( colourTextMenuItem.isSelected() );\r
 443        }\r
 444      }\r
 445      else\r
 446      {\r
 447        SequenceGroup sg = viewport.alignment.findGroup( (Sequence) viewport.sel.sequenceAt(0));\r
 448        if (alignPanel.seqPanel.isNewSelection(sg))\r
 449        {\r
 450          sg = viewport.getAlignment().addGroup();\r
 451          for (int i = 0; i < viewport.getSelection().size(); i++)\r
 452          {\r
 453            viewport.alignment.removeFromGroup(viewport.alignment.findGroup( (\r
 454                Sequence) viewport.sel.sequenceAt(i)),\r
 455                                               (Sequence) viewport.sel.sequenceAt(\r
 456                i));\r
 457            viewport.alignment.addToGroup(sg,\r
 458                                          (Sequence) viewport.sel.sequenceAt(i));\r
 459          }\r
 460        }\r
 461 \r
 462        sg.setDisplayBoxes(viewBoxesMenuItem.isSelected());\r
 463        sg.setDisplayText(viewTextMenuItem.isSelected());\r
 464        sg.setColourText(colourTextMenuItem.isSelected());\r
 465      }\r
 466     alignPanel.RefreshPanels();\r
 467   }\r
 468 \r
 469 \r
 470   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 471   {\r
 472     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
 473   }\r
 474 \r
 475   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 476   {\r
 477 \r
 478     JInternalFrame frame = new JInternalFrame();\r
 479     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 480    try{\r
 481      overview = new OverviewPanel(alignPanel, viewport);\r
 482      frame.setContentPane(overview);\r
 483     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 484                              frame.getWidth(), frame.getHeight());\r
 485     frame.pack();\r
 486     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 487     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 488       {\r
 489             alignPanel.setOverviewPanel(null);\r
 490       };\r
 491     });\r
 492     alignPanel.setOverviewPanel( overview );\r
 493 \r
 494   }catch(java.lang.OutOfMemoryError ex)\r
 495    {\r
 496      JOptionPane.showMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 497                                    +"\nTry reducing the font size.",\r
 498                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 499    }\r
 500 \r
 501 \r
 502   }\r
 503 \r
 504   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 505   {\r
 506     alignPanel.setColourScheme(null, false);\r
 507   }\r
 508 \r
 509 \r
 510   public void clustalColour_actionPerformed(ActionEvent e)\r
 511   {\r
 512    // alignPanel.setColourScheme( new ClustalxColourScheme() );\r
 513   }\r
 514 \r
 515   public void zappoColour_actionPerformed(ActionEvent e)\r
 516   {\r
 517     alignPanel.setColourScheme( new ZappoColourScheme(), conservationMenuItem.isSelected() );\r
 518   }\r
 519 \r
 520   public void taylorColour_actionPerformed(ActionEvent e)\r
 521   {\r
 522     alignPanel.setColourScheme( new TaylorColourScheme(),conservationMenuItem.isSelected() );\r
 523   }\r
 524 \r
 525 \r
 526   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 527   {\r
 528     alignPanel.setColourScheme( new HydrophobicColourScheme(),conservationMenuItem.isSelected() );\r
 529   }\r
 530 \r
 531   public void helixColour_actionPerformed(ActionEvent e)\r
 532   {\r
 533     alignPanel.setColourScheme( new HelixColourScheme(),conservationMenuItem.isSelected() );\r
 534   }\r
 535 \r
 536 \r
 537   public void strandColour_actionPerformed(ActionEvent e)\r
 538   {\r
 539     alignPanel.setColourScheme( new StrandColourScheme() ,conservationMenuItem.isSelected() );\r
 540   }\r
 541 \r
 542 \r
 543   public void turnColour_actionPerformed(ActionEvent e)\r
 544   {\r
 545     alignPanel.setColourScheme( new TurnColourScheme() ,conservationMenuItem.isSelected() );\r
 546   }\r
 547 \r
 548 \r
 549   public void buriedColour_actionPerformed(ActionEvent e)\r
 550   {\r
 551     alignPanel.setColourScheme( new BuriedColourScheme() ,conservationMenuItem.isSelected() );\r
 552   }\r
 553 \r
 554 \r
 555   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 556   {\r
 557     alignPanel.setColourScheme ( alignPanel.seqPanel.getColourScheme(),conservationMenuItem.isSelected() );\r
 558     conservationColourIncMenuItem.setEnabled( conservationMenuItem.isSelected() );\r
 559   }\r
 560 \r
 561 \r
 562 \r
 563   public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
 564  {\r
 565    ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);\r
 566    JInternalFrame frame = new JInternalFrame();\r
 567    frame.setContentPane(cip);\r
 568    Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);\r
 569    frame.setMaximizable(false);\r
 570  }\r
 571 \r
 572 \r
 573   public void abovePIDColour_actionPerformed(ActionEvent e)\r
 574   {\r
 575     alignPanel.setColourScheme( new PIDColourScheme() ,conservationMenuItem.isSelected() );\r
 576   }\r
 577 \r
 578 \r
 579   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 580   {\r
 581     JInternalFrame frame = new JInternalFrame();\r
 582     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel.seqPanel );\r
 583     frame.setContentPane(chooser);\r
 584     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 585     frame.setResizable(false);\r
 586     frame.setIconifiable(false);\r
 587     frame.setMaximizable(false);\r
 588   }\r
 589 \r
 590   public void PIDColour_actionPerformed(ActionEvent e)\r
 591   {\r
 592     alignPanel.setColourScheme( new PIDColourScheme(),conservationMenuItem.isSelected() );\r
 593   }\r
 594 \r
 595 \r
 596   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 597   {\r
 598     alignPanel.setColourScheme( new Blosum62ColourScheme(viewport) ,conservationMenuItem.isSelected() );\r
 599   }\r
 600 \r
 601 \r
 602 \r
 603   protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
 604   {\r
 605     ColourKey colourKey = new ColourKey( alignPanel.seqPanel.getColourScheme() );\r
 606     Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);\r
 607   }\r
 608 \r
 609 \r
 610   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 611   {\r
 612     addHistoryItem("sort");\r
 613     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 614     alignPanel.RefreshPanels();\r
 615   }\r
 616 \r
 617   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 618   {\r
 619     addHistoryItem("sort");\r
 620     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 621     alignPanel.RefreshPanels();\r
 622   }\r
 623 \r
 624   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 625   {\r
 626     addHistoryItem("sort");\r
 627     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 628     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 629     alignPanel.RefreshPanels();\r
 630   }\r
 631 \r
 632   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 633   {\r
 634     addHistoryItem("sort");\r
 635     if(viewport.getCurrentTree()==null)\r
 636       return;\r
 637 \r
 638     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 639     alignPanel.RefreshPanels();\r
 640   }\r
 641 \r
 642   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 643   {\r
 644 \r
 645   }\r
 646 \r
 647   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 648   {\r
 649     if(viewport.getSelection().size()<2)\r
 650       JOptionPane.showMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 651     else\r
 652     {\r
 653       JInternalFrame frame = new JInternalFrame();\r
 654       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 655       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 656     }\r
 657   }\r
 658 \r
 659   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 660   {\r
 661     if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)\r
 662        || viewport.getAlignment().getHeight()<4)\r
 663     {\r
 664       JOptionPane.showMessageDialog(this, "Principal component analysis must take\n"\r
 665                                     +"at least 4 input sequences.",\r
 666                                     "Sequence selection insufficient",\r
 667                                     JOptionPane.WARNING_MESSAGE);\r
 668       return;\r
 669     }\r
 670 \r
 671     try{\r
 672       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 673       JInternalFrame frame = new JInternalFrame();\r
 674       frame.setContentPane(pcaPanel);\r
 675       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 676    }catch(java.lang.OutOfMemoryError ex)\r
 677    {\r
 678      JOptionPane.showMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 679                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 680    }\r
 681 \r
 682 \r
 683   }\r
 684 \r
 685   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 686   {\r
 687     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 688   }\r
 689 \r
 690   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 691   {\r
 692     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 693   }\r
 694 \r
 695 \r
 696   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 697   {\r
 698     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 699   }\r
 700 \r
 701   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 702   {\r
 703     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 704   }\r
 705 \r
 706   void NewTreePanel(String type, String pwType, String title)\r
 707   {\r
 708     JInternalFrame frame = new javax.swing.JInternalFrame();\r
 709     TreePanel tp=null;\r
 710    if (viewport.getSelection() != null && viewport.getSelection().size() > 3)\r
 711    {\r
 712      tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,\r
 713                          viewport.getStartRes(), viewport.getEndRes());\r
 714    }\r
 715    else\r
 716    {\r
 717      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 718                          type, pwType, viewport.getStartRes(),\r
 719                          viewport.getEndRes());\r
 720    }\r
 721 \r
 722    frame.setContentPane(tp);\r
 723    Desktop.addInternalFrame(frame, title, 600, 500);\r
 724   }\r
 725 \r
 726 \r
 727 \r
 728   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 729   {\r
 730     JOptionPane.showMessageDialog(this, "Jalview is currently being reengineered"\r
 731                                   +"\nwithin the Barton Group, Dundee University."\r
 732                                   +"\nThis will be available as a web service 2005",\r
 733                                   "Web service", JOptionPane.INFORMATION_MESSAGE);\r
 734   }\r
 735 \r
 736   public void pdbTest_actionPerformed(ActionEvent e)\r
 737   {\r
 738    String reply = JOptionPane.showInputDialog(this, "Enter pdb code", "PDB test viewer", JOptionPane.QUESTION_MESSAGE);\r
 739 \r
 740    String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";\r
 741    if (reply.length()>1)\r
 742      url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id="+reply;\r
 743 \r
 744    try\r
 745    {\r
 746      PDBfile pdb = new PDBfile(url,\r
 747                                "URL");\r
 748     Sequence seq = (Sequence)viewport.getAlignment().getSequenceAt(0);\r
 749     seq.setPDBfile(pdb);\r
 750      ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).isVisible = true;\r
 751      ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).sequence = seq;\r
 752   // ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).colourBySequence();\r
 753 \r
 754      rotCanvas rc = new rotCanvas(pdb);\r
 755      JInternalFrame frame = new JInternalFrame();\r
 756      frame.setContentPane(rc);\r
 757      Desktop.addInternalFrame(frame, url, 400,400);\r
 758    }\r
 759    catch (Exception ex)\r
 760    {\r
 761      ex.printStackTrace();\r
 762    }\r
 763 \r
 764   }\r
 765 \r
 766 }\r