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