src/jalview/gui/AlignFrame.java

   1 /********************\r
   2  * 2004 Jalview Reengineered\r
   3  * Barton Group\r
   4  * Dundee University\r
   5  *\r
   6  * AM Waterhouse\r
   7  *******************/\r
   8 \r
   9 \r
  10 \r
  11 \r
  12 package jalview.gui;\r
  13 \r
  14 import jalview.jbgui.GAlignFrame;\r
  15 import jalview.schemes.*;\r
  16 import jalview.datamodel.*;\r
  17 import jalview.analysis.*;\r
  18 import jalview.io.*;\r
  19 import jalview.ws.*;\r
  20 import java.awt.*;\r
  21 import java.awt.event.*;\r
  22 import java.awt.print.*;\r
  23 import javax.swing.*;\r
  24 import javax.swing.event.*;\r
  25 import java.util.*;\r
  26 import  java.awt.datatransfer.*;\r
  27 \r
  28 \r
  29 public class AlignFrame extends GAlignFrame\r
  30 {\r
  31   final AlignmentPanel alignPanel;\r
  32   final AlignViewport viewport;\r
  33   public AlignFrame(AlignmentI al)\r
  34   {\r
  35     super();\r
  36     viewport = new AlignViewport(al,true,true,true,false);\r
  37     alignPanel = new AlignmentPanel(this, viewport);\r
  38     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
  39     fontNameMenuItem.setText(viewport.getFont().getName());\r
  40     fontSizeMenuItem.setText(viewport.getFont().getSize()+"");\r
  41 \r
  42     addInternalFrameListener(new InternalFrameAdapter()\r
  43    {\r
  44      public void internalFrameActivated(InternalFrameEvent evt)\r
  45      {\r
  46           javax.swing.SwingUtilities.invokeLater(new Runnable()\r
  47           {\r
  48             public void run()\r
  49             {      alignPanel.requestFocus();    }\r
  50           });\r
  51 \r
  52      }\r
  53    });\r
  54 \r
  55    AlignmentUtil.fetchSequenceFeatures(al, alignPanel);\r
  56   }\r
  57 \r
  58   protected void saveAs_actionPerformed(ActionEvent e)\r
  59   {\r
  60     JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
  61     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
  62     chooser.setToolTipText("Save");\r
  63     int value = chooser.showSaveDialog(this);\r
  64     if(value == JFileChooser.APPROVE_OPTION)\r
  65     {\r
  66       String choice =  chooser.getSelectedFile().getPath();\r
  67       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
  68       String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
  69       try{\r
  70         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
  71         out.println(output);\r
  72         out.close();\r
  73       }\r
  74       catch(Exception ex){}\r
  75     }\r
  76 \r
  77   }\r
  78 \r
  79   protected void outputText_actionPerformed(ActionEvent e)\r
  80   {\r
  81      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
  82      JInternalFrame frame = new JInternalFrame();\r
  83      cap.formatForOutput();\r
  84      frame.setContentPane(cap);\r
  85      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
  86      cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
  87   }\r
  88 \r
  89   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
  90   {\r
  91     HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
  92     htmlOutput = null;\r
  93   }\r
  94 \r
  95   public void printMenuItem_actionPerformed(ActionEvent e)\r
  96   {\r
  97     //Putting in a thread avoids Swing painting problems\r
  98     PrintThread thread = new PrintThread();\r
  99     thread.start();\r
 100   }\r
 101 \r
 102   class PrintThread extends Thread\r
 103   {\r
 104     public void run()\r
 105     {\r
 106       PrinterJob printJob = PrinterJob.getPrinterJob();\r
 107       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
 108       printJob.setPrintable(alignPanel, pf);\r
 109       if (printJob.printDialog())\r
 110       {\r
 111         try\r
 112         {\r
 113           printJob.print();\r
 114         }\r
 115         catch (Exception PrintException)\r
 116         {\r
 117           PrintException.printStackTrace();\r
 118         }\r
 119       }\r
 120     }\r
 121 \r
 122   }\r
 123 \r
 124 \r
 125 \r
 126 \r
 127   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 128   {\r
 129     try{\r
 130       this.setClosed(true);\r
 131     }catch(Exception ex){}\r
 132   }\r
 133 \r
 134   ArrayList  historyList = new ArrayList();\r
 135   ArrayList redoList = new ArrayList();\r
 136 \r
 137   void updateEditMenuBar()\r
 138   {\r
 139     if(historyList.size()>0)\r
 140      {\r
 141        undoMenuItem.setEnabled(true);\r
 142        Object [] history = (Object[])historyList.get(0);\r
 143        undoMenuItem.setText("Undo "+history[0]);\r
 144      }\r
 145     else\r
 146     {\r
 147       undoMenuItem.setEnabled(false);\r
 148       undoMenuItem.setText("Undo");\r
 149     }\r
 150 \r
 151     if(redoList.size()>0)\r
 152      {\r
 153        redoMenuItem.setEnabled(true);\r
 154        Object [] history = (Object[])redoList.get(0);\r
 155        redoMenuItem.setText("Redo "+history[0]);\r
 156      }\r
 157     else\r
 158     {\r
 159       redoMenuItem.setEnabled(false);\r
 160       redoMenuItem.setText("Redo");\r
 161     }\r
 162   }\r
 163 \r
 164   public void addHistoryItem(String type)\r
 165   {\r
 166     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 167     redoList.clear();\r
 168     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 169     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 170     {\r
 171       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 172                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 173     }\r
 174 \r
 175     historyList.add(0, new Object[]{type,  seq} );\r
 176     updateEditMenuBar();\r
 177   }\r
 178 \r
 179   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 180   {\r
 181     Object [] history = (Object[])historyList.remove(0);\r
 182     // add the redo state before continuing!!\r
 183     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 184     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
 185     {\r
 186       seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
 187                             viewport.getAlignment().getSequenceAt(i).\r
 188                             getSequence());\r
 189     }\r
 190     /////////\r
 191 \r
 192     redoList.add(0, new Object[] {history[0], seq});\r
 193 \r
 194       seq = (SequenceI[]) history[1];\r
 195       viewport.setAlignment( new Alignment(seq) );\r
 196       updateEditMenuBar();\r
 197       alignPanel.RefreshPanels();\r
 198   }\r
 199 \r
 200   protected void copy_actionPerformed(ActionEvent e)\r
 201   {\r
 202    if(viewport.getRubberbandGroup()==null)\r
 203      return;\r
 204 \r
 205    SequenceGroup sg = viewport.getRubberbandGroup();\r
 206 \r
 207      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 208      StringBuffer buffer= new StringBuffer();\r
 209 \r
 210        for(int i=0; i<sg.getSize(); i++)\r
 211        {\r
 212          SequenceI seq = sg.getSequenceAt(i);\r
 213          buffer.append( seq.getName()+"\t"+seq.getStart() +"\t"+seq.getEnd()+"\t"\r
 214                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
 215        }\r
 216      c.setContents( new StringSelection( buffer.toString()) , null ) ;\r
 217 \r
 218   }\r
 219 \r
 220 \r
 221   protected void pasteNew_actionPerformed(ActionEvent e)\r
 222   {\r
 223     paste(true);\r
 224   }\r
 225 \r
 226   protected void pasteThis_actionPerformed(ActionEvent e)\r
 227   {\r
 228     paste(false);\r
 229   }\r
 230 \r
 231   void paste(boolean newAlignment)\r
 232   {\r
 233     try{\r
 234       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 235       Transferable contents = c.getContents(this);\r
 236       if (contents == null)\r
 237         return;\r
 238 \r
 239       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
 240       StringTokenizer st = new StringTokenizer(str);\r
 241       ArrayList seqs = new ArrayList();\r
 242       while (st.hasMoreElements())\r
 243       {\r
 244         String name = st.nextToken();\r
 245         int start = Integer.parseInt(st.nextToken());\r
 246         int end = Integer.parseInt(st.nextToken());\r
 247 \r
 248         Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
 249         if(!newAlignment)\r
 250           viewport.alignment.addSequence(sequence);\r
 251         else\r
 252           seqs.add(sequence);\r
 253       }\r
 254 \r
 255       if(newAlignment)\r
 256       {\r
 257         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 258         seqs.toArray(newSeqs);\r
 259         AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
 260         int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;\r
 261         if (newHeight > 500)\r
 262           newHeight = 500;\r
 263         Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
 264       }\r
 265       else\r
 266       {\r
 267         viewport.setEndSeq(viewport.alignment.getHeight());\r
 268         viewport.alignment.getWidth();\r
 269         alignPanel.RefreshPanels();\r
 270       }\r
 271 \r
 272     }catch(Exception ex){}// could be anything being pasted in here\r
 273 \r
 274   }\r
 275 \r
 276 \r
 277   protected void cut_actionPerformed(ActionEvent e)\r
 278   {\r
 279     copy_actionPerformed(null);\r
 280     delete_actionPerformed(null);\r
 281   }\r
 282 \r
 283   protected void delete_actionPerformed(ActionEvent e)\r
 284   {\r
 285     if (viewport.getRubberbandGroup() == null)\r
 286       return;\r
 287 \r
 288      SequenceGroup sg = viewport.getRubberbandGroup();\r
 289      for (int i=0;i < sg.sequences.size(); i++)\r
 290              viewport.getAlignment().deleteSequence(sg.getSequenceAt(i));\r
 291 \r
 292      viewport.alignment.deleteGroup(sg);\r
 293      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());\r
 294      if(viewport.getAlignment().getHeight()<1)\r
 295      try\r
 296      {\r
 297        this.setClosed(true);\r
 298      }catch(Exception ex){}\r
 299      alignPanel.RefreshPanels();\r
 300 \r
 301   }\r
 302 \r
 303 \r
 304 \r
 305   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 306   {\r
 307      Object [] history = (Object[])redoList.remove(0);\r
 308      SequenceI[] seq = (SequenceI[]) history[1];\r
 309      viewport.setAlignment( new Alignment(seq) );\r
 310      updateEditMenuBar();\r
 311      alignPanel.RefreshPanels();\r
 312   }\r
 313 \r
 314 \r
 315   public void groupsMenuItem_actionPerformed(ActionEvent e)\r
 316   {\r
 317     GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
 318     JInternalFrame frame = new JInternalFrame();\r
 319     frame.setContentPane(geditor);\r
 320     Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
 321     frame.setResizable(false);\r
 322   }\r
 323 \r
 324   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 325   {\r
 326     viewport.alignment.deleteAllGroups();\r
 327     viewport.getSelection().clear();\r
 328 \r
 329     alignPanel.RefreshPanels();\r
 330   }\r
 331 \r
 332 \r
 333 \r
 334   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 335   {\r
 336     Selection sel = viewport.getSelection();\r
 337     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 338       sel.addElement( viewport.getAlignment().getSequenceAt(i));\r
 339     PaintRefresher.Refresh(null);\r
 340   }\r
 341 \r
 342   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 343   {\r
 344     viewport.setRubberbandGroup(null);\r
 345     viewport.getSelection().clear();\r
 346     PaintRefresher.Refresh(null);\r
 347   }\r
 348 \r
 349   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 350   {\r
 351     Selection sel = viewport.getSelection();\r
 352     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 353     {\r
 354       if (sel.contains(viewport.getAlignment().getSequenceAt(i)))\r
 355         sel.removeElement(viewport.getAlignment().getSequenceAt(i));\r
 356       else\r
 357         sel.addElement(viewport.getAlignment().getSequenceAt(i));\r
 358     }\r
 359     PaintRefresher.Refresh(null);\r
 360   }\r
 361 \r
 362 \r
 363   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 364   {\r
 365     viewport.getColumnSelection().clear();\r
 366     repaint();\r
 367   }\r
 368 \r
 369   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 370   {\r
 371     addHistoryItem("delete columns");\r
 372     ColumnSelection colSel = viewport.getColumnSelection();\r
 373     if (colSel.size() > 0)\r
 374     {\r
 375       int min = colSel.getMin();\r
 376       viewport.getAlignment().trimLeft(min);\r
 377       colSel.compensateForEdit(0,min);\r
 378       alignPanel.RefreshPanels();\r
 379     }\r
 380   }\r
 381 \r
 382   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 383   {\r
 384     addHistoryItem("delete columns");\r
 385     ColumnSelection colSel = viewport.getColumnSelection();\r
 386     if (colSel.size() > 0)\r
 387     {\r
 388       int max = colSel.getMax();\r
 389       if(max>1)\r
 390         viewport.getAlignment().trimRight(max);\r
 391 \r
 392       alignPanel.RefreshPanels();\r
 393     }\r
 394 \r
 395   }\r
 396 \r
 397   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 398   {\r
 399     addHistoryItem("delete gapped columns");\r
 400     viewport.getAlignment().removeGaps();\r
 401     alignPanel.RefreshPanels();\r
 402   }\r
 403 \r
 404   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 405   {\r
 406     addHistoryItem("delete all gaps");\r
 407     SequenceI current;\r
 408     int jSize;\r
 409     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 410     {\r
 411       current = viewport.getAlignment().getSequenceAt(i);\r
 412       jSize = current.getLength();\r
 413       for (int j=0; j < jSize; j++)\r
 414         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 415         {\r
 416           current.deleteCharAt(j);\r
 417           j--;\r
 418           jSize--;\r
 419         }\r
 420     }\r
 421 \r
 422     alignPanel.RefreshPanels();\r
 423   }\r
 424 \r
 425   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 426   {\r
 427     char thisChar = '-';\r
 428     char nextChar = '.';\r
 429     if(viewport.getGapCharacter()=='-')\r
 430     {\r
 431       thisChar = '.';\r
 432       nextChar = '-';\r
 433     }\r
 434     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 435     viewport.setGapCharacter(thisChar);\r
 436     alignPanel.RefreshPanels();\r
 437   }\r
 438 \r
 439   public void findMenuItem_actionPerformed(ActionEvent e)\r
 440   {\r
 441     JOptionPane op = new JOptionPane();\r
 442     JInternalFrame frame =  op.createInternalFrame(this, "Find");\r
 443     Finder finder = new Finder(viewport, alignPanel, frame);\r
 444     frame.setClosable(true);\r
 445     frame.setContentPane(finder);\r
 446     frame.setSize(340,110);\r
 447     frame.setVisible(true);\r
 448   }\r
 449 \r
 450 \r
 451 \r
 452   public void fontNameMenuItem_actionPerformed(ActionEvent e)\r
 453   {\r
 454     String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();\r
 455 \r
 456 \r
 457     String selection = JOptionPane.showInternalInputDialog(this,\r
 458                                 "Select font",\r
 459                                 "Font selection",\r
 460                                 JOptionPane.QUESTION_MESSAGE,\r
 461                                 null,fonts\r
 462                                 ,fontNameMenuItem.getText()).toString();\r
 463     if(selection!=null)\r
 464     {\r
 465        fontNameMenuItem.setText(selection);\r
 466        SetFont();\r
 467      }\r
 468 \r
 469   }\r
 470 \r
 471   public void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
 472   {\r
 473     String selection = JOptionPane.showInternalInputDialog(this,\r
 474                                 "Select font size",\r
 475                                 "Font size",\r
 476                                 JOptionPane.QUESTION_MESSAGE,\r
 477                                 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
 478                                 ,fontSizeMenuItem.getText()).toString();\r
 479     if(selection!=null)\r
 480      {\r
 481        fontSizeMenuItem.setText(selection);\r
 482        SetFont();\r
 483      }\r
 484   }\r
 485 \r
 486   public void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
 487   {\r
 488     String selection = JOptionPane.showInternalInputDialog(this,\r
 489                                 "Select font style",\r
 490                                 "Font style",\r
 491                                 JOptionPane.QUESTION_MESSAGE,\r
 492                                 null, new String[]{"plain", "bold", "italic"}\r
 493                                 ,fontStyleMenuItem.getText()).toString();\r
 494     if(selection!=null)\r
 495     {\r
 496       fontStyleMenuItem.setText(selection);\r
 497       SetFont();\r
 498     }\r
 499 \r
 500   }\r
 501 \r
 502   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 503   {\r
 504       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 505       alignPanel.RefreshPanels();\r
 506   }\r
 507 \r
 508   void SetFont()\r
 509   {\r
 510       int style = java.awt.Font.PLAIN;\r
 511       if(fontStyleMenuItem.getText().equals("bold"))\r
 512         style = java.awt.Font.BOLD;\r
 513       else if(fontStyleMenuItem.getText().equals("italic"))\r
 514         style = java.awt.Font.ITALIC;\r
 515 \r
 516       viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),\r
 517                                            style,\r
 518                                            Integer.parseInt(fontSizeMenuItem.getText())));\r
 519       alignPanel.RefreshPanels();\r
 520 \r
 521   }\r
 522 \r
 523   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 524   {\r
 525     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 526     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
 527   }\r
 528 \r
 529 \r
 530   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 531   {\r
 532     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 533     alignPanel.RefreshPanels();\r
 534   }\r
 535 \r
 536   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 537   {\r
 538     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 539     alignPanel.RefreshPanels();\r
 540   }\r
 541 \r
 542 \r
 543   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 544   {\r
 545     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 546     alignPanel.RefreshPanels();\r
 547   }\r
 548 \r
 549   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
 550   {\r
 551     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 552     alignPanel.RefreshPanels();\r
 553   }\r
 554 \r
 555   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 556   {\r
 557     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
 558   }\r
 559 \r
 560   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 561   {\r
 562     if (alignPanel.overviewPanel != null)\r
 563       return;\r
 564 \r
 565     JInternalFrame frame = new JInternalFrame();\r
 566     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 567    try{\r
 568      overview = new OverviewPanel(alignPanel, viewport);\r
 569      frame.setContentPane(overview);\r
 570     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 571                              frame.getWidth(), frame.getHeight());\r
 572     frame.pack();\r
 573     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 574     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 575       {\r
 576             alignPanel.setOverviewPanel(null);\r
 577       };\r
 578     });\r
 579     alignPanel.setOverviewPanel( overview );\r
 580 \r
 581   }catch(java.lang.OutOfMemoryError ex)\r
 582    {\r
 583      JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 584                                    +"\nTry reducing the font size.",\r
 585                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 586    }\r
 587 \r
 588 \r
 589   }\r
 590 \r
 591   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 592   {\r
 593     viewport.setGlobalColourScheme( null );\r
 594     changeColour();\r
 595   }\r
 596 \r
 597 \r
 598   public void clustalColour_actionPerformed(ActionEvent e)\r
 599   {\r
 600     viewport.setGlobalColourScheme(\r
 601       new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 602     abovePIDThreshold.setSelected(false);\r
 603     changeColour();\r
 604   }\r
 605 \r
 606   public void zappoColour_actionPerformed(ActionEvent e)\r
 607   {\r
 608     viewport.setGlobalColourScheme(new ZappoColourScheme() );\r
 609     changeColour();\r
 610   }\r
 611 \r
 612   public void taylorColour_actionPerformed(ActionEvent e)\r
 613   {\r
 614     viewport.setGlobalColourScheme(new TaylorColourScheme() );\r
 615     changeColour();\r
 616   }\r
 617 \r
 618 \r
 619   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 620   {\r
 621     viewport.setGlobalColourScheme( new HydrophobicColourScheme() );\r
 622     changeColour();\r
 623   }\r
 624 \r
 625   public void helixColour_actionPerformed(ActionEvent e)\r
 626   {\r
 627     viewport.setGlobalColourScheme( new HelixColourScheme()  );\r
 628     changeColour();\r
 629   }\r
 630 \r
 631 \r
 632   public void strandColour_actionPerformed(ActionEvent e)\r
 633   {\r
 634     viewport.setGlobalColourScheme(new StrandColourScheme() );\r
 635     changeColour();\r
 636   }\r
 637 \r
 638 \r
 639   public void turnColour_actionPerformed(ActionEvent e)\r
 640   {\r
 641     viewport.setGlobalColourScheme(new TurnColourScheme() );\r
 642     changeColour();\r
 643   }\r
 644 \r
 645 \r
 646   public void buriedColour_actionPerformed(ActionEvent e)\r
 647   {\r
 648     viewport.setGlobalColourScheme( new BuriedColourScheme() );\r
 649     changeColour();\r
 650   }\r
 651 \r
 652   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 653   {\r
 654     viewport.setGlobalColourScheme( new NucleotideColourScheme() );\r
 655     changeColour();\r
 656   }\r
 657 \r
 658 \r
 659   void changeColour()\r
 660   {\r
 661     if(abovePIDThreshold.isSelected())\r
 662       abovePIDThreshold_actionPerformed(null);\r
 663     else if(conservationMenuItem.isSelected())\r
 664       conservationMenuItem_actionPerformed(null);\r
 665 \r
 666     alignPanel.RefreshPanels();\r
 667   }\r
 668 \r
 669 \r
 670   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 671   {\r
 672    if(abovePIDThreshold.isSelected())\r
 673    {\r
 674      abovePIDThreshold.setSelected(false);\r
 675      Desktop.hidePIDSlider();\r
 676    }\r
 677 \r
 678    viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 679 \r
 680    ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
 681 \r
 682    ConservationColourScheme ccs = null;\r
 683    if (oldCs instanceof ConservationColourScheme)\r
 684          ccs = (ConservationColourScheme) oldCs;\r
 685 \r
 686        if (conservationMenuItem.isSelected())\r
 687        {\r
 688          Alignment al = (Alignment) viewport.alignment;\r
 689          Conservation c = new Conservation("All",\r
 690                                            ResidueProperties.propHash, 3,\r
 691                                            al.getSequences(), 0,\r
 692                                            al.getWidth());\r
 693 \r
 694          c.calculate();\r
 695          c.verdict(false, 100);\r
 696 \r
 697          if (ccs != null)\r
 698            ccs = new ConservationColourScheme(c, ccs.cs);\r
 699          else\r
 700            ccs = new ConservationColourScheme(c, oldCs);\r
 701 \r
 702 \r
 703          int threshold = Desktop.setConservationSliderSource(alignPanel, ccs, "Background");\r
 704 \r
 705          ccs.inc = threshold;\r
 706 \r
 707          if (ccs.cs instanceof ResidueColourScheme)\r
 708            ((ResidueColourScheme) ccs.cs).setThreshold(0);\r
 709          else if (ccs.cs instanceof ScoreColourScheme)\r
 710            ((ScoreColourScheme)ccs.cs).setThreshold(0);\r
 711 \r
 712          viewport.setGlobalColourScheme(ccs);\r
 713 \r
 714 \r
 715        }\r
 716        else if (oldCs instanceof ConservationColourScheme)\r
 717        {\r
 718          /// ie, if we remove ConservationColourScheme from backgroundColour\r
 719          oldCs = ccs.cs;\r
 720          viewport.setGlobalColourScheme(oldCs);\r
 721          Desktop.hideConservationSlider();\r
 722        }\r
 723 \r
 724        if(e!=null)\r
 725          alignPanel.RefreshPanels();\r
 726   }\r
 727 \r
 728 \r
 729   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 730   {\r
 731       if(conservationMenuItem.isSelected())\r
 732         conservationMenuItem.setSelected(false);\r
 733 \r
 734       ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
 735       int threshold = 0;\r
 736       if (oldCs instanceof ConservationColourScheme)\r
 737      {\r
 738        ConservationColourScheme ccs = (ConservationColourScheme) oldCs;\r
 739        oldCs = ccs.cs;\r
 740      }\r
 741 \r
 742      if(abovePIDThreshold.isSelected())\r
 743      {\r
 744        threshold = Desktop.setPIDSliderSource(alignPanel, oldCs, "Background");\r
 745        Desktop.hideConservationSlider();\r
 746      }\r
 747      else\r
 748        Desktop.hidePIDSlider();\r
 749 \r
 750       if (oldCs instanceof ResidueColourScheme)\r
 751           ((ResidueColourScheme) oldCs).setThreshold(threshold);\r
 752       else if (oldCs instanceof ScoreColourScheme)\r
 753           ((ScoreColourScheme)oldCs).setThreshold(threshold);\r
 754 \r
 755     viewport.setGlobalColourScheme(oldCs);\r
 756      if(e!=null)\r
 757         alignPanel.RefreshPanels();\r
 758   }\r
 759 \r
 760 \r
 761 \r
 762   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 763   {\r
 764     JInternalFrame frame = new JInternalFrame();\r
 765     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 766     frame.setContentPane(chooser);\r
 767     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 768     frame.setResizable(false);\r
 769     frame.setIconifiable(false);\r
 770     frame.setMaximizable(false);\r
 771   }\r
 772 \r
 773   public void PIDColour_actionPerformed(ActionEvent e)\r
 774   {\r
 775     viewport.setGlobalColourScheme( new PIDColourScheme() );\r
 776     alignPanel.setColourScheme( );\r
 777   }\r
 778 \r
 779 \r
 780   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 781   {\r
 782     viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport)  );\r
 783     changeColour();\r
 784   }\r
 785 \r
 786 \r
 787 \r
 788   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 789   {\r
 790     addHistoryItem("sort");\r
 791     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 792     alignPanel.RefreshPanels();\r
 793   }\r
 794 \r
 795   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 796   {\r
 797     addHistoryItem("sort");\r
 798     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 799     alignPanel.RefreshPanels();\r
 800   }\r
 801 \r
 802   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 803   {\r
 804     addHistoryItem("sort");\r
 805     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 806     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 807     alignPanel.RefreshPanels();\r
 808   }\r
 809 \r
 810   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 811   {\r
 812     addHistoryItem("sort");\r
 813     if(viewport.getCurrentTree()==null)\r
 814       return;\r
 815 \r
 816     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 817     alignPanel.RefreshPanels();\r
 818   }\r
 819 \r
 820   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 821   {\r
 822     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 823     JInternalFrame frame = new JInternalFrame();\r
 824     frame.setContentPane(sp);\r
 825     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);\r
 826     frame.setMaximizable(false);\r
 827     frame.setResizable(false);\r
 828 \r
 829   }\r
 830 \r
 831   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 832   {\r
 833     if(viewport.getSelection().size()<2)\r
 834       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 835     else\r
 836     {\r
 837       JInternalFrame frame = new JInternalFrame();\r
 838       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 839       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 840     }\r
 841   }\r
 842 \r
 843   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 844   {\r
 845     if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)\r
 846        || viewport.getAlignment().getHeight()<4)\r
 847     {\r
 848       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
 849                                     +"at least 4 input sequences.",\r
 850                                     "Sequence selection insufficient",\r
 851                                     JOptionPane.WARNING_MESSAGE);\r
 852       return;\r
 853     }\r
 854 \r
 855     try{\r
 856       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 857       JInternalFrame frame = new JInternalFrame();\r
 858       frame.setContentPane(pcaPanel);\r
 859       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 860    }catch(java.lang.OutOfMemoryError ex)\r
 861    {\r
 862      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 863                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 864    }\r
 865 \r
 866 \r
 867   }\r
 868 \r
 869   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 870   {\r
 871     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 872   }\r
 873 \r
 874   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 875   {\r
 876     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 877   }\r
 878 \r
 879 \r
 880   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 881   {\r
 882     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 883   }\r
 884 \r
 885   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 886   {\r
 887     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 888   }\r
 889 \r
 890   void NewTreePanel(String type, String pwType, String title)\r
 891   {\r
 892     //are the sequences aligned?\r
 893     if(!viewport.alignment.isAligned())\r
 894     {\r
 895       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
 896                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
 897       return;\r
 898     }\r
 899 \r
 900     JInternalFrame frame = new javax.swing.JInternalFrame();\r
 901     TreePanel tp=null;\r
 902    if (viewport.getSelection() != null && viewport.getSelection().size() > 3)\r
 903    {\r
 904      tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,\r
 905                          viewport.getStartRes(), viewport.getEndRes());\r
 906    }\r
 907    else\r
 908    {\r
 909      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 910                          type, pwType, viewport.getStartRes(),\r
 911                          viewport.getEndRes());\r
 912    }\r
 913 \r
 914    frame.setContentPane(tp);\r
 915    Desktop.addInternalFrame(frame, title, 600, 500);\r
 916   }\r
 917 \r
 918 \r
 919 \r
 920 \r
 921   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 922   {\r
 923     JInternalFrame frame = new JInternalFrame();\r
 924     ClustalThread ct = new ClustalThread(frame);\r
 925     Thread t = new Thread(ct);\r
 926     t.start();\r
 927     frame.setContentPane(ct);\r
 928      Desktop.addInternalFrame(frame, title, 300, 80);\r
 929 \r
 930   }\r
 931 \r
 932   class ClustalThread extends JPanel implements Runnable\r
 933   {\r
 934     Image [] image;\r
 935     int imageIndex = 0;\r
 936     boolean webServiceRunning = false;\r
 937     JInternalFrame frame;\r
 938     public ClustalThread(JInternalFrame frame)\r
 939     {\r
 940       this.frame = frame;\r
 941       image = new Image[9];\r
 942       for(int i=0; i<9; i++)\r
 943       {\r
 944         java.net.URL url = getClass().getResource("/dna" + (i+1) + ".gif");\r
 945         if (url != null)\r
 946         {\r
 947           image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
 948           MediaTracker mt = new MediaTracker(this);\r
 949           mt.addImage(image[i], i);\r
 950           try{mt.waitForID(i);}\r
 951           catch(Exception ex){}\r
 952         }\r
 953       }\r
 954       DNATwirler twirler = new DNATwirler();\r
 955       twirler.start();\r
 956       webServiceRunning = true;\r
 957     }\r
 958 \r
 959     class DNATwirler extends Thread\r
 960     {\r
 961       public void run()\r
 962       {\r
 963         while(webServiceRunning)\r
 964         {\r
 965           try{\r
 966             Thread.sleep(100);\r
 967             imageIndex++;\r
 968             imageIndex %=9;\r
 969             repaint();\r
 970           }\r
 971           catch(Exception ex){}\r
 972         }\r
 973       }\r
 974     }\r
 975 \r
 976     // JBPNote\r
 977     // Should check to see if the server settings are valid\r
 978     // Need visual-delay indication here.\r
 979     public void run()\r
 980        {\r
 981          jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
 982          Vector sv = viewport.getAlignment().getSequences();\r
 983          SequenceI[] seqs = new SequenceI[sv.size()];\r
 984 \r
 985          int i = 0;\r
 986          do\r
 987          {\r
 988            seqs[i] = (SequenceI) sv.elementAt(i);\r
 989          }\r
 990          while (++i < sv.size());\r
 991 \r
 992          SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
 993 \r
 994          if (alignment != null)\r
 995          {\r
 996            AlignFrame af = new AlignFrame(new Alignment(alignment));\r
 997           af.clustalColour.setSelected(true);\r
 998           af.clustalColour_actionPerformed(null);\r
 999            Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),\r
1000                                     700, 500); // JBPNote - is there a new window geom. property ?\r
1001          }\r
1002          else\r
1003            JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",\r
1004                                          JOptionPane.WARNING_MESSAGE);\r
1005 \r
1006          webServiceRunning = false;\r
1007          try{\r
1008            frame.setClosed(true);\r
1009          }catch(Exception ex){}\r
1010        }\r
1011 \r
1012        public void paintComponent(Graphics g)\r
1013        {\r
1014          g.setColor(Color.white);\r
1015          g.fillRect(0,0,getWidth(), getHeight());\r
1016          if(image!=null)\r
1017          {\r
1018            g.drawImage(image[imageIndex],10,10,this);\r
1019          }\r
1020          g.setFont(new Font("Arial", Font.BOLD, 12));\r
1021          g.setColor(Color.black);\r
1022          g.drawString("Clustal Alignment Web Service running", 30,30);\r
1023        }\r
1024   }\r
1025 }\r