src/jalview/gui/PopupMenu.java

   1 package jalview.gui;\r
   2 \r
   3 import jalview.datamodel.*;\r
   4 import jalview.analysis.*;\r
   5 import jalview.schemes.*;\r
   6 import javax.swing.*;\r
   7 import java.awt.event.*;\r
   8 \r
   9 \r
  10 public class PopupMenu extends JPopupMenu\r
  11 {\r
  12   JMenu groupMenu = new JMenu();\r
  13   JMenuItem copyGroup = new JMenuItem();\r
  14   JMenuItem moveGroup = new JMenuItem();\r
  15   JMenuItem deleteSequences = new JMenuItem();\r
  16   JMenuItem analyze = new JMenuItem();\r
  17   JMenu defineMenu = new JMenu();\r
  18   JMenuItem groupName = new JMenuItem();\r
  19   JMenuItem groupAnnotation = new JMenuItem();\r
  20   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  21   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  22   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  23   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
  24   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  25   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  26   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  27   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  28   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();\r
  29   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  30   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  31   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  32   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  33   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  34 \r
  35 \r
  36   AlignmentPanel ap;\r
  37   JMenu sequenceMenu = new JMenu();\r
  38   JMenuItem sequenceName = new JMenuItem();\r
  39   JMenu residueMenu = new JMenu();\r
  40   JMenuItem annotateResidue = new JMenuItem();\r
  41 \r
  42   SequenceI sequence;\r
  43   JMenuItem unGroupMenuItem = new JMenuItem();\r
  44 \r
  45   public PopupMenu(AlignmentPanel ap, SequenceI seq)\r
  46   {\r
  47     ///////////////////////////////////////////////////////////\r
  48     // If this is activated from the sequence panel, the user may want to\r
  49     // edit or annotate a particular residue. Therefore display the residue menu\r
  50     //\r
  51     // If from the IDPanel, we must display the sequence menu\r
  52     //////////////////////////////////////////////////////////\r
  53 \r
  54     this.ap = ap;\r
  55     sequence = seq;\r
  56 \r
  57     ButtonGroup colours = new ButtonGroup();\r
  58     colours.add(noColourmenuItem);\r
  59     colours.add(clustalColour);\r
  60     colours.add(zappoColour);\r
  61     colours.add(taylorColour);\r
  62     colours.add(hydrophobicityColour);\r
  63     colours.add(helixColour);\r
  64     colours.add(strandColour);\r
  65     colours.add(turnColour);\r
  66     colours.add(buriedColour);\r
  67     colours.add(abovePIDColour);\r
  68     colours.add(userDefinedColour);\r
  69     colours.add(PIDColour);\r
  70     colours.add(BLOSUM62Colour);\r
  71 \r
  72     try\r
  73     {     jbInit();   }\r
  74     catch(Exception e)\r
  75     {    e.printStackTrace();    }\r
  76 \r
  77     SequenceGroup sg = ap.av.getRubberbandGroup();\r
  78     if(sg!=null)\r
  79     {\r
  80       groupName.setText(sg.getName());\r
  81       if(sg.cs instanceof ZappoColourScheme)\r
  82         zappoColour.setSelected(true);\r
  83       else if(sg.cs instanceof TaylorColourScheme)\r
  84         taylorColour.setSelected(true);\r
  85       else if (sg.cs instanceof PIDColourScheme)\r
  86         PIDColour.setSelected(true);\r
  87       else if (sg.cs instanceof Blosum62ColourScheme)\r
  88         BLOSUM62Colour.setSelected(true);\r
  89       else if (sg.cs instanceof UserColourScheme)\r
  90         userDefinedColour.setSelected(true);\r
  91       else if (sg.cs instanceof HydrophobicColourScheme)\r
  92         hydrophobicityColour.setSelected(true);\r
  93       else if (sg.cs instanceof HelixColourScheme)\r
  94         helixColour.setSelected(true);\r
  95       else if (sg.cs instanceof StrandColourScheme)\r
  96         strandColour.setSelected(true);\r
  97       else if (sg.cs instanceof TurnColourScheme)\r
  98         turnColour.setSelected(true);\r
  99       else if (sg.cs instanceof BuriedColourScheme)\r
 100         buriedColour.setSelected(true);\r
 101       else if (sg.cs instanceof ClustalxColourScheme)\r
 102         clustalColour.setSelected(true);\r
 103       else\r
 104         noColourmenuItem.setSelected(true);\r
 105 \r
 106       if (sg.cs instanceof ConservationColourScheme)\r
 107         conservationMenuItem.setSelected(true);\r
 108     }\r
 109 \r
 110 \r
 111     if(seq!=null)\r
 112     {\r
 113       residueMenu.setVisible(false);\r
 114       sequenceName.setText( sequence.getName() );\r
 115     }\r
 116     else\r
 117       sequenceMenu.setVisible(false);\r
 118 \r
 119   }\r
 120   private void jbInit() throws Exception\r
 121   {\r
 122     groupMenu.setText("Group");\r
 123     copyGroup.setText("Copy region to new Alignment");\r
 124     copyGroup.addActionListener(new java.awt.event.ActionListener()\r
 125     {\r
 126       public void actionPerformed(ActionEvent e)\r
 127       {\r
 128         copyGroup_actionPerformed(e);\r
 129       }\r
 130     });\r
 131     moveGroup.setText("Move sequences to new Alignment");\r
 132     moveGroup.addActionListener(new java.awt.event.ActionListener()\r
 133     {\r
 134       public void actionPerformed(ActionEvent e)\r
 135       {\r
 136         moveGroup_actionPerformed(e);\r
 137       }\r
 138     });\r
 139     deleteSequences.setText("Delete sequences");\r
 140     deleteSequences.addActionListener(new java.awt.event.ActionListener()\r
 141     {\r
 142       public void actionPerformed(ActionEvent e)\r
 143       {\r
 144         deleteSequences_actionPerformed(e);\r
 145       }\r
 146     });\r
 147     analyze.setText("Analyze");\r
 148     analyze.addActionListener(new java.awt.event.ActionListener()\r
 149     {\r
 150       public void actionPerformed(ActionEvent e)\r
 151       {\r
 152         analyze_actionPerformed(e);\r
 153       }\r
 154     });\r
 155     defineMenu.setText("Define");\r
 156     groupName.setText("Name");\r
 157     groupName.addActionListener(new java.awt.event.ActionListener()\r
 158     {\r
 159       public void actionPerformed(ActionEvent e)\r
 160       {\r
 161         groupName_actionPerformed(e);\r
 162       }\r
 163     });\r
 164     groupAnnotation.setText("Annotation");\r
 165     groupAnnotation.addActionListener(new java.awt.event.ActionListener()\r
 166     {\r
 167       public void actionPerformed(ActionEvent e)\r
 168       {\r
 169         groupAnnotation_actionPerformed(e);\r
 170       }\r
 171     });\r
 172     sequenceMenu.setText("Sequence");\r
 173     sequenceName.setText("sequenceName");\r
 174     sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 175     {\r
 176       public void actionPerformed(ActionEvent e)\r
 177       {\r
 178         sequenceName_actionPerformed(e);\r
 179       }\r
 180     });\r
 181     residueMenu.setText("Residue");\r
 182     annotateResidue.setText("annotate residue???");\r
 183     PIDColour.setFocusPainted(false);\r
 184     unGroupMenuItem.setText("Remove Group");\r
 185     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 186     {\r
 187       public void actionPerformed(ActionEvent e)\r
 188       {\r
 189         unGroupMenuItem_actionPerformed(e);\r
 190       }\r
 191     });\r
 192     add(groupMenu);\r
 193     this.add(sequenceMenu);\r
 194     this.add(residueMenu);\r
 195     groupMenu.add(defineMenu);\r
 196     groupMenu.add(unGroupMenuItem);\r
 197     groupMenu.addSeparator();\r
 198     groupMenu.add(copyGroup);\r
 199     groupMenu.add(moveGroup);\r
 200     groupMenu.add(deleteSequences);\r
 201     groupMenu.addSeparator();\r
 202     groupMenu.add(analyze);\r
 203     defineMenu.add(groupName);\r
 204     defineMenu.add(groupAnnotation);\r
 205     defineMenu.addSeparator();\r
 206     defineMenu.add(noColourmenuItem);\r
 207     defineMenu.add(clustalColour);\r
 208     defineMenu.add(zappoColour);\r
 209     defineMenu.add(taylorColour);\r
 210     defineMenu.add(hydrophobicityColour);\r
 211     defineMenu.add(helixColour);\r
 212     defineMenu.add(strandColour);\r
 213     defineMenu.add(turnColour);\r
 214     defineMenu.add(buriedColour);\r
 215     defineMenu.add(userDefinedColour);\r
 216     defineMenu.add(PIDColour);\r
 217     defineMenu.add(BLOSUM62Colour);\r
 218     defineMenu.addSeparator();\r
 219     defineMenu.add(abovePIDColour);\r
 220     defineMenu.add(conservationMenuItem);\r
 221 \r
 222     sequenceMenu.add(sequenceName);\r
 223     residueMenu.add(annotateResidue);\r
 224 \r
 225     noColourmenuItem.setText("None");\r
 226     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 227     {\r
 228       public void actionPerformed(ActionEvent e)\r
 229       {\r
 230         noColourmenuItem_actionPerformed(e);\r
 231       }\r
 232     });\r
 233 \r
 234     clustalColour.setText("Clustalx colours");\r
 235     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 236     {\r
 237       public void actionPerformed(ActionEvent e)\r
 238       {\r
 239         clustalColour_actionPerformed(e);\r
 240       }\r
 241     });\r
 242     zappoColour.setText("Zappo colour scheme");\r
 243     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 244     {\r
 245       public void actionPerformed(ActionEvent e)\r
 246       {\r
 247         zappoColour_actionPerformed(e);\r
 248       }\r
 249     });\r
 250     taylorColour.setText("Taylor colour scheme");\r
 251     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 252     {\r
 253       public void actionPerformed(ActionEvent e)\r
 254       {\r
 255         taylorColour_actionPerformed(e);\r
 256       }\r
 257     });\r
 258     hydrophobicityColour.setText("By hydrophobicity");\r
 259     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 260     {\r
 261       public void actionPerformed(ActionEvent e)\r
 262       {\r
 263         hydrophobicityColour_actionPerformed(e);\r
 264       }\r
 265     });\r
 266     helixColour.setText("Helix propensity");\r
 267     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 268     {\r
 269       public void actionPerformed(ActionEvent e)\r
 270       {\r
 271         helixColour_actionPerformed(e);\r
 272       }\r
 273     });\r
 274     strandColour.setText("Strand propensity");\r
 275     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 276     {\r
 277       public void actionPerformed(ActionEvent e)\r
 278       {\r
 279         strandColour_actionPerformed(e);\r
 280       }\r
 281     });\r
 282     turnColour.setText("Turn propensity");\r
 283     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 284     {\r
 285       public void actionPerformed(ActionEvent e)\r
 286       {\r
 287         turnColour_actionPerformed(e);\r
 288       }\r
 289     });\r
 290     buriedColour.setText("Buried index");\r
 291     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 292     {\r
 293       public void actionPerformed(ActionEvent e)\r
 294       {\r
 295         buriedColour_actionPerformed(e);\r
 296       }\r
 297     });\r
 298     abovePIDColour.setText("Above PID threshold only");\r
 299     abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 300     {\r
 301       public void actionPerformed(ActionEvent e)\r
 302       {\r
 303         abovePIDColour_actionPerformed(e);\r
 304       }\r
 305     });\r
 306     userDefinedColour.setText("User defined colours");\r
 307     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 308     {\r
 309       public void actionPerformed(ActionEvent e)\r
 310       {\r
 311         userDefinedColour_actionPerformed(e);\r
 312       }\r
 313     });\r
 314     PIDColour.setText("Percentage Identity");\r
 315     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 316     {\r
 317       public void actionPerformed(ActionEvent e)\r
 318       {\r
 319         PIDColour_actionPerformed(e);\r
 320       }\r
 321     });\r
 322     BLOSUM62Colour.setText("BLOSUM62 score");\r
 323     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 324     {\r
 325       public void actionPerformed(ActionEvent e)\r
 326       {\r
 327         BLOSUM62Colour_actionPerformed(e);\r
 328       }\r
 329     });\r
 330     conservationMenuItem.setText("By conservation");\r
 331    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 332    {\r
 333      public void actionPerformed(ActionEvent e)\r
 334      {\r
 335        conservationMenuItem_actionPerformed(e);\r
 336      }\r
 337    });\r
 338 \r
 339 \r
 340 \r
 341   }\r
 342 \r
 343   void refresh()\r
 344   {\r
 345     SequenceGroup sg = getGroup();\r
 346     SuperGroup superG = ap.av.alignment.getSuperGroup( sg );\r
 347     if( superG !=null)\r
 348       superG.setSuperGroupProperties( sg );\r
 349 \r
 350     ap.seqPanel.seqCanvas.paintFlag=true;\r
 351     ap.seqPanel.repaint();\r
 352   }\r
 353 \r
 354   protected void clustalColour_actionPerformed(ActionEvent e)\r
 355   {\r
 356     SequenceGroup sg = getGroup();\r
 357     sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());\r
 358     refresh();\r
 359   }\r
 360 \r
 361   protected void zappoColour_actionPerformed(ActionEvent e)\r
 362   {\r
 363     getGroup().cs = new ZappoColourScheme();\r
 364     refresh();\r
 365   }\r
 366 \r
 367   protected void taylorColour_actionPerformed(ActionEvent e)\r
 368   {\r
 369     getGroup().cs = new TaylorColourScheme();\r
 370     refresh();\r
 371   }\r
 372 \r
 373 \r
 374   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 375   {\r
 376     getGroup().cs = new HydrophobicColourScheme();\r
 377     refresh();\r
 378   }\r
 379 \r
 380   protected void helixColour_actionPerformed(ActionEvent e)\r
 381   {\r
 382     getGroup().cs = new HelixColourScheme();\r
 383     refresh();\r
 384   }\r
 385 \r
 386   protected void strandColour_actionPerformed(ActionEvent e)\r
 387   {\r
 388     getGroup().cs = new StrandColourScheme();\r
 389     refresh();\r
 390   }\r
 391 \r
 392   protected void turnColour_actionPerformed(ActionEvent e)\r
 393   {\r
 394     getGroup().cs = new TurnColourScheme();\r
 395     refresh();\r
 396   }\r
 397 \r
 398   protected void buriedColour_actionPerformed(ActionEvent e)\r
 399   {\r
 400     getGroup().cs = new BuriedColourScheme();\r
 401     refresh();\r
 402   }\r
 403 \r
 404 \r
 405   protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 406   {\r
 407     Desktop.setPIDSliderSource(ap, getGroup().cs, getGroup().getName());\r
 408   }\r
 409 \r
 410 \r
 411   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 412   {\r
 413     JInternalFrame frame = new JInternalFrame();\r
 414     UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup());\r
 415     frame.setContentPane(chooser);\r
 416     Desktop.addInternalFrame(frame,"User defined colours ("+getGroup().getName()+")", 450,540 );\r
 417     frame.setResizable(false);\r
 418     frame.setIconifiable(false);\r
 419     frame.setMaximizable(false);\r
 420 \r
 421   }\r
 422 \r
 423   protected void PIDColour_actionPerformed(ActionEvent e)\r
 424   {\r
 425 \r
 426   }\r
 427 \r
 428   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 429   {\r
 430     getGroup().cs = new Blosum62ColourScheme(ap.av);\r
 431     refresh();\r
 432   }\r
 433 \r
 434 \r
 435   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 436   {\r
 437     getGroup().cs = null;\r
 438     refresh();\r
 439   }\r
 440 \r
 441   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 442   {\r
 443     SequenceGroup sg = getGroup();\r
 444 \r
 445     if(conservationMenuItem.isSelected())\r
 446     {\r
 447 \r
 448         Conservation c = new Conservation("Group",\r
 449                                           ResidueProperties.propHash, 3,\r
 450                                           sg.sequences, 0,\r
 451                                           ap.av.alignment.getWidth());\r
 452 \r
 453         c.calculate();\r
 454         c.verdict(false, 100);\r
 455         ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 456 \r
 457 \r
 458       sg.cs = ccs;\r
 459 \r
 460       Desktop.setConservationSliderSource(ap, ccs, sg.getName());\r
 461     }\r
 462     else // remove ConservationColouring\r
 463     {\r
 464         ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
 465         sg.cs = ccs.cs;\r
 466     }\r
 467 \r
 468      refresh();\r
 469   }\r
 470 \r
 471   protected void groupAnnotation_actionPerformed(ActionEvent e)\r
 472   {\r
 473 \r
 474   }\r
 475 \r
 476   protected void groupName_actionPerformed(ActionEvent e)\r
 477   {\r
 478     SequenceGroup sg = getGroup();\r
 479     String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);\r
 480     if(reply==null)\r
 481       return;\r
 482 \r
 483     sg.setName(reply);\r
 484     groupName.setText(reply);\r
 485   }\r
 486 \r
 487   protected void copyGroup_actionPerformed(ActionEvent e)\r
 488   {\r
 489     SequenceGroup sg = ap.av.getRubberbandGroup();\r
 490 \r
 491     SequenceI[] s = new Sequence[sg.sequences.size()];\r
 492      for (int i=0; i < sg.sequences.size(); i++)\r
 493      {\r
 494        s[i] = new Sequence( sg.getSequenceAt(i));\r
 495        s[i].setSequence( s[i].getSequence(sg.getStartRes(), sg.getEndRes()+1) );\r
 496      }\r
 497      AlignFrame af = new AlignFrame(new Alignment(s));\r
 498      int newHeight = s.length * af.viewport.getCharHeight() + 200;\r
 499      if (newHeight > 500)\r
 500        newHeight = 500;\r
 501      Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
 502    }\r
 503 \r
 504   protected  void moveGroup_actionPerformed(ActionEvent e)\r
 505   {\r
 506     SequenceGroup sg = ap.av.getRubberbandGroup();\r
 507 \r
 508     SequenceI[] s = new Sequence[sg.sequences.size()];\r
 509 \r
 510      for (int i=0; i < sg.sequences.size(); i++)\r
 511        s[i] = new Sequence( sg.getSequenceAt(i));\r
 512 \r
 513      AlignFrame af = new AlignFrame(new Alignment(s));\r
 514      int newHeight = s.length * af.viewport.getCharHeight() + 200;\r
 515      if(newHeight>500)\r
 516        newHeight=500;\r
 517      Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);\r
 518 \r
 519 \r
 520      for (int i=0; i < sg.sequences.size(); i++)\r
 521        ap.av.alignment.deleteSequence(sg.getSequenceAt(i));\r
 522 \r
 523 \r
 524      ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());\r
 525      ap.RefreshPanels();\r
 526 \r
 527 \r
 528   }\r
 529 \r
 530   protected void deleteSequences_actionPerformed(ActionEvent e)\r
 531   {\r
 532     SequenceGroup sg = ap.av.getRubberbandGroup();\r
 533     for (int i=0;i < sg.sequences.size(); i++)\r
 534             ap.av.getAlignment().deleteSequence(sg.getSequenceAt(i));\r
 535 \r
 536     ap.av.alignment.deleteGroup(sg);\r
 537     ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());\r
 538     ap.RefreshPanels();\r
 539 \r
 540   }\r
 541 \r
 542   protected void analyze_actionPerformed(ActionEvent e)\r
 543   {\r
 544      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
 545      JInternalFrame frame = new JInternalFrame();\r
 546      cap.formatForOutput();\r
 547      frame.setContentPane(cap);\r
 548      Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
 549      SequenceGroup sg = getGroup();\r
 550      StringBuffer sb = new StringBuffer();\r
 551 \r
 552      for(int i=0; i<sg.sequences.size(); i++)\r
 553      {\r
 554        Sequence tmp = (Sequence)sg.sequences.get(i);\r
 555        sb.append(  tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));\r
 556        sb.append("\n");\r
 557      }\r
 558 \r
 559      sb.append("Something amazing will happen soon");\r
 560      cap.setText( sb.toString() );\r
 561 \r
 562   }\r
 563 \r
 564   SequenceGroup getGroup()\r
 565   {\r
 566     SequenceGroup sg = ap.av.getRubberbandGroup();\r
 567 \r
 568     // this method won't add a new group if it already exists\r
 569     ap.av.alignment.addGroup(sg);\r
 570     return sg;\r
 571   }\r
 572 \r
 573   void sequenceName_actionPerformed(ActionEvent e)\r
 574   {\r
 575     String id = sequence.getName();\r
 576     String s = (String)JOptionPane.showInternalInputDialog(\r
 577                 ap,\r
 578                 "Edit sequence name",\r
 579                 "Edit sequence name",\r
 580                 JOptionPane.PLAIN_MESSAGE,\r
 581                 null,\r
 582                 null,\r
 583                 id);\r
 584 \r
 585     if(s!=null)\r
 586     {\r
 587       sequence.setName(s);\r
 588       ap.RefreshPanels();\r
 589     }\r
 590 \r
 591   }\r
 592 \r
 593   void unGroupMenuItem_actionPerformed(ActionEvent e)\r
 594   {\r
 595      SequenceGroup sg = ap.av.getRubberbandGroup();\r
 596      ap.av.alignment.deleteGroup(sg);\r
 597      ap.av.setRubberbandGroup(null);\r
 598      ap.RefreshPanels();\r
 599   }\r
 600 }\r