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