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