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     else\r
 117       groupMenu.insertSeparator(3);\r
 118 \r
 119     if(seq==null)\r
 120        sequenceMenu.setVisible(false);\r
 121 \r
 122   }\r
 123   private void jbInit() throws Exception\r
 124   {\r
 125     groupMenu.setText("Group");\r
 126     groupMenu.setText("Define");\r
 127     groupName.setText("Name");\r
 128     groupName.addActionListener(new java.awt.event.ActionListener()\r
 129     {\r
 130       public void actionPerformed(ActionEvent e)\r
 131       {\r
 132         groupName_actionPerformed(e);\r
 133       }\r
 134     });\r
 135     sequenceMenu.setText("Sequence");\r
 136     sequenceName.setText("Edit name");\r
 137     sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 138     {\r
 139       public void actionPerformed(ActionEvent e)\r
 140       {\r
 141         sequenceName_actionPerformed(e);\r
 142       }\r
 143     });\r
 144     PIDColour.setFocusPainted(false);\r
 145     unGroupMenuItem.setText("Remove Group");\r
 146     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 147     {\r
 148       public void actionPerformed(ActionEvent e)\r
 149       {\r
 150         unGroupMenuItem_actionPerformed(e);\r
 151       }\r
 152     });\r
 153     pdbMenuItem.setText("View PDB structure");\r
 154     pdbMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 155     {\r
 156       public void actionPerformed(ActionEvent e)\r
 157       {\r
 158         pdbMenuItem_actionPerformed(e);\r
 159       }\r
 160     });\r
 161     outline.setText("Border colour");\r
 162     outline.addActionListener(new java.awt.event.ActionListener()\r
 163     {\r
 164       public void actionPerformed(ActionEvent e)\r
 165       {\r
 166         outline_actionPerformed(e);\r
 167       }\r
 168     });\r
 169     nucleotideMenuItem.setText("Nucleotide");\r
 170     nucleotideMenuItem.addActionListener(new ActionListener()\r
 171     {\r
 172       public void actionPerformed(ActionEvent e)\r
 173       {\r
 174         nucleotideMenuItem_actionPerformed(e);\r
 175       }\r
 176     });\r
 177     colourMenu.setText("Group Colour");\r
 178     showBoxes.setText("Boxes");\r
 179     showBoxes.setState(true);\r
 180     showBoxes.addActionListener(new ActionListener()\r
 181     {\r
 182       public void actionPerformed(ActionEvent e)\r
 183       {\r
 184         showBoxes_actionPerformed(e);\r
 185       }\r
 186     });\r
 187     showText.setText("Text");\r
 188     showText.setState(true);\r
 189     showText.addActionListener(new ActionListener()\r
 190     {\r
 191       public void actionPerformed(ActionEvent e)\r
 192       {\r
 193         showText_actionPerformed(e);\r
 194       }\r
 195     });\r
 196     showColourText.setText("Colour Text");\r
 197     showColourText.addActionListener(new ActionListener()\r
 198     {\r
 199       public void actionPerformed(ActionEvent e)\r
 200       {\r
 201         showColourText_actionPerformed(e);\r
 202       }\r
 203     });\r
 204     add(groupMenu);\r
 205     add(sequenceMenu);\r
 206     groupMenu.add(groupName);\r
 207     groupMenu.addSeparator();\r
 208     groupMenu.add(unGroupMenuItem);\r
 209     groupMenu.add(colourMenu);\r
 210     groupMenu.addSeparator();\r
 211     groupMenu.add(showBoxes);\r
 212     groupMenu.add(showText);\r
 213     groupMenu.add(showColourText);\r
 214     groupMenu.addSeparator();\r
 215     groupMenu.add(outline);\r
 216     sequenceMenu.add(sequenceName);\r
 217     sequenceMenu.add(pdbMenuItem);\r
 218     colourMenu.add(noColourmenuItem);\r
 219     colourMenu.add(clustalColour);\r
 220     colourMenu.add(BLOSUM62Colour);\r
 221     colourMenu.add(PIDColour);\r
 222     colourMenu.add(zappoColour);\r
 223     colourMenu.add(taylorColour);\r
 224     colourMenu.add(hydrophobicityColour);\r
 225     colourMenu.add(helixColour);\r
 226     colourMenu.add(strandColour);\r
 227     colourMenu.add(turnColour);\r
 228     colourMenu.add(buriedColour);\r
 229     colourMenu.add(nucleotideMenuItem);\r
 230     colourMenu.add(userDefinedColour);\r
 231     colourMenu.addSeparator();\r
 232     colourMenu.add(abovePIDColour);\r
 233     colourMenu.add(conservationMenuItem);\r
 234     noColourmenuItem.setText("None");\r
 235     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 236     {\r
 237       public void actionPerformed(ActionEvent e)\r
 238       {\r
 239         noColourmenuItem_actionPerformed(e);\r
 240       }\r
 241     });\r
 242 \r
 243     clustalColour.setText("Clustalx colours");\r
 244     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 245     {\r
 246       public void actionPerformed(ActionEvent e)\r
 247       {\r
 248         clustalColour_actionPerformed(e);\r
 249       }\r
 250     });\r
 251     zappoColour.setText("Zappo");\r
 252     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 253     {\r
 254       public void actionPerformed(ActionEvent e)\r
 255       {\r
 256         zappoColour_actionPerformed(e);\r
 257       }\r
 258     });\r
 259     taylorColour.setText("Taylor");\r
 260     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 261     {\r
 262       public void actionPerformed(ActionEvent e)\r
 263       {\r
 264         taylorColour_actionPerformed(e);\r
 265       }\r
 266     });\r
 267     hydrophobicityColour.setText("Hydrophobicity");\r
 268     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 269     {\r
 270       public void actionPerformed(ActionEvent e)\r
 271       {\r
 272         hydrophobicityColour_actionPerformed(e);\r
 273       }\r
 274     });\r
 275     helixColour.setText("Helix propensity");\r
 276     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 277     {\r
 278       public void actionPerformed(ActionEvent e)\r
 279       {\r
 280         helixColour_actionPerformed(e);\r
 281       }\r
 282     });\r
 283     strandColour.setText("Strand propensity");\r
 284     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 285     {\r
 286       public void actionPerformed(ActionEvent e)\r
 287       {\r
 288         strandColour_actionPerformed(e);\r
 289       }\r
 290     });\r
 291     turnColour.setText("Turn propensity");\r
 292     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 293     {\r
 294       public void actionPerformed(ActionEvent e)\r
 295       {\r
 296         turnColour_actionPerformed(e);\r
 297       }\r
 298     });\r
 299     buriedColour.setText("Buried Index");\r
 300     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 301     {\r
 302       public void actionPerformed(ActionEvent e)\r
 303       {\r
 304         buriedColour_actionPerformed(e);\r
 305       }\r
 306     });\r
 307     abovePIDColour.setText("Above % Identity");\r
 308     abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 309     {\r
 310       public void actionPerformed(ActionEvent e)\r
 311       {\r
 312         abovePIDColour_actionPerformed(e);\r
 313       }\r
 314     });\r
 315     userDefinedColour.setText("User Defined");\r
 316     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 317     {\r
 318       public void actionPerformed(ActionEvent e)\r
 319       {\r
 320         userDefinedColour_actionPerformed(e);\r
 321       }\r
 322     });\r
 323     PIDColour.setText("Percentage Identity");\r
 324     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 325     {\r
 326       public void actionPerformed(ActionEvent e)\r
 327       {\r
 328         PIDColour_actionPerformed(e);\r
 329       }\r
 330     });\r
 331     BLOSUM62Colour.setText("BLOSUM62");\r
 332     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 333     {\r
 334       public void actionPerformed(ActionEvent e)\r
 335       {\r
 336         BLOSUM62Colour_actionPerformed(e);\r
 337       }\r
 338     });\r
 339     conservationMenuItem.setText("Conservation");\r
 340    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 341    {\r
 342      public void actionPerformed(ActionEvent e)\r
 343      {\r
 344        conservationMenuItem_actionPerformed(e);\r
 345      }\r
 346    });\r
 347 \r
 348 \r
 349 \r
 350   }\r
 351 \r
 352   void refresh()\r
 353   {\r
 354     SequenceGroup sg = getGroup();\r
 355     SuperGroup superG = ap.av.alignment.getSuperGroup( sg );\r
 356     if( superG !=null)\r
 357       superG.setSuperGroupProperties( sg );\r
 358 \r
 359     ap.seqPanel.repaint();\r
 360   }\r
 361 \r
 362   protected void clustalColour_actionPerformed(ActionEvent e)\r
 363   {\r
 364     SequenceGroup sg = getGroup();\r
 365     sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());\r
 366     refresh();\r
 367   }\r
 368 \r
 369   protected void zappoColour_actionPerformed(ActionEvent e)\r
 370   {\r
 371     getGroup().cs = new ZappoColourScheme();\r
 372     refresh();\r
 373   }\r
 374 \r
 375   protected void taylorColour_actionPerformed(ActionEvent e)\r
 376   {\r
 377     getGroup().cs = new TaylorColourScheme();\r
 378     refresh();\r
 379   }\r
 380 \r
 381 \r
 382   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 383   {\r
 384     getGroup().cs = new HydrophobicColourScheme();\r
 385     refresh();\r
 386   }\r
 387 \r
 388   protected void helixColour_actionPerformed(ActionEvent e)\r
 389   {\r
 390     getGroup().cs = new HelixColourScheme();\r
 391     refresh();\r
 392   }\r
 393 \r
 394   protected void strandColour_actionPerformed(ActionEvent e)\r
 395   {\r
 396     getGroup().cs = new StrandColourScheme();\r
 397     refresh();\r
 398   }\r
 399 \r
 400   protected void turnColour_actionPerformed(ActionEvent e)\r
 401   {\r
 402     getGroup().cs = new TurnColourScheme();\r
 403     refresh();\r
 404   }\r
 405 \r
 406   protected void buriedColour_actionPerformed(ActionEvent e)\r
 407   {\r
 408     getGroup().cs = new BuriedColourScheme();\r
 409     refresh();\r
 410   }\r
 411 \r
 412   public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
 413   {\r
 414     getGroup().cs = new NucleotideColourScheme();\r
 415     refresh();\r
 416   }\r
 417 \r
 418 \r
 419 \r
 420   protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 421   {\r
 422     SequenceGroup sg = getGroup();\r
 423     if (abovePIDColour.isSelected())\r
 424     {\r
 425       sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 426                                                ap.av.alignment.getWidth()));\r
 427       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());\r
 428       if (sg.cs instanceof ResidueColourScheme)\r
 429         ( (ResidueColourScheme)sg. cs).setThreshold(threshold);\r
 430       else if (sg.cs instanceof ScoreColourScheme)\r
 431         ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
 432 \r
 433       SliderPanel.showPIDSlider();\r
 434 \r
 435 \r
 436     }\r
 437     else // remove PIDColouring\r
 438     {\r
 439       ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;\r
 440       rcs.setThreshold(0);\r
 441       sg.cs = rcs;\r
 442     }\r
 443 \r
 444     refresh();\r
 445 \r
 446   }\r
 447 \r
 448 \r
 449   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 450   {\r
 451     new UserDefinedColours( ap, getGroup());\r
 452   }\r
 453 \r
 454   protected void PIDColour_actionPerformed(ActionEvent e)\r
 455   {\r
 456     SequenceGroup sg = getGroup();\r
 457     sg.cs = new PIDColourScheme();\r
 458     sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 459                                                ap.av.alignment.getWidth()));\r
 460     refresh();\r
 461   }\r
 462 \r
 463   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 464   {\r
 465     SequenceGroup sg = getGroup();\r
 466 \r
 467     sg.cs = new Blosum62ColourScheme();\r
 468 \r
 469     sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 470                                                ap.av.alignment.getWidth()));\r
 471 \r
 472     refresh();\r
 473   }\r
 474 \r
 475 \r
 476   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 477   {\r
 478     getGroup().cs = null;\r
 479     refresh();\r
 480   }\r
 481 \r
 482   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 483   {\r
 484     SequenceGroup sg = getGroup();\r
 485 \r
 486     if(conservationMenuItem.isSelected())\r
 487     {\r
 488 \r
 489         Conservation c = new Conservation("Group",\r
 490                                           ResidueProperties.propHash, 3,\r
 491                                           sg.sequences, 0,\r
 492                                           ap.av.alignment.getWidth());\r
 493 \r
 494         c.calculate();\r
 495         c.verdict(false, ap.av.ConsPercGaps);\r
 496         ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 497 \r
 498 \r
 499       sg.cs = ccs;\r
 500 \r
 501       SliderPanel.setConservationSlider(ap, ccs, sg.getName());\r
 502       SliderPanel.showConservationSlider();\r
 503     }\r
 504     else // remove ConservationColouring\r
 505     {\r
 506         ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
 507         sg.cs = ccs.cs;\r
 508     }\r
 509 \r
 510      refresh();\r
 511   }\r
 512 \r
 513 \r
 514   protected void groupName_actionPerformed(ActionEvent e)\r
 515   {\r
 516     SequenceGroup sg = getGroup();\r
 517     String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);\r
 518     if(reply==null)\r
 519       return;\r
 520 \r
 521     sg.setName(reply);\r
 522     groupName.setText(reply);\r
 523   }\r
 524 \r
 525 \r
 526   protected void analyze_actionPerformed(ActionEvent e)\r
 527   {\r
 528      CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 529      JInternalFrame frame = new JInternalFrame();\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