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 import jalview.io.*;\r
   9 import MCview.*;\r
  10 \r
  11 public class PopupMenu extends JPopupMenu\r
  12 {\r
  13   JMenu groupMenu = new JMenu();\r
  14   JMenuItem copyGroup = new JMenuItem();\r
  15   JMenuItem moveGroup = new JMenuItem();\r
  16   JMenuItem deleteSequences = new JMenuItem();\r
  17   JMenuItem analyze = new JMenuItem();\r
  18   JMenu defineMenu = new JMenu();\r
  19   JMenuItem groupName = new JMenuItem();\r
  20   JMenuItem groupAnnotation = new JMenuItem();\r
  21   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  22   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  23   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  24   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
  25   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  26   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  27   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  28   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  29   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();\r
  30   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  31   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  32   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  33   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  34   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  35 \r
  36 \r
  37   AlignmentPanel ap;\r
  38   JMenu sequenceMenu = new JMenu();\r
  39   JMenuItem sequenceName = new JMenuItem();\r
  40   JMenu residueMenu = new JMenu();\r
  41   JMenuItem annotateResidue = new JMenuItem();\r
  42 \r
  43   Sequence sequence;\r
  44   JMenuItem unGroupMenuItem = new JMenuItem();\r
  45   JMenuItem pdbMenuItem = new JMenuItem();\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.getRubberbandGroup();\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     copyGroup.setText("Copy region to new Alignment");\r
 123     copyGroup.addActionListener(new java.awt.event.ActionListener()\r
 124     {\r
 125       public void actionPerformed(ActionEvent e)\r
 126       {\r
 127         copyGroup_actionPerformed(e);\r
 128       }\r
 129     });\r
 130     moveGroup.setText("Move sequences to new Alignment");\r
 131     moveGroup.addActionListener(new java.awt.event.ActionListener()\r
 132     {\r
 133       public void actionPerformed(ActionEvent e)\r
 134       {\r
 135         moveGroup_actionPerformed(e);\r
 136       }\r
 137     });\r
 138     deleteSequences.setText("Delete sequences");\r
 139     deleteSequences.addActionListener(new java.awt.event.ActionListener()\r
 140     {\r
 141       public void actionPerformed(ActionEvent e)\r
 142       {\r
 143         deleteSequences_actionPerformed(e);\r
 144       }\r
 145     });\r
 146     analyze.setText("Analyze");\r
 147     analyze.addActionListener(new java.awt.event.ActionListener()\r
 148     {\r
 149       public void actionPerformed(ActionEvent e)\r
 150       {\r
 151         analyze_actionPerformed(e);\r
 152       }\r
 153     });\r
 154     defineMenu.setText("Define");\r
 155     groupName.setText("Name");\r
 156     groupName.addActionListener(new java.awt.event.ActionListener()\r
 157     {\r
 158       public void actionPerformed(ActionEvent e)\r
 159       {\r
 160         groupName_actionPerformed(e);\r
 161       }\r
 162     });\r
 163     groupAnnotation.setText("Annotation");\r
 164     groupAnnotation.addActionListener(new java.awt.event.ActionListener()\r
 165     {\r
 166       public void actionPerformed(ActionEvent e)\r
 167       {\r
 168         groupAnnotation_actionPerformed(e);\r
 169       }\r
 170     });\r
 171     sequenceMenu.setText("Sequence");\r
 172     sequenceName.setText("Edit name");\r
 173     sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 174     {\r
 175       public void actionPerformed(ActionEvent e)\r
 176       {\r
 177         sequenceName_actionPerformed(e);\r
 178       }\r
 179     });\r
 180     residueMenu.setText("Residue");\r
 181     annotateResidue.setText("annotate residue???");\r
 182     PIDColour.setFocusPainted(false);\r
 183     unGroupMenuItem.setText("Remove Group");\r
 184     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 185     {\r
 186       public void actionPerformed(ActionEvent e)\r
 187       {\r
 188         unGroupMenuItem_actionPerformed(e);\r
 189       }\r
 190     });\r
 191     pdbMenuItem.setText("View PDB structure");\r
 192     pdbMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 193     {\r
 194       public void actionPerformed(ActionEvent e)\r
 195       {\r
 196         pdbMenuItem_actionPerformed(e);\r
 197       }\r
 198     });\r
 199     add(groupMenu);\r
 200     this.add(sequenceMenu);\r
 201     this.add(residueMenu);\r
 202     groupMenu.add(defineMenu);\r
 203     groupMenu.add(unGroupMenuItem);\r
 204     groupMenu.addSeparator();\r
 205     groupMenu.add(copyGroup);\r
 206     groupMenu.add(moveGroup);\r
 207     groupMenu.add(deleteSequences);\r
 208     groupMenu.addSeparator();\r
 209     groupMenu.add(analyze);\r
 210     defineMenu.add(groupName);\r
 211     defineMenu.add(groupAnnotation);\r
 212     defineMenu.addSeparator();\r
 213     defineMenu.add(noColourmenuItem);\r
 214     defineMenu.add(clustalColour);\r
 215     defineMenu.add(zappoColour);\r
 216     defineMenu.add(taylorColour);\r
 217     defineMenu.add(hydrophobicityColour);\r
 218     defineMenu.add(helixColour);\r
 219     defineMenu.add(strandColour);\r
 220     defineMenu.add(turnColour);\r
 221     defineMenu.add(buriedColour);\r
 222     defineMenu.add(userDefinedColour);\r
 223     defineMenu.add(PIDColour);\r
 224     defineMenu.add(BLOSUM62Colour);\r
 225     defineMenu.addSeparator();\r
 226     defineMenu.add(abovePIDColour);\r
 227     defineMenu.add(conservationMenuItem);\r
 228 \r
 229     sequenceMenu.add(sequenceName);\r
 230     sequenceMenu.add(pdbMenuItem);\r
 231     residueMenu.add(annotateResidue);\r
 232 \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 colour scheme");\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 colour scheme");\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("By 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 PID threshold only");\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 colours");\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 score");\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("By 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.seqCanvas.paintFlag=true;\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 \r
 413   protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 414   {\r
 415     Desktop.setPIDSliderSource(ap, getGroup().cs, getGroup().getName());\r
 416   }\r
 417 \r
 418 \r
 419   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 420   {\r
 421     JInternalFrame frame = new JInternalFrame();\r
 422     UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup());\r
 423     frame.setContentPane(chooser);\r
 424     Desktop.addInternalFrame(frame,"User defined colours ("+getGroup().getName()+")", 450,540 );\r
 425     frame.setResizable(false);\r
 426     frame.setIconifiable(false);\r
 427     frame.setMaximizable(false);\r
 428 \r
 429   }\r
 430 \r
 431   protected void PIDColour_actionPerformed(ActionEvent e)\r
 432   {\r
 433 \r
 434   }\r
 435 \r
 436   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 437   {\r
 438     getGroup().cs = new Blosum62ColourScheme(ap.av);\r
 439     refresh();\r
 440   }\r
 441 \r
 442 \r
 443   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 444   {\r
 445     getGroup().cs = null;\r
 446     refresh();\r
 447   }\r
 448 \r
 449   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 450   {\r
 451     SequenceGroup sg = getGroup();\r
 452 \r
 453     if(conservationMenuItem.isSelected())\r
 454     {\r
 455 \r
 456         Conservation c = new Conservation("Group",\r
 457                                           ResidueProperties.propHash, 3,\r
 458                                           sg.sequences, 0,\r
 459                                           ap.av.alignment.getWidth());\r
 460 \r
 461         c.calculate();\r
 462         c.verdict(false, 100);\r
 463         ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 464 \r
 465 \r
 466       sg.cs = ccs;\r
 467 \r
 468       Desktop.setConservationSliderSource(ap, ccs, sg.getName());\r
 469     }\r
 470     else // remove ConservationColouring\r
 471     {\r
 472         ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
 473         sg.cs = ccs.cs;\r
 474     }\r
 475 \r
 476      refresh();\r
 477   }\r
 478 \r
 479   protected void groupAnnotation_actionPerformed(ActionEvent e)\r
 480   {\r
 481 \r
 482   }\r
 483 \r
 484   protected void groupName_actionPerformed(ActionEvent e)\r
 485   {\r
 486     SequenceGroup sg = getGroup();\r
 487     String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);\r
 488     if(reply==null)\r
 489       return;\r
 490 \r
 491     sg.setName(reply);\r
 492     groupName.setText(reply);\r
 493   }\r
 494 \r
 495   protected void copyGroup_actionPerformed(ActionEvent e)\r
 496   {\r
 497     SequenceGroup sg = ap.av.getRubberbandGroup();\r
 498 \r
 499     SequenceI[] s = new Sequence[sg.sequences.size()];\r
 500      for (int i=0; i < sg.sequences.size(); i++)\r
 501      {\r
 502        s[i] = new Sequence( sg.getSequenceAt(i));\r
 503        s[i].setSequence( s[i].getSequence(sg.getStartRes(), sg.getEndRes()+1) );\r
 504      }\r
 505      AlignFrame af = new AlignFrame(new Alignment(s));\r
 506      int newHeight = s.length * af.viewport.getCharHeight() + 200;\r
 507      if (newHeight > 500)\r
 508        newHeight = 500;\r
 509      Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
 510    }\r
 511 \r
 512   protected  void moveGroup_actionPerformed(ActionEvent e)\r
 513   {\r
 514     SequenceGroup sg = ap.av.getRubberbandGroup();\r
 515 \r
 516     SequenceI[] s = new Sequence[sg.sequences.size()];\r
 517 \r
 518      for (int i=0; i < sg.sequences.size(); i++)\r
 519        s[i] = new Sequence( sg.getSequenceAt(i));\r
 520 \r
 521      AlignFrame af = new AlignFrame(new Alignment(s));\r
 522      int newHeight = s.length * af.viewport.getCharHeight() + 200;\r
 523      if(newHeight>500)\r
 524        newHeight=500;\r
 525      Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);\r
 526 \r
 527 \r
 528      for (int i=0; i < sg.sequences.size(); i++)\r
 529        ap.av.alignment.deleteSequence(sg.getSequenceAt(i));\r
 530 \r
 531 \r
 532      ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());\r
 533      ap.RefreshPanels();\r
 534 \r
 535 \r
 536   }\r
 537 \r
 538   protected void deleteSequences_actionPerformed(ActionEvent e)\r
 539   {\r
 540     SequenceGroup sg = ap.av.getRubberbandGroup();\r
 541     for (int i=0;i < sg.sequences.size(); i++)\r
 542             ap.av.getAlignment().deleteSequence(sg.getSequenceAt(i));\r
 543 \r
 544     ap.av.alignment.deleteGroup(sg);\r
 545     ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());\r
 546     ap.RefreshPanels();\r
 547 \r
 548   }\r
 549 \r
 550   protected void analyze_actionPerformed(ActionEvent e)\r
 551   {\r
 552      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
 553      JInternalFrame frame = new JInternalFrame();\r
 554      cap.formatForOutput();\r
 555      frame.setContentPane(cap);\r
 556      Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
 557      SequenceGroup sg = getGroup();\r
 558      StringBuffer sb = new StringBuffer();\r
 559 \r
 560      for(int i=0; i<sg.sequences.size(); i++)\r
 561      {\r
 562        Sequence tmp = (Sequence)sg.sequences.get(i);\r
 563        sb.append(  tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));\r
 564        sb.append("\n");\r
 565      }\r
 566 \r
 567      sb.append("Something amazing will happen soon");\r
 568      cap.setText( sb.toString() );\r
 569 \r
 570   }\r
 571 \r
 572   SequenceGroup getGroup()\r
 573   {\r
 574     SequenceGroup sg = ap.av.getRubberbandGroup();\r
 575 \r
 576     // this method won't add a new group if it already exists\r
 577     ap.av.alignment.addGroup(sg);\r
 578     return sg;\r
 579   }\r
 580 \r
 581   void sequenceName_actionPerformed(ActionEvent e)\r
 582   {\r
 583     String id = sequence.getName();\r
 584     String s = (String)JOptionPane.showInternalInputDialog(\r
 585                 ap,\r
 586                 "Edit sequence name",\r
 587                 "Edit sequence name ("+sequence.getName()+")",\r
 588                 JOptionPane.PLAIN_MESSAGE,\r
 589                 null,\r
 590                 null,\r
 591                 id);\r
 592 \r
 593     if(s!=null)\r
 594     {\r
 595       sequence.setName(s);\r
 596       ap.RefreshPanels();\r
 597     }\r
 598 \r
 599   }\r
 600 \r
 601   void unGroupMenuItem_actionPerformed(ActionEvent e)\r
 602   {\r
 603      SequenceGroup sg = ap.av.getRubberbandGroup();\r
 604      ap.av.alignment.deleteGroup(sg);\r
 605      ap.av.setRubberbandGroup(null);\r
 606      ap.RefreshPanels();\r
 607   }\r
 608 \r
 609   void pdbMenuItem_actionPerformed(ActionEvent e)\r
 610   {\r
 611     if(sequence.getPDBId()==null)\r
 612       return;\r
 613 \r
 614     try\r
 615     {\r
 616       EBIFetchClient ebi = new EBIFetchClient();\r
 617       String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null);\r
 618 \r
 619       PDBfile pdb = new PDBfile(result);\r
 620       sequence.setPDBfile(pdb);\r
 621 \r
 622       ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).isVisible = true;\r
 623       ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).sequence = sequence;\r
 624     //  ( (PDBChain)pdb.chains.elementAt(sequence.maxchain)).colourBySequence();\r
 625 \r
 626       rotCanvas rc = new rotCanvas(pdb);\r
 627       JInternalFrame frame = new JInternalFrame();\r
 628       frame.setContentPane(rc);\r
 629       Desktop.addInternalFrame(frame,sequence.getName()+" "+ sequence.getPDBId(), 400, 400);\r
 630     }\r
 631     catch (Exception ex)\r
 632     {\r
 633       ex.printStackTrace();\r
 634     }\r
 635   }\r
 636 \r
 637 }\r