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     {\r
 115       residueMenu.setVisible(false);\r
 116       sequenceName.setText( sequence.getName() );\r
 117     }\r
 118     else\r
 119       sequenceMenu.setVisible(false);\r
 120 \r
 121   }\r
 122   private void jbInit() throws Exception\r
 123   {\r
 124     groupMenu.setText("Group");\r
 125     copyGroup.setText("Copy region to new Alignment");\r
 126     copyGroup.addActionListener(new java.awt.event.ActionListener()\r
 127     {\r
 128       public void actionPerformed(ActionEvent e)\r
 129       {\r
 130         copyGroup_actionPerformed(e);\r
 131       }\r
 132     });\r
 133     moveGroup.setText("Move sequences to new Alignment");\r
 134     moveGroup.addActionListener(new java.awt.event.ActionListener()\r
 135     {\r
 136       public void actionPerformed(ActionEvent e)\r
 137       {\r
 138         moveGroup_actionPerformed(e);\r
 139       }\r
 140     });\r
 141     deleteSequences.setText("Delete sequences");\r
 142     deleteSequences.addActionListener(new java.awt.event.ActionListener()\r
 143     {\r
 144       public void actionPerformed(ActionEvent e)\r
 145       {\r
 146         deleteSequences_actionPerformed(e);\r
 147       }\r
 148     });\r
 149     analyze.setText("Analyze");\r
 150     analyze.addActionListener(new java.awt.event.ActionListener()\r
 151     {\r
 152       public void actionPerformed(ActionEvent e)\r
 153       {\r
 154         analyze_actionPerformed(e);\r
 155       }\r
 156     });\r
 157     defineMenu.setText("Define");\r
 158     groupName.setText("Name");\r
 159     groupName.addActionListener(new java.awt.event.ActionListener()\r
 160     {\r
 161       public void actionPerformed(ActionEvent e)\r
 162       {\r
 163         groupName_actionPerformed(e);\r
 164       }\r
 165     });\r
 166     groupAnnotation.setText("Annotation");\r
 167     groupAnnotation.addActionListener(new java.awt.event.ActionListener()\r
 168     {\r
 169       public void actionPerformed(ActionEvent e)\r
 170       {\r
 171         groupAnnotation_actionPerformed(e);\r
 172       }\r
 173     });\r
 174     sequenceMenu.setText("Sequence");\r
 175     sequenceName.setText("sequenceName");\r
 176     sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 177     {\r
 178       public void actionPerformed(ActionEvent e)\r
 179       {\r
 180         sequenceName_actionPerformed(e);\r
 181       }\r
 182     });\r
 183     residueMenu.setText("Residue");\r
 184     annotateResidue.setText("annotate residue???");\r
 185     PIDColour.setFocusPainted(false);\r
 186     unGroupMenuItem.setText("Remove Group");\r
 187     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 188     {\r
 189       public void actionPerformed(ActionEvent e)\r
 190       {\r
 191         unGroupMenuItem_actionPerformed(e);\r
 192       }\r
 193     });\r
 194     pdbMenuItem.setText("View PDB structure");\r
 195     pdbMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 196     {\r
 197       public void actionPerformed(ActionEvent e)\r
 198       {\r
 199         pdbMenuItem_actionPerformed(e);\r
 200       }\r
 201     });\r
 202     add(groupMenu);\r
 203     this.add(sequenceMenu);\r
 204     this.add(residueMenu);\r
 205     groupMenu.add(defineMenu);\r
 206     groupMenu.add(unGroupMenuItem);\r
 207     groupMenu.addSeparator();\r
 208     groupMenu.add(copyGroup);\r
 209     groupMenu.add(moveGroup);\r
 210     groupMenu.add(deleteSequences);\r
 211     groupMenu.addSeparator();\r
 212     groupMenu.add(analyze);\r
 213     defineMenu.add(groupName);\r
 214     defineMenu.add(groupAnnotation);\r
 215     defineMenu.addSeparator();\r
 216     defineMenu.add(noColourmenuItem);\r
 217     defineMenu.add(clustalColour);\r
 218     defineMenu.add(zappoColour);\r
 219     defineMenu.add(taylorColour);\r
 220     defineMenu.add(hydrophobicityColour);\r
 221     defineMenu.add(helixColour);\r
 222     defineMenu.add(strandColour);\r
 223     defineMenu.add(turnColour);\r
 224     defineMenu.add(buriedColour);\r
 225     defineMenu.add(userDefinedColour);\r
 226     defineMenu.add(PIDColour);\r
 227     defineMenu.add(BLOSUM62Colour);\r
 228     defineMenu.addSeparator();\r
 229     defineMenu.add(abovePIDColour);\r
 230     defineMenu.add(conservationMenuItem);\r
 231 \r
 232     sequenceMenu.add(sequenceName);\r
 233     sequenceMenu.add(pdbMenuItem);\r
 234     residueMenu.add(annotateResidue);\r
 235 \r
 236     noColourmenuItem.setText("None");\r
 237     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 238     {\r
 239       public void actionPerformed(ActionEvent e)\r
 240       {\r
 241         noColourmenuItem_actionPerformed(e);\r
 242       }\r
 243     });\r
 244 \r
 245     clustalColour.setText("Clustalx colours");\r
 246     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 247     {\r
 248       public void actionPerformed(ActionEvent e)\r
 249       {\r
 250         clustalColour_actionPerformed(e);\r
 251       }\r
 252     });\r
 253     zappoColour.setText("Zappo colour scheme");\r
 254     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 255     {\r
 256       public void actionPerformed(ActionEvent e)\r
 257       {\r
 258         zappoColour_actionPerformed(e);\r
 259       }\r
 260     });\r
 261     taylorColour.setText("Taylor colour scheme");\r
 262     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 263     {\r
 264       public void actionPerformed(ActionEvent e)\r
 265       {\r
 266         taylorColour_actionPerformed(e);\r
 267       }\r
 268     });\r
 269     hydrophobicityColour.setText("By hydrophobicity");\r
 270     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 271     {\r
 272       public void actionPerformed(ActionEvent e)\r
 273       {\r
 274         hydrophobicityColour_actionPerformed(e);\r
 275       }\r
 276     });\r
 277     helixColour.setText("Helix propensity");\r
 278     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 279     {\r
 280       public void actionPerformed(ActionEvent e)\r
 281       {\r
 282         helixColour_actionPerformed(e);\r
 283       }\r
 284     });\r
 285     strandColour.setText("Strand propensity");\r
 286     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 287     {\r
 288       public void actionPerformed(ActionEvent e)\r
 289       {\r
 290         strandColour_actionPerformed(e);\r
 291       }\r
 292     });\r
 293     turnColour.setText("Turn propensity");\r
 294     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 295     {\r
 296       public void actionPerformed(ActionEvent e)\r
 297       {\r
 298         turnColour_actionPerformed(e);\r
 299       }\r
 300     });\r
 301     buriedColour.setText("Buried index");\r
 302     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 303     {\r
 304       public void actionPerformed(ActionEvent e)\r
 305       {\r
 306         buriedColour_actionPerformed(e);\r
 307       }\r
 308     });\r
 309     abovePIDColour.setText("Above PID threshold only");\r
 310     abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 311     {\r
 312       public void actionPerformed(ActionEvent e)\r
 313       {\r
 314         abovePIDColour_actionPerformed(e);\r
 315       }\r
 316     });\r
 317     userDefinedColour.setText("User defined colours");\r
 318     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 319     {\r
 320       public void actionPerformed(ActionEvent e)\r
 321       {\r
 322         userDefinedColour_actionPerformed(e);\r
 323       }\r
 324     });\r
 325     PIDColour.setText("Percentage Identity");\r
 326     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 327     {\r
 328       public void actionPerformed(ActionEvent e)\r
 329       {\r
 330         PIDColour_actionPerformed(e);\r
 331       }\r
 332     });\r
 333     BLOSUM62Colour.setText("BLOSUM62 score");\r
 334     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 335     {\r
 336       public void actionPerformed(ActionEvent e)\r
 337       {\r
 338         BLOSUM62Colour_actionPerformed(e);\r
 339       }\r
 340     });\r
 341     conservationMenuItem.setText("By conservation");\r
 342    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 343    {\r
 344      public void actionPerformed(ActionEvent e)\r
 345      {\r
 346        conservationMenuItem_actionPerformed(e);\r
 347      }\r
 348    });\r
 349 \r
 350 \r
 351 \r
 352   }\r
 353 \r
 354   void refresh()\r
 355   {\r
 356     SequenceGroup sg = getGroup();\r
 357     SuperGroup superG = ap.av.alignment.getSuperGroup( sg );\r
 358     if( superG !=null)\r
 359       superG.setSuperGroupProperties( sg );\r
 360 \r
 361     ap.seqPanel.seqCanvas.paintFlag=true;\r
 362     ap.seqPanel.repaint();\r
 363   }\r
 364 \r
 365   protected void clustalColour_actionPerformed(ActionEvent e)\r
 366   {\r
 367     SequenceGroup sg = getGroup();\r
 368     sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());\r
 369     refresh();\r
 370   }\r
 371 \r
 372   protected void zappoColour_actionPerformed(ActionEvent e)\r
 373   {\r
 374     getGroup().cs = new ZappoColourScheme();\r
 375     refresh();\r
 376   }\r
 377 \r
 378   protected void taylorColour_actionPerformed(ActionEvent e)\r
 379   {\r
 380     getGroup().cs = new TaylorColourScheme();\r
 381     refresh();\r
 382   }\r
 383 \r
 384 \r
 385   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 386   {\r
 387     getGroup().cs = new HydrophobicColourScheme();\r
 388     refresh();\r
 389   }\r
 390 \r
 391   protected void helixColour_actionPerformed(ActionEvent e)\r
 392   {\r
 393     getGroup().cs = new HelixColourScheme();\r
 394     refresh();\r
 395   }\r
 396 \r
 397   protected void strandColour_actionPerformed(ActionEvent e)\r
 398   {\r
 399     getGroup().cs = new StrandColourScheme();\r
 400     refresh();\r
 401   }\r
 402 \r
 403   protected void turnColour_actionPerformed(ActionEvent e)\r
 404   {\r
 405     getGroup().cs = new TurnColourScheme();\r
 406     refresh();\r
 407   }\r
 408 \r
 409   protected void buriedColour_actionPerformed(ActionEvent e)\r
 410   {\r
 411     getGroup().cs = new BuriedColourScheme();\r
 412     refresh();\r
 413   }\r
 414 \r
 415 \r
 416   protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 417   {\r
 418     Desktop.setPIDSliderSource(ap, getGroup().cs, getGroup().getName());\r
 419   }\r
 420 \r
 421 \r
 422   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 423   {\r
 424     JInternalFrame frame = new JInternalFrame();\r
 425     UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup());\r
 426     frame.setContentPane(chooser);\r
 427     Desktop.addInternalFrame(frame,"User defined colours ("+getGroup().getName()+")", 450,540 );\r
 428     frame.setResizable(false);\r
 429     frame.setIconifiable(false);\r
 430     frame.setMaximizable(false);\r
 431 \r
 432   }\r
 433 \r
 434   protected void PIDColour_actionPerformed(ActionEvent e)\r
 435   {\r
 436 \r
 437   }\r
 438 \r
 439   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 440   {\r
 441     getGroup().cs = new Blosum62ColourScheme(ap.av);\r
 442     refresh();\r
 443   }\r
 444 \r
 445 \r
 446   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 447   {\r
 448     getGroup().cs = null;\r
 449     refresh();\r
 450   }\r
 451 \r
 452   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 453   {\r
 454     SequenceGroup sg = getGroup();\r
 455 \r
 456     if(conservationMenuItem.isSelected())\r
 457     {\r
 458 \r
 459         Conservation c = new Conservation("Group",\r
 460                                           ResidueProperties.propHash, 3,\r
 461                                           sg.sequences, 0,\r
 462                                           ap.av.alignment.getWidth());\r
 463 \r
 464         c.calculate();\r
 465         c.verdict(false, 100);\r
 466         ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 467 \r
 468 \r
 469       sg.cs = ccs;\r
 470 \r
 471       Desktop.setConservationSliderSource(ap, ccs, sg.getName());\r
 472     }\r
 473     else // remove ConservationColouring\r
 474     {\r
 475         ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
 476         sg.cs = ccs.cs;\r
 477     }\r
 478 \r
 479      refresh();\r
 480   }\r
 481 \r
 482   protected void groupAnnotation_actionPerformed(ActionEvent e)\r
 483   {\r
 484 \r
 485   }\r
 486 \r
 487   protected void groupName_actionPerformed(ActionEvent e)\r
 488   {\r
 489     SequenceGroup sg = getGroup();\r
 490     String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);\r
 491     if(reply==null)\r
 492       return;\r
 493 \r
 494     sg.setName(reply);\r
 495     groupName.setText(reply);\r
 496   }\r
 497 \r
 498   protected void copyGroup_actionPerformed(ActionEvent e)\r
 499   {\r
 500     SequenceGroup sg = ap.av.getRubberbandGroup();\r
 501 \r
 502     SequenceI[] s = new Sequence[sg.sequences.size()];\r
 503      for (int i=0; i < sg.sequences.size(); i++)\r
 504      {\r
 505        s[i] = new Sequence( sg.getSequenceAt(i));\r
 506        s[i].setSequence( s[i].getSequence(sg.getStartRes(), sg.getEndRes()+1) );\r
 507      }\r
 508      AlignFrame af = new AlignFrame(new Alignment(s));\r
 509      int newHeight = s.length * af.viewport.getCharHeight() + 200;\r
 510      if (newHeight > 500)\r
 511        newHeight = 500;\r
 512      Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
 513    }\r
 514 \r
 515   protected  void moveGroup_actionPerformed(ActionEvent e)\r
 516   {\r
 517     SequenceGroup sg = ap.av.getRubberbandGroup();\r
 518 \r
 519     SequenceI[] s = new Sequence[sg.sequences.size()];\r
 520 \r
 521      for (int i=0; i < sg.sequences.size(); i++)\r
 522        s[i] = new Sequence( sg.getSequenceAt(i));\r
 523 \r
 524      AlignFrame af = new AlignFrame(new Alignment(s));\r
 525      int newHeight = s.length * af.viewport.getCharHeight() + 200;\r
 526      if(newHeight>500)\r
 527        newHeight=500;\r
 528      Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);\r
 529 \r
 530 \r
 531      for (int i=0; i < sg.sequences.size(); i++)\r
 532        ap.av.alignment.deleteSequence(sg.getSequenceAt(i));\r
 533 \r
 534 \r
 535      ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());\r
 536      ap.RefreshPanels();\r
 537 \r
 538 \r
 539   }\r
 540 \r
 541   protected void deleteSequences_actionPerformed(ActionEvent e)\r
 542   {\r
 543     SequenceGroup sg = ap.av.getRubberbandGroup();\r
 544     for (int i=0;i < sg.sequences.size(); i++)\r
 545             ap.av.getAlignment().deleteSequence(sg.getSequenceAt(i));\r
 546 \r
 547     ap.av.alignment.deleteGroup(sg);\r
 548     ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());\r
 549     ap.RefreshPanels();\r
 550 \r
 551   }\r
 552 \r
 553   protected void analyze_actionPerformed(ActionEvent e)\r
 554   {\r
 555      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
 556      JInternalFrame frame = new JInternalFrame();\r
 557      cap.formatForOutput();\r
 558      frame.setContentPane(cap);\r
 559      Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
 560      SequenceGroup sg = getGroup();\r
 561      StringBuffer sb = new StringBuffer();\r
 562 \r
 563      for(int i=0; i<sg.sequences.size(); i++)\r
 564      {\r
 565        Sequence tmp = (Sequence)sg.sequences.get(i);\r
 566        sb.append(  tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));\r
 567        sb.append("\n");\r
 568      }\r
 569 \r
 570      sb.append("Something amazing will happen soon");\r
 571      cap.setText( sb.toString() );\r
 572 \r
 573   }\r
 574 \r
 575   SequenceGroup getGroup()\r
 576   {\r
 577     SequenceGroup sg = ap.av.getRubberbandGroup();\r
 578 \r
 579     // this method won't add a new group if it already exists\r
 580     ap.av.alignment.addGroup(sg);\r
 581     return sg;\r
 582   }\r
 583 \r
 584   void sequenceName_actionPerformed(ActionEvent e)\r
 585   {\r
 586     String id = sequence.getName();\r
 587     String s = (String)JOptionPane.showInternalInputDialog(\r
 588                 ap,\r
 589                 "Edit sequence name",\r
 590                 "Edit sequence name",\r
 591                 JOptionPane.PLAIN_MESSAGE,\r
 592                 null,\r
 593                 null,\r
 594                 id);\r
 595 \r
 596     if(s!=null)\r
 597     {\r
 598       sequence.setName(s);\r
 599       ap.RefreshPanels();\r
 600     }\r
 601 \r
 602   }\r
 603 \r
 604   void unGroupMenuItem_actionPerformed(ActionEvent e)\r
 605   {\r
 606      SequenceGroup sg = ap.av.getRubberbandGroup();\r
 607      ap.av.alignment.deleteGroup(sg);\r
 608      ap.av.setRubberbandGroup(null);\r
 609      ap.RefreshPanels();\r
 610   }\r
 611 \r
 612   void pdbMenuItem_actionPerformed(ActionEvent e)\r
 613   {\r
 614     if(sequence.getPDBId()==null)\r
 615       return;\r
 616 \r
 617     try\r
 618     {\r
 619       EBIFetchClient ebi = new EBIFetchClient();\r
 620       String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null);\r
 621 \r
 622       PDBfile pdb = new PDBfile(result);\r
 623       sequence.setPDBfile(pdb);\r
 624 \r
 625       ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).isVisible = true;\r
 626       ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).sequence = sequence;\r
 627     //  ( (PDBChain)pdb.chains.elementAt(sequence.maxchain)).colourBySequence();\r
 628 \r
 629       rotCanvas rc = new rotCanvas(pdb);\r
 630       JInternalFrame frame = new JInternalFrame();\r
 631       frame.setContentPane(rc);\r
 632       Desktop.addInternalFrame(frame,sequence.getName()+" "+ sequence.getPDBId(), 400, 400);\r
 633     }\r
 634     catch (Exception ex)\r
 635     {\r
 636       ex.printStackTrace();\r
 637     }\r
 638   }\r
 639 \r
 640 }\r