src/jalview/gui/PopupMenu.java

   1 /*\r
   2 * Jalview - A Sequence Alignment Editor and Viewer\r
   3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4 *\r
   5 * This program is free software; you can redistribute it and/or\r
   6 * modify it under the terms of the GNU General Public License\r
   7 * as published by the Free Software Foundation; either version 2\r
   8 * of the License, or (at your option) any later version.\r
   9 *\r
  10 * This program is distributed in the hope that it will be useful,\r
  11 * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13 * GNU General Public License for more details.\r
  14 *\r
  15 * You should have received a copy of the GNU General Public License\r
  16 * along with this program; if not, write to the Free Software\r
  17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18 */\r
  19 \r
  20 package jalview.gui;\r
  21 \r
  22 import jalview.datamodel.*;\r
  23 import jalview.analysis.*;\r
  24 import jalview.schemes.*;\r
  25 import java.awt.*;\r
  26 import javax.swing.*;\r
  27 import java.awt.event.*;\r
  28 import jalview.io.*;\r
  29 import MCview.*;\r
  30 \r
  31 public class PopupMenu extends JPopupMenu\r
  32 {\r
  33   JMenu groupMenu = new JMenu();\r
  34   JMenuItem groupName = new JMenuItem();\r
  35   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  36   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  37   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  38   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
  39   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  40   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  41   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  42   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  43   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();\r
  44   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  45   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  46   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  47   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  48   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  49 \r
  50 \r
  51   AlignmentPanel ap;\r
  52   JMenu sequenceMenu = new JMenu();\r
  53   JMenuItem sequenceName = new JMenuItem();\r
  54   Sequence sequence;\r
  55   JMenuItem unGroupMenuItem = new JMenuItem();\r
  56   JMenuItem pdbMenuItem = new JMenuItem();\r
  57   JMenuItem outline = new JMenuItem();\r
  58   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
  59   JMenu colourMenu = new JMenu();\r
  60   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
  61   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
  62   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
  63 \r
  64   public PopupMenu(AlignmentPanel ap, Sequence seq)\r
  65   {\r
  66     ///////////////////////////////////////////////////////////\r
  67     // If this is activated from the sequence panel, the user may want to\r
  68     // edit or annotate a particular residue. Therefore display the residue menu\r
  69     //\r
  70     // If from the IDPanel, we must display the sequence menu\r
  71     //////////////////////////////////////////////////////////\r
  72 \r
  73     this.ap = ap;\r
  74     sequence = seq;\r
  75 \r
  76     ButtonGroup colours = new ButtonGroup();\r
  77     colours.add(noColourmenuItem);\r
  78     colours.add(clustalColour);\r
  79     colours.add(zappoColour);\r
  80     colours.add(taylorColour);\r
  81     colours.add(hydrophobicityColour);\r
  82     colours.add(helixColour);\r
  83     colours.add(strandColour);\r
  84     colours.add(turnColour);\r
  85     colours.add(buriedColour);\r
  86     colours.add(abovePIDColour);\r
  87     colours.add(userDefinedColour);\r
  88     colours.add(PIDColour);\r
  89     colours.add(BLOSUM62Colour);\r
  90 \r
  91     try\r
  92     {     jbInit();   }\r
  93     catch(Exception e)\r
  94     {    e.printStackTrace();    }\r
  95 \r
  96     SequenceGroup sg = ap.av.getSelectionGroup();\r
  97     if(sg!=null)\r
  98     {\r
  99       groupName.setText(sg.getName());\r
 100       if(sg.cs instanceof ZappoColourScheme)\r
 101         zappoColour.setSelected(true);\r
 102       else if(sg.cs instanceof TaylorColourScheme)\r
 103         taylorColour.setSelected(true);\r
 104       else if (sg.cs instanceof PIDColourScheme)\r
 105         PIDColour.setSelected(true);\r
 106       else if (sg.cs instanceof Blosum62ColourScheme)\r
 107         BLOSUM62Colour.setSelected(true);\r
 108       else if (sg.cs instanceof UserColourScheme)\r
 109         userDefinedColour.setSelected(true);\r
 110       else if (sg.cs instanceof HydrophobicColourScheme)\r
 111         hydrophobicityColour.setSelected(true);\r
 112       else if (sg.cs instanceof HelixColourScheme)\r
 113         helixColour.setSelected(true);\r
 114       else if (sg.cs instanceof StrandColourScheme)\r
 115         strandColour.setSelected(true);\r
 116       else if (sg.cs instanceof TurnColourScheme)\r
 117         turnColour.setSelected(true);\r
 118       else if (sg.cs instanceof BuriedColourScheme)\r
 119         buriedColour.setSelected(true);\r
 120       else if (sg.cs instanceof ClustalxColourScheme)\r
 121         clustalColour.setSelected(true);\r
 122       else\r
 123         noColourmenuItem.setSelected(true);\r
 124 \r
 125       if (sg.cs instanceof ConservationColourScheme)\r
 126         conservationMenuItem.setSelected(true);\r
 127 \r
 128       showText.setSelected(sg.getDisplayText());\r
 129       showColourText.setSelected(sg.getColourText());\r
 130       showBoxes.setSelected(sg.getDisplayBoxes());\r
 131     }\r
 132 \r
 133     if( !ap.av.alignment.getGroups().contains(sg))\r
 134       unGroupMenuItem.setVisible(false);\r
 135     else\r
 136       groupMenu.insertSeparator(3);\r
 137 \r
 138     if(seq==null)\r
 139        sequenceMenu.setVisible(false);\r
 140 \r
 141   }\r
 142   private void jbInit() throws Exception\r
 143   {\r
 144     groupMenu.setText("Group");\r
 145     groupMenu.setText("Define");\r
 146     groupName.setText("Name");\r
 147     groupName.addActionListener(new java.awt.event.ActionListener()\r
 148     {\r
 149       public void actionPerformed(ActionEvent e)\r
 150       {\r
 151         groupName_actionPerformed(e);\r
 152       }\r
 153     });\r
 154     sequenceMenu.setText("Sequence");\r
 155     sequenceName.setText("Edit name");\r
 156     sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 157     {\r
 158       public void actionPerformed(ActionEvent e)\r
 159       {\r
 160         sequenceName_actionPerformed(e);\r
 161       }\r
 162     });\r
 163     PIDColour.setFocusPainted(false);\r
 164     unGroupMenuItem.setText("Remove Group");\r
 165     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 166     {\r
 167       public void actionPerformed(ActionEvent e)\r
 168       {\r
 169         unGroupMenuItem_actionPerformed(e);\r
 170       }\r
 171     });\r
 172     pdbMenuItem.setText("View PDB structure");\r
 173     pdbMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 174     {\r
 175       public void actionPerformed(ActionEvent e)\r
 176       {\r
 177         pdbMenuItem_actionPerformed(e);\r
 178       }\r
 179     });\r
 180     outline.setText("Border colour");\r
 181     outline.addActionListener(new java.awt.event.ActionListener()\r
 182     {\r
 183       public void actionPerformed(ActionEvent e)\r
 184       {\r
 185         outline_actionPerformed(e);\r
 186       }\r
 187     });\r
 188     nucleotideMenuItem.setText("Nucleotide");\r
 189     nucleotideMenuItem.addActionListener(new ActionListener()\r
 190     {\r
 191       public void actionPerformed(ActionEvent e)\r
 192       {\r
 193         nucleotideMenuItem_actionPerformed(e);\r
 194       }\r
 195     });\r
 196     colourMenu.setText("Group Colour");\r
 197     showBoxes.setText("Boxes");\r
 198     showBoxes.setState(true);\r
 199     showBoxes.addActionListener(new ActionListener()\r
 200     {\r
 201       public void actionPerformed(ActionEvent e)\r
 202       {\r
 203         showBoxes_actionPerformed(e);\r
 204       }\r
 205     });\r
 206     showText.setText("Text");\r
 207     showText.setState(true);\r
 208     showText.addActionListener(new ActionListener()\r
 209     {\r
 210       public void actionPerformed(ActionEvent e)\r
 211       {\r
 212         showText_actionPerformed(e);\r
 213       }\r
 214     });\r
 215     showColourText.setText("Colour Text");\r
 216     showColourText.addActionListener(new ActionListener()\r
 217     {\r
 218       public void actionPerformed(ActionEvent e)\r
 219       {\r
 220         showColourText_actionPerformed(e);\r
 221       }\r
 222     });\r
 223     add(groupMenu);\r
 224     add(sequenceMenu);\r
 225     groupMenu.add(groupName);\r
 226     groupMenu.addSeparator();\r
 227     groupMenu.add(unGroupMenuItem);\r
 228     groupMenu.add(colourMenu);\r
 229     groupMenu.addSeparator();\r
 230     groupMenu.add(showBoxes);\r
 231     groupMenu.add(showText);\r
 232     groupMenu.add(showColourText);\r
 233     groupMenu.addSeparator();\r
 234     groupMenu.add(outline);\r
 235     sequenceMenu.add(sequenceName);\r
 236     sequenceMenu.add(pdbMenuItem);\r
 237     colourMenu.add(noColourmenuItem);\r
 238     colourMenu.add(clustalColour);\r
 239     colourMenu.add(BLOSUM62Colour);\r
 240     colourMenu.add(PIDColour);\r
 241     colourMenu.add(zappoColour);\r
 242     colourMenu.add(taylorColour);\r
 243     colourMenu.add(hydrophobicityColour);\r
 244     colourMenu.add(helixColour);\r
 245     colourMenu.add(strandColour);\r
 246     colourMenu.add(turnColour);\r
 247     colourMenu.add(buriedColour);\r
 248     colourMenu.add(nucleotideMenuItem);\r
 249     colourMenu.add(userDefinedColour);\r
 250     colourMenu.addSeparator();\r
 251     colourMenu.add(abovePIDColour);\r
 252     colourMenu.add(conservationMenuItem);\r
 253     noColourmenuItem.setText("None");\r
 254     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 255     {\r
 256       public void actionPerformed(ActionEvent e)\r
 257       {\r
 258         noColourmenuItem_actionPerformed(e);\r
 259       }\r
 260     });\r
 261 \r
 262     clustalColour.setText("Clustalx colours");\r
 263     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 264     {\r
 265       public void actionPerformed(ActionEvent e)\r
 266       {\r
 267         clustalColour_actionPerformed(e);\r
 268       }\r
 269     });\r
 270     zappoColour.setText("Zappo");\r
 271     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 272     {\r
 273       public void actionPerformed(ActionEvent e)\r
 274       {\r
 275         zappoColour_actionPerformed(e);\r
 276       }\r
 277     });\r
 278     taylorColour.setText("Taylor");\r
 279     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 280     {\r
 281       public void actionPerformed(ActionEvent e)\r
 282       {\r
 283         taylorColour_actionPerformed(e);\r
 284       }\r
 285     });\r
 286     hydrophobicityColour.setText("Hydrophobicity");\r
 287     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 288     {\r
 289       public void actionPerformed(ActionEvent e)\r
 290       {\r
 291         hydrophobicityColour_actionPerformed(e);\r
 292       }\r
 293     });\r
 294     helixColour.setText("Helix propensity");\r
 295     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 296     {\r
 297       public void actionPerformed(ActionEvent e)\r
 298       {\r
 299         helixColour_actionPerformed(e);\r
 300       }\r
 301     });\r
 302     strandColour.setText("Strand propensity");\r
 303     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 304     {\r
 305       public void actionPerformed(ActionEvent e)\r
 306       {\r
 307         strandColour_actionPerformed(e);\r
 308       }\r
 309     });\r
 310     turnColour.setText("Turn propensity");\r
 311     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 312     {\r
 313       public void actionPerformed(ActionEvent e)\r
 314       {\r
 315         turnColour_actionPerformed(e);\r
 316       }\r
 317     });\r
 318     buriedColour.setText("Buried Index");\r
 319     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 320     {\r
 321       public void actionPerformed(ActionEvent e)\r
 322       {\r
 323         buriedColour_actionPerformed(e);\r
 324       }\r
 325     });\r
 326     abovePIDColour.setText("Above % Identity");\r
 327     abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 328     {\r
 329       public void actionPerformed(ActionEvent e)\r
 330       {\r
 331         abovePIDColour_actionPerformed(e);\r
 332       }\r
 333     });\r
 334     userDefinedColour.setText("User Defined");\r
 335     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 336     {\r
 337       public void actionPerformed(ActionEvent e)\r
 338       {\r
 339         userDefinedColour_actionPerformed(e);\r
 340       }\r
 341     });\r
 342     PIDColour.setText("Percentage Identity");\r
 343     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 344     {\r
 345       public void actionPerformed(ActionEvent e)\r
 346       {\r
 347         PIDColour_actionPerformed(e);\r
 348       }\r
 349     });\r
 350     BLOSUM62Colour.setText("BLOSUM62");\r
 351     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 352     {\r
 353       public void actionPerformed(ActionEvent e)\r
 354       {\r
 355         BLOSUM62Colour_actionPerformed(e);\r
 356       }\r
 357     });\r
 358     conservationMenuItem.setText("Conservation");\r
 359    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 360    {\r
 361      public void actionPerformed(ActionEvent e)\r
 362      {\r
 363        conservationMenuItem_actionPerformed(e);\r
 364      }\r
 365    });\r
 366 \r
 367 \r
 368 \r
 369   }\r
 370 \r
 371   void refresh()\r
 372   {\r
 373     SequenceGroup sg = getGroup();\r
 374     SuperGroup superG = ap.av.alignment.getSuperGroup( sg );\r
 375     if( superG !=null)\r
 376       superG.setSuperGroupProperties( sg );\r
 377 \r
 378     ap.seqPanel.repaint();\r
 379   }\r
 380 \r
 381   protected void clustalColour_actionPerformed(ActionEvent e)\r
 382   {\r
 383     SequenceGroup sg = getGroup();\r
 384     sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());\r
 385     refresh();\r
 386   }\r
 387 \r
 388   protected void zappoColour_actionPerformed(ActionEvent e)\r
 389   {\r
 390     getGroup().cs = new ZappoColourScheme();\r
 391     refresh();\r
 392   }\r
 393 \r
 394   protected void taylorColour_actionPerformed(ActionEvent e)\r
 395   {\r
 396     getGroup().cs = new TaylorColourScheme();\r
 397     refresh();\r
 398   }\r
 399 \r
 400 \r
 401   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 402   {\r
 403     getGroup().cs = new HydrophobicColourScheme();\r
 404     refresh();\r
 405   }\r
 406 \r
 407   protected void helixColour_actionPerformed(ActionEvent e)\r
 408   {\r
 409     getGroup().cs = new HelixColourScheme();\r
 410     refresh();\r
 411   }\r
 412 \r
 413   protected void strandColour_actionPerformed(ActionEvent e)\r
 414   {\r
 415     getGroup().cs = new StrandColourScheme();\r
 416     refresh();\r
 417   }\r
 418 \r
 419   protected void turnColour_actionPerformed(ActionEvent e)\r
 420   {\r
 421     getGroup().cs = new TurnColourScheme();\r
 422     refresh();\r
 423   }\r
 424 \r
 425   protected void buriedColour_actionPerformed(ActionEvent e)\r
 426   {\r
 427     getGroup().cs = new BuriedColourScheme();\r
 428     refresh();\r
 429   }\r
 430 \r
 431   public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
 432   {\r
 433     getGroup().cs = new NucleotideColourScheme();\r
 434     refresh();\r
 435   }\r
 436 \r
 437 \r
 438 \r
 439   protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 440   {\r
 441     SequenceGroup sg = getGroup();\r
 442     if (abovePIDColour.isSelected())\r
 443     {\r
 444       sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 445                                                ap.av.alignment.getWidth()));\r
 446       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());\r
 447       if (sg.cs instanceof ResidueColourScheme)\r
 448         ( (ResidueColourScheme)sg. cs).setThreshold(threshold);\r
 449       else if (sg.cs instanceof ScoreColourScheme)\r
 450         ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
 451 \r
 452       SliderPanel.showPIDSlider();\r
 453 \r
 454 \r
 455     }\r
 456     else // remove PIDColouring\r
 457     {\r
 458       ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;\r
 459       rcs.setThreshold(0);\r
 460       sg.cs = rcs;\r
 461     }\r
 462 \r
 463     refresh();\r
 464 \r
 465   }\r
 466 \r
 467 \r
 468   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 469   {\r
 470     new UserDefinedColours( ap, getGroup());\r
 471   }\r
 472 \r
 473   protected void PIDColour_actionPerformed(ActionEvent e)\r
 474   {\r
 475     SequenceGroup sg = getGroup();\r
 476     sg.cs = new PIDColourScheme();\r
 477     sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 478                                                ap.av.alignment.getWidth()));\r
 479     refresh();\r
 480   }\r
 481 \r
 482   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 483   {\r
 484     SequenceGroup sg = getGroup();\r
 485 \r
 486     sg.cs = new Blosum62ColourScheme();\r
 487 \r
 488     sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 489                                                ap.av.alignment.getWidth()));\r
 490 \r
 491     refresh();\r
 492   }\r
 493 \r
 494 \r
 495   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 496   {\r
 497     getGroup().cs = null;\r
 498     refresh();\r
 499   }\r
 500 \r
 501   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 502   {\r
 503     SequenceGroup sg = getGroup();\r
 504 \r
 505     if(conservationMenuItem.isSelected())\r
 506     {\r
 507 \r
 508         Conservation c = new Conservation("Group",\r
 509                                           ResidueProperties.propHash, 3,\r
 510                                           sg.sequences, 0,\r
 511                                           ap.av.alignment.getWidth());\r
 512 \r
 513         c.calculate();\r
 514         c.verdict(false, ap.av.ConsPercGaps);\r
 515         ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 516 \r
 517 \r
 518       sg.cs = ccs;\r
 519 \r
 520       SliderPanel.setConservationSlider(ap, ccs, sg.getName());\r
 521       SliderPanel.showConservationSlider();\r
 522     }\r
 523     else // remove ConservationColouring\r
 524     {\r
 525         ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
 526         sg.cs = ccs.cs;\r
 527     }\r
 528 \r
 529      refresh();\r
 530   }\r
 531 \r
 532 \r
 533   protected void groupName_actionPerformed(ActionEvent e)\r
 534   {\r
 535     SequenceGroup sg = getGroup();\r
 536     String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);\r
 537     if(reply==null)\r
 538       return;\r
 539 \r
 540     sg.setName(reply);\r
 541     groupName.setText(reply);\r
 542   }\r
 543 \r
 544 \r
 545   protected void analyze_actionPerformed(ActionEvent e)\r
 546   {\r
 547      CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 548      JInternalFrame frame = new JInternalFrame();\r
 549      frame.setContentPane(cap);\r
 550      Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
 551      SequenceGroup sg = getGroup();\r
 552      StringBuffer sb = new StringBuffer();\r
 553 \r
 554      for(int i=0; i<sg.sequences.size(); i++)\r
 555      {\r
 556        Sequence tmp = (Sequence)sg.sequences.get(i);\r
 557        sb.append(  tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));\r
 558        sb.append("\n");\r
 559      }\r
 560 \r
 561      sb.append("Something amazing will happen soon");\r
 562      cap.setText( sb.toString() );\r
 563 \r
 564   }\r
 565 \r
 566   SequenceGroup getGroup()\r
 567   {\r
 568     SequenceGroup sg = ap.av.getSelectionGroup();\r
 569 \r
 570     // this method won't add a new group if it already exists\r
 571     ap.av.alignment.addGroup(sg);\r
 572 \r
 573     return sg;\r
 574   }\r
 575 \r
 576   void sequenceName_actionPerformed(ActionEvent e)\r
 577   {\r
 578     String id = sequence.getName();\r
 579     String s = (String)JOptionPane.showInternalInputDialog(\r
 580                 ap,\r
 581                 "Edit sequence name",\r
 582                 "Edit sequence name ("+sequence.getName()+")",\r
 583                 JOptionPane.PLAIN_MESSAGE,\r
 584                 null,\r
 585                 null,\r
 586                 id);\r
 587 \r
 588     if(s!=null)\r
 589     {\r
 590       sequence.setName(s);\r
 591       ap.repaint();\r
 592     }\r
 593 \r
 594   }\r
 595 \r
 596   void unGroupMenuItem_actionPerformed(ActionEvent e)\r
 597   {\r
 598      SequenceGroup sg = ap.av.getSelectionGroup();\r
 599      ap.av.alignment.deleteGroup(sg);\r
 600      ap.av.setSelectionGroup(null);\r
 601      ap.repaint();\r
 602   }\r
 603 \r
 604   void pdbMenuItem_actionPerformed(ActionEvent e)\r
 605   {\r
 606     if(sequence.getPDBId()==null)\r
 607       return;\r
 608 \r
 609     try\r
 610     {\r
 611       EBIFetchClient ebi = new EBIFetchClient();\r
 612       String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null);\r
 613 \r
 614       PDBfile pdb = new PDBfile(result);\r
 615 \r
 616       rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);\r
 617       JInternalFrame frame = new JInternalFrame();\r
 618       frame.setContentPane(rc);\r
 619       Desktop.addInternalFrame(frame,sequence.getName()+" "+ sequence.getPDBId(), 400, 400);\r
 620     }\r
 621     catch (Exception ex)\r
 622     {\r
 623       ex.printStackTrace();\r
 624     }\r
 625   }\r
 626 \r
 627   protected void outline_actionPerformed(ActionEvent e)\r
 628   {\r
 629     SequenceGroup sg = getGroup();\r
 630     Color col = JColorChooser.showDialog(this, "Select Outline Colour", Color.BLUE);\r
 631     if(col!=null)\r
 632       sg.setOutlineColour(col);\r
 633     ap.repaint();\r
 634   }\r
 635 \r
 636   public void showBoxes_actionPerformed(ActionEvent e)\r
 637   {\r
 638     getGroup().setDisplayBoxes(showBoxes.isSelected());\r
 639     refresh();\r
 640   }\r
 641 \r
 642   public void showText_actionPerformed(ActionEvent e)\r
 643   {\r
 644     getGroup().setDisplayText(showText.isSelected());\r
 645     refresh();\r
 646   }\r
 647 \r
 648   public void showColourText_actionPerformed(ActionEvent e)\r
 649   {\r
 650     getGroup().setColourText(showColourText.isSelected());\r
 651     refresh();\r
 652   }\r
 653 \r
 654 }\r