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 package jalview.gui;\r
  20 \r
  21 import MCview.*;\r
  22 \r
  23 import jalview.analysis.*;\r
  24 \r
  25 import jalview.datamodel.*;\r
  26 \r
  27 \r
  28 import jalview.schemes.*;\r
  29 \r
  30 import java.awt.*;\r
  31 import java.awt.event.*;\r
  32 \r
  33 import javax.swing.*;\r
  34 \r
  35 import java.util.Vector;\r
  36 import jalview.io.FormatAdapter;\r
  37 \r
  38 \r
  39 /**\r
  40  * DOCUMENT ME!\r
  41  *\r
  42  * @author $author$\r
  43  * @version $Revision$\r
  44  */\r
  45 public class PopupMenu extends JPopupMenu\r
  46 {\r
  47     JMenu groupMenu = new JMenu();\r
  48     JMenuItem groupName = new JMenuItem();\r
  49     protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  50     protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  51     protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  52     protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
  53     protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  54     protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  55     protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  56     protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  57     protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();\r
  58     protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  59     protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  60     protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  61     JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  62     protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  63     AlignmentPanel ap;\r
  64     JMenu sequenceMenu = new JMenu();\r
  65     JMenuItem sequenceName = new JMenuItem();\r
  66     Sequence sequence;\r
  67     JMenuItem unGroupMenuItem = new JMenuItem();\r
  68     JMenuItem outline = new JMenuItem();\r
  69     JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
  70     JMenu colourMenu = new JMenu();\r
  71     JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
  72     JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
  73     JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
  74   JMenu editMenu = new JMenu();\r
  75   JMenuItem cut = new JMenuItem();\r
  76   JMenuItem copy = new JMenuItem();\r
  77   JMenuItem upperCase = new JMenuItem();\r
  78   JMenuItem lowerCase = new JMenuItem();\r
  79   JMenuItem toggle = new JMenuItem();\r
  80   JMenu pdbMenu = new JMenu();\r
  81   JMenuItem pdbFromFile = new JMenuItem();\r
  82   JMenuItem enterPDB = new JMenuItem();\r
  83   JMenuItem discoverPDB = new JMenuItem();\r
  84   JMenu outputMenu = new JMenu();\r
  85 \r
  86   /**\r
  87      * Creates a new PopupMenu object.\r
  88      *\r
  89      * @param ap DOCUMENT ME!\r
  90      * @param seq DOCUMENT ME!\r
  91      */\r
  92     public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)\r
  93     {\r
  94         ///////////////////////////////////////////////////////////\r
  95         // If this is activated from the sequence panel, the user may want to\r
  96         // edit or annotate a particular residue. Therefore display the residue menu\r
  97         //\r
  98         // If from the IDPanel, we must display the sequence menu\r
  99         //////////////////////////////////////////////////////////\r
 100         this.ap = ap;\r
 101         sequence = seq;\r
 102 \r
 103         ButtonGroup colours = new ButtonGroup();\r
 104         colours.add(noColourmenuItem);\r
 105         colours.add(clustalColour);\r
 106         colours.add(zappoColour);\r
 107         colours.add(taylorColour);\r
 108         colours.add(hydrophobicityColour);\r
 109         colours.add(helixColour);\r
 110         colours.add(strandColour);\r
 111         colours.add(turnColour);\r
 112         colours.add(buriedColour);\r
 113         colours.add(abovePIDColour);\r
 114         colours.add(userDefinedColour);\r
 115         colours.add(PIDColour);\r
 116         colours.add(BLOSUM62Colour);\r
 117 \r
 118         for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-1; i++)\r
 119         {\r
 120           JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
 121                                          elementAt(\r
 122                                              i));\r
 123           item.addActionListener(new java.awt.event.ActionListener()\r
 124           {\r
 125             public void actionPerformed(ActionEvent e)\r
 126             {\r
 127               outputText_actionPerformed(e);\r
 128             }\r
 129           });\r
 130 \r
 131           outputMenu.add(item);\r
 132         }\r
 133 \r
 134 \r
 135         try\r
 136         {\r
 137             jbInit();\r
 138         }\r
 139         catch (Exception e)\r
 140         {\r
 141             e.printStackTrace();\r
 142         }\r
 143 \r
 144 \r
 145         if (seq != null)\r
 146         {\r
 147           int start = Math.max(sequence.getName().length()-15, 0);\r
 148           sequenceMenu.setText(sequence.getName().substring(start));\r
 149 \r
 150           JMenuItem menuItem;\r
 151           if( seq.getDatasetSequence().getPDBId() != null)\r
 152           {\r
 153             java.util.Enumeration e = seq.getDatasetSequence().getPDBId().\r
 154                 elements();\r
 155 \r
 156             while (e.hasMoreElements())\r
 157             {\r
 158               final PDBEntry pdb = (PDBEntry) e.nextElement();\r
 159 \r
 160               menuItem = new JMenuItem();\r
 161               menuItem.setText("View PDB entry: " + pdb.getId());\r
 162               menuItem.addActionListener(new java.awt.event.ActionListener()\r
 163               {\r
 164                 public void actionPerformed(ActionEvent e)\r
 165                 {\r
 166                   new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);\r
 167                 }\r
 168               });\r
 169               sequenceMenu.add(menuItem);\r
 170             }\r
 171           }\r
 172 \r
 173           menuItem = new JMenuItem("Hide Sequences");\r
 174           menuItem.addActionListener(new java.awt.event.ActionListener()\r
 175               {\r
 176                 public void actionPerformed(ActionEvent e)\r
 177                 {\r
 178                   hideSequences(false);\r
 179                 }\r
 180               });\r
 181           add(menuItem);\r
 182 \r
 183           if(ap.av.getSelectionGroup() !=null\r
 184              && ap.av.getSelectionGroup().getSize(false)>1)\r
 185           {\r
 186             menuItem = new JMenuItem("Represent Group with " + seq.getName());\r
 187             menuItem.addActionListener(new java.awt.event.ActionListener()\r
 188             {\r
 189               public void actionPerformed(ActionEvent e)\r
 190               {\r
 191                 hideSequences(true);\r
 192               }\r
 193             });\r
 194             sequenceMenu.add(menuItem);\r
 195           }\r
 196 \r
 197           if (ap.av.hasHiddenRows)\r
 198           {\r
 199             final int index = ap.av.alignment.findIndex(seq);\r
 200 \r
 201             if (ap.av.adjustForHiddenSeqs(index) -\r
 202                 ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
 203             {\r
 204               menuItem = new JMenuItem("Reveal Sequences");\r
 205               menuItem.addActionListener(new ActionListener()\r
 206               {\r
 207                 public void actionPerformed(ActionEvent e)\r
 208                 {\r
 209                   ap.av.showSequence(index);\r
 210                   ap.repaint();\r
 211                   if (ap.overviewPanel != null)\r
 212                     ap.overviewPanel.updateOverviewImage();\r
 213                 }\r
 214               });\r
 215               add(menuItem);\r
 216             }\r
 217 \r
 218             menuItem = new JMenuItem("Reveal All");\r
 219             menuItem.addActionListener(new ActionListener()\r
 220                 {\r
 221                   public void actionPerformed(ActionEvent e)\r
 222                   {\r
 223                     ap.av.showAllHiddenSeqs();\r
 224                     ap.repaint();\r
 225                     if (ap.overviewPanel != null)\r
 226                       ap.overviewPanel.updateOverviewImage();\r
 227                       }\r
 228                 });\r
 229 \r
 230             add(menuItem);\r
 231           }\r
 232 \r
 233 \r
 234         }\r
 235 \r
 236 \r
 237 \r
 238         SequenceGroup sg = ap.av.getSelectionGroup();\r
 239 \r
 240         if (sg != null)\r
 241         {\r
 242             groupName.setText(sg.getName());\r
 243 \r
 244             if (sg.cs instanceof ZappoColourScheme)\r
 245             {\r
 246                 zappoColour.setSelected(true);\r
 247             }\r
 248             else if (sg.cs instanceof TaylorColourScheme)\r
 249             {\r
 250                 taylorColour.setSelected(true);\r
 251             }\r
 252             else if (sg.cs instanceof PIDColourScheme)\r
 253             {\r
 254                 PIDColour.setSelected(true);\r
 255             }\r
 256             else if (sg.cs instanceof Blosum62ColourScheme)\r
 257             {\r
 258                 BLOSUM62Colour.setSelected(true);\r
 259             }\r
 260             else if (sg.cs instanceof UserColourScheme)\r
 261             {\r
 262                 userDefinedColour.setSelected(true);\r
 263             }\r
 264             else if (sg.cs instanceof HydrophobicColourScheme)\r
 265             {\r
 266                 hydrophobicityColour.setSelected(true);\r
 267             }\r
 268             else if (sg.cs instanceof HelixColourScheme)\r
 269             {\r
 270                 helixColour.setSelected(true);\r
 271             }\r
 272             else if (sg.cs instanceof StrandColourScheme)\r
 273             {\r
 274                 strandColour.setSelected(true);\r
 275             }\r
 276             else if (sg.cs instanceof TurnColourScheme)\r
 277             {\r
 278                 turnColour.setSelected(true);\r
 279             }\r
 280             else if (sg.cs instanceof BuriedColourScheme)\r
 281             {\r
 282                 buriedColour.setSelected(true);\r
 283             }\r
 284             else if (sg.cs instanceof ClustalxColourScheme)\r
 285             {\r
 286                 clustalColour.setSelected(true);\r
 287             }\r
 288             else\r
 289             {\r
 290                 noColourmenuItem.setSelected(true);\r
 291             }\r
 292 \r
 293             if (sg.cs!=null && sg.cs.conservationApplied())\r
 294             {\r
 295                 conservationMenuItem.setSelected(true);\r
 296             }\r
 297 \r
 298             showText.setSelected(sg.getDisplayText());\r
 299             showColourText.setSelected(sg.getColourText());\r
 300             showBoxes.setSelected(sg.getDisplayBoxes());\r
 301         }\r
 302         else\r
 303         {\r
 304           groupMenu.setVisible(false);\r
 305           editMenu.setVisible(false);\r
 306         }\r
 307 \r
 308         if (!ap.av.alignment.getGroups().contains(sg))\r
 309         {\r
 310             unGroupMenuItem.setVisible(false);\r
 311         }\r
 312 \r
 313 \r
 314         if (seq == null)\r
 315         {\r
 316             sequenceMenu.setVisible(false);\r
 317             pdbMenu.setVisible(false);\r
 318         }\r
 319 \r
 320         if(links != null && links.size()>0)\r
 321         {\r
 322           JMenu linkMenu = new JMenu("Link");\r
 323           JMenuItem item;\r
 324           for(int i=0; i<links.size(); i++)\r
 325           {\r
 326             String link = links.elementAt(i).toString();\r
 327             final String label = link.substring(0, link.indexOf("|"));\r
 328             item = new JMenuItem(label);\r
 329             final String url;\r
 330 \r
 331             if (link.indexOf("$SEQUENCE_ID$") > -1)\r
 332             {\r
 333               String id = seq.getName();\r
 334               if (id.indexOf("|") > -1)\r
 335                 id = id.substring(id.lastIndexOf("|") + 1);\r
 336 \r
 337               url = link.substring(link.indexOf("|") + 1,\r
 338                                    link.indexOf("$SEQUENCE_ID$"))\r
 339                   + id +\r
 340                   link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
 341             }\r
 342             else\r
 343               url = link.substring(link.lastIndexOf("|")+1);\r
 344 \r
 345 \r
 346             item.addActionListener(new java.awt.event.ActionListener()\r
 347             {\r
 348                 public void actionPerformed(ActionEvent e)\r
 349                 {\r
 350                     showLink(url);\r
 351                 }\r
 352             });\r
 353 \r
 354             linkMenu.add(item);\r
 355           }\r
 356           if(sequence!=null)\r
 357             sequenceMenu.add(linkMenu);\r
 358           else\r
 359             add(linkMenu);\r
 360         }\r
 361     }\r
 362 \r
 363 \r
 364     /**\r
 365      * DOCUMENT ME!\r
 366      *\r
 367      * @throws Exception DOCUMENT ME!\r
 368      */\r
 369     private void jbInit() throws Exception\r
 370     {\r
 371         groupMenu.setText("Group");\r
 372         groupMenu.setText("Selection");\r
 373         groupName.setText("Name");\r
 374         groupName.addActionListener(new java.awt.event.ActionListener()\r
 375             {\r
 376                 public void actionPerformed(ActionEvent e)\r
 377                 {\r
 378                     groupName_actionPerformed(e);\r
 379                 }\r
 380             });\r
 381         sequenceMenu.setText("Sequence");\r
 382         sequenceName.setText("Edit Name/Description");\r
 383         sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 384             {\r
 385                 public void actionPerformed(ActionEvent e)\r
 386                 {\r
 387                     sequenceName_actionPerformed(e);\r
 388                 }\r
 389             });\r
 390         PIDColour.setFocusPainted(false);\r
 391         unGroupMenuItem.setText("Remove Group");\r
 392         unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 393             {\r
 394                 public void actionPerformed(ActionEvent e)\r
 395                 {\r
 396                     unGroupMenuItem_actionPerformed(e);\r
 397                 }\r
 398             });\r
 399 \r
 400         outline.setText("Border colour");\r
 401         outline.addActionListener(new java.awt.event.ActionListener()\r
 402             {\r
 403                 public void actionPerformed(ActionEvent e)\r
 404                 {\r
 405                     outline_actionPerformed(e);\r
 406                 }\r
 407             });\r
 408         nucleotideMenuItem.setText("Nucleotide");\r
 409         nucleotideMenuItem.addActionListener(new ActionListener()\r
 410             {\r
 411                 public void actionPerformed(ActionEvent e)\r
 412                 {\r
 413                     nucleotideMenuItem_actionPerformed(e);\r
 414                 }\r
 415             });\r
 416         colourMenu.setText("Group Colour");\r
 417         showBoxes.setText("Boxes");\r
 418         showBoxes.setState(true);\r
 419         showBoxes.addActionListener(new ActionListener()\r
 420             {\r
 421                 public void actionPerformed(ActionEvent e)\r
 422                 {\r
 423                     showBoxes_actionPerformed(e);\r
 424                 }\r
 425             });\r
 426         showText.setText("Text");\r
 427         showText.setState(true);\r
 428         showText.addActionListener(new ActionListener()\r
 429             {\r
 430                 public void actionPerformed(ActionEvent e)\r
 431                 {\r
 432                     showText_actionPerformed(e);\r
 433                 }\r
 434             });\r
 435         showColourText.setText("Colour Text");\r
 436         showColourText.addActionListener(new ActionListener()\r
 437             {\r
 438                 public void actionPerformed(ActionEvent e)\r
 439                 {\r
 440                     showColourText_actionPerformed(e);\r
 441                 }\r
 442             });\r
 443     editMenu.setText("Edit");\r
 444     cut.setText("Cut");\r
 445     cut.addActionListener(new ActionListener()\r
 446     {\r
 447       public void actionPerformed(ActionEvent e)\r
 448       {\r
 449         cut_actionPerformed(e);\r
 450       }\r
 451     });\r
 452     upperCase.setText("To Upper Case");\r
 453     upperCase.addActionListener(new ActionListener()\r
 454     {\r
 455       public void actionPerformed(ActionEvent e)\r
 456       {\r
 457         upperCase_actionPerformed(e);\r
 458       }\r
 459     });\r
 460     copy.setText("Copy");\r
 461     copy.addActionListener(new ActionListener()\r
 462     {\r
 463       public void actionPerformed(ActionEvent e)\r
 464       {\r
 465         copy_actionPerformed(e);\r
 466       }\r
 467     });\r
 468     lowerCase.setText("To Lower Case");\r
 469     lowerCase.addActionListener(new ActionListener()\r
 470     {\r
 471       public void actionPerformed(ActionEvent e)\r
 472       {\r
 473         lowerCase_actionPerformed(e);\r
 474       }\r
 475     });\r
 476     toggle.setText("Toggle Case");\r
 477     toggle.addActionListener(new ActionListener()\r
 478     {\r
 479       public void actionPerformed(ActionEvent e)\r
 480       {\r
 481         toggle_actionPerformed(e);\r
 482       }\r
 483     });\r
 484     pdbMenu.setText("Associate Structure with Sequence");\r
 485     pdbFromFile.setText("From File");\r
 486     pdbFromFile.addActionListener(new ActionListener()\r
 487     {\r
 488       public void actionPerformed(ActionEvent e)\r
 489       {\r
 490         pdbFromFile_actionPerformed(e);\r
 491       }\r
 492     });\r
 493     enterPDB.setText("Enter PDB Id");\r
 494     enterPDB.addActionListener(new ActionListener()\r
 495     {\r
 496       public void actionPerformed(ActionEvent e)\r
 497       {\r
 498         enterPDB_actionPerformed(e);\r
 499       }\r
 500     });\r
 501     discoverPDB.setText("Discover PDB ids");\r
 502     discoverPDB.addActionListener(new ActionListener()\r
 503     {\r
 504       public void actionPerformed(ActionEvent e)\r
 505       {\r
 506         discoverPDB_actionPerformed(e);\r
 507       }\r
 508     });\r
 509     outputMenu.setText("Output to Textbox...");\r
 510     add(groupMenu);\r
 511 \r
 512     add(sequenceMenu);\r
 513     groupMenu.add(editMenu);\r
 514     groupMenu.add(outputMenu);\r
 515     groupMenu.addSeparator();\r
 516     groupMenu.add(groupName);\r
 517     groupMenu.add(unGroupMenuItem);\r
 518         groupMenu.add(colourMenu);\r
 519     groupMenu.add(showBoxes);\r
 520         groupMenu.add(showText);\r
 521         groupMenu.add(showColourText);\r
 522     groupMenu.add(outline);\r
 523         sequenceMenu.add(sequenceName);\r
 524     sequenceMenu.add(pdbMenu);\r
 525     colourMenu.add(noColourmenuItem);\r
 526         colourMenu.add(clustalColour);\r
 527         colourMenu.add(BLOSUM62Colour);\r
 528         colourMenu.add(PIDColour);\r
 529         colourMenu.add(zappoColour);\r
 530         colourMenu.add(taylorColour);\r
 531         colourMenu.add(hydrophobicityColour);\r
 532         colourMenu.add(helixColour);\r
 533         colourMenu.add(strandColour);\r
 534         colourMenu.add(turnColour);\r
 535         colourMenu.add(buriedColour);\r
 536         colourMenu.add(nucleotideMenuItem);\r
 537         colourMenu.add(userDefinedColour);\r
 538 \r
 539         if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 540         {\r
 541           java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 542               getUserColourSchemes().keys();\r
 543 \r
 544           while (userColours.hasMoreElements())\r
 545           {\r
 546             JMenuItem item = new JMenuItem(userColours.\r
 547                 nextElement().toString());\r
 548             item.addActionListener(new ActionListener()\r
 549             {\r
 550               public void actionPerformed(ActionEvent evt)\r
 551               {\r
 552                 userDefinedColour_actionPerformed(evt);\r
 553               }\r
 554             });\r
 555             colourMenu.add(item);\r
 556           }\r
 557         }\r
 558 \r
 559 \r
 560         colourMenu.addSeparator();\r
 561         colourMenu.add(abovePIDColour);\r
 562         colourMenu.add(conservationMenuItem);\r
 563     editMenu.add(copy);\r
 564     editMenu.add(cut);\r
 565     editMenu.add(upperCase);\r
 566     editMenu.add(lowerCase);\r
 567     editMenu.add(toggle);\r
 568     pdbMenu.add(pdbFromFile);\r
 569     pdbMenu.add(enterPDB);\r
 570     pdbMenu.add(discoverPDB);\r
 571     noColourmenuItem.setText("None");\r
 572         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 573             {\r
 574                 public void actionPerformed(ActionEvent e)\r
 575                 {\r
 576                     noColourmenuItem_actionPerformed(e);\r
 577                 }\r
 578             });\r
 579 \r
 580         clustalColour.setText("Clustalx colours");\r
 581         clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 582             {\r
 583                 public void actionPerformed(ActionEvent e)\r
 584                 {\r
 585                     clustalColour_actionPerformed(e);\r
 586                 }\r
 587             });\r
 588         zappoColour.setText("Zappo");\r
 589         zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 590             {\r
 591                 public void actionPerformed(ActionEvent e)\r
 592                 {\r
 593                     zappoColour_actionPerformed(e);\r
 594                 }\r
 595             });\r
 596         taylorColour.setText("Taylor");\r
 597         taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 598             {\r
 599                 public void actionPerformed(ActionEvent e)\r
 600                 {\r
 601                     taylorColour_actionPerformed(e);\r
 602                 }\r
 603             });\r
 604         hydrophobicityColour.setText("Hydrophobicity");\r
 605         hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 606             {\r
 607                 public void actionPerformed(ActionEvent e)\r
 608                 {\r
 609                     hydrophobicityColour_actionPerformed(e);\r
 610                 }\r
 611             });\r
 612         helixColour.setText("Helix propensity");\r
 613         helixColour.addActionListener(new java.awt.event.ActionListener()\r
 614             {\r
 615                 public void actionPerformed(ActionEvent e)\r
 616                 {\r
 617                     helixColour_actionPerformed(e);\r
 618                 }\r
 619             });\r
 620         strandColour.setText("Strand propensity");\r
 621         strandColour.addActionListener(new java.awt.event.ActionListener()\r
 622             {\r
 623                 public void actionPerformed(ActionEvent e)\r
 624                 {\r
 625                     strandColour_actionPerformed(e);\r
 626                 }\r
 627             });\r
 628         turnColour.setText("Turn propensity");\r
 629         turnColour.addActionListener(new java.awt.event.ActionListener()\r
 630             {\r
 631                 public void actionPerformed(ActionEvent e)\r
 632                 {\r
 633                     turnColour_actionPerformed(e);\r
 634                 }\r
 635             });\r
 636         buriedColour.setText("Buried Index");\r
 637         buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 638             {\r
 639                 public void actionPerformed(ActionEvent e)\r
 640                 {\r
 641                     buriedColour_actionPerformed(e);\r
 642                 }\r
 643             });\r
 644         abovePIDColour.setText("Above % Identity");\r
 645         abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 646             {\r
 647                 public void actionPerformed(ActionEvent e)\r
 648                 {\r
 649                     abovePIDColour_actionPerformed(e);\r
 650                 }\r
 651             });\r
 652         userDefinedColour.setText("User Defined...");\r
 653         userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 654             {\r
 655                 public void actionPerformed(ActionEvent e)\r
 656                 {\r
 657                     userDefinedColour_actionPerformed(e);\r
 658                 }\r
 659             });\r
 660         PIDColour.setText("Percentage Identity");\r
 661         PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 662             {\r
 663                 public void actionPerformed(ActionEvent e)\r
 664                 {\r
 665                     PIDColour_actionPerformed(e);\r
 666                 }\r
 667             });\r
 668         BLOSUM62Colour.setText("BLOSUM62");\r
 669         BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 670             {\r
 671                 public void actionPerformed(ActionEvent e)\r
 672                 {\r
 673                     BLOSUM62Colour_actionPerformed(e);\r
 674                 }\r
 675             });\r
 676         conservationMenuItem.setText("Conservation");\r
 677         conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 678             {\r
 679                 public void actionPerformed(ActionEvent e)\r
 680                 {\r
 681                     conservationMenuItem_actionPerformed(e);\r
 682                 }\r
 683             });\r
 684     }\r
 685 \r
 686     /**\r
 687      * DOCUMENT ME!\r
 688      */\r
 689     void refresh()\r
 690     {\r
 691         if (ap.overviewPanel != null)\r
 692           ap.overviewPanel.updateOverviewImage();\r
 693 \r
 694         ap.seqPanel.repaint();\r
 695     }\r
 696 \r
 697     /**\r
 698      * DOCUMENT ME!\r
 699      *\r
 700      * @param e DOCUMENT ME!\r
 701      */\r
 702     protected void clustalColour_actionPerformed(ActionEvent e)\r
 703     {\r
 704         SequenceGroup sg = getGroup();\r
 705         sg.cs = new ClustalxColourScheme(sg.getSequences(true),\r
 706                 ap.av.alignment.getWidth());\r
 707         refresh();\r
 708     }\r
 709 \r
 710     /**\r
 711      * DOCUMENT ME!\r
 712      *\r
 713      * @param e DOCUMENT ME!\r
 714      */\r
 715     protected void zappoColour_actionPerformed(ActionEvent e)\r
 716     {\r
 717         getGroup().cs = new ZappoColourScheme();\r
 718         refresh();\r
 719     }\r
 720 \r
 721     /**\r
 722      * DOCUMENT ME!\r
 723      *\r
 724      * @param e DOCUMENT ME!\r
 725      */\r
 726     protected void taylorColour_actionPerformed(ActionEvent e)\r
 727     {\r
 728         getGroup().cs = new TaylorColourScheme();\r
 729         refresh();\r
 730     }\r
 731 \r
 732     /**\r
 733      * DOCUMENT ME!\r
 734      *\r
 735      * @param e DOCUMENT ME!\r
 736      */\r
 737     protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 738     {\r
 739         getGroup().cs = new HydrophobicColourScheme();\r
 740         refresh();\r
 741     }\r
 742 \r
 743     /**\r
 744      * DOCUMENT ME!\r
 745      *\r
 746      * @param e DOCUMENT ME!\r
 747      */\r
 748     protected void helixColour_actionPerformed(ActionEvent e)\r
 749     {\r
 750         getGroup().cs = new HelixColourScheme();\r
 751         refresh();\r
 752     }\r
 753 \r
 754     /**\r
 755      * DOCUMENT ME!\r
 756      *\r
 757      * @param e DOCUMENT ME!\r
 758      */\r
 759     protected void strandColour_actionPerformed(ActionEvent e)\r
 760     {\r
 761         getGroup().cs = new StrandColourScheme();\r
 762         refresh();\r
 763     }\r
 764 \r
 765     /**\r
 766      * DOCUMENT ME!\r
 767      *\r
 768      * @param e DOCUMENT ME!\r
 769      */\r
 770     protected void turnColour_actionPerformed(ActionEvent e)\r
 771     {\r
 772         getGroup().cs = new TurnColourScheme();\r
 773         refresh();\r
 774     }\r
 775 \r
 776     /**\r
 777      * DOCUMENT ME!\r
 778      *\r
 779      * @param e DOCUMENT ME!\r
 780      */\r
 781     protected void buriedColour_actionPerformed(ActionEvent e)\r
 782     {\r
 783         getGroup().cs = new BuriedColourScheme();\r
 784         refresh();\r
 785     }\r
 786 \r
 787     /**\r
 788      * DOCUMENT ME!\r
 789      *\r
 790      * @param e DOCUMENT ME!\r
 791      */\r
 792     public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
 793     {\r
 794         getGroup().cs = new NucleotideColourScheme();\r
 795         refresh();\r
 796     }\r
 797 \r
 798     /**\r
 799      * DOCUMENT ME!\r
 800      *\r
 801      * @param e DOCUMENT ME!\r
 802      */\r
 803     protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 804     {\r
 805         SequenceGroup sg = getGroup();\r
 806         if(sg.cs==null)\r
 807           return;\r
 808 \r
 809         if (abovePIDColour.isSelected())\r
 810         {\r
 811             sg.cs.setConsensus(AAFrequency.calculate(\r
 812                     sg.getSequences(true), 0,\r
 813                     ap.av.alignment.getWidth()));\r
 814 \r
 815             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
 816                     getGroup().getName());\r
 817 \r
 818            sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
 819 \r
 820             SliderPanel.showPIDSlider();\r
 821         }\r
 822         else // remove PIDColouring\r
 823         {\r
 824             sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
 825         }\r
 826 \r
 827         refresh();\r
 828     }\r
 829 \r
 830     /**\r
 831      * DOCUMENT ME!\r
 832      *\r
 833      * @param e DOCUMENT ME!\r
 834      */\r
 835     protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 836     {\r
 837        SequenceGroup sg = getGroup();\r
 838 \r
 839        if (e.getActionCommand().equals("User Defined..."))\r
 840          new UserDefinedColours(ap, sg);\r
 841        else\r
 842        {\r
 843          UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
 844              getUserColourSchemes().get(e.getActionCommand());\r
 845 \r
 846          sg.cs = udc;\r
 847        }\r
 848      }\r
 849     /**\r
 850      * DOCUMENT ME!\r
 851      *\r
 852      * @param e DOCUMENT ME!\r
 853      */\r
 854     protected void PIDColour_actionPerformed(ActionEvent e)\r
 855     {\r
 856         SequenceGroup sg = getGroup();\r
 857         sg.cs = new PIDColourScheme();\r
 858         sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
 859                 ap.av.alignment.getWidth()));\r
 860         refresh();\r
 861     }\r
 862 \r
 863     /**\r
 864      * DOCUMENT ME!\r
 865      *\r
 866      * @param e DOCUMENT ME!\r
 867      */\r
 868     protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 869     {\r
 870         SequenceGroup sg = getGroup();\r
 871 \r
 872         sg.cs = new Blosum62ColourScheme();\r
 873 \r
 874         sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
 875                 ap.av.alignment.getWidth()));\r
 876 \r
 877         refresh();\r
 878     }\r
 879 \r
 880     /**\r
 881      * DOCUMENT ME!\r
 882      *\r
 883      * @param e DOCUMENT ME!\r
 884      */\r
 885     protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 886     {\r
 887         getGroup().cs = null;\r
 888         refresh();\r
 889     }\r
 890 \r
 891     /**\r
 892      * DOCUMENT ME!\r
 893      *\r
 894      * @param e DOCUMENT ME!\r
 895      */\r
 896     protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 897     {\r
 898         SequenceGroup sg = getGroup();\r
 899         if(sg.cs==null)\r
 900           return;\r
 901 \r
 902         if (conservationMenuItem.isSelected())\r
 903         {\r
 904             Conservation c = new Conservation("Group",\r
 905                     ResidueProperties.propHash, 3,\r
 906                     sg.getSequences(true), 0,\r
 907                     ap.av.alignment.getWidth());\r
 908 \r
 909             c.calculate();\r
 910             c.verdict(false, ap.av.ConsPercGaps);\r
 911 \r
 912             sg.cs.setConservation(c);\r
 913 \r
 914             SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
 915             SliderPanel.showConservationSlider();\r
 916         }\r
 917         else // remove ConservationColouring\r
 918         {\r
 919             sg.cs.setConservation(null);\r
 920         }\r
 921 \r
 922         refresh();\r
 923     }\r
 924 \r
 925     /**\r
 926      * DOCUMENT ME!\r
 927      *\r
 928      * @param e DOCUMENT ME!\r
 929      */\r
 930     protected void groupName_actionPerformed(ActionEvent e)\r
 931     {\r
 932         SequenceGroup sg = getGroup();\r
 933         String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
 934                 "Enter new group name", "Edit group name",\r
 935                 JOptionPane.QUESTION_MESSAGE);\r
 936 \r
 937         if (reply == null)\r
 938         {\r
 939             return;\r
 940         }\r
 941 \r
 942         sg.setName(reply);\r
 943         groupName.setText(reply);\r
 944     }\r
 945 \r
 946     /**\r
 947      * DOCUMENT ME!\r
 948      *\r
 949      * @param e DOCUMENT ME!\r
 950      */\r
 951     protected void analyze_actionPerformed(ActionEvent e)\r
 952     {\r
 953         CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 954         JInternalFrame frame = new JInternalFrame();\r
 955         frame.setContentPane(cap);\r
 956         Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
 957 \r
 958         SequenceGroup sg = getGroup();\r
 959         StringBuffer sb = new StringBuffer();\r
 960 \r
 961         for (int i = 0; i < sg.getSize(false); i++)\r
 962         {\r
 963             Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i);\r
 964             sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
 965             sb.append("\n");\r
 966         }\r
 967 \r
 968         sb.append("Something amazing will happen soon");\r
 969         cap.setText(sb.toString());\r
 970     }\r
 971 \r
 972     /**\r
 973      * DOCUMENT ME!\r
 974      *\r
 975      * @return DOCUMENT ME!\r
 976      */\r
 977     SequenceGroup getGroup()\r
 978     {\r
 979         SequenceGroup sg = ap.av.getSelectionGroup();\r
 980       // this method won't add a new group if it already exists\r
 981         if(sg!=null)\r
 982           ap.av.alignment.addGroup(sg);\r
 983 \r
 984         return sg;\r
 985     }\r
 986 \r
 987     /**\r
 988      * DOCUMENT ME!\r
 989      *\r
 990      * @param e DOCUMENT ME!\r
 991      */\r
 992     void sequenceName_actionPerformed(ActionEvent e)\r
 993     {\r
 994       JLabel idlabel = new JLabel(  "       Sequence Name ");\r
 995       JLabel desclabel = new JLabel("Sequence Description ");\r
 996       idlabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
 997       desclabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
 998       JTextField id = new JTextField(sequence.getName(), 40);\r
 999       JTextField description = new JTextField(sequence.getDescription(), 40);\r
1000       JPanel panel = new JPanel(new BorderLayout());\r
1001       JPanel panel2 = new JPanel(new BorderLayout());\r
1002       panel2.add(idlabel, BorderLayout.WEST);\r
1003       panel2.add(id, BorderLayout.CENTER);\r
1004       panel.add(panel2, BorderLayout.NORTH);\r
1005       panel2 = new JPanel(new BorderLayout());\r
1006       panel2.add(desclabel, BorderLayout.WEST);\r
1007       panel2.add(description, BorderLayout.CENTER);\r
1008       panel.add(panel2, BorderLayout.SOUTH);\r
1009 \r
1010 \r
1011        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
1012           panel, "Edit Sequence Name/Description",\r
1013           JOptionPane.OK_CANCEL_OPTION );\r
1014 \r
1015 \r
1016         if (reply != JOptionPane.OK_OPTION )\r
1017         {\r
1018             return;\r
1019         }\r
1020 \r
1021         String s = id.getText();\r
1022 \r
1023         if (s != null)\r
1024         {\r
1025             if (s.indexOf(" ") > -1)\r
1026             {\r
1027                 JOptionPane.showMessageDialog(ap,\r
1028                     "Spaces have been converted to \"_\"",\r
1029                     "No spaces allowed in Sequence Name",\r
1030                     JOptionPane.WARNING_MESSAGE);\r
1031             }\r
1032 \r
1033             s = s.replace(' ', '_');\r
1034             sequence.getDatasetSequence().setName(s);\r
1035             sequence.setName(s);\r
1036             ap.repaint();\r
1037         }\r
1038 \r
1039         sequence.getDatasetSequence().setDescription(description.getText());\r
1040         sequence.setDescription(description.getText());\r
1041     }\r
1042 \r
1043     /**\r
1044      * DOCUMENT ME!\r
1045      *\r
1046      * @param e DOCUMENT ME!\r
1047      */\r
1048     void unGroupMenuItem_actionPerformed(ActionEvent e)\r
1049     {\r
1050         SequenceGroup sg = ap.av.getSelectionGroup();\r
1051         ap.av.alignment.deleteGroup(sg);\r
1052         ap.av.setSelectionGroup(null);\r
1053         refresh();\r
1054     }\r
1055 \r
1056 \r
1057     /**\r
1058      * DOCUMENT ME!\r
1059      *\r
1060      * @param e DOCUMENT ME!\r
1061      */\r
1062     protected void outline_actionPerformed(ActionEvent e)\r
1063     {\r
1064         SequenceGroup sg = getGroup();\r
1065         Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
1066                 Color.BLUE);\r
1067 \r
1068         if (col != null)\r
1069         {\r
1070             sg.setOutlineColour(col);\r
1071         }\r
1072 \r
1073         refresh();\r
1074     }\r
1075 \r
1076     /**\r
1077      * DOCUMENT ME!\r
1078      *\r
1079      * @param e DOCUMENT ME!\r
1080      */\r
1081     public void showBoxes_actionPerformed(ActionEvent e)\r
1082     {\r
1083         getGroup().setDisplayBoxes(showBoxes.isSelected());\r
1084         refresh();\r
1085     }\r
1086 \r
1087     /**\r
1088      * DOCUMENT ME!\r
1089      *\r
1090      * @param e DOCUMENT ME!\r
1091      */\r
1092     public void showText_actionPerformed(ActionEvent e)\r
1093     {\r
1094         getGroup().setDisplayText(showText.isSelected());\r
1095         refresh();\r
1096     }\r
1097 \r
1098     /**\r
1099      * DOCUMENT ME!\r
1100      *\r
1101      * @param e DOCUMENT ME!\r
1102      */\r
1103     public void showColourText_actionPerformed(ActionEvent e)\r
1104     {\r
1105         getGroup().setColourText(showColourText.isSelected());\r
1106         refresh();\r
1107     }\r
1108 \r
1109     public void showLink(String url)\r
1110     {\r
1111       try\r
1112       {\r
1113         jalview.util.BrowserLauncher.openURL(url);\r
1114       }\r
1115       catch (Exception ex)\r
1116       {\r
1117         JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
1118             "Unixers: Couldn't find default web browser."\r
1119            +"\nAdd the full path to your browser in Preferences.",\r
1120            "Web browser not found", JOptionPane.WARNING_MESSAGE );\r
1121 \r
1122 \r
1123         ex.printStackTrace();\r
1124       }\r
1125     }\r
1126 \r
1127     void hideSequences(boolean representGroup)\r
1128     {\r
1129       SequenceGroup sg = ap.av.getSelectionGroup();\r
1130       if(sg==null || sg.getSize(false)<1)\r
1131       {\r
1132         ap.av.hideSequence(sequence);\r
1133         return;\r
1134       }\r
1135 \r
1136         int index = 0;\r
1137         while(index < sg.getSize(false))\r
1138         {\r
1139           if(representGroup && sg.getSequenceAt(index)!=sequence)\r
1140           {\r
1141             sequence.addHiddenSequence(sg.getSequenceAt(index));\r
1142             ap.av.hideSequence(sg.getSequenceAt(index));\r
1143           }\r
1144           else if(!representGroup)\r
1145           {\r
1146             ap.av.hideSequence(sg.getSequenceAt(index));\r
1147           }\r
1148           index ++;\r
1149         }\r
1150 \r
1151         ap.av.setSelectionGroup(null);\r
1152         ap.repaint();\r
1153         refresh();\r
1154     }\r
1155 \r
1156   public void copy_actionPerformed(ActionEvent e)\r
1157   {\r
1158     ap.alignFrame.copy_actionPerformed(null);\r
1159   }\r
1160 \r
1161   public void cut_actionPerformed(ActionEvent e)\r
1162   {\r
1163     ap.alignFrame.cut_actionPerformed(null);\r
1164   }\r
1165 \r
1166   public void upperCase_actionPerformed(ActionEvent e)\r
1167   {\r
1168     SequenceGroup sg = ap.av.getSelectionGroup();\r
1169     if(sg==null)\r
1170       return;\r
1171 \r
1172     for(int g=0; g<sg.getSize(true); g++)\r
1173     {\r
1174     ( (SequenceI)sg.getSequences(true).elementAt(g))\r
1175         .changeCase(true, sg.getStartRes(), sg.getEndRes()+1);\r
1176     }\r
1177     ap.repaint();\r
1178   }\r
1179 \r
1180   public void lowerCase_actionPerformed(ActionEvent e)\r
1181   {\r
1182     SequenceGroup sg = ap.av.getSelectionGroup();\r
1183     if(sg==null)\r
1184       return;\r
1185 \r
1186     for(int g=0; g<sg.getSize(true); g++)\r
1187     {\r
1188        ( (SequenceI)sg.getSequences(true).elementAt(g))\r
1189            .changeCase(false, sg.getStartRes(), sg.getEndRes()+1);\r
1190     }\r
1191     ap.repaint();\r
1192   }\r
1193 \r
1194   public void toggle_actionPerformed(ActionEvent e)\r
1195   {\r
1196     SequenceGroup sg = ap.av.getSelectionGroup();\r
1197     if (sg == null)\r
1198       return;\r
1199 \r
1200     for (int g = 0; g < sg.getSize(true); g++)\r
1201     {\r
1202       ( (SequenceI)sg.getSequences(true).elementAt(g))\r
1203           .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);\r
1204     }\r
1205 \r
1206     ap.repaint();\r
1207   }\r
1208 \r
1209   public void outputText_actionPerformed(ActionEvent e)\r
1210   {\r
1211     CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
1212     Desktop.addInternalFrame(cap,\r
1213                              "Alignment output - " + e.getActionCommand(), 600,\r
1214                              500);\r
1215 \r
1216     String [] omitHidden = null;\r
1217 \r
1218     if(ap.av.hasHiddenColumns)\r
1219     {\r
1220       System.out.println("PROMPT USER HERE");\r
1221       omitHidden = ap.av.getViewAsString(true);\r
1222     }\r
1223 \r
1224     cap.setText(new FormatAdapter().formatSequences(\r
1225         e.getActionCommand(),\r
1226         ap.av.getSelectionAsNewSequence(),\r
1227         omitHidden));\r
1228   }\r
1229 \r
1230 \r
1231   public void pdbFromFile_actionPerformed(ActionEvent e)\r
1232   {\r
1233      jalview.io.JalviewFileChooser chooser\r
1234          = new jalview.io.JalviewFileChooser(jalview.bin.Cache.\r
1235          getProperty(\r
1236              "LAST_DIRECTORY"));\r
1237      chooser.setFileView(new jalview.io.JalviewFileView());\r
1238      chooser.setDialogTitle("Select a PDB file");\r
1239      chooser.setToolTipText("Load a PDB file");\r
1240 \r
1241      int value = chooser.showOpenDialog(null);\r
1242 \r
1243      if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
1244      {\r
1245        PDBEntry entry = new PDBEntry();\r
1246        String choice = chooser.getSelectedFile().getPath();\r
1247        jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1248        try\r
1249        {\r
1250          MCview.PDBfile pdbfile = new MCview.PDBfile(choice,\r
1251                                        jalview.io.AppletFormatAdapter.FILE);\r
1252 \r
1253          if (pdbfile.id == null)\r
1254          {\r
1255            String reply = JOptionPane.showInternalInputDialog(\r
1256                Desktop.desktop,\r
1257                "Couldn't find a PDB id in the file supplied."\r
1258                + "Please enter an Id to identify this structure.",\r
1259                "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);\r
1260            if (reply == null)\r
1261              return;\r
1262 \r
1263            entry.setId(reply);\r
1264          }\r
1265          else\r
1266            entry.setId(pdbfile.id);\r
1267        }\r
1268        catch (java.io.IOException ex)\r
1269        {\r
1270          ex.printStackTrace();\r
1271        }\r
1272 \r
1273        entry.setFile(choice);\r
1274        sequence.getDatasetSequence().addPDBId(entry);\r
1275      }\r
1276 \r
1277   }\r
1278 \r
1279   public void enterPDB_actionPerformed(ActionEvent e)\r
1280   {\r
1281     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
1282         "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);\r
1283 \r
1284     if (id != null && id.length() > 0)\r
1285     {\r
1286       PDBEntry entry = new PDBEntry();\r
1287       entry.setId(id);\r
1288       sequence.getDatasetSequence()\r
1289           .addPDBId(entry);\r
1290     }\r
1291   }\r
1292 \r
1293   public void discoverPDB_actionPerformed(ActionEvent e)\r
1294   {\r
1295     new jalview.io.DBRefFetcher(\r
1296              ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);\r
1297   }\r
1298 }\r