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