src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.jbgui;
  22
  23 import java.awt.BorderLayout;
  24 import java.awt.Color;
  25 import java.awt.GridLayout;
  26 import java.awt.event.ActionEvent;
  27 import java.awt.event.ActionListener;
  28 import java.awt.event.FocusAdapter;
  29 import java.awt.event.FocusEvent;
  30 import java.awt.event.KeyEvent;
  31 import java.awt.event.MouseAdapter;
  32 import java.awt.event.MouseEvent;
  33 import java.util.HashMap;
  34 import java.util.Map;
  35
  36 import javax.swing.BorderFactory;
  37 import javax.swing.ButtonGroup;
  38 import javax.swing.JCheckBoxMenuItem;
  39 import javax.swing.JInternalFrame;
  40 import javax.swing.JLabel;
  41 import javax.swing.JMenu;
  42 import javax.swing.JMenuBar;
  43 import javax.swing.JMenuItem;
  44 import javax.swing.JPanel;
  45 import javax.swing.JRadioButtonMenuItem;
  46 import javax.swing.JTabbedPane;
  47 import javax.swing.KeyStroke;
  48 import javax.swing.event.ChangeEvent;
  49 import javax.swing.event.MenuEvent;
  50 import javax.swing.event.MenuListener;
  51
  52 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  53 import jalview.analysis.GeneticCodeI;
  54 import jalview.analysis.GeneticCodes;
  55 import jalview.api.SplitContainerI;
  56 import jalview.bin.Cache;
  57 import jalview.gui.JvSwingUtils;
  58 import jalview.gui.Preferences;
  59 import jalview.io.FileFormats;
  60 import jalview.schemes.ResidueColourScheme;
  61 import jalview.util.MessageManager;
  62 import jalview.util.Platform;
  63
  64 @SuppressWarnings("serial")
  65 public class GAlignFrame extends JInternalFrame
  66 {
  67   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  68
  69   protected JMenuItem closeMenuItem = new JMenuItem();
  70
  71   public JMenu webService = new JMenu();// BH 2019 was protected, but not
  72                                         // sufficient for AlignFrame thread run
  73
  74   public JMenuItem webServiceNoServices;// BH 2019 was protected, but not
  75                                         // sufficient for AlignFrame thread run
  76
  77   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  78
  79   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  80
  81   protected JMenu sortByAnnotScore = new JMenu();
  82
  83   public JLabel statusBar = new JLabel(); // BH 2019 was protected, but not
  84                                           // sufficient for
  85                                           // AlignFrame.printWriter
  86
  87   protected JMenu outputTextboxMenu = new JMenu();
  88
  89   protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
  90
  91   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
  92
  93   protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
  94
  95   protected JMenuItem undoMenuItem = new JMenuItem();
  96
  97   protected JMenuItem redoMenuItem = new JMenuItem();
  98
  99   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 100
 101   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 102
 103   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 104
 105   JMenuItem copy = new JMenuItem();
 106
 107   JMenuItem copyHighlighted = new JMenuItem();
 108
 109   JMenuItem cut = new JMenuItem();
 110
 111   JMenu pasteMenu = new JMenu();
 112
 113   protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 114
 115   protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 116
 117   protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 118
 119   protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 120
 121   protected JCheckBoxMenuItem applyToAllGroups;
 122
 123   protected JMenu colourMenu = new JMenu();
 124
 125   protected JMenuItem textColour;
 126
 127   protected JCheckBoxMenuItem conservationMenuItem;
 128
 129   protected JMenuItem modifyConservation;
 130
 131   protected JCheckBoxMenuItem abovePIDThreshold;
 132
 133   protected JMenuItem modifyPID;
 134
 135   protected JRadioButtonMenuItem annotationColour;
 136
 137   protected JMenu sortByTreeMenu = new JMenu();
 138
 139   protected JMenu sort = new JMenu();
 140
 141   protected JMenuItem calculateTree = new JMenuItem();
 142
 143   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 144
 145   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 146
 147   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 148
 149   protected JMenu showTranslation = new JMenu();
 150
 151   protected JMenuItem showReverse = new JMenuItem();
 152
 153   protected JMenuItem showReverseComplement = new JMenuItem();
 154
 155   protected JMenu showProducts = new JMenu();
 156
 157   protected JMenuItem runGroovy = new JMenuItem();
 158
 159   protected JMenuItem loadVcf;
 160
 161   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 162
 163   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 164
 165   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 166
 167   protected JPanel statusPanel = new JPanel();
 168
 169   protected JMenuItem showAllSeqAnnotations = new JMenuItem();
 170
 171   protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
 172
 173   protected JMenuItem showAllAlAnnotations = new JMenuItem();
 174
 175   protected JMenuItem hideAllAlAnnotations = new JMenuItem();
 176
 177   protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
 178
 179   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 180
 181   protected JTabbedPane tabbedPane = new JTabbedPane();
 182
 183   protected JMenuItem reload = new JMenuItem();
 184
 185   protected JMenu formatMenu = new JMenu();
 186
 187   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 188
 189   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 190
 191   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 192
 193   protected JMenuItem gatherViews = new JMenuItem();
 194
 195   protected JMenuItem expandViews = new JMenuItem();
 196
 197   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 198
 199   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 200
 201   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 202
 203   protected JCheckBoxMenuItem showSSConsensusHistogram = new JCheckBoxMenuItem();
 204
 205   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 206
 207   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 208
 209   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 210
 211   protected JMenuItem openFeatureSettings;
 212
 213   private SequenceAnnotationOrder annotationSortOrder;
 214
 215   private boolean showAutoCalculatedAbove = false;
 216
 217   private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
 218
 219   private SplitContainerI splitFrame;
 220
 221   public GAlignFrame()
 222   {
 223     try
 224     {
 225       setFrameIcon(null);
 226
 227       // for Web-page embedding using id=align-frame-div
 228       setName("jalview-alignment");
 229
 230       jbInit();
 231       setJMenuBar(alignFrameMenuBar);
 232
 233       // dynamically fill save as menu with available formats
 234       for (String ff : FileFormats.getInstance().getWritableFormats(true))
 235       {
 236         JMenuItem item = new JMenuItem(ff);
 237
 238         item.addActionListener(new ActionListener()
 239         {
 240           @Override
 241           public void actionPerformed(ActionEvent e)
 242           {
 243             outputText_actionPerformed(e.getActionCommand());
 244           }
 245         });
 246
 247         outputTextboxMenu.add(item);
 248       }
 249     } catch (Exception e)
 250     {
 251       jalview.bin.Console.errPrintln(e.toString());
 252     }
 253
 254     if (Platform.allowMnemonics()) // was "not mac and not JS"
 255     {
 256       closeMenuItem.setMnemonic('C');
 257       outputTextboxMenu.setMnemonic('T');
 258       undoMenuItem.setMnemonic('Z');
 259       redoMenuItem.setMnemonic('0');
 260       copy.setMnemonic('C');
 261       cut.setMnemonic('U');
 262       pasteMenu.setMnemonic('P');
 263       reload.setMnemonic('R');
 264     }
 265   }
 266
 267   private void jbInit() throws Exception
 268   {
 269     setFrameIcon(null);
 270     initColourMenu();
 271
 272     JMenuItem saveAs = new JMenuItem(
 273             MessageManager.getString("action.save_as"));
 274     ActionListener al = new ActionListener()
 275     {
 276       @Override
 277       public void actionPerformed(ActionEvent e)
 278       {
 279         saveAs_actionPerformed();
 280       }
 281     };
 282
 283     // FIXME getDefaultToolkit throws an exception in Headless mode
 284     KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
 285             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
 286                     | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
 287             false);
 288     addMenuActionAndAccelerator(keyStroke, saveAs, al);
 289
 290     closeMenuItem.setText(MessageManager.getString("action.close"));
 291     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
 292             jalview.util.ShortcutKeyMaskExWrapper
 293                     .getMenuShortcutKeyMaskEx(),
 294             false);
 295     al = new ActionListener()
 296     {
 297       @Override
 298       public void actionPerformed(ActionEvent e)
 299       {
 300         closeMenuItem_actionPerformed(false);
 301       }
 302     };
 303     addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
 304
 305     JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
 306     JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
 307     JMenu annotationsMenu = new JMenu(
 308             MessageManager.getString("action.annotations"));
 309     JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
 310     colourMenu.setText(MessageManager.getString("action.colour"));
 311     JMenu calculateMenu = new JMenu(
 312             MessageManager.getString("action.calculate"));
 313     webService.setText(MessageManager.getString("action.web_service"));
 314     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
 315             MessageManager.getString("action.select_all"));
 316     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
 317             jalview.util.ShortcutKeyMaskExWrapper
 318                     .getMenuShortcutKeyMaskEx(),
 319             false);
 320     al = new ActionListener()
 321     {
 322       @Override
 323       public void actionPerformed(ActionEvent e)
 324       {
 325         selectAllSequenceMenuItem_actionPerformed(e);
 326       }
 327     };
 328     addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
 329
 330     JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
 331             MessageManager.getString("action.deselect_all"));
 332     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
 333     al = new ActionListener()
 334     {
 335       @Override
 336       public void actionPerformed(ActionEvent e)
 337       {
 338         deselectAllSequenceMenuItem_actionPerformed(e);
 339       }
 340     };
 341     addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
 342
 343     JMenuItem invertSequenceMenuItem = new JMenuItem(
 344             MessageManager.getString("action.invert_sequence_selection"));
 345     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
 346             jalview.util.ShortcutKeyMaskExWrapper
 347                     .getMenuShortcutKeyMaskEx(),
 348             false);
 349     al = new ActionListener()
 350     {
 351       @Override
 352       public void actionPerformed(ActionEvent e)
 353       {
 354         invertSequenceMenuItem_actionPerformed(e);
 355       }
 356     };
 357     addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
 358
 359     JMenuItem grpsFromSelection = new JMenuItem(
 360             MessageManager.getString("action.make_groups_selection"));
 361     grpsFromSelection.addActionListener(new ActionListener()
 362     {
 363       @Override
 364       public void actionPerformed(ActionEvent e)
 365       {
 366         makeGrpsFromSelection_actionPerformed(e);
 367       }
 368     });
 369     JMenuItem expandAlignment = new JMenuItem(
 370             MessageManager.getString("action.view_flanking_regions"));
 371     expandAlignment.setToolTipText(
 372             MessageManager.getString("label.view_flanking_regions"));
 373     expandAlignment.addActionListener(new ActionListener()
 374     {
 375       @Override
 376       public void actionPerformed(ActionEvent e)
 377       {
 378         expand_newalign(e);
 379       }
 380     });
 381     JMenuItem remove2LeftMenuItem = new JMenuItem(
 382             MessageManager.getString("action.remove_left"));
 383     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
 384             jalview.util.ShortcutKeyMaskExWrapper
 385                     .getMenuShortcutKeyMaskEx(),
 386             false);
 387     al = new ActionListener()
 388     {
 389       @Override
 390       public void actionPerformed(ActionEvent e)
 391       {
 392         remove2LeftMenuItem_actionPerformed(e);
 393       }
 394     };
 395     addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
 396
 397     JMenuItem remove2RightMenuItem = new JMenuItem(
 398             MessageManager.getString("action.remove_right"));
 399     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
 400             jalview.util.ShortcutKeyMaskExWrapper
 401                     .getMenuShortcutKeyMaskEx(),
 402             false);
 403     al = new ActionListener()
 404     {
 405       @Override
 406       public void actionPerformed(ActionEvent e)
 407       {
 408         remove2RightMenuItem_actionPerformed(e);
 409       }
 410     };
 411     addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
 412
 413     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
 414             MessageManager.getString("action.remove_empty_columns"));
 415     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
 416             jalview.util.ShortcutKeyMaskExWrapper
 417                     .getMenuShortcutKeyMaskEx(),
 418             false);
 419     al = new ActionListener()
 420     {
 421       @Override
 422       public void actionPerformed(ActionEvent e)
 423       {
 424         removeGappedColumnMenuItem_actionPerformed(e);
 425       }
 426     };
 427     addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
 428
 429     JMenuItem removeAllGapsMenuItem = new JMenuItem(
 430             MessageManager.getString("action.remove_all_gaps"));
 431     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
 432             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
 433                     | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
 434             false);
 435     al = new ActionListener()
 436     {
 437       @Override
 438       public void actionPerformed(ActionEvent e)
 439       {
 440         removeAllGapsMenuItem_actionPerformed(e);
 441       }
 442     };
 443     addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
 444
 445     JMenuItem justifyLeftMenuItem = new JMenuItem(
 446             MessageManager.getString("action.left_justify_alignment"));
 447     justifyLeftMenuItem.addActionListener(new ActionListener()
 448     {
 449       @Override
 450       public void actionPerformed(ActionEvent e)
 451       {
 452         justifyLeftMenuItem_actionPerformed(e);
 453       }
 454     });
 455     JMenuItem justifyRightMenuItem = new JMenuItem(
 456             MessageManager.getString("action.right_justify_alignment"));
 457     justifyRightMenuItem.addActionListener(new ActionListener()
 458     {
 459       @Override
 460       public void actionPerformed(ActionEvent e)
 461       {
 462         justifyRightMenuItem_actionPerformed(e);
 463       }
 464     });
 465     viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
 466     viewBoxesMenuItem.setState(true);
 467     viewBoxesMenuItem.addActionListener(new ActionListener()
 468     {
 469       @Override
 470       public void actionPerformed(ActionEvent e)
 471       {
 472         viewBoxesMenuItem_actionPerformed(e);
 473       }
 474     });
 475     viewTextMenuItem.setText(MessageManager.getString("action.text"));
 476     viewTextMenuItem.setState(true);
 477     viewTextMenuItem.addActionListener(new ActionListener()
 478     {
 479       @Override
 480       public void actionPerformed(ActionEvent e)
 481       {
 482         viewTextMenuItem_actionPerformed(e);
 483       }
 484     });
 485     showNonconservedMenuItem
 486             .setText(MessageManager.getString("label.show_non_conserved"));
 487     showNonconservedMenuItem.setState(false);
 488     showNonconservedMenuItem.addActionListener(new ActionListener()
 489     {
 490       @Override
 491       public void actionPerformed(ActionEvent e)
 492       {
 493         showUnconservedMenuItem_actionPerformed(e);
 494       }
 495     });
 496     JMenuItem sortPairwiseMenuItem = new JMenuItem(
 497             MessageManager.getString("action.by_pairwise_id"));
 498     sortPairwiseMenuItem.addActionListener(new ActionListener()
 499     {
 500       @Override
 501       public void actionPerformed(ActionEvent e)
 502       {
 503         sortPairwiseMenuItem_actionPerformed(e);
 504       }
 505     });
 506     JMenuItem sortIDMenuItem = new JMenuItem(
 507             MessageManager.getString("action.by_id"));
 508     sortIDMenuItem.addActionListener(new ActionListener()
 509     {
 510       @Override
 511       public void actionPerformed(ActionEvent e)
 512       {
 513         sortIDMenuItem_actionPerformed(e);
 514       }
 515     });
 516     JMenuItem sortLengthMenuItem = new JMenuItem(
 517             MessageManager.getString("action.by_length"));
 518     sortLengthMenuItem.addActionListener(new ActionListener()
 519     {
 520       @Override
 521       public void actionPerformed(ActionEvent e)
 522       {
 523         sortLengthMenuItem_actionPerformed(e);
 524       }
 525     });
 526     JMenuItem sortGroupMenuItem = new JMenuItem(
 527             MessageManager.getString("action.by_group"));
 528     sortGroupMenuItem.addActionListener(new ActionListener()
 529     {
 530       @Override
 531       public void actionPerformed(ActionEvent e)
 532       {
 533         sortGroupMenuItem_actionPerformed(e);
 534       }
 535     });
 536
 537     JMenuItem removeRedundancyMenuItem = new JMenuItem(
 538             MessageManager.getString("action.remove_redundancy"));
 539     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
 540             jalview.util.ShortcutKeyMaskExWrapper
 541                     .getMenuShortcutKeyMaskEx(),
 542             false);
 543     al = new ActionListener()
 544     {
 545       @Override
 546       public void actionPerformed(ActionEvent e)
 547       {
 548         removeRedundancyMenuItem_actionPerformed(e);
 549       }
 550     };
 551     addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
 552
 553     JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
 554             MessageManager.getString("action.pairwise_alignment"));
 555     pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
 556     {
 557       @Override
 558       public void actionPerformed(ActionEvent e)
 559       {
 560         pairwiseAlignmentMenuItem_actionPerformed(e);
 561       }
 562     });
 563
 564     this.getContentPane().setLayout(new BorderLayout());
 565     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 566     statusBar.setBackground(Color.white);
 567     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 568     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 569     statusBar.setText(MessageManager.getString("label.status_bar"));
 570     outputTextboxMenu
 571             .setText(MessageManager.getString("label.out_to_textbox"));
 572
 573     annotationPanelMenuItem.setActionCommand("");
 574     annotationPanelMenuItem
 575             .setText(MessageManager.getString("label.show_annotations"));
 576     annotationPanelMenuItem
 577             .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
 578     annotationPanelMenuItem.addActionListener(new ActionListener()
 579     {
 580       @Override
 581       public void actionPerformed(ActionEvent e)
 582       {
 583         annotationPanelMenuItem_actionPerformed(e);
 584       }
 585     });
 586     showAllAlAnnotations.setText(
 587             MessageManager.getString("label.show_all_al_annotations"));
 588     final boolean isAnnotationPanelShown = annotationPanelMenuItem
 589             .getState();
 590     showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 591     showAllAlAnnotations.addActionListener(new ActionListener()
 592     {
 593       @Override
 594       public void actionPerformed(ActionEvent e)
 595       {
 596         showAllAnnotations_actionPerformed(false, true);
 597       }
 598     });
 599     hideAllAlAnnotations.setText(
 600             MessageManager.getString("label.hide_all_al_annotations"));
 601     hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 602     hideAllAlAnnotations.addActionListener(new ActionListener()
 603     {
 604       @Override
 605       public void actionPerformed(ActionEvent e)
 606       {
 607         hideAllAnnotations_actionPerformed(false, true);
 608       }
 609     });
 610     showAllSeqAnnotations.setText(
 611             MessageManager.getString("label.show_all_seq_annotations"));
 612     showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 613     showAllSeqAnnotations.addActionListener(new ActionListener()
 614     {
 615       @Override
 616       public void actionPerformed(ActionEvent e)
 617       {
 618         showAllAnnotations_actionPerformed(true, false);
 619       }
 620     });
 621     hideAllSeqAnnotations.setText(
 622             MessageManager.getString("label.hide_all_seq_annotations"));
 623     hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 624     hideAllSeqAnnotations.addActionListener(new ActionListener()
 625     {
 626       @Override
 627       public void actionPerformed(ActionEvent e)
 628       {
 629         hideAllAnnotations_actionPerformed(true, false);
 630       }
 631     });
 632     SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
 633             .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
 634                     SequenceAnnotationOrder.NONE.name()));
 635     final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
 636             MessageManager.getString("label.sort_annotations_by_sequence"));
 637     final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
 638             MessageManager.getString("label.sort_annotations_by_label"));
 639
 640     sortAnnBySequence.setSelected(
 641             sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
 642     sortAnnBySequence.addActionListener(new ActionListener()
 643     {
 644       @Override
 645       public void actionPerformed(ActionEvent e)
 646       {
 647         boolean newState = sortAnnBySequence.getState();
 648         sortAnnByLabel.setSelected(false);
 649         setAnnotationSortOrder(
 650                 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 651                         : SequenceAnnotationOrder.NONE);
 652         sortAnnotations_actionPerformed();
 653       }
 654     });
 655     sortAnnByLabel.setSelected(
 656             sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
 657     sortAnnByLabel.addActionListener(new ActionListener()
 658     {
 659       @Override
 660       public void actionPerformed(ActionEvent e)
 661       {
 662         boolean newState = sortAnnByLabel.getState();
 663         sortAnnBySequence.setSelected(false);
 664         setAnnotationSortOrder(
 665                 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 666                         : SequenceAnnotationOrder.NONE);
 667         sortAnnotations_actionPerformed();
 668       }
 669     });
 670     colourTextMenuItem = new JCheckBoxMenuItem(
 671             MessageManager.getString("label.colour_text"));
 672     colourTextMenuItem.addActionListener(new ActionListener()
 673     {
 674       @Override
 675       public void actionPerformed(ActionEvent e)
 676       {
 677         colourTextMenuItem_actionPerformed(e);
 678       }
 679     });
 680
 681     JMenuItem htmlMenuItem = new JMenuItem(
 682             MessageManager.getString("label.html"));
 683     htmlMenuItem.addActionListener(new ActionListener()
 684     {
 685       @Override
 686       public void actionPerformed(ActionEvent e)
 687       {
 688         htmlMenuItem_actionPerformed(e);
 689       }
 690     });
 691
 692     JMenuItem createBioJS = new JMenuItem(
 693             MessageManager.getString("label.biojs_html_export"));
 694     createBioJS.addActionListener(new java.awt.event.ActionListener()
 695     {
 696       @Override
 697       public void actionPerformed(ActionEvent e)
 698       {
 699         bioJSMenuItem_actionPerformed(e);
 700       }
 701     });
 702
 703     JMenuItem overviewMenuItem = new JMenuItem(
 704             MessageManager.getString("label.overview_window"));
 705     overviewMenuItem.addActionListener(new ActionListener()
 706     {
 707       @Override
 708       public void actionPerformed(ActionEvent e)
 709       {
 710         overviewMenuItem_actionPerformed(e);
 711       }
 712     });
 713
 714     undoMenuItem.setEnabled(false);
 715     undoMenuItem.setText(MessageManager.getString("action.undo"));
 716     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
 717             jalview.util.ShortcutKeyMaskExWrapper
 718                     .getMenuShortcutKeyMaskEx(),
 719             false);
 720     al = new ActionListener()
 721     {
 722       @Override
 723       public void actionPerformed(ActionEvent e)
 724       {
 725         undoMenuItem_actionPerformed(e);
 726       }
 727     };
 728     addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
 729
 730     redoMenuItem.setEnabled(false);
 731     redoMenuItem.setText(MessageManager.getString("action.redo"));
 732     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
 733             jalview.util.ShortcutKeyMaskExWrapper
 734                     .getMenuShortcutKeyMaskEx(),
 735             false);
 736     al = new ActionListener()
 737     {
 738       @Override
 739       public void actionPerformed(ActionEvent e)
 740       {
 741         redoMenuItem_actionPerformed(e);
 742       }
 743     };
 744     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
 745
 746     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
 747     wrapMenuItem.addActionListener(new ActionListener()
 748     {
 749       @Override
 750       public void actionPerformed(ActionEvent e)
 751       {
 752         wrapMenuItem_actionPerformed(e);
 753       }
 754     });
 755
 756     JMenuItem printMenuItem = new JMenuItem(
 757             MessageManager.getString("action.print"));
 758     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
 759             jalview.util.ShortcutKeyMaskExWrapper
 760                     .getMenuShortcutKeyMaskEx(),
 761             false);
 762     al = new ActionListener()
 763     {
 764       @Override
 765       public void actionPerformed(ActionEvent e)
 766       {
 767         printMenuItem_actionPerformed(e);
 768       }
 769     };
 770     addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
 771
 772     renderGapsMenuItem
 773             .setText(MessageManager.getString("action.show_gaps"));
 774     renderGapsMenuItem.setState(true);
 775     renderGapsMenuItem.addActionListener(new ActionListener()
 776     {
 777       @Override
 778       public void actionPerformed(ActionEvent e)
 779       {
 780         renderGapsMenuItem_actionPerformed(e);
 781       }
 782     });
 783
 784     JMenuItem findMenuItem = new JMenuItem(
 785             MessageManager.getString("action.find"));
 786     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
 787             jalview.util.ShortcutKeyMaskExWrapper
 788                     .getMenuShortcutKeyMaskEx(),
 789             false);
 790     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
 791             MessageManager.getString("label.find_tip")));
 792     al = new ActionListener()
 793     {
 794       @Override
 795       public void actionPerformed(ActionEvent e)
 796       {
 797         findMenuItem_actionPerformed(e);
 798       }
 799     };
 800     addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
 801
 802     showSeqFeatures.setText(
 803             MessageManager.getString("label.show_sequence_features"));
 804     showSeqFeatures.addActionListener(new ActionListener()
 805     {
 806       @Override
 807       public void actionPerformed(ActionEvent actionEvent)
 808       {
 809         showSeqFeatures_actionPerformed(actionEvent);
 810       }
 811     });
 812     /*
 813      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
 814      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
 815      * void actionPerformed(ActionEvent actionEvent) {
 816      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
 817      */
 818     showDbRefsMenuitem
 819             .setText(MessageManager.getString("label.show_database_refs"));
 820     showDbRefsMenuitem.addActionListener(new ActionListener()
 821     {
 822
 823       @Override
 824       public void actionPerformed(ActionEvent e)
 825       {
 826         showDbRefs_actionPerformed(e);
 827       }
 828
 829     });
 830     showNpFeatsMenuitem.setText(
 831             MessageManager.getString("label.show_non_positional_features"));
 832     showNpFeatsMenuitem.addActionListener(new ActionListener()
 833     {
 834
 835       @Override
 836       public void actionPerformed(ActionEvent e)
 837       {
 838         showNpFeats_actionPerformed(e);
 839       }
 840
 841     });
 842     showGroupConservation
 843             .setText(MessageManager.getString("label.group_conservation"));
 844     showGroupConservation.addActionListener(new ActionListener()
 845     {
 846
 847       @Override
 848       public void actionPerformed(ActionEvent e)
 849       {
 850         showGroupConservation_actionPerformed(e);
 851       }
 852
 853     });
 854
 855     showGroupConsensus
 856             .setText(MessageManager.getString("label.group_consensus"));
 857     showGroupConsensus.addActionListener(new ActionListener()
 858     {
 859
 860       @Override
 861       public void actionPerformed(ActionEvent e)
 862       {
 863         showGroupConsensus_actionPerformed(e);
 864       }
 865
 866     });
 867     showConsensusHistogram.setText(
 868             MessageManager.getString("label.show_consensus_histogram"));
 869     showConsensusHistogram.addActionListener(new ActionListener()
 870     {
 871
 872       @Override
 873       public void actionPerformed(ActionEvent e)
 874       {
 875         showConsensusHistogram_actionPerformed(e);
 876       }
 877
 878     });
 879     showSSConsensusHistogram.setText(
 880             MessageManager.getString("label.show_ssconsensus_histogram"));
 881     showSSConsensusHistogram.addActionListener(new ActionListener()
 882     {
 883
 884       @Override
 885       public void actionPerformed(ActionEvent e)
 886       {
 887         showConsensusHistogram_actionPerformed(e);
 888       }
 889
 890     });
 891     showSequenceLogo
 892             .setText(MessageManager.getString("label.show_consensus_logo"));
 893     showSequenceLogo.addActionListener(new ActionListener()
 894     {
 895
 896       @Override
 897       public void actionPerformed(ActionEvent e)
 898       {
 899         showSequenceLogo_actionPerformed(e);
 900       }
 901
 902     });
 903     normaliseSequenceLogo
 904             .setText(MessageManager.getString("label.norm_consensus_logo"));
 905     normaliseSequenceLogo.addActionListener(new ActionListener()
 906     {
 907
 908       @Override
 909       public void actionPerformed(ActionEvent e)
 910       {
 911         normaliseSequenceLogo_actionPerformed(e);
 912       }
 913
 914     });
 915     applyAutoAnnotationSettings
 916             .setText(MessageManager.getString("label.apply_all_groups"));
 917     applyAutoAnnotationSettings.setState(false);
 918     applyAutoAnnotationSettings.setVisible(true);
 919     applyAutoAnnotationSettings.addActionListener(new ActionListener()
 920     {
 921       @Override
 922       public void actionPerformed(ActionEvent e)
 923       {
 924         applyAutoAnnotationSettings_actionPerformed(e);
 925       }
 926     });
 927
 928     ButtonGroup buttonGroup = new ButtonGroup();
 929     final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
 930             MessageManager.getString("label.show_first"));
 931     final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
 932             MessageManager.getString("label.show_last"));
 933     buttonGroup.add(showAutoFirst);
 934     buttonGroup.add(showAutoLast);
 935     final boolean autoFirst = Cache
 936             .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
 937     showAutoFirst.setSelected(autoFirst);
 938     setShowAutoCalculatedAbove(autoFirst);
 939     showAutoFirst.addActionListener(new ActionListener()
 940     {
 941       @Override
 942       public void actionPerformed(ActionEvent e)
 943       {
 944         setShowAutoCalculatedAbove(showAutoFirst.isSelected());
 945         sortAnnotations_actionPerformed();
 946       }
 947     });
 948     showAutoLast.setSelected(!showAutoFirst.isSelected());
 949     showAutoLast.addActionListener(new ActionListener()
 950     {
 951       @Override
 952       public void actionPerformed(ActionEvent e)
 953       {
 954         setShowAutoCalculatedAbove(!showAutoLast.isSelected());
 955         sortAnnotations_actionPerformed();
 956       }
 957     });
 958
 959     JMenuItem deleteGroups = new JMenuItem(
 960             MessageManager.getString("action.undefine_groups"));
 961     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
 962             jalview.util.ShortcutKeyMaskExWrapper
 963                     .getMenuShortcutKeyMaskEx(),
 964             false);
 965     al = new ActionListener()
 966     {
 967       @Override
 968       public void actionPerformed(ActionEvent e)
 969       {
 970         deleteGroups_actionPerformed(e);
 971       }
 972     };
 973     addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
 974
 975     JMenuItem annotationColumn = new JMenuItem(
 976             MessageManager.getString("action.select_by_annotation"));
 977     annotationColumn.addActionListener(new ActionListener()
 978     {
 979       @Override
 980       public void actionPerformed(ActionEvent e)
 981       {
 982         annotationColumn_actionPerformed(e);
 983       }
 984     });
 985
 986     JMenuItem createGroup = new JMenuItem(
 987             MessageManager.getString("action.create_group"));
 988     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
 989             jalview.util.ShortcutKeyMaskExWrapper
 990                     .getMenuShortcutKeyMaskEx(),
 991             false);
 992     al = new ActionListener()
 993     {
 994       @Override
 995       public void actionPerformed(ActionEvent e)
 996       {
 997         createGroup_actionPerformed(e);
 998       }
 999     };
1000     addMenuActionAndAccelerator(keyStroke, createGroup, al);
1001
1002     JMenuItem unGroup = new JMenuItem(
1003             MessageManager.getString("action.remove_group"));
1004     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
1005             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1006                     | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
1007             false);
1008     al = new ActionListener()
1009     {
1010       @Override
1011       public void actionPerformed(ActionEvent e)
1012       {
1013         unGroup_actionPerformed(e);
1014       }
1015     };
1016     addMenuActionAndAccelerator(keyStroke, unGroup, al);
1017
1018     copy.setText(MessageManager.getString("action.copy"));
1019     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
1020             jalview.util.ShortcutKeyMaskExWrapper
1021                     .getMenuShortcutKeyMaskEx(),
1022             false);
1023
1024     al = new ActionListener()
1025     {
1026       @Override
1027       public void actionPerformed(ActionEvent e)
1028       {
1029         copy_actionPerformed();
1030       }
1031     };
1032     addMenuActionAndAccelerator(keyStroke, copy, al);
1033
1034     cut.setText(MessageManager.getString("action.cut"));
1035     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
1036             jalview.util.ShortcutKeyMaskExWrapper
1037                     .getMenuShortcutKeyMaskEx(),
1038             false);
1039     al = new ActionListener()
1040     {
1041       @Override
1042       public void actionPerformed(ActionEvent e)
1043       {
1044         cut_actionPerformed();
1045       }
1046     };
1047     addMenuActionAndAccelerator(keyStroke, cut, al);
1048
1049     JMenuItem delete = new JMenuItem(
1050             MessageManager.getString("action.delete"));
1051     delete.addActionListener(new ActionListener()
1052     {
1053       @Override
1054       public void actionPerformed(ActionEvent e)
1055       {
1056         delete_actionPerformed();
1057       }
1058     });
1059
1060     pasteMenu.setText(MessageManager.getString("action.paste"));
1061     JMenuItem pasteNew = new JMenuItem(
1062             MessageManager.getString("label.to_new_alignment"));
1063     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1064             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1065                     | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
1066             false);
1067     al = new ActionListener()
1068     {
1069       @Override
1070       public void actionPerformed(ActionEvent e)
1071       {
1072         pasteNew_actionPerformed(e);
1073       }
1074     };
1075     addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1076
1077     JMenuItem pasteThis = new JMenuItem(
1078             MessageManager.getString("label.to_this_alignment"));
1079     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1080             jalview.util.ShortcutKeyMaskExWrapper
1081                     .getMenuShortcutKeyMaskEx(),
1082             false);
1083     al = new ActionListener()
1084     {
1085       @Override
1086       public void actionPerformed(ActionEvent e)
1087       {
1088         pasteThis_actionPerformed(e);
1089       }
1090     };
1091     addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1092
1093     JMenuItem createPNG = new JMenuItem("PNG");
1094     createPNG.addActionListener(new ActionListener()
1095     {
1096       @Override
1097       public void actionPerformed(ActionEvent e)
1098       {
1099         createPNG_actionPerformed(e);
1100       }
1101     });
1102     createPNG.setActionCommand(
1103             MessageManager.getString("label.save_png_image"));
1104
1105     JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1106     font.addActionListener(new ActionListener()
1107     {
1108       @Override
1109       public void actionPerformed(ActionEvent e)
1110       {
1111         font_actionPerformed(e);
1112       }
1113     });
1114     seqLimits.setText(
1115             MessageManager.getString("label.show_sequence_limits"));
1116     seqLimits.setState(Cache.getDefault("SHOW_JVSUFFIX", true));
1117     seqLimits.addActionListener(new ActionListener()
1118     {
1119       @Override
1120       public void actionPerformed(ActionEvent e)
1121       {
1122         seqLimit_actionPerformed(e);
1123       }
1124     });
1125     JMenuItem epsFile = new JMenuItem("EPS");
1126     epsFile.addActionListener(new ActionListener()
1127     {
1128       @Override
1129       public void actionPerformed(ActionEvent e)
1130       {
1131         createEPS_actionPerformed(e);
1132       }
1133     });
1134
1135     JMenuItem createSVG = new JMenuItem("SVG");
1136     createSVG.addActionListener(new ActionListener()
1137     {
1138       @Override
1139       public void actionPerformed(ActionEvent e)
1140       {
1141         createSVG_actionPerformed(e);
1142       }
1143     });
1144
1145     JMenuItem loadTreeMenuItem = new JMenuItem(
1146             MessageManager.getString("label.load_associated_tree"));
1147     loadTreeMenuItem.setActionCommand(
1148             MessageManager.getString("label.load_tree_for_sequence_set"));
1149     loadTreeMenuItem.addActionListener(new ActionListener()
1150     {
1151       @Override
1152       public void actionPerformed(ActionEvent e)
1153       {
1154         loadTreeMenuItem_actionPerformed(e);
1155       }
1156     });
1157
1158     scaleAbove.setVisible(false);
1159     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1160     scaleAbove.addActionListener(new ActionListener()
1161     {
1162       @Override
1163       public void actionPerformed(ActionEvent e)
1164       {
1165         scaleAbove_actionPerformed(e);
1166       }
1167     });
1168     scaleLeft.setVisible(false);
1169     scaleLeft.setSelected(true);
1170     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1171     scaleLeft.addActionListener(new ActionListener()
1172     {
1173       @Override
1174       public void actionPerformed(ActionEvent e)
1175       {
1176         scaleLeft_actionPerformed(e);
1177       }
1178     });
1179     scaleRight.setVisible(false);
1180     scaleRight.setSelected(true);
1181     scaleRight.setText(MessageManager.getString("action.scale_right"));
1182     scaleRight.addActionListener(new ActionListener()
1183     {
1184       @Override
1185       public void actionPerformed(ActionEvent e)
1186       {
1187         scaleRight_actionPerformed(e);
1188       }
1189     });
1190     centreColumnLabelsMenuItem.setVisible(true);
1191     centreColumnLabelsMenuItem.setState(false);
1192     centreColumnLabelsMenuItem.setText(
1193             MessageManager.getString("label.centre_column_labels"));
1194     centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1195     {
1196       @Override
1197       public void actionPerformed(ActionEvent e)
1198       {
1199         centreColumnLabels_actionPerformed(e);
1200       }
1201     });
1202     followHighlightMenuItem.setVisible(true);
1203     followHighlightMenuItem.setState(true);
1204     followHighlightMenuItem
1205             .setText(MessageManager.getString("label.automatic_scrolling"));
1206     followHighlightMenuItem.addActionListener(new ActionListener()
1207     {
1208
1209       @Override
1210       public void actionPerformed(ActionEvent e)
1211       {
1212         followHighlight_actionPerformed();
1213       }
1214
1215     });
1216
1217     sortByTreeMenu
1218             .setText(MessageManager.getString("action.by_tree_order"));
1219     sort.setText(MessageManager.getString("action.sort"));
1220     sort.addMenuListener(new MenuListener()
1221     {
1222       @Override
1223       public void menuSelected(MenuEvent e)
1224       {
1225         buildTreeSortMenu();
1226       }
1227
1228       @Override
1229       public void menuDeselected(MenuEvent e)
1230       {
1231       }
1232
1233       @Override
1234       public void menuCanceled(MenuEvent e)
1235       {
1236       }
1237     });
1238     sortByAnnotScore
1239             .setText(MessageManager.getString("label.sort_by_score"));
1240     sort.add(sortByAnnotScore);
1241     sort.addMenuListener(new javax.swing.event.MenuListener()
1242     {
1243
1244       @Override
1245       public void menuCanceled(MenuEvent e)
1246       {
1247       }
1248
1249       @Override
1250       public void menuDeselected(MenuEvent e)
1251       {
1252       }
1253
1254       @Override
1255       public void menuSelected(MenuEvent e)
1256       {
1257         buildSortByAnnotationScoresMenu();
1258       }
1259     });
1260     sortByAnnotScore.setVisible(false);
1261
1262     calculateTree
1263             .setText(MessageManager.getString("action.calculate_tree_pca"));
1264
1265     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1266     padGapsMenuitem.setState(Cache.getDefault("PAD_GAPS", false));
1267     padGapsMenuitem.addActionListener(new ActionListener()
1268     {
1269       @Override
1270       public void actionPerformed(ActionEvent e)
1271       {
1272         padGapsMenuitem_actionPerformed(e);
1273       }
1274     });
1275     JMenuItem vamsasStore = new JMenuItem(
1276             MessageManager.getString("label.vamsas_store"));
1277     vamsasStore.setVisible(false);
1278     vamsasStore.addActionListener(new ActionListener()
1279     {
1280       @Override
1281       public void actionPerformed(ActionEvent e)
1282       {
1283         vamsasStore_actionPerformed(e);
1284       }
1285     });
1286
1287     /*
1288      * Translate as cDNA with sub-menu of translation tables
1289      */
1290     showTranslation
1291             .setText(MessageManager.getString("label.translate_cDNA"));
1292     boolean first = true;
1293     for (final GeneticCodeI table : GeneticCodes.getInstance()
1294             .getCodeTables())
1295     {
1296       JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
1297       showTranslation.add(item);
1298       item.addActionListener(new ActionListener()
1299       {
1300         @Override
1301         public void actionPerformed(ActionEvent e)
1302         {
1303           showTranslation_actionPerformed(table);
1304         }
1305       });
1306       if (first)
1307       {
1308         showTranslation.addSeparator();
1309       }
1310       first = false;
1311     }
1312
1313     showReverse.setText(MessageManager.getString("label.reverse"));
1314     showReverse.addActionListener(new ActionListener()
1315     {
1316       @Override
1317       public void actionPerformed(ActionEvent e)
1318       {
1319         showReverse_actionPerformed(false);
1320       }
1321     });
1322     showReverseComplement
1323             .setText(MessageManager.getString("label.reverse_complement"));
1324     showReverseComplement.addActionListener(new ActionListener()
1325     {
1326       @Override
1327       public void actionPerformed(ActionEvent e)
1328       {
1329         showReverse_actionPerformed(true);
1330       }
1331     });
1332
1333     JMenuItem extractScores = new JMenuItem(
1334             MessageManager.getString("label.extract_scores"));
1335     extractScores.addActionListener(new ActionListener()
1336     {
1337       @Override
1338       public void actionPerformed(ActionEvent e)
1339       {
1340         extractScores_actionPerformed(e);
1341       }
1342     });
1343     extractScores.setVisible(true);
1344     // JBPNote: TODO: make gui for regex based score extraction
1345
1346     // for show products actions see AlignFrame.canShowProducts
1347     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1348
1349     runGroovy.setText(MessageManager.getString("label.run_groovy"));
1350     runGroovy.setToolTipText(
1351             MessageManager.getString("label.run_groovy_tip"));
1352     runGroovy.addActionListener(new ActionListener()
1353     {
1354       @Override
1355       public void actionPerformed(ActionEvent e)
1356       {
1357         runGroovy_actionPerformed();
1358       }
1359     });
1360
1361     openFeatureSettings = new JMenuItem(
1362             MessageManager.getString("action.feature_settings"));
1363     openFeatureSettings.addActionListener(new ActionListener()
1364     {
1365       @Override
1366       public void actionPerformed(ActionEvent e)
1367       {
1368         featureSettings_actionPerformed(e);
1369       }
1370     });
1371
1372     /*
1373      * add sub-menu of database we can fetch from
1374      */
1375     JMenuItem fetchSequence = new JMenuItem(
1376             MessageManager.getString("label.fetch_sequences"));
1377     fetchSequence.addActionListener(new ActionListener()
1378     {
1379       @Override
1380       public void actionPerformed(ActionEvent e)
1381       {
1382         fetchSequence_actionPerformed();
1383       }
1384     });
1385
1386     JMenuItem associatedData = new JMenuItem(
1387             MessageManager.getString("label.load_features_annotations"));
1388     associatedData.addActionListener(new ActionListener()
1389     {
1390       @Override
1391       public void actionPerformed(ActionEvent e)
1392       {
1393         associatedData_actionPerformed(e);
1394       }
1395     });
1396     loadVcf = new JMenuItem(
1397             MessageManager.getString("label.load_vcf_file"));
1398     loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
1399     loadVcf.addActionListener(new ActionListener()
1400     {
1401       @Override
1402       public void actionPerformed(ActionEvent e)
1403       {
1404         loadVcf_actionPerformed();
1405       }
1406     });
1407     autoCalculate.setText(
1408             MessageManager.getString("label.autocalculate_consensus"));
1409     autoCalculate.setState(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1410     autoCalculate.addActionListener(new ActionListener()
1411     {
1412       @Override
1413       public void actionPerformed(ActionEvent e)
1414       {
1415         autoCalculate_actionPerformed(e);
1416       }
1417     });
1418     sortByTree.setText(
1419             MessageManager.getString("label.sort_alignment_new_tree"));
1420     sortByTree.setToolTipText("<html>" + MessageManager.getString(
1421             "label.enable_automatically_sort_alignment_when_open_new_tree"));
1422     sortByTree.setState(Cache.getDefault("SORT_BY_TREE", false));
1423     sortByTree.addActionListener(new ActionListener()
1424     {
1425       @Override
1426       public void actionPerformed(ActionEvent e)
1427       {
1428         sortByTreeOption_actionPerformed(e);
1429       }
1430     });
1431
1432     listenToViewSelections.setText(
1433             MessageManager.getString("label.listen_for_selections"));
1434     listenToViewSelections
1435             .setToolTipText("<html>" + MessageManager.getString(
1436                     "label.selections_mirror_selections_made_same_sequences_other_views"));
1437     listenToViewSelections.setState(false);
1438     listenToViewSelections.addActionListener(new ActionListener()
1439     {
1440       @Override
1441       public void actionPerformed(ActionEvent e)
1442       {
1443         listenToViewSelections_actionPerformed(e);
1444       }
1445     });
1446
1447     JMenu addSequenceMenu = new JMenu(
1448             MessageManager.getString("label.add_sequences"));
1449     JMenuItem addFromFile = new JMenuItem(
1450             MessageManager.getString("label.from_file"));
1451     addFromFile.addActionListener(new ActionListener()
1452     {
1453       @Override
1454       public void actionPerformed(ActionEvent e)
1455       {
1456         addFromFile_actionPerformed(e);
1457       }
1458     });
1459     JMenuItem addFromText = new JMenuItem(
1460             MessageManager.getString("label.from_textbox"));
1461     addFromText.addActionListener(new ActionListener()
1462     {
1463       @Override
1464       public void actionPerformed(ActionEvent e)
1465       {
1466         addFromText_actionPerformed(e);
1467       }
1468     });
1469     JMenuItem addFromURL = new JMenuItem(
1470             MessageManager.getString("label.from_url"));
1471     addFromURL.addActionListener(new ActionListener()
1472     {
1473       @Override
1474       public void actionPerformed(ActionEvent e)
1475       {
1476         addFromURL_actionPerformed(e);
1477       }
1478     });
1479     JMenuItem exportFeatures = new JMenuItem(
1480             MessageManager.getString("label.export_features"));
1481     exportFeatures.addActionListener(new ActionListener()
1482     {
1483       @Override
1484       public void actionPerformed(ActionEvent e)
1485       {
1486         exportFeatures_actionPerformed(e);
1487       }
1488     });
1489     JMenuItem exportAnnotations = new JMenuItem(
1490             MessageManager.getString("label.export_annotations"));
1491     exportAnnotations.addActionListener(new ActionListener()
1492     {
1493       @Override
1494       public void actionPerformed(ActionEvent e)
1495       {
1496         exportAnnotations_actionPerformed(e);
1497       }
1498     });
1499     statusPanel.setLayout(new GridLayout());
1500     JMenuItem showAllSeqs = new JMenuItem(
1501             MessageManager.getString("label.all_sequences"));
1502     showAllSeqs.setToolTipText(
1503             MessageManager.getString("label.toggle_sequence_visibility"));
1504     showAllSeqs.addActionListener(new ActionListener()
1505     {
1506       @Override
1507       public void actionPerformed(ActionEvent e)
1508       {
1509         showAllSeqs_actionPerformed(e);
1510       }
1511     });
1512     JMenuItem showAllColumns = new JMenuItem(
1513             MessageManager.getString("label.all_columns"));
1514     showAllColumns.setToolTipText(
1515             MessageManager.getString("label.toggle_columns_visibility"));
1516     showAllColumns.addActionListener(new ActionListener()
1517     {
1518       @Override
1519       public void actionPerformed(ActionEvent e)
1520       {
1521         showAllColumns_actionPerformed(e);
1522       }
1523     });
1524     JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1525     JMenuItem hideSelSequences = new JMenuItem(
1526             MessageManager.getString("label.selected_sequences"));
1527     hideSelSequences.setToolTipText(
1528             MessageManager.getString("label.toggle_sequence_visibility"));
1529     hideSelSequences.addActionListener(new ActionListener()
1530     {
1531       @Override
1532       public void actionPerformed(ActionEvent e)
1533       {
1534         hideSelSequences_actionPerformed(e);
1535       }
1536     });
1537     JMenuItem hideSelColumns = new JMenuItem(
1538             MessageManager.getString("label.selected_columns"));
1539     hideSelColumns.setToolTipText(
1540             MessageManager.getString("label.toggle_columns_visibility"));
1541     hideSelColumns.addActionListener(new ActionListener()
1542     {
1543       @Override
1544       public void actionPerformed(ActionEvent e)
1545       {
1546         hideSelColumns_actionPerformed(e);
1547       }
1548     });
1549     JMenuItem hideAllSelection = new JMenuItem(
1550             MessageManager.getString("label.selected_region"));
1551     hideAllSelection.addActionListener(new ActionListener()
1552     {
1553       @Override
1554       public void actionPerformed(ActionEvent e)
1555       {
1556         hideAllSelection_actionPerformed(e);
1557       }
1558     });
1559     // TODO: should be hidden if no selection exists.
1560     JMenuItem hideAllButSelection = new JMenuItem(
1561             MessageManager.getString("label.all_but_selected_region"));
1562     hideAllButSelection.addActionListener(new ActionListener()
1563     {
1564       @Override
1565       public void actionPerformed(ActionEvent e)
1566       {
1567         hideAllButSelection_actionPerformed(e);
1568       }
1569     });
1570     JMenuItem showAllhidden = new JMenuItem(
1571             MessageManager.getString("label.all_sequences_columns"));
1572     showAllhidden.setToolTipText(MessageManager
1573             .getString("label.toggles_visibility_hidden_selected_regions"));
1574     showAllhidden.addActionListener(new ActionListener()
1575     {
1576       @Override
1577       public void actionPerformed(ActionEvent e)
1578       {
1579         showAllhidden_actionPerformed(e);
1580       }
1581     });
1582     hiddenMarkers.setText(
1583             MessageManager.getString("action.show_hidden_markers"));
1584     hiddenMarkers.addActionListener(new ActionListener()
1585     {
1586       @Override
1587       public void actionPerformed(ActionEvent e)
1588       {
1589         hiddenMarkers_actionPerformed(e);
1590       }
1591     });
1592
1593     JMenuItem invertColSel = new JMenuItem(
1594             MessageManager.getString("action.invert_column_selection"));
1595     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1596             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1597                     | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
1598             false);
1599     al = new ActionListener()
1600     {
1601       @Override
1602       public void actionPerformed(ActionEvent e)
1603       {
1604         invertColSel_actionPerformed(e);
1605       }
1606     };
1607     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1608
1609     showComplementMenuItem.setVisible(false);
1610     showComplementMenuItem.addActionListener(new ActionListener()
1611     {
1612       @Override
1613       public void actionPerformed(ActionEvent e)
1614       {
1615         showComplement_actionPerformed(showComplementMenuItem.getState());
1616       }
1617     });
1618
1619     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1620     {
1621       @Override
1622       public void stateChanged(ChangeEvent evt)
1623       {
1624         JTabbedPane pane = (JTabbedPane) evt.getSource();
1625         int sel = pane.getSelectedIndex();
1626         tabSelectionChanged(sel);
1627       }
1628     });
1629     tabbedPane.addMouseListener(new MouseAdapter()
1630     {
1631       @Override
1632       public void mousePressed(MouseEvent e)
1633       {
1634         if (e.isPopupTrigger()) // Mac
1635         {
1636           tabbedPane_mousePressed(e);
1637         }
1638       }
1639
1640       @Override
1641       public void mouseReleased(MouseEvent e)
1642       {
1643         if (e.isPopupTrigger()) // Windows
1644         {
1645           tabbedPane_mousePressed(e);
1646         }
1647       }
1648     });
1649     tabbedPane.addFocusListener(new FocusAdapter()
1650     {
1651       @Override
1652       public void focusGained(FocusEvent e)
1653       {
1654         tabbedPane_focusGained(e);
1655       }
1656     });
1657
1658     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1659     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1660             jalview.util.ShortcutKeyMaskExWrapper
1661                     .getMenuShortcutKeyMaskEx(),
1662             false);
1663     al = new ActionListener()
1664     {
1665       @Override
1666       public void actionPerformed(ActionEvent e)
1667       {
1668         save_actionPerformed(e);
1669       }
1670     };
1671     addMenuActionAndAccelerator(keyStroke, save, al);
1672
1673     reload.setEnabled(false);
1674     reload.setText(MessageManager.getString("action.reload"));
1675     reload.addActionListener(new ActionListener()
1676     {
1677       @Override
1678       public void actionPerformed(ActionEvent e)
1679       {
1680         reload_actionPerformed(e);
1681       }
1682     });
1683
1684     JMenuItem newView = new JMenuItem(
1685             MessageManager.getString("action.new_view"));
1686     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1687             jalview.util.ShortcutKeyMaskExWrapper
1688                     .getMenuShortcutKeyMaskEx(),
1689             false);
1690     al = new ActionListener()
1691     {
1692       @Override
1693       public void actionPerformed(ActionEvent e)
1694       {
1695         newView_actionPerformed(e);
1696       }
1697     };
1698     addMenuActionAndAccelerator(keyStroke, newView, al);
1699
1700     tabbedPane.setToolTipText("<html><i>"
1701             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1702             + "</i></html>");
1703
1704     formatMenu.setText(MessageManager.getString("action.format"));
1705     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1706
1707     idRightAlign.setText(
1708             MessageManager.getString("label.right_align_sequence_id"));
1709     idRightAlign.addActionListener(new ActionListener()
1710     {
1711       @Override
1712       public void actionPerformed(ActionEvent e)
1713       {
1714         idRightAlign_actionPerformed(e);
1715       }
1716     });
1717
1718     gatherViews.setEnabled(false);
1719     gatherViews.setText(MessageManager.getString("action.gather_views"));
1720     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1721     al = new ActionListener()
1722     {
1723       @Override
1724       public void actionPerformed(ActionEvent e)
1725       {
1726         gatherViews_actionPerformed(e);
1727       }
1728     };
1729     addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1730
1731     expandViews.setEnabled(false);
1732     expandViews.setText(MessageManager.getString("action.expand_views"));
1733     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1734     al = new ActionListener()
1735     {
1736       @Override
1737       public void actionPerformed(ActionEvent e)
1738       {
1739         expandViews_actionPerformed(e);
1740       }
1741     };
1742     addMenuActionAndAccelerator(keyStroke, expandViews, al);
1743
1744     JMenuItem pageSetup = new JMenuItem(
1745             MessageManager.getString("action.page_setup"));
1746     pageSetup.addActionListener(new ActionListener()
1747     {
1748       @Override
1749       public void actionPerformed(ActionEvent e)
1750       {
1751         pageSetup_actionPerformed(e);
1752       }
1753     });
1754     JMenuItem alignmentProperties = new JMenuItem(
1755             MessageManager.getString("label.alignment_props"));
1756     alignmentProperties.addActionListener(new ActionListener()
1757     {
1758       @Override
1759       public void actionPerformed(ActionEvent actionEvent)
1760       {
1761         alignmentProperties();
1762       }
1763     });
1764     JMenuItem selectHighlighted = new JMenuItem(
1765             MessageManager.getString("action.select_highlighted_columns"));
1766     selectHighlighted.setToolTipText(
1767             MessageManager.getString("tooltip.select_highlighted_columns"));
1768     al = new ActionListener()
1769     {
1770       @Override
1771       public void actionPerformed(ActionEvent actionEvent)
1772       {
1773         selectHighlightedColumns_actionPerformed(actionEvent);
1774       }
1775     };
1776     selectHighlighted.addActionListener(al);
1777
1778     copyHighlighted = new JMenuItem(
1779             MessageManager.getString("action.copy_highlighted_regions"));
1780     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
1781             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1782                     + jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
1783             false);
1784     copyHighlighted.setToolTipText(
1785             MessageManager.getString("tooltip.copy_highlighted_regions"));
1786     al = new ActionListener()
1787     {
1788       @Override
1789       public void actionPerformed(ActionEvent actionEvent)
1790       {
1791         copyHighlightedColumns_actionPerformed(actionEvent);
1792       }
1793     };
1794     addMenuActionAndAccelerator(keyStroke, copyHighlighted, al);
1795     copyHighlighted.addActionListener(al);
1796
1797     JMenu tooltipSettingsMenu = new JMenu(
1798             MessageManager.getString("label.sequence_id_tooltip"));
1799     JMenu autoAnnMenu = new JMenu(
1800             MessageManager.getString("label.autocalculated_annotation"));
1801
1802     JMenu exportImageMenu = new JMenu(
1803             MessageManager.getString("label.export_image"));
1804     JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1805     alignFrameMenuBar.add(fileMenu);
1806     alignFrameMenuBar.add(editMenu);
1807     alignFrameMenuBar.add(selectMenu);
1808     alignFrameMenuBar.add(viewMenu);
1809     alignFrameMenuBar.add(annotationsMenu);
1810     alignFrameMenuBar.add(formatMenu);
1811     alignFrameMenuBar.add(colourMenu);
1812     alignFrameMenuBar.add(calculateMenu);
1813     if (!Platform.isJS())
1814     {
1815       alignFrameMenuBar.add(webService);
1816     }
1817
1818     fileMenu.add(fetchSequence);
1819     fileMenu.add(addSequenceMenu);
1820     fileMenu.add(reload);
1821     fileMenu.addSeparator();
1822     fileMenu.add(vamsasStore);
1823     fileMenu.add(save);
1824     fileMenu.add(saveAs);
1825     fileMenu.add(outputTextboxMenu);
1826     fileMenu.add(pageSetup);
1827     fileMenu.add(printMenuItem);
1828     fileMenu.addSeparator();
1829     fileMenu.add(exportImageMenu);
1830     fileMenu.add(exportFeatures);
1831     fileMenu.add(exportAnnotations);
1832     fileMenu.add(loadTreeMenuItem);
1833     fileMenu.add(associatedData);
1834     if (!Platform.isJS())
1835     {
1836       fileMenu.add(loadVcf);
1837     }
1838     fileMenu.addSeparator();
1839     fileMenu.add(closeMenuItem);
1840
1841     pasteMenu.add(pasteNew);
1842     pasteMenu.add(pasteThis);
1843     editMenu.add(undoMenuItem);
1844     editMenu.add(redoMenuItem);
1845     editMenu.add(cut);
1846     editMenu.add(copy);
1847     editMenu.add(copyHighlighted);
1848     editMenu.add(pasteMenu);
1849     editMenu.add(delete);
1850     editMenu.addSeparator();
1851     editMenu.add(remove2LeftMenuItem);
1852     editMenu.add(remove2RightMenuItem);
1853     editMenu.add(removeGappedColumnMenuItem);
1854     editMenu.add(removeAllGapsMenuItem);
1855     editMenu.add(removeRedundancyMenuItem);
1856     editMenu.addSeparator();
1857     // dont add these yet in the CVS build - they cannot be undone!
1858     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1859     // editMenu.add(justifyLeftMenuItem);
1860     // editMenu.add(justifyRightMenuItem);
1861     // editMenu.addSeparator();
1862     editMenu.add(padGapsMenuitem);
1863
1864     showMenu.add(showAllColumns);
1865     showMenu.add(showAllSeqs);
1866     showMenu.add(showAllhidden);
1867     hideMenu.add(hideSelColumns);
1868     hideMenu.add(hideSelSequences);
1869     hideMenu.add(hideAllSelection);
1870     hideMenu.add(hideAllButSelection);
1871     viewMenu.add(newView);
1872     viewMenu.add(expandViews);
1873     viewMenu.add(gatherViews);
1874     viewMenu.addSeparator();
1875     viewMenu.add(showMenu);
1876     viewMenu.add(hideMenu);
1877     viewMenu.add(showComplementMenuItem);
1878     viewMenu.addSeparator();
1879     viewMenu.add(followHighlightMenuItem);
1880     viewMenu.addSeparator();
1881     viewMenu.add(showSeqFeatures);
1882     // viewMenu.add(showSeqFeaturesHeight);
1883     viewMenu.add(openFeatureSettings);
1884     tooltipSettingsMenu.add(showDbRefsMenuitem);
1885     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1886     viewMenu.add(tooltipSettingsMenu);
1887     viewMenu.addSeparator();
1888     viewMenu.add(alignmentProperties);
1889     viewMenu.addSeparator();
1890     viewMenu.add(overviewMenuItem);
1891
1892     annotationsMenu.add(annotationPanelMenuItem);
1893     annotationsMenu.addSeparator();
1894     annotationsMenu.add(showAllAlAnnotations);
1895     annotationsMenu.add(hideAllAlAnnotations);
1896     annotationsMenu.addSeparator();
1897     annotationsMenu.add(showAllSeqAnnotations);
1898     annotationsMenu.add(hideAllSeqAnnotations);
1899     annotationsMenu.add(sortAnnBySequence);
1900     annotationsMenu.add(sortAnnByLabel);
1901     annotationsMenu.addSeparator();
1902     autoAnnMenu.add(showAutoFirst);
1903     autoAnnMenu.add(showAutoLast);
1904     autoAnnMenu.addSeparator();
1905     autoAnnMenu.add(applyAutoAnnotationSettings);
1906     autoAnnMenu.add(showConsensusHistogram);
1907     autoAnnMenu.add(showSSConsensusHistogram);
1908     autoAnnMenu.add(showSequenceLogo);
1909     autoAnnMenu.add(normaliseSequenceLogo);
1910     autoAnnMenu.addSeparator();
1911     autoAnnMenu.add(showGroupConservation);
1912     autoAnnMenu.add(showGroupConsensus);
1913     annotationsMenu.add(autoAnnMenu);
1914
1915     sort.add(sortIDMenuItem);
1916     sort.add(sortLengthMenuItem);
1917     sort.add(sortGroupMenuItem);
1918     sort.add(sortPairwiseMenuItem);
1919     sort.add(sortByTreeMenu);
1920     calculateMenu.add(sort);
1921     calculateMenu.add(calculateTree);
1922     calculateMenu.addSeparator();
1923     calculateMenu.add(pairwiseAlignmentMenuItem);
1924     calculateMenu.addSeparator();
1925     calculateMenu.add(showTranslation);
1926     calculateMenu.add(showReverse);
1927     calculateMenu.add(showReverseComplement);
1928     calculateMenu.add(showProducts);
1929     calculateMenu.add(autoCalculate);
1930     calculateMenu.add(sortByTree);
1931     calculateMenu.addSeparator();
1932     calculateMenu.add(expandAlignment);
1933     calculateMenu.add(extractScores);
1934     if (!Platform.isJS())
1935     {
1936       calculateMenu.addSeparator();
1937       calculateMenu.add(runGroovy);
1938     }
1939
1940     webServiceNoServices = new JMenuItem(
1941             MessageManager.getString("label.no_services"));
1942     webService.add(webServiceNoServices);
1943     if (!Platform.isJS())
1944     {
1945       exportImageMenu.add(htmlMenuItem);
1946     }
1947     exportImageMenu.add(epsFile);
1948     exportImageMenu.add(createPNG);
1949     if (!Platform.isJS())
1950     {
1951       exportImageMenu.add(createBioJS);
1952       exportImageMenu.add(createSVG);
1953     }
1954     addSequenceMenu.add(addFromFile);
1955     addSequenceMenu.add(addFromText);
1956     addSequenceMenu.add(addFromURL);
1957     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1958     statusPanel.add(statusBar, null);
1959     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1960
1961     formatMenu.add(font);
1962     formatMenu.addSeparator();
1963     formatMenu.add(wrapMenuItem);
1964     formatMenu.add(scaleAbove);
1965     formatMenu.add(scaleLeft);
1966     formatMenu.add(scaleRight);
1967     formatMenu.add(seqLimits);
1968     formatMenu.add(idRightAlign);
1969     formatMenu.add(hiddenMarkers);
1970     formatMenu.add(viewBoxesMenuItem);
1971     formatMenu.add(viewTextMenuItem);
1972     formatMenu.add(colourTextMenuItem);
1973     formatMenu.add(renderGapsMenuItem);
1974     formatMenu.add(centreColumnLabelsMenuItem);
1975     formatMenu.add(showNonconservedMenuItem);
1976     selectMenu.add(findMenuItem);
1977     selectMenu.addSeparator();
1978     selectMenu.add(selectAllSequenceMenuItem);
1979     selectMenu.add(deselectAllSequenceMenuItem);
1980     selectMenu.add(invertSequenceMenuItem);
1981     selectMenu.add(invertColSel);
1982     selectMenu.add(createGroup);
1983     selectMenu.add(unGroup);
1984     selectMenu.add(grpsFromSelection);
1985     selectMenu.add(deleteGroups);
1986     selectMenu.add(annotationColumn);
1987     selectMenu.add(selectHighlighted);
1988     // TODO - determine if the listenToViewSelections button is needed : see bug
1989     // JAL-574
1990     // selectMenu.addSeparator();
1991     // selectMenu.add(listenToViewSelections);
1992   }
1993
1994   protected void createPNG_actionPerformed(ActionEvent object)
1995   {
1996     // TODO Auto-generated method stub
1997
1998   }
1999
2000   protected void createEPS_actionPerformed(ActionEvent object)
2001   {
2002     // TODO Auto-generated method stub
2003
2004   }
2005
2006   protected void createSVG_actionPerformed(ActionEvent object)
2007   {
2008     // TODO Auto-generated method stub
2009
2010   }
2011
2012   protected void copyHighlightedColumns_actionPerformed(
2013           ActionEvent actionEvent)
2014   {
2015
2016   }
2017
2018   protected void loadVcf_actionPerformed()
2019   {
2020   }
2021
2022   /**
2023    * Constructs the entries on the Colour menu (but does not add them to the
2024    * menu).
2025    */
2026   protected void initColourMenu()
2027   {
2028     applyToAllGroups = new JCheckBoxMenuItem(
2029             MessageManager.getString("label.apply_colour_to_all_groups"));
2030     applyToAllGroups.addActionListener(new ActionListener()
2031     {
2032       @Override
2033       public void actionPerformed(ActionEvent e)
2034       {
2035         applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
2036       }
2037     });
2038
2039     textColour = new JMenuItem(
2040             MessageManager.getString("label.text_colour"));
2041     textColour.addActionListener(new ActionListener()
2042     {
2043       @Override
2044       public void actionPerformed(ActionEvent e)
2045       {
2046         textColour_actionPerformed();
2047       }
2048     });
2049
2050     conservationMenuItem = new JCheckBoxMenuItem(
2051             MessageManager.getString("action.by_conservation"));
2052     conservationMenuItem.addActionListener(new ActionListener()
2053     {
2054       @Override
2055       public void actionPerformed(ActionEvent e)
2056       {
2057         conservationMenuItem_actionPerformed(
2058                 conservationMenuItem.isSelected());
2059       }
2060     });
2061
2062     abovePIDThreshold = new JCheckBoxMenuItem(
2063             MessageManager.getString("label.above_identity_threshold"));
2064     abovePIDThreshold.addActionListener(new ActionListener()
2065     {
2066       @Override
2067       public void actionPerformed(ActionEvent e)
2068       {
2069         abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
2070       }
2071     });
2072     modifyPID = new JMenuItem(
2073             MessageManager.getString("label.modify_identity_threshold"));
2074     modifyPID.addActionListener(new ActionListener()
2075     {
2076       @Override
2077       public void actionPerformed(ActionEvent e)
2078       {
2079         modifyPID_actionPerformed();
2080       }
2081     });
2082     modifyConservation = new JMenuItem(MessageManager
2083             .getString("label.modify_conservation_threshold"));
2084     modifyConservation.addActionListener(new ActionListener()
2085     {
2086       @Override
2087       public void actionPerformed(ActionEvent e)
2088       {
2089         modifyConservation_actionPerformed();
2090       }
2091     });
2092
2093     annotationColour = new JRadioButtonMenuItem(
2094             MessageManager.getString("action.by_annotation"));
2095     annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
2096     annotationColour.addActionListener(new ActionListener()
2097     {
2098       @Override
2099       public void actionPerformed(ActionEvent e)
2100       {
2101         annotationColour_actionPerformed();
2102       }
2103     });
2104   }
2105
2106   protected void selectHighlightedColumns_actionPerformed(
2107           ActionEvent actionEvent)
2108   {
2109     // TODO Auto-generated method stub
2110
2111   }
2112
2113   /**
2114    * Generate the reverse sequence (or reverse complement if the flag is true)
2115    * and add it to the alignment
2116    *
2117    * @param complement
2118    */
2119   protected void showReverse_actionPerformed(boolean complement)
2120   {
2121   }
2122
2123   /**
2124    * Try to run script in a Groovy console, having first ensured that this
2125    * alignframe is set as currentAlignFrame in Desktop
2126    */
2127   protected void runGroovy_actionPerformed()
2128   {
2129
2130   }
2131
2132   /**
2133    * Adds the given action listener and key accelerator to the given menu item.
2134    * Also saves in a lookup table to support lookup of action by key stroke.
2135    *
2136    * @param keyStroke
2137    * @param menuItem
2138    * @param actionListener
2139    */
2140   protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2141           JMenuItem menuItem, ActionListener actionListener)
2142   {
2143     menuItem.setAccelerator(keyStroke);
2144     accelerators.put(keyStroke, menuItem);
2145     menuItem.addActionListener(actionListener);
2146   }
2147
2148   /**
2149    * Action on clicking sort annotations by type.
2150    *
2151    * @param sortOrder
2152    */
2153   protected void sortAnnotations_actionPerformed()
2154   {
2155   }
2156
2157   /**
2158    * Action on clicking Show all annotations.
2159    *
2160    * @param forSequences
2161    *          update sequence-related annotations
2162    * @param forAlignment
2163    *          update non-sequence-related annotations
2164    */
2165   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2166           boolean forAlignment)
2167   {
2168     setAnnotationsVisibility(true, forSequences, forAlignment);
2169   }
2170
2171   /**
2172    * Action on clicking Hide all annotations.
2173    *
2174    * @param forSequences
2175    *          update sequence-related annotations
2176    * @param forAlignment
2177    *          update non-sequence-related annotations
2178    */
2179   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2180           boolean forAlignment)
2181   {
2182     setAnnotationsVisibility(false, forSequences, forAlignment);
2183   }
2184
2185   /**
2186    * Set the visibility of annotations to true or false. Can act on
2187    * sequence-related annotations, or alignment-related, or both.
2188    *
2189    * @param visible
2190    * @param forSequences
2191    *          update sequence-related annotations
2192    * @param forAlignment
2193    *          update non-sequence-related annotations
2194    */
2195   public void setAnnotationsVisibility(boolean visible,
2196           boolean forSequences, boolean forAlignment)
2197   {
2198
2199   }
2200
2201   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2202   {
2203     // TODO Auto-generated method stub
2204
2205   }
2206
2207   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2208   {
2209     // TODO Auto-generated method stub
2210
2211   }
2212
2213   protected void showAllhidden_actionPerformed(ActionEvent e)
2214   {
2215     // TODO Auto-generated method stub
2216
2217   }
2218
2219   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2220   {
2221     // TODO Auto-generated method stub
2222
2223   }
2224
2225   protected void hideAllSelection_actionPerformed(ActionEvent e)
2226   {
2227     // TODO Auto-generated method stub
2228
2229   }
2230
2231   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2232   {
2233     // TODO Auto-generated method stub
2234
2235   }
2236
2237   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2238   {
2239     // TODO Auto-generated method stub
2240
2241   }
2242
2243   protected void showSSConsensusHistogram_actionPerformed(ActionEvent e)
2244   {
2245     // TODO Auto-generated method stub
2246
2247   }
2248
2249   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2250   {
2251     // TODO Auto-generated method stub
2252
2253   }
2254
2255   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2256   {
2257     // TODO Auto-generated method stub
2258
2259   }
2260
2261   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2262   {
2263     // TODO Auto-generated method stub
2264
2265   }
2266
2267   protected void showGroupConservation_actionPerformed(ActionEvent e)
2268   {
2269     // TODO Auto-generated method stub
2270
2271   }
2272
2273   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2274   {
2275     // TODO Auto-generated method stub
2276
2277   }
2278
2279   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2280   {
2281     // TODO Auto-generated method stub
2282
2283   }
2284
2285   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2286   {
2287     // TODO Auto-generated method stub
2288
2289   }
2290
2291   protected void followHighlight_actionPerformed()
2292   {
2293     // TODO Auto-generated method stub
2294
2295   }
2296
2297   protected void showNpFeats_actionPerformed(ActionEvent e)
2298   {
2299     // TODO Auto-generated method stub
2300
2301   }
2302
2303   protected void showDbRefs_actionPerformed(ActionEvent e)
2304   {
2305     // TODO Auto-generated method stub
2306
2307   }
2308
2309   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2310   {
2311   }
2312
2313   protected void buildSortByAnnotationScoresMenu()
2314   {
2315   }
2316
2317   protected void extractScores_actionPerformed(ActionEvent e)
2318   {
2319   }
2320
2321   protected void outputText_actionPerformed(String formatName)
2322   {
2323   }
2324
2325   public void addFromFile_actionPerformed(ActionEvent e)
2326   {
2327
2328   }
2329
2330   public void addFromText_actionPerformed(ActionEvent e)
2331   {
2332
2333   }
2334
2335   public void addFromURL_actionPerformed(ActionEvent e)
2336   {
2337
2338   }
2339
2340   public void exportFeatures_actionPerformed(ActionEvent e)
2341   {
2342
2343   }
2344
2345   public void exportAnnotations_actionPerformed(ActionEvent e)
2346   {
2347
2348   }
2349
2350   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2351   {
2352   }
2353
2354   protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2355   {
2356
2357   }
2358
2359   protected void closeMenuItem_actionPerformed(boolean b)
2360   {
2361   }
2362
2363   protected void redoMenuItem_actionPerformed(ActionEvent e)
2364   {
2365   }
2366
2367   protected void undoMenuItem_actionPerformed(ActionEvent e)
2368   {
2369   }
2370
2371   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2372   {
2373   }
2374
2375   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2376   {
2377   }
2378
2379   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2380   {
2381   }
2382
2383   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2384   {
2385   }
2386
2387   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2388   {
2389   }
2390
2391   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2392   {
2393   }
2394
2395   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2396   {
2397   }
2398
2399   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2400   {
2401   }
2402
2403   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2404   {
2405   }
2406
2407   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2408   {
2409   }
2410
2411   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2412   {
2413   }
2414
2415   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2416   {
2417   }
2418
2419   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2420   {
2421   }
2422
2423   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2424   {
2425   }
2426
2427   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2428   {
2429   }
2430
2431   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2432   {
2433   }
2434
2435   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2436   {
2437   }
2438
2439   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2440   {
2441   }
2442
2443   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2444   {
2445   }
2446
2447   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2448   {
2449   }
2450
2451   protected void conservationMenuItem_actionPerformed(boolean selected)
2452   {
2453   }
2454
2455   protected void printMenuItem_actionPerformed(ActionEvent e)
2456   {
2457   }
2458
2459   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2460   {
2461   }
2462
2463   protected void findMenuItem_actionPerformed(ActionEvent e)
2464   {
2465   }
2466
2467   protected void abovePIDThreshold_actionPerformed(boolean selected)
2468   {
2469   }
2470
2471   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2472   {
2473   }
2474
2475   protected void deleteGroups_actionPerformed(ActionEvent e)
2476   {
2477   }
2478
2479   protected void createGroup_actionPerformed(ActionEvent e)
2480   {
2481   }
2482
2483   protected void unGroup_actionPerformed(ActionEvent e)
2484   {
2485   }
2486
2487   protected void copy_actionPerformed()
2488   {
2489   }
2490
2491   protected void cut_actionPerformed()
2492   {
2493   }
2494
2495   protected void delete_actionPerformed()
2496   {
2497   }
2498
2499   protected void pasteNew_actionPerformed(ActionEvent e)
2500   {
2501   }
2502
2503   protected void pasteThis_actionPerformed(ActionEvent e)
2504   {
2505   }
2506
2507   protected void applyToAllGroups_actionPerformed(boolean selected)
2508   {
2509   }
2510
2511   protected void font_actionPerformed(ActionEvent e)
2512   {
2513   }
2514
2515   protected void seqLimit_actionPerformed(ActionEvent e)
2516   {
2517   }
2518
2519   public void seqDBRef_actionPerformed(ActionEvent e)
2520   {
2521
2522   }
2523
2524   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2525   {
2526
2527   }
2528
2529   /**
2530    * Template method to handle the 'load T-Coffee scores' menu event.
2531    * <p>
2532    * Subclasses override this method to provide a custom action.
2533    *
2534    * @param event
2535    *          The raised event
2536    */
2537   protected void loadScores_actionPerformed(ActionEvent event)
2538   {
2539
2540   }
2541
2542   protected void jpred_actionPerformed(ActionEvent e)
2543   {
2544   }
2545
2546   protected void scaleAbove_actionPerformed(ActionEvent e)
2547   {
2548   }
2549
2550   protected void scaleLeft_actionPerformed(ActionEvent e)
2551   {
2552   }
2553
2554   protected void scaleRight_actionPerformed(ActionEvent e)
2555   {
2556   }
2557
2558   protected void modifyPID_actionPerformed()
2559   {
2560   }
2561
2562   protected void modifyConservation_actionPerformed()
2563   {
2564   }
2565
2566   protected void saveAs_actionPerformed()
2567   {
2568   }
2569
2570   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2571   {
2572   }
2573
2574   public void vamsasStore_actionPerformed(ActionEvent e)
2575   {
2576
2577   }
2578
2579   public void vamsasLoad_actionPerformed(ActionEvent e)
2580   {
2581
2582   }
2583
2584   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
2585   {
2586
2587   }
2588
2589   public void featureSettings_actionPerformed(ActionEvent e)
2590   {
2591
2592   }
2593
2594   public void fetchSequence_actionPerformed()
2595   {
2596
2597   }
2598
2599   public void smoothFont_actionPerformed(ActionEvent e)
2600   {
2601
2602   }
2603
2604   public void annotationColour_actionPerformed()
2605   {
2606   }
2607
2608   public void annotationColumn_actionPerformed(ActionEvent e)
2609   {
2610   }
2611
2612   public void associatedData_actionPerformed(ActionEvent e)
2613   {
2614
2615   }
2616
2617   public void autoCalculate_actionPerformed(ActionEvent e)
2618   {
2619
2620   }
2621
2622   public void sortByTreeOption_actionPerformed(ActionEvent e)
2623   {
2624
2625   }
2626
2627   public void showAllSeqs_actionPerformed(ActionEvent e)
2628   {
2629
2630   }
2631
2632   public void showAllColumns_actionPerformed(ActionEvent e)
2633   {
2634
2635   }
2636
2637   public void hideSelSequences_actionPerformed(ActionEvent e)
2638   {
2639
2640   }
2641
2642   public void hideSelColumns_actionPerformed(ActionEvent e)
2643   {
2644
2645   }
2646
2647   public void hiddenMarkers_actionPerformed(ActionEvent e)
2648   {
2649
2650   }
2651
2652   public void findPdbId_actionPerformed(ActionEvent e)
2653   {
2654
2655   }
2656
2657   public void enterPdbId_actionPerformed(ActionEvent e)
2658   {
2659
2660   }
2661
2662   public void pdbFile_actionPerformed(ActionEvent e)
2663   {
2664
2665   }
2666
2667   public void invertColSel_actionPerformed(ActionEvent e)
2668   {
2669
2670   }
2671
2672   public void tabSelectionChanged(int sel)
2673   {
2674
2675   }
2676
2677   public void tabbedPane_mousePressed(MouseEvent e)
2678   {
2679
2680   }
2681
2682   public void tabbedPane_focusGained(FocusEvent e)
2683   {
2684     requestFocus();
2685   }
2686
2687   public void save_actionPerformed(ActionEvent e)
2688   {
2689
2690   }
2691
2692   public void reload_actionPerformed(ActionEvent e)
2693   {
2694
2695   }
2696
2697   public void newView_actionPerformed(ActionEvent e)
2698   {
2699
2700   }
2701
2702   public void textColour_actionPerformed()
2703   {
2704
2705   }
2706
2707   public void idRightAlign_actionPerformed(ActionEvent e)
2708   {
2709
2710   }
2711
2712   public void expandViews_actionPerformed(ActionEvent e)
2713   {
2714
2715   }
2716
2717   public void gatherViews_actionPerformed(ActionEvent e)
2718   {
2719
2720   }
2721
2722   public void buildTreeSortMenu()
2723   {
2724
2725   }
2726
2727   public void pageSetup_actionPerformed(ActionEvent e)
2728   {
2729
2730   }
2731
2732   public void alignmentProperties()
2733   {
2734
2735   }
2736
2737   protected void expand_newalign(ActionEvent e)
2738   {
2739     // TODO Auto-generated method stub
2740
2741   }
2742
2743   protected boolean isShowAutoCalculatedAbove()
2744   {
2745     return showAutoCalculatedAbove;
2746   }
2747
2748   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2749   {
2750     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2751   }
2752
2753   protected SequenceAnnotationOrder getAnnotationSortOrder()
2754   {
2755     return annotationSortOrder;
2756   }
2757
2758   protected void setAnnotationSortOrder(
2759           SequenceAnnotationOrder annotationSortOrder)
2760   {
2761     this.annotationSortOrder = annotationSortOrder;
2762   }
2763
2764   public Map<KeyStroke, JMenuItem> getAccelerators()
2765   {
2766     return this.accelerators;
2767   }
2768
2769   /**
2770    * Returns the selected index of the tabbed pane, or -1 if none selected
2771    * (including the case where the tabbed pane has not been made visible).
2772    *
2773    * @return
2774    */
2775   public int getTabIndex()
2776   {
2777     return tabbedPane.getSelectedIndex();
2778   }
2779
2780   public JPanel getStatusPanel()
2781   {
2782     return statusPanel;
2783   }
2784
2785   /**
2786    * Sets a reference to the containing split frame. Also makes the 'toggle
2787    * split view' menu item visible and checked.
2788    *
2789    * @param sf
2790    */
2791   public void setSplitFrame(SplitContainerI sf)
2792   {
2793     this.splitFrame = sf;
2794     if (sf != null)
2795     {
2796       this.showComplementMenuItem.setVisible(true);
2797       this.showComplementMenuItem.setState(true);
2798     }
2799   }
2800
2801   public SplitContainerI getSplitViewContainer()
2802   {
2803     return this.splitFrame;
2804   }
2805
2806   protected void showComplement_actionPerformed(boolean complement)
2807   {
2808   }
2809 }