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