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