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