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     createEPS.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);
1103       }
1104     });
1105
1106     JMenuItem loadTreeMenuItem = new JMenuItem(
1107             MessageManager.getString("label.load_associated_tree"));
1108     loadTreeMenuItem.setActionCommand(
1109             MessageManager.getString("label.load_tree_for_sequence_set"));
1110     loadTreeMenuItem.addActionListener(new ActionListener()
1111     {
1112       @Override
1113       public void actionPerformed(ActionEvent e)
1114       {
1115         loadTreeMenuItem_actionPerformed(e);
1116       }
1117     });
1118
1119     scaleAbove.setVisible(false);
1120     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1121     scaleAbove.addActionListener(new ActionListener()
1122     {
1123       @Override
1124       public void actionPerformed(ActionEvent e)
1125       {
1126         scaleAbove_actionPerformed(e);
1127       }
1128     });
1129     scaleLeft.setVisible(false);
1130     scaleLeft.setSelected(true);
1131     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1132     scaleLeft.addActionListener(new ActionListener()
1133     {
1134       @Override
1135       public void actionPerformed(ActionEvent e)
1136       {
1137         scaleLeft_actionPerformed(e);
1138       }
1139     });
1140     scaleRight.setVisible(false);
1141     scaleRight.setSelected(true);
1142     scaleRight.setText(MessageManager.getString("action.scale_right"));
1143     scaleRight.addActionListener(new ActionListener()
1144     {
1145       @Override
1146       public void actionPerformed(ActionEvent e)
1147       {
1148         scaleRight_actionPerformed(e);
1149       }
1150     });
1151     centreColumnLabelsMenuItem.setVisible(true);
1152     centreColumnLabelsMenuItem.setState(false);
1153     centreColumnLabelsMenuItem.setText(
1154             MessageManager.getString("label.centre_column_labels"));
1155     centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1156     {
1157       @Override
1158       public void actionPerformed(ActionEvent e)
1159       {
1160         centreColumnLabels_actionPerformed(e);
1161       }
1162     });
1163     followHighlightMenuItem.setVisible(true);
1164     followHighlightMenuItem.setState(true);
1165     followHighlightMenuItem
1166             .setText(MessageManager.getString("label.automatic_scrolling"));
1167     followHighlightMenuItem.addActionListener(new ActionListener()
1168     {
1169
1170       @Override
1171       public void actionPerformed(ActionEvent e)
1172       {
1173         followHighlight_actionPerformed();
1174       }
1175
1176     });
1177
1178     sortByTreeMenu
1179             .setText(MessageManager.getString("action.by_tree_order"));
1180     sort.setText(MessageManager.getString("action.sort"));
1181     sort.addMenuListener(new MenuListener()
1182     {
1183       @Override
1184       public void menuSelected(MenuEvent e)
1185       {
1186         buildTreeSortMenu();
1187       }
1188
1189       @Override
1190       public void menuDeselected(MenuEvent e)
1191       {
1192       }
1193
1194       @Override
1195       public void menuCanceled(MenuEvent e)
1196       {
1197       }
1198     });
1199     sortByAnnotScore
1200             .setText(MessageManager.getString("label.sort_by_score"));
1201     sort.add(sortByAnnotScore);
1202     sort.addMenuListener(new javax.swing.event.MenuListener()
1203     {
1204
1205       @Override
1206       public void menuCanceled(MenuEvent e)
1207       {
1208       }
1209
1210       @Override
1211       public void menuDeselected(MenuEvent e)
1212       {
1213       }
1214
1215       @Override
1216       public void menuSelected(MenuEvent e)
1217       {
1218         buildSortByAnnotationScoresMenu();
1219       }
1220     });
1221     sortByAnnotScore.setVisible(false);
1222
1223     calculateTree
1224             .setText(MessageManager.getString("action.calculate_tree_pca"));
1225
1226     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1227     padGapsMenuitem
1228             .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
1229     padGapsMenuitem.addActionListener(new ActionListener()
1230     {
1231       @Override
1232       public void actionPerformed(ActionEvent e)
1233       {
1234         padGapsMenuitem_actionPerformed(e);
1235       }
1236     });
1237     JMenuItem vamsasStore = new JMenuItem(
1238             MessageManager.getString("label.vamsas_store"));
1239     vamsasStore.setVisible(false);
1240     vamsasStore.addActionListener(new ActionListener()
1241     {
1242       @Override
1243       public void actionPerformed(ActionEvent e)
1244       {
1245         vamsasStore_actionPerformed(e);
1246       }
1247     });
1248
1249     /*
1250      * Translate as cDNA with sub-menu of translation tables
1251      */
1252     showTranslation.setText(MessageManager
1253             .getString("label.translate_cDNA"));
1254     boolean first = true;
1255     for (final GeneticCodeI table : GeneticCodes.getInstance()
1256             .getCodeTables())
1257     {
1258       JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
1259       showTranslation.add(item);
1260       item.addActionListener(new ActionListener()
1261       {
1262         @Override
1263         public void actionPerformed(ActionEvent e)
1264         {
1265           showTranslation_actionPerformed(table);
1266         }
1267       });
1268       if (first)
1269       {
1270         showTranslation.addSeparator();
1271       }
1272       first = false;
1273     }
1274
1275     showReverse.setText(MessageManager.getString("label.reverse"));
1276     showReverse.addActionListener(new ActionListener()
1277     {
1278       @Override
1279       public void actionPerformed(ActionEvent e)
1280       {
1281         showReverse_actionPerformed(false);
1282       }
1283     });
1284     showReverseComplement
1285             .setText(MessageManager.getString("label.reverse_complement"));
1286     showReverseComplement.addActionListener(new ActionListener()
1287     {
1288       @Override
1289       public void actionPerformed(ActionEvent e)
1290       {
1291         showReverse_actionPerformed(true);
1292       }
1293     });
1294
1295     JMenuItem extractScores = new JMenuItem(
1296             MessageManager.getString("label.extract_scores"));
1297     extractScores.addActionListener(new ActionListener()
1298     {
1299       @Override
1300       public void actionPerformed(ActionEvent e)
1301       {
1302         extractScores_actionPerformed(e);
1303       }
1304     });
1305     extractScores.setVisible(true);
1306     // JBPNote: TODO: make gui for regex based score extraction
1307
1308     // for show products actions see AlignFrame.canShowProducts
1309     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1310
1311     runGroovy.setText(MessageManager.getString("label.run_groovy"));
1312     runGroovy.setToolTipText(
1313             MessageManager.getString("label.run_groovy_tip"));
1314     runGroovy.addActionListener(new ActionListener()
1315     {
1316       @Override
1317       public void actionPerformed(ActionEvent e)
1318       {
1319         runGroovy_actionPerformed();
1320       }
1321     });
1322
1323     JMenuItem openFeatureSettings = new JMenuItem(
1324             MessageManager.getString("action.feature_settings"));
1325     openFeatureSettings.addActionListener(new ActionListener()
1326     {
1327       @Override
1328       public void actionPerformed(ActionEvent e)
1329       {
1330         featureSettings_actionPerformed(e);
1331       }
1332     });
1333     JMenuItem fetchSequence = new JMenuItem(
1334             MessageManager.getString("label.fetch_sequences"));
1335     fetchSequence.addActionListener(new ActionListener()
1336     {
1337       @Override
1338       public void actionPerformed(ActionEvent e)
1339       {
1340         fetchSequence_actionPerformed(e);
1341       }
1342     });
1343
1344     JMenuItem associatedData = new JMenuItem(
1345             MessageManager.getString("label.load_features_annotations"));
1346     associatedData.addActionListener(new ActionListener()
1347     {
1348       @Override
1349       public void actionPerformed(ActionEvent e)
1350       {
1351         associatedData_actionPerformed(e);
1352       }
1353     });
1354     loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
1355     loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
1356     loadVcf.addActionListener(new ActionListener()
1357     {
1358       @Override
1359       public void actionPerformed(ActionEvent e)
1360       {
1361         loadVcf_actionPerformed();
1362       }
1363     });
1364     autoCalculate.setText(
1365             MessageManager.getString("label.autocalculate_consensus"));
1366     autoCalculate.setState(
1367             jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1368     autoCalculate.addActionListener(new ActionListener()
1369     {
1370       @Override
1371       public void actionPerformed(ActionEvent e)
1372       {
1373         autoCalculate_actionPerformed(e);
1374       }
1375     });
1376     sortByTree.setText(
1377             MessageManager.getString("label.sort_alignment_new_tree"));
1378     sortByTree.setToolTipText("<html>" + MessageManager.getString(
1379             "label.enable_automatically_sort_alignment_when_open_new_tree"));
1380     sortByTree
1381             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1382     sortByTree.addActionListener(new ActionListener()
1383     {
1384       @Override
1385       public void actionPerformed(ActionEvent e)
1386       {
1387         sortByTreeOption_actionPerformed(e);
1388       }
1389     });
1390
1391     listenToViewSelections.setText(
1392             MessageManager.getString("label.listen_for_selections"));
1393     listenToViewSelections
1394             .setToolTipText("<html>" + MessageManager.getString(
1395                     "label.selections_mirror_selections_made_same_sequences_other_views"));
1396     listenToViewSelections.setState(false);
1397     listenToViewSelections.addActionListener(new ActionListener()
1398     {
1399       @Override
1400       public void actionPerformed(ActionEvent e)
1401       {
1402         listenToViewSelections_actionPerformed(e);
1403       }
1404     });
1405
1406     JMenu addSequenceMenu = new JMenu(
1407             MessageManager.getString("label.add_sequences"));
1408     JMenuItem addFromFile = new JMenuItem(
1409             MessageManager.getString("label.from_file"));
1410     addFromFile.addActionListener(new ActionListener()
1411     {
1412       @Override
1413       public void actionPerformed(ActionEvent e)
1414       {
1415         addFromFile_actionPerformed(e);
1416       }
1417     });
1418     JMenuItem addFromText = new JMenuItem(
1419             MessageManager.getString("label.from_textbox"));
1420     addFromText.addActionListener(new ActionListener()
1421     {
1422       @Override
1423       public void actionPerformed(ActionEvent e)
1424       {
1425         addFromText_actionPerformed(e);
1426       }
1427     });
1428     JMenuItem addFromURL = new JMenuItem(
1429             MessageManager.getString("label.from_url"));
1430     addFromURL.addActionListener(new ActionListener()
1431     {
1432       @Override
1433       public void actionPerformed(ActionEvent e)
1434       {
1435         addFromURL_actionPerformed(e);
1436       }
1437     });
1438     JMenuItem exportFeatures = new JMenuItem(
1439             MessageManager.getString("label.export_features"));
1440     exportFeatures.addActionListener(new ActionListener()
1441     {
1442       @Override
1443       public void actionPerformed(ActionEvent e)
1444       {
1445         exportFeatures_actionPerformed(e);
1446       }
1447     });
1448     JMenuItem exportAnnotations = new JMenuItem(
1449             MessageManager.getString("label.export_annotations"));
1450     exportAnnotations.addActionListener(new ActionListener()
1451     {
1452       @Override
1453       public void actionPerformed(ActionEvent e)
1454       {
1455         exportAnnotations_actionPerformed(e);
1456       }
1457     });
1458     statusPanel.setLayout(new GridLayout());
1459     JMenuItem showAllSeqs = new JMenuItem(
1460             MessageManager.getString("label.all_sequences"));
1461     showAllSeqs.setToolTipText(
1462             MessageManager.getString("label.toggle_sequence_visibility"));
1463     showAllSeqs.addActionListener(new ActionListener()
1464     {
1465       @Override
1466       public void actionPerformed(ActionEvent e)
1467       {
1468         showAllSeqs_actionPerformed(e);
1469       }
1470     });
1471     JMenuItem showAllColumns = new JMenuItem(
1472             MessageManager.getString("label.all_columns"));
1473     showAllColumns.setToolTipText(
1474             MessageManager.getString("label.toggle_columns_visibility"));
1475     showAllColumns.addActionListener(new ActionListener()
1476     {
1477       @Override
1478       public void actionPerformed(ActionEvent e)
1479       {
1480         showAllColumns_actionPerformed(e);
1481       }
1482     });
1483     JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1484     JMenuItem hideSelSequences = new JMenuItem(
1485             MessageManager.getString("label.selected_sequences"));
1486     hideSelSequences.setToolTipText(
1487             MessageManager.getString("label.toggle_sequence_visibility"));
1488     hideSelSequences.addActionListener(new ActionListener()
1489     {
1490       @Override
1491       public void actionPerformed(ActionEvent e)
1492       {
1493         hideSelSequences_actionPerformed(e);
1494       }
1495     });
1496     JMenuItem hideSelColumns = new JMenuItem(
1497             MessageManager.getString("label.selected_columns"));
1498     hideSelColumns.setToolTipText(
1499             MessageManager.getString("label.toggle_columns_visibility"));
1500     hideSelColumns.addActionListener(new ActionListener()
1501     {
1502       @Override
1503       public void actionPerformed(ActionEvent e)
1504       {
1505         hideSelColumns_actionPerformed(e);
1506       }
1507     });
1508     JMenuItem hideAllSelection = new JMenuItem(
1509             MessageManager.getString("label.selected_region"));
1510     hideAllSelection.addActionListener(new ActionListener()
1511     {
1512       @Override
1513       public void actionPerformed(ActionEvent e)
1514       {
1515         hideAllSelection_actionPerformed(e);
1516       }
1517     });
1518     // TODO: should be hidden if no selection exists.
1519     JMenuItem hideAllButSelection = new JMenuItem(
1520             MessageManager.getString("label.all_but_selected_region"));
1521     hideAllButSelection.addActionListener(new ActionListener()
1522     {
1523       @Override
1524       public void actionPerformed(ActionEvent e)
1525       {
1526         hideAllButSelection_actionPerformed(e);
1527       }
1528     });
1529     JMenuItem showAllhidden = new JMenuItem(
1530             MessageManager.getString("label.all_sequences_columns"));
1531     showAllhidden.setToolTipText(MessageManager
1532             .getString("label.toggles_visibility_hidden_selected_regions"));
1533     showAllhidden.addActionListener(new ActionListener()
1534     {
1535       @Override
1536       public void actionPerformed(ActionEvent e)
1537       {
1538         showAllhidden_actionPerformed(e);
1539       }
1540     });
1541     hiddenMarkers.setText(
1542             MessageManager.getString("action.show_hidden_markers"));
1543     hiddenMarkers.addActionListener(new ActionListener()
1544     {
1545       @Override
1546       public void actionPerformed(ActionEvent e)
1547       {
1548         hiddenMarkers_actionPerformed(e);
1549       }
1550     });
1551
1552     JMenuItem invertColSel = new JMenuItem(
1553             MessageManager.getString("action.invert_column_selection"));
1554     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1555             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1556                     | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
1557             false);
1558     al = new ActionListener()
1559     {
1560       @Override
1561       public void actionPerformed(ActionEvent e)
1562       {
1563         invertColSel_actionPerformed(e);
1564       }
1565     };
1566     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1567
1568     showComplementMenuItem.setVisible(false);
1569     showComplementMenuItem.addActionListener(new ActionListener()
1570     {
1571       @Override
1572       public void actionPerformed(ActionEvent e)
1573       {
1574         showComplement_actionPerformed(showComplementMenuItem.getState());
1575       }
1576     });
1577
1578     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1579     {
1580       @Override
1581       public void stateChanged(ChangeEvent evt)
1582       {
1583         JTabbedPane pane = (JTabbedPane) evt.getSource();
1584         int sel = pane.getSelectedIndex();
1585         tabSelectionChanged(sel);
1586       }
1587     });
1588     tabbedPane.addMouseListener(new MouseAdapter()
1589     {
1590       @Override
1591       public void mousePressed(MouseEvent e)
1592       {
1593         if (e.isPopupTrigger()) // Mac
1594         {
1595           tabbedPane_mousePressed(e);
1596         }
1597       }
1598
1599       @Override
1600       public void mouseReleased(MouseEvent e)
1601       {
1602         if (e.isPopupTrigger()) // Windows
1603         {
1604           tabbedPane_mousePressed(e);
1605         }
1606       }
1607     });
1608     tabbedPane.addFocusListener(new FocusAdapter()
1609     {
1610       @Override
1611       public void focusGained(FocusEvent e)
1612       {
1613         tabbedPane_focusGained(e);
1614       }
1615     });
1616
1617     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1618     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1619             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
1620     al = new ActionListener()
1621     {
1622       @Override
1623       public void actionPerformed(ActionEvent e)
1624       {
1625         save_actionPerformed(e);
1626       }
1627     };
1628     addMenuActionAndAccelerator(keyStroke, save, al);
1629
1630     reload.setEnabled(false);
1631     reload.setText(MessageManager.getString("action.reload"));
1632     reload.addActionListener(new ActionListener()
1633     {
1634       @Override
1635       public void actionPerformed(ActionEvent e)
1636       {
1637         reload_actionPerformed(e);
1638       }
1639     });
1640
1641     JMenuItem newView = new JMenuItem(
1642             MessageManager.getString("action.new_view"));
1643     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1644             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
1645     al = new ActionListener()
1646     {
1647       @Override
1648       public void actionPerformed(ActionEvent e)
1649       {
1650         newView_actionPerformed(e);
1651       }
1652     };
1653     addMenuActionAndAccelerator(keyStroke, newView, al);
1654
1655     tabbedPane.setToolTipText("<html><i>"
1656             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1657             + "</i></html>");
1658
1659     formatMenu.setText(MessageManager.getString("action.format"));
1660     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1661
1662     idRightAlign.setText(
1663             MessageManager.getString("label.right_align_sequence_id"));
1664     idRightAlign.addActionListener(new ActionListener()
1665     {
1666       @Override
1667       public void actionPerformed(ActionEvent e)
1668       {
1669         idRightAlign_actionPerformed(e);
1670       }
1671     });
1672
1673     gatherViews.setEnabled(false);
1674     gatherViews.setText(MessageManager.getString("action.gather_views"));
1675     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1676     al = new ActionListener()
1677     {
1678       @Override
1679       public void actionPerformed(ActionEvent e)
1680       {
1681         gatherViews_actionPerformed(e);
1682       }
1683     };
1684     addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1685
1686     expandViews.setEnabled(false);
1687     expandViews.setText(MessageManager.getString("action.expand_views"));
1688     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1689     al = new ActionListener()
1690     {
1691       @Override
1692       public void actionPerformed(ActionEvent e)
1693       {
1694         expandViews_actionPerformed(e);
1695       }
1696     };
1697     addMenuActionAndAccelerator(keyStroke, expandViews, al);
1698
1699     JMenuItem pageSetup = new JMenuItem(
1700             MessageManager.getString("action.page_setup"));
1701     pageSetup.addActionListener(new ActionListener()
1702     {
1703       @Override
1704       public void actionPerformed(ActionEvent e)
1705       {
1706         pageSetup_actionPerformed(e);
1707       }
1708     });
1709     JMenuItem alignmentProperties = new JMenuItem(
1710             MessageManager.getString("label.alignment_props"));
1711     alignmentProperties.addActionListener(new ActionListener()
1712     {
1713       @Override
1714       public void actionPerformed(ActionEvent actionEvent)
1715       {
1716         alignmentProperties();
1717       }
1718     });
1719     JMenuItem selectHighlighted = new JMenuItem(
1720             MessageManager.getString("action.select_highlighted_columns"));
1721     selectHighlighted.setToolTipText(
1722             MessageManager.getString("tooltip.select_highlighted_columns"));
1723     al = new ActionListener()
1724     {
1725       @Override
1726       public void actionPerformed(ActionEvent actionEvent)
1727       {
1728         selectHighlightedColumns_actionPerformed(actionEvent);
1729       }
1730     };
1731     selectHighlighted.addActionListener(al);
1732     JMenu tooltipSettingsMenu = new JMenu(
1733             MessageManager.getString("label.sequence_id_tooltip"));
1734     JMenu autoAnnMenu = new JMenu(
1735             MessageManager.getString("label.autocalculated_annotation"));
1736
1737     JMenu exportImageMenu = new JMenu(
1738             MessageManager.getString("label.export_image"));
1739     exportSplitFrameMenu = new JMenu(
1740             MessageManager.getString("label.export_split_frame"));
1741     exportSplitFrameMenu.setVisible(false);
1742     JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1743     alignFrameMenuBar.add(fileMenu);
1744     alignFrameMenuBar.add(editMenu);
1745     alignFrameMenuBar.add(selectMenu);
1746     alignFrameMenuBar.add(viewMenu);
1747     alignFrameMenuBar.add(annotationsMenu);
1748     alignFrameMenuBar.add(formatMenu);
1749     alignFrameMenuBar.add(colourMenu);
1750     alignFrameMenuBar.add(calculateMenu);
1751     alignFrameMenuBar.add(webService);
1752
1753     fileMenu.add(fetchSequence);
1754     fileMenu.add(addSequenceMenu);
1755     fileMenu.add(reload);
1756     fileMenu.addSeparator();
1757     fileMenu.add(vamsasStore);
1758     fileMenu.add(save);
1759     fileMenu.add(saveAs);
1760     fileMenu.add(outputTextboxMenu);
1761     fileMenu.add(pageSetup);
1762     fileMenu.add(printMenuItem);
1763     fileMenu.addSeparator();
1764     fileMenu.add(exportImageMenu);
1765     fileMenu.add(exportSplitFrameMenu);
1766     fileMenu.add(exportFeatures);
1767     fileMenu.add(exportAnnotations);
1768     fileMenu.add(loadTreeMenuItem);
1769     fileMenu.add(associatedData);
1770     fileMenu.add(loadVcf);
1771     fileMenu.addSeparator();
1772     fileMenu.add(closeMenuItem);
1773
1774     pasteMenu.add(pasteNew);
1775     pasteMenu.add(pasteThis);
1776     editMenu.add(undoMenuItem);
1777     editMenu.add(redoMenuItem);
1778     editMenu.add(cut);
1779     editMenu.add(copy);
1780     editMenu.add(pasteMenu);
1781     editMenu.add(delete);
1782     editMenu.addSeparator();
1783     editMenu.add(remove2LeftMenuItem);
1784     editMenu.add(remove2RightMenuItem);
1785     editMenu.add(removeGappedColumnMenuItem);
1786     editMenu.add(removeAllGapsMenuItem);
1787     editMenu.add(removeRedundancyMenuItem);
1788     editMenu.addSeparator();
1789     // dont add these yet in the CVS build - they cannot be undone!
1790     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1791     // editMenu.add(justifyLeftMenuItem);
1792     // editMenu.add(justifyRightMenuItem);
1793     // editMenu.addSeparator();
1794     editMenu.add(padGapsMenuitem);
1795
1796     showMenu.add(showAllColumns);
1797     showMenu.add(showAllSeqs);
1798     showMenu.add(showAllhidden);
1799     hideMenu.add(hideSelColumns);
1800     hideMenu.add(hideSelSequences);
1801     hideMenu.add(hideAllSelection);
1802     hideMenu.add(hideAllButSelection);
1803     viewMenu.add(newView);
1804     viewMenu.add(expandViews);
1805     viewMenu.add(gatherViews);
1806     viewMenu.addSeparator();
1807     viewMenu.add(showMenu);
1808     viewMenu.add(hideMenu);
1809     viewMenu.add(showComplementMenuItem);
1810     viewMenu.addSeparator();
1811     viewMenu.add(followHighlightMenuItem);
1812     viewMenu.addSeparator();
1813     viewMenu.add(showSeqFeatures);
1814     // viewMenu.add(showSeqFeaturesHeight);
1815     viewMenu.add(openFeatureSettings);
1816     tooltipSettingsMenu.add(showDbRefsMenuitem);
1817     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1818     viewMenu.add(tooltipSettingsMenu);
1819     viewMenu.addSeparator();
1820     viewMenu.add(alignmentProperties);
1821     viewMenu.addSeparator();
1822     viewMenu.add(overviewMenuItem);
1823
1824     annotationsMenu.add(annotationPanelMenuItem);
1825     annotationsMenu.addSeparator();
1826     annotationsMenu.add(showAllAlAnnotations);
1827     annotationsMenu.add(hideAllAlAnnotations);
1828     annotationsMenu.addSeparator();
1829     annotationsMenu.add(showAllSeqAnnotations);
1830     annotationsMenu.add(hideAllSeqAnnotations);
1831     annotationsMenu.add(sortAnnBySequence);
1832     annotationsMenu.add(sortAnnByLabel);
1833     annotationsMenu.addSeparator();
1834     autoAnnMenu.add(showAutoFirst);
1835     autoAnnMenu.add(showAutoLast);
1836     autoAnnMenu.addSeparator();
1837     autoAnnMenu.add(applyAutoAnnotationSettings);
1838     autoAnnMenu.add(showConsensusHistogram);
1839     autoAnnMenu.add(showSequenceLogo);
1840     autoAnnMenu.add(normaliseSequenceLogo);
1841     autoAnnMenu.addSeparator();
1842     autoAnnMenu.add(showGroupConservation);
1843     autoAnnMenu.add(showGroupConsensus);
1844     annotationsMenu.add(autoAnnMenu);
1845
1846     sort.add(sortIDMenuItem);
1847     sort.add(sortLengthMenuItem);
1848     sort.add(sortGroupMenuItem);
1849     sort.add(sortPairwiseMenuItem);
1850     sort.add(sortByTreeMenu);
1851     calculateMenu.add(sort);
1852     calculateMenu.add(calculateTree);
1853     calculateMenu.addSeparator();
1854     calculateMenu.add(pairwiseAlignmentMenuItem);
1855     calculateMenu.addSeparator();
1856     calculateMenu.add(showTranslation);
1857     calculateMenu.add(showReverse);
1858     calculateMenu.add(showReverseComplement);
1859     calculateMenu.add(showProducts);
1860     calculateMenu.add(autoCalculate);
1861     calculateMenu.add(sortByTree);
1862     calculateMenu.addSeparator();
1863     calculateMenu.add(expandAlignment);
1864     calculateMenu.add(extractScores);
1865     calculateMenu.addSeparator();
1866     calculateMenu.add(runGroovy);
1867
1868     webServiceNoServices = new JMenuItem(
1869             MessageManager.getString("label.no_services"));
1870     webService.add(webServiceNoServices);
1871     exportImageMenu.add(htmlMenuItem);
1872     exportImageMenu.add(createEPS);
1873     exportImageMenu.add(createPNG);
1874     exportImageMenu.add(createBioJS);
1875     exportImageMenu.add(createSVG);
1876     exportSplitFrameMenu.add(createSplitFrameEPS);
1877     exportSplitFrameMenu.add(createSplitFramePNG);
1878     addSequenceMenu.add(addFromFile);
1879     addSequenceMenu.add(addFromText);
1880     addSequenceMenu.add(addFromURL);
1881     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1882     statusPanel.add(statusBar, null);
1883     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1884
1885     formatMenu.add(font);
1886     formatMenu.addSeparator();
1887     formatMenu.add(wrapMenuItem);
1888     formatMenu.add(scaleAbove);
1889     formatMenu.add(scaleLeft);
1890     formatMenu.add(scaleRight);
1891     formatMenu.add(seqLimits);
1892     formatMenu.add(idRightAlign);
1893     formatMenu.add(hiddenMarkers);
1894     formatMenu.add(viewBoxesMenuItem);
1895     formatMenu.add(viewTextMenuItem);
1896     formatMenu.add(colourTextMenuItem);
1897     formatMenu.add(renderGapsMenuItem);
1898     formatMenu.add(centreColumnLabelsMenuItem);
1899     formatMenu.add(showNonconservedMenuItem);
1900     selectMenu.add(findMenuItem);
1901     selectMenu.addSeparator();
1902     selectMenu.add(selectAllSequenceMenuItem);
1903     selectMenu.add(deselectAllSequenceMenuItem);
1904     selectMenu.add(invertSequenceMenuItem);
1905     selectMenu.add(invertColSel);
1906     selectMenu.add(createGroup);
1907     selectMenu.add(unGroup);
1908     selectMenu.add(grpsFromSelection);
1909     selectMenu.add(deleteGroups);
1910     selectMenu.add(annotationColumn);
1911     selectMenu.add(selectHighlighted);
1912     // TODO - determine if the listenToViewSelections button is needed : see bug
1913     // JAL-574
1914     // selectMenu.addSeparator();
1915     // selectMenu.add(listenToViewSelections);
1916   }
1917
1918   protected void loadVcf_actionPerformed()
1919   {
1920   }
1921
1922   /**
1923    * Constructs the entries on the Colour menu (but does not add them to the
1924    * menu).
1925    */
1926   protected void initColourMenu()
1927   {
1928     applyToAllGroups = new JCheckBoxMenuItem(
1929             MessageManager.getString("label.apply_colour_to_all_groups"));
1930     applyToAllGroups.addActionListener(new ActionListener()
1931     {
1932       @Override
1933       public void actionPerformed(ActionEvent e)
1934       {
1935         applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1936       }
1937     });
1938
1939     textColour = new JMenuItem(
1940             MessageManager.getString("label.text_colour"));
1941     textColour.addActionListener(new ActionListener()
1942     {
1943       @Override
1944       public void actionPerformed(ActionEvent e)
1945       {
1946         textColour_actionPerformed();
1947       }
1948     });
1949
1950     conservationMenuItem = new JCheckBoxMenuItem(
1951             MessageManager.getString("action.by_conservation"));
1952     conservationMenuItem.addActionListener(new ActionListener()
1953     {
1954       @Override
1955       public void actionPerformed(ActionEvent e)
1956       {
1957         conservationMenuItem_actionPerformed(
1958                 conservationMenuItem.isSelected());
1959       }
1960     });
1961
1962     abovePIDThreshold = new JCheckBoxMenuItem(
1963             MessageManager.getString("label.above_identity_threshold"));
1964     abovePIDThreshold.addActionListener(new ActionListener()
1965     {
1966       @Override
1967       public void actionPerformed(ActionEvent e)
1968       {
1969         abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
1970       }
1971     });
1972     modifyPID = new JMenuItem(
1973             MessageManager.getString("label.modify_identity_threshold"));
1974     modifyPID.addActionListener(new ActionListener()
1975     {
1976       @Override
1977       public void actionPerformed(ActionEvent e)
1978       {
1979         modifyPID_actionPerformed();
1980       }
1981     });
1982     modifyConservation = new JMenuItem(MessageManager
1983             .getString("label.modify_conservation_threshold"));
1984     modifyConservation.addActionListener(new ActionListener()
1985     {
1986       @Override
1987       public void actionPerformed(ActionEvent e)
1988       {
1989         modifyConservation_actionPerformed();
1990       }
1991     });
1992
1993     annotationColour = new JRadioButtonMenuItem(
1994             MessageManager.getString("action.by_annotation"));
1995     annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
1996     annotationColour.addActionListener(new ActionListener()
1997     {
1998       @Override
1999       public void actionPerformed(ActionEvent e)
2000       {
2001         annotationColour_actionPerformed();
2002       }
2003     });
2004   }
2005
2006   protected void selectHighlightedColumns_actionPerformed(
2007           ActionEvent actionEvent)
2008   {
2009     // TODO Auto-generated method stub
2010
2011   }
2012
2013   /**
2014    * Generate the reverse sequence (or reverse complement if the flag is true)
2015    * and add it to the alignment
2016    *
2017    * @param complement
2018    */
2019   protected void showReverse_actionPerformed(boolean complement)
2020   {
2021   }
2022
2023   /**
2024    * Try to run script in a Groovy console, having first ensured that this
2025    * alignframe is set as currentAlignFrame in Desktop
2026    */
2027   protected void runGroovy_actionPerformed()
2028   {
2029
2030   }
2031
2032   /**
2033    * Adds the given action listener and key accelerator to the given menu item.
2034    * Also saves in a lookup table to support lookup of action by key stroke.
2035    *
2036    * @param keyStroke
2037    * @param menuItem
2038    * @param actionListener
2039    */
2040   protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2041           JMenuItem menuItem, ActionListener actionListener)
2042   {
2043     menuItem.setAccelerator(keyStroke);
2044     accelerators.put(keyStroke, menuItem);
2045     menuItem.addActionListener(actionListener);
2046   }
2047
2048   /**
2049    * Action on clicking sort annotations by type.
2050    *
2051    * @param sortOrder
2052    */
2053   protected void sortAnnotations_actionPerformed()
2054   {
2055   }
2056
2057   /**
2058    * Action on clicking Show all annotations.
2059    *
2060    * @param forSequences
2061    *          update sequence-related annotations
2062    * @param forAlignment
2063    *          update non-sequence-related annotations
2064    */
2065   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2066           boolean forAlignment)
2067   {
2068     setAnnotationsVisibility(true, forSequences, forAlignment);
2069   }
2070
2071   /**
2072    * Action on clicking Hide all annotations.
2073    *
2074    * @param forSequences
2075    *          update sequence-related annotations
2076    * @param forAlignment
2077    *          update non-sequence-related annotations
2078    */
2079   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2080           boolean forAlignment)
2081   {
2082     setAnnotationsVisibility(false, forSequences, forAlignment);
2083   }
2084
2085   /**
2086    * Set the visibility of annotations to true or false. Can act on
2087    * sequence-related annotations, or alignment-related, or both.
2088    *
2089    * @param visible
2090    * @param forSequences
2091    *          update sequence-related annotations
2092    * @param forAlignment
2093    *          update non-sequence-related annotations
2094    */
2095   protected void setAnnotationsVisibility(boolean visible,
2096           boolean forSequences, boolean forAlignment)
2097   {
2098
2099   }
2100
2101   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2102   {
2103     // TODO Auto-generated method stub
2104
2105   }
2106
2107   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2108   {
2109     // TODO Auto-generated method stub
2110
2111   }
2112
2113   protected void showAllhidden_actionPerformed(ActionEvent e)
2114   {
2115     // TODO Auto-generated method stub
2116
2117   }
2118
2119   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2120   {
2121     // TODO Auto-generated method stub
2122
2123   }
2124
2125   protected void hideAllSelection_actionPerformed(ActionEvent e)
2126   {
2127     // TODO Auto-generated method stub
2128
2129   }
2130
2131   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2132   {
2133     // TODO Auto-generated method stub
2134
2135   }
2136
2137   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2138   {
2139     // TODO Auto-generated method stub
2140
2141   }
2142
2143   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2144   {
2145     // TODO Auto-generated method stub
2146
2147   }
2148
2149   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2150   {
2151     // TODO Auto-generated method stub
2152
2153   }
2154
2155   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2156   {
2157     // TODO Auto-generated method stub
2158
2159   }
2160
2161   protected void showGroupConservation_actionPerformed(ActionEvent e)
2162   {
2163     // TODO Auto-generated method stub
2164
2165   }
2166
2167   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2168   {
2169     // TODO Auto-generated method stub
2170
2171   }
2172
2173   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2174   {
2175     // TODO Auto-generated method stub
2176
2177   }
2178
2179   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2180   {
2181     // TODO Auto-generated method stub
2182
2183   }
2184
2185   protected void followHighlight_actionPerformed()
2186   {
2187     // TODO Auto-generated method stub
2188
2189   }
2190
2191   protected void showNpFeats_actionPerformed(ActionEvent e)
2192   {
2193     // TODO Auto-generated method stub
2194
2195   }
2196
2197   protected void showDbRefs_actionPerformed(ActionEvent e)
2198   {
2199     // TODO Auto-generated method stub
2200
2201   }
2202
2203   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2204   {
2205   }
2206
2207   protected void buildSortByAnnotationScoresMenu()
2208   {
2209   }
2210
2211   protected void extractScores_actionPerformed(ActionEvent e)
2212   {
2213   }
2214
2215   protected void outputText_actionPerformed(ActionEvent e)
2216   {
2217   }
2218
2219   public void addFromFile_actionPerformed(ActionEvent e)
2220   {
2221
2222   }
2223
2224   public void addFromText_actionPerformed(ActionEvent e)
2225   {
2226
2227   }
2228
2229   public void addFromURL_actionPerformed(ActionEvent e)
2230   {
2231
2232   }
2233
2234   public void exportFeatures_actionPerformed(ActionEvent e)
2235   {
2236
2237   }
2238
2239   public void exportAnnotations_actionPerformed(ActionEvent e)
2240   {
2241
2242   }
2243
2244   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2245   {
2246   }
2247
2248   protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2249   {
2250
2251   }
2252
2253   protected void closeMenuItem_actionPerformed(boolean b)
2254   {
2255   }
2256
2257   protected void redoMenuItem_actionPerformed(ActionEvent e)
2258   {
2259   }
2260
2261   protected void undoMenuItem_actionPerformed(ActionEvent e)
2262   {
2263   }
2264
2265   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2266   {
2267   }
2268
2269   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2270   {
2271   }
2272
2273   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2274   {
2275   }
2276
2277   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2278   {
2279   }
2280
2281   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2282   {
2283   }
2284
2285   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2286   {
2287   }
2288
2289   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2290   {
2291   }
2292
2293   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2294   {
2295   }
2296
2297   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2298   {
2299   }
2300
2301   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2302   {
2303   }
2304
2305   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2306   {
2307   }
2308
2309   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2310   {
2311   }
2312
2313   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2314   {
2315   }
2316
2317   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2318   {
2319   }
2320
2321   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2322   {
2323   }
2324
2325   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2326   {
2327   }
2328
2329   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2330   {
2331   }
2332
2333   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2334   {
2335   }
2336
2337   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2338   {
2339   }
2340
2341   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2342   {
2343   }
2344
2345   protected void conservationMenuItem_actionPerformed(boolean selected)
2346   {
2347   }
2348
2349   protected void printMenuItem_actionPerformed(ActionEvent e)
2350   {
2351   }
2352
2353   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2354   {
2355   }
2356
2357   protected void findMenuItem_actionPerformed(ActionEvent e)
2358   {
2359   }
2360
2361   protected void abovePIDThreshold_actionPerformed(boolean selected)
2362   {
2363   }
2364
2365   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2366   {
2367   }
2368
2369   protected void deleteGroups_actionPerformed(ActionEvent e)
2370   {
2371   }
2372
2373   protected void createGroup_actionPerformed(ActionEvent e)
2374   {
2375   }
2376
2377   protected void unGroup_actionPerformed(ActionEvent e)
2378   {
2379   }
2380
2381   protected void copy_actionPerformed(ActionEvent e)
2382   {
2383   }
2384
2385   protected void cut_actionPerformed(ActionEvent e)
2386   {
2387   }
2388
2389   protected void delete_actionPerformed(ActionEvent e)
2390   {
2391   }
2392
2393   protected void pasteNew_actionPerformed(ActionEvent e)
2394   {
2395   }
2396
2397   protected void pasteThis_actionPerformed(ActionEvent e)
2398   {
2399   }
2400
2401   protected void applyToAllGroups_actionPerformed(boolean selected)
2402   {
2403   }
2404
2405   public void createPNG(File f, boolean forSplitFrame)
2406   {
2407   }
2408
2409   protected void font_actionPerformed(ActionEvent e)
2410   {
2411   }
2412
2413   protected void seqLimit_actionPerformed(ActionEvent e)
2414   {
2415   }
2416
2417   public void seqDBRef_actionPerformed(ActionEvent e)
2418   {
2419
2420   }
2421
2422   public void createEPS(File f, boolean forSplitFrame)
2423   {
2424   }
2425
2426   public void createSVG(File f)
2427   {
2428
2429   }
2430
2431   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2432   {
2433
2434   }
2435
2436   /**
2437    * Template method to handle the 'load T-Coffee scores' menu event.
2438    * <p>
2439    * Subclasses override this method to provide a custom action.
2440    *
2441    * @param event
2442    *          The raised event
2443    */
2444   protected void loadScores_actionPerformed(ActionEvent event)
2445   {
2446
2447   }
2448
2449   protected void jpred_actionPerformed(ActionEvent e)
2450   {
2451   }
2452
2453   protected void scaleAbove_actionPerformed(ActionEvent e)
2454   {
2455   }
2456
2457   protected void scaleLeft_actionPerformed(ActionEvent e)
2458   {
2459   }
2460
2461   protected void scaleRight_actionPerformed(ActionEvent e)
2462   {
2463   }
2464
2465   protected void modifyPID_actionPerformed()
2466   {
2467   }
2468
2469   protected void modifyConservation_actionPerformed()
2470   {
2471   }
2472
2473   protected void saveAs_actionPerformed(ActionEvent e)
2474   {
2475   }
2476
2477   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2478   {
2479   }
2480
2481   public void vamsasStore_actionPerformed(ActionEvent e)
2482   {
2483
2484   }
2485
2486   public void vamsasLoad_actionPerformed(ActionEvent e)
2487   {
2488
2489   }
2490
2491   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
2492   {
2493
2494   }
2495
2496   public void featureSettings_actionPerformed(ActionEvent e)
2497   {
2498
2499   }
2500
2501   public void fetchSequence_actionPerformed(ActionEvent e)
2502   {
2503
2504   }
2505
2506   public void smoothFont_actionPerformed(ActionEvent e)
2507   {
2508
2509   }
2510
2511   public void annotationColour_actionPerformed()
2512   {
2513   }
2514
2515   public void annotationColumn_actionPerformed(ActionEvent e)
2516   {
2517   }
2518
2519   public void associatedData_actionPerformed(ActionEvent e)
2520   {
2521
2522   }
2523
2524   public void autoCalculate_actionPerformed(ActionEvent e)
2525   {
2526
2527   }
2528
2529   public void sortByTreeOption_actionPerformed(ActionEvent e)
2530   {
2531
2532   }
2533
2534   public void showAllSeqs_actionPerformed(ActionEvent e)
2535   {
2536
2537   }
2538
2539   public void showAllColumns_actionPerformed(ActionEvent e)
2540   {
2541
2542   }
2543
2544   public void hideSelSequences_actionPerformed(ActionEvent e)
2545   {
2546
2547   }
2548
2549   public void hideSelColumns_actionPerformed(ActionEvent e)
2550   {
2551
2552   }
2553
2554   public void hiddenMarkers_actionPerformed(ActionEvent e)
2555   {
2556
2557   }
2558
2559   public void findPdbId_actionPerformed(ActionEvent e)
2560   {
2561
2562   }
2563
2564   public void enterPdbId_actionPerformed(ActionEvent e)
2565   {
2566
2567   }
2568
2569   public void pdbFile_actionPerformed(ActionEvent e)
2570   {
2571
2572   }
2573
2574   public void invertColSel_actionPerformed(ActionEvent e)
2575   {
2576
2577   }
2578
2579   public void tabSelectionChanged(int sel)
2580   {
2581
2582   }
2583
2584   public void tabbedPane_mousePressed(MouseEvent e)
2585   {
2586
2587   }
2588
2589   public void tabbedPane_focusGained(FocusEvent e)
2590   {
2591     requestFocus();
2592   }
2593
2594   public void save_actionPerformed(ActionEvent e)
2595   {
2596
2597   }
2598
2599   public void reload_actionPerformed(ActionEvent e)
2600   {
2601
2602   }
2603
2604   public void newView_actionPerformed(ActionEvent e)
2605   {
2606
2607   }
2608
2609   public void textColour_actionPerformed()
2610   {
2611
2612   }
2613
2614   public void idRightAlign_actionPerformed(ActionEvent e)
2615   {
2616
2617   }
2618
2619   public void expandViews_actionPerformed(ActionEvent e)
2620   {
2621
2622   }
2623
2624   public void gatherViews_actionPerformed(ActionEvent e)
2625   {
2626
2627   }
2628
2629   public void buildTreeSortMenu()
2630   {
2631
2632   }
2633
2634   public void pageSetup_actionPerformed(ActionEvent e)
2635   {
2636
2637   }
2638
2639   public void alignmentProperties()
2640   {
2641
2642   }
2643
2644   protected void expand_newalign(ActionEvent e)
2645   {
2646     // TODO Auto-generated method stub
2647
2648   }
2649
2650   protected boolean isShowAutoCalculatedAbove()
2651   {
2652     return showAutoCalculatedAbove;
2653   }
2654
2655   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2656   {
2657     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2658   }
2659
2660   protected SequenceAnnotationOrder getAnnotationSortOrder()
2661   {
2662     return annotationSortOrder;
2663   }
2664
2665   protected void setAnnotationSortOrder(
2666           SequenceAnnotationOrder annotationSortOrder)
2667   {
2668     this.annotationSortOrder = annotationSortOrder;
2669   }
2670
2671   public Map<KeyStroke, JMenuItem> getAccelerators()
2672   {
2673     return this.accelerators;
2674   }
2675
2676   /**
2677    * Returns the selected index of the tabbed pane, or -1 if none selected
2678    * (including the case where the tabbed pane has not been made visible).
2679    *
2680    * @return
2681    */
2682   public int getTabIndex()
2683   {
2684     return tabbedPane.getSelectedIndex();
2685   }
2686
2687   public JPanel getStatusPanel()
2688   {
2689     return statusPanel;
2690   }
2691
2692   /**
2693    * Sets a reference to the containing split frame. Also makes the 'toggle split
2694    * view' menu item visible and checked, and makes the 'export split frame image'
2695    * menu visible.
2696    *
2697    * @param sf
2698    */
2699   public void setSplitFrame(SplitContainerI sf, boolean asTopFrame)
2700   {
2701     this.splitFrame = sf;
2702     if (sf != null)
2703     {
2704       this.showComplementMenuItem.setVisible(true);
2705       this.showComplementMenuItem.setState(true);
2706       this.exportSplitFrameMenu.setVisible(true);
2707       String biotype = asTopFrame
2708               ? MessageManager.getString("label.nucleotide")
2709               : MessageManager.getString("label.protein");
2710       this.exportSplitFrameMenu.setToolTipText(MessageManager
2711               .formatMessage("label.export_tooltip", biotype));
2712     }
2713   }
2714
2715   public SplitContainerI getSplitViewContainer()
2716   {
2717     return this.splitFrame;
2718   }
2719
2720   protected void showComplement_actionPerformed(boolean complement)
2721   {
2722   }
2723 }