src/jalview/jbgui/GAlignFrame.java

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