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 colourGapsMenuItem = new JCheckBoxMenuItem();
  94
  95   protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
  96
  97   protected JMenuItem undoMenuItem = new JMenuItem();
  98
  99   protected JMenuItem redoMenuItem = new JMenuItem();
 100
 101   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 102
 103   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 104
 105   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 106
 107   JMenuItem copy = new JMenuItem();
 108
 109   JMenuItem cut = new JMenuItem();
 110
 111   JMenu pasteMenu = new JMenu();
 112
 113   protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 114
 115   protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 116
 117   protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 118
 119   protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 120
 121   protected JCheckBoxMenuItem applyToAllGroups;
 122
 123   protected JMenu colourMenu = new JMenu();
 124
 125   protected JMenuItem textColour;
 126
 127   protected JCheckBoxMenuItem conservationMenuItem;
 128
 129   protected JMenuItem modifyConservation;
 130
 131   protected JCheckBoxMenuItem abovePIDThreshold;
 132
 133   protected JMenuItem modifyPID;
 134
 135   protected JRadioButtonMenuItem annotationColour;
 136
 137   protected JMenu sortByTreeMenu = new JMenu();
 138
 139   protected JMenu sort = new JMenu();
 140
 141   protected JMenuItem calculateTree = new JMenuItem();
 142
 143   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 144
 145   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 146
 147   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 148
 149   protected JMenu showTranslation = new JMenu();
 150
 151   protected JMenuItem showReverse = new JMenuItem();
 152
 153   protected JMenuItem showReverseComplement = new JMenuItem();
 154
 155   protected JMenu showProducts = new JMenu();
 156
 157   protected JMenuItem runGroovy = new JMenuItem();
 158
 159   protected JMenuItem loadVcf;
 160
 161   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 162
 163   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 164
 165   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 166
 167   protected JPanel statusPanel = new JPanel();
 168
 169   protected JMenuItem showAllSeqAnnotations = new JMenuItem();
 170
 171   protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
 172
 173   protected JMenuItem showAllAlAnnotations = new JMenuItem();
 174
 175   protected JMenuItem hideAllAlAnnotations = new JMenuItem();
 176
 177   protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
 178
 179   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 180
 181   protected JTabbedPane tabbedPane = new JTabbedPane();
 182
 183   protected JMenuItem reload = new JMenuItem();
 184
 185   protected JMenu formatMenu = new JMenu();
 186
 187   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 188
 189   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 190
 191   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 192
 193   protected JMenuItem gatherViews = new JMenuItem();
 194
 195   protected JMenuItem expandViews = new JMenuItem();
 196
 197   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 198
 199   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 200
 201   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 202
 203   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 204
 205   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 206
 207   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 208
 209   protected JMenuItem openFeatureSettings;
 210
 211   private SequenceAnnotationOrder annotationSortOrder;
 212
 213   private boolean showAutoCalculatedAbove = false;
 214
 215   private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
 216
 217   private SplitContainerI splitFrame;
 218
 219   public GAlignFrame()
 220   {
 221     try
 222     {
 223
 224       // for Web-page embedding using id=align-frame-div
 225       setName("jalview-alignment");
 226
 227       jbInit();
 228       setJMenuBar(alignFrameMenuBar);
 229
 230       // dynamically fill save as menu with available formats
 231       for (String ff : FileFormats.getInstance().getWritableFormats(true))
 232       {
 233         JMenuItem item = new JMenuItem(ff);
 234
 235         item.addActionListener(new ActionListener()
 236         {
 237           @Override
 238           public void actionPerformed(ActionEvent e)
 239           {
 240             outputText_actionPerformed(e.getActionCommand());
 241           }
 242         });
 243
 244         outputTextboxMenu.add(item);
 245       }
 246     } catch (Exception e)
 247     {
 248       System.err.println(e.toString());
 249     }
 250
 251     if (Platform.allowMnemonics()) // was "not mac and not JS"
 252     {
 253       closeMenuItem.setMnemonic('C');
 254       outputTextboxMenu.setMnemonic('T');
 255       undoMenuItem.setMnemonic('Z');
 256       redoMenuItem.setMnemonic('0');
 257       copy.setMnemonic('C');
 258       cut.setMnemonic('U');
 259       pasteMenu.setMnemonic('P');
 260       reload.setMnemonic('R');
 261     }
 262   }
 263
 264   private void jbInit() throws Exception
 265   {
 266     initColourMenu();
 267
 268     JMenuItem saveAs = new JMenuItem(
 269             MessageManager.getString("action.save_as"));
 270     ActionListener al = new ActionListener()
 271     {
 272       @Override
 273       public void actionPerformed(ActionEvent e)
 274       {
 275         saveAs_actionPerformed();
 276       }
 277     };
 278
 279     // FIXME getDefaultToolkit throws an exception in Headless mode
 280     KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
 281             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
 282                     | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
 283             false);
 284     addMenuActionAndAccelerator(keyStroke, saveAs, al);
 285
 286     closeMenuItem.setText(MessageManager.getString("action.close"));
 287     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
 288             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 289     al = new ActionListener()
 290     {
 291       @Override
 292       public void actionPerformed(ActionEvent e)
 293       {
 294         closeMenuItem_actionPerformed(false);
 295       }
 296     };
 297     addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
 298
 299     JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
 300     JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
 301     JMenu annotationsMenu = new JMenu(
 302             MessageManager.getString("action.annotations"));
 303     JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
 304     colourMenu.setText(MessageManager.getString("action.colour"));
 305     JMenu calculateMenu = new JMenu(
 306             MessageManager.getString("action.calculate"));
 307     webService.setText(MessageManager.getString("action.web_service"));
 308     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
 309             MessageManager.getString("action.select_all"));
 310     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
 311             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 312     al = new ActionListener()
 313     {
 314       @Override
 315       public void actionPerformed(ActionEvent e)
 316       {
 317         selectAllSequenceMenuItem_actionPerformed(e);
 318       }
 319     };
 320     addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
 321
 322     JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
 323             MessageManager.getString("action.deselect_all"));
 324     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
 325     al = new ActionListener()
 326     {
 327       @Override
 328       public void actionPerformed(ActionEvent e)
 329       {
 330         deselectAllSequenceMenuItem_actionPerformed(e);
 331       }
 332     };
 333     addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
 334
 335     JMenuItem invertSequenceMenuItem = new JMenuItem(
 336             MessageManager.getString("action.invert_sequence_selection"));
 337     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
 338             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 339     al = new ActionListener()
 340     {
 341       @Override
 342       public void actionPerformed(ActionEvent e)
 343       {
 344         invertSequenceMenuItem_actionPerformed(e);
 345       }
 346     };
 347     addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
 348
 349     JMenuItem grpsFromSelection = new JMenuItem(
 350             MessageManager.getString("action.make_groups_selection"));
 351     grpsFromSelection.addActionListener(new ActionListener()
 352     {
 353       @Override
 354       public void actionPerformed(ActionEvent e)
 355       {
 356         makeGrpsFromSelection_actionPerformed(e);
 357       }
 358     });
 359     JMenuItem expandAlignment = new JMenuItem(
 360             MessageManager.getString("action.view_flanking_regions"));
 361     expandAlignment.setToolTipText(
 362             MessageManager.getString("label.view_flanking_regions"));
 363     expandAlignment.addActionListener(new ActionListener()
 364     {
 365       @Override
 366       public void actionPerformed(ActionEvent e)
 367       {
 368         expand_newalign(e);
 369       }
 370     });
 371     JMenuItem remove2LeftMenuItem = new JMenuItem(
 372             MessageManager.getString("action.remove_left"));
 373     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
 374             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 375     al = new ActionListener()
 376     {
 377       @Override
 378       public void actionPerformed(ActionEvent e)
 379       {
 380         remove2LeftMenuItem_actionPerformed(e);
 381       }
 382     };
 383     addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
 384
 385     JMenuItem remove2RightMenuItem = new JMenuItem(
 386             MessageManager.getString("action.remove_right"));
 387     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
 388             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 389     al = new ActionListener()
 390     {
 391       @Override
 392       public void actionPerformed(ActionEvent e)
 393       {
 394         remove2RightMenuItem_actionPerformed(e);
 395       }
 396     };
 397     addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
 398
 399     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
 400             MessageManager.getString("action.remove_empty_columns"));
 401     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
 402             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 403     al = new ActionListener()
 404     {
 405       @Override
 406       public void actionPerformed(ActionEvent e)
 407       {
 408         removeGappedColumnMenuItem_actionPerformed(e);
 409       }
 410     };
 411     addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
 412
 413     JMenuItem removeAllGapsMenuItem = new JMenuItem(
 414             MessageManager.getString("action.remove_all_gaps"));
 415     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
 416             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
 417                     | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
 418             false);
 419     al = new ActionListener()
 420     {
 421       @Override
 422       public void actionPerformed(ActionEvent e)
 423       {
 424         removeAllGapsMenuItem_actionPerformed(e);
 425       }
 426     };
 427     addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
 428
 429     JMenuItem justifyLeftMenuItem = new JMenuItem(
 430             MessageManager.getString("action.left_justify_alignment"));
 431     justifyLeftMenuItem.addActionListener(new ActionListener()
 432     {
 433       @Override
 434       public void actionPerformed(ActionEvent e)
 435       {
 436         justifyLeftMenuItem_actionPerformed(e);
 437       }
 438     });
 439     JMenuItem justifyRightMenuItem = new JMenuItem(
 440             MessageManager.getString("action.right_justify_alignment"));
 441     justifyRightMenuItem.addActionListener(new ActionListener()
 442     {
 443       @Override
 444       public void actionPerformed(ActionEvent e)
 445       {
 446         justifyRightMenuItem_actionPerformed(e);
 447       }
 448     });
 449     viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
 450     viewBoxesMenuItem.setState(true);
 451     viewBoxesMenuItem.addActionListener(new ActionListener()
 452     {
 453       @Override
 454       public void actionPerformed(ActionEvent e)
 455       {
 456         viewBoxesMenuItem_actionPerformed(e);
 457       }
 458     });
 459     viewTextMenuItem.setText(MessageManager.getString("action.text"));
 460     viewTextMenuItem.setState(true);
 461     viewTextMenuItem.addActionListener(new ActionListener()
 462     {
 463       @Override
 464       public void actionPerformed(ActionEvent e)
 465       {
 466         viewTextMenuItem_actionPerformed(e);
 467       }
 468     });
 469     showNonconservedMenuItem
 470             .setText(MessageManager.getString("label.show_non_conserved"));
 471     showNonconservedMenuItem.setState(false);
 472     showNonconservedMenuItem.addActionListener(new ActionListener()
 473     {
 474       @Override
 475       public void actionPerformed(ActionEvent e)
 476       {
 477         showUnconservedMenuItem_actionPerformed(e);
 478       }
 479     });
 480     JMenuItem sortPairwiseMenuItem = new JMenuItem(
 481             MessageManager.getString("action.by_pairwise_id"));
 482     sortPairwiseMenuItem.addActionListener(new ActionListener()
 483     {
 484       @Override
 485       public void actionPerformed(ActionEvent e)
 486       {
 487         sortPairwiseMenuItem_actionPerformed(e);
 488       }
 489     });
 490     JMenuItem sortIDMenuItem = new JMenuItem(
 491             MessageManager.getString("action.by_id"));
 492     sortIDMenuItem.addActionListener(new ActionListener()
 493     {
 494       @Override
 495       public void actionPerformed(ActionEvent e)
 496       {
 497         sortIDMenuItem_actionPerformed(e);
 498       }
 499     });
 500     JMenuItem sortLengthMenuItem = new JMenuItem(
 501             MessageManager.getString("action.by_length"));
 502     sortLengthMenuItem.addActionListener(new ActionListener()
 503     {
 504       @Override
 505       public void actionPerformed(ActionEvent e)
 506       {
 507         sortLengthMenuItem_actionPerformed(e);
 508       }
 509     });
 510     JMenuItem sortGroupMenuItem = new JMenuItem(
 511             MessageManager.getString("action.by_group"));
 512     sortGroupMenuItem.addActionListener(new ActionListener()
 513     {
 514       @Override
 515       public void actionPerformed(ActionEvent e)
 516       {
 517         sortGroupMenuItem_actionPerformed(e);
 518       }
 519     });
 520
 521     JMenuItem removeRedundancyMenuItem = new JMenuItem(
 522             MessageManager.getString("action.remove_redundancy"));
 523     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
 524             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 525     al = new ActionListener()
 526     {
 527       @Override
 528       public void actionPerformed(ActionEvent e)
 529       {
 530         removeRedundancyMenuItem_actionPerformed(e);
 531       }
 532     };
 533     addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
 534
 535     JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
 536             MessageManager.getString("action.pairwise_alignment"));
 537     pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
 538     {
 539       @Override
 540       public void actionPerformed(ActionEvent e)
 541       {
 542         pairwiseAlignmentMenuItem_actionPerformed(e);
 543       }
 544     });
 545
 546     this.getContentPane().setLayout(new BorderLayout());
 547     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 548     statusBar.setBackground(Color.white);
 549     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 550     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 551     statusBar.setText(MessageManager.getString("label.status_bar"));
 552     outputTextboxMenu
 553             .setText(MessageManager.getString("label.out_to_textbox"));
 554
 555     annotationPanelMenuItem.setActionCommand("");
 556     annotationPanelMenuItem
 557             .setText(MessageManager.getString("label.show_annotations"));
 558     annotationPanelMenuItem
 559             .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
 560     annotationPanelMenuItem.addActionListener(new ActionListener()
 561     {
 562       @Override
 563       public void actionPerformed(ActionEvent e)
 564       {
 565         annotationPanelMenuItem_actionPerformed(e);
 566       }
 567     });
 568     showAllAlAnnotations.setText(
 569             MessageManager.getString("label.show_all_al_annotations"));
 570     final boolean isAnnotationPanelShown = annotationPanelMenuItem
 571             .getState();
 572     showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 573     showAllAlAnnotations.addActionListener(new ActionListener()
 574     {
 575       @Override
 576       public void actionPerformed(ActionEvent e)
 577       {
 578         showAllAnnotations_actionPerformed(false, true);
 579       }
 580     });
 581     hideAllAlAnnotations.setText(
 582             MessageManager.getString("label.hide_all_al_annotations"));
 583     hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 584     hideAllAlAnnotations.addActionListener(new ActionListener()
 585     {
 586       @Override
 587       public void actionPerformed(ActionEvent e)
 588       {
 589         hideAllAnnotations_actionPerformed(false, true);
 590       }
 591     });
 592     showAllSeqAnnotations.setText(
 593             MessageManager.getString("label.show_all_seq_annotations"));
 594     showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 595     showAllSeqAnnotations.addActionListener(new ActionListener()
 596     {
 597       @Override
 598       public void actionPerformed(ActionEvent e)
 599       {
 600         showAllAnnotations_actionPerformed(true, false);
 601       }
 602     });
 603     hideAllSeqAnnotations.setText(
 604             MessageManager.getString("label.hide_all_seq_annotations"));
 605     hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 606     hideAllSeqAnnotations.addActionListener(new ActionListener()
 607     {
 608       @Override
 609       public void actionPerformed(ActionEvent e)
 610       {
 611         hideAllAnnotations_actionPerformed(true, false);
 612       }
 613     });
 614     SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
 615             .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
 616                     SequenceAnnotationOrder.NONE.name()));
 617     final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
 618             MessageManager.getString("label.sort_annotations_by_sequence"));
 619     final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
 620             MessageManager.getString("label.sort_annotations_by_label"));
 621
 622     sortAnnBySequence.setSelected(
 623             sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
 624     sortAnnBySequence.addActionListener(new ActionListener()
 625     {
 626       @Override
 627       public void actionPerformed(ActionEvent e)
 628       {
 629         boolean newState = sortAnnBySequence.getState();
 630         sortAnnByLabel.setSelected(false);
 631         setAnnotationSortOrder(
 632                 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 633                         : SequenceAnnotationOrder.NONE);
 634         sortAnnotations_actionPerformed();
 635       }
 636     });
 637     sortAnnByLabel.setSelected(
 638             sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
 639     sortAnnByLabel.addActionListener(new ActionListener()
 640     {
 641       @Override
 642       public void actionPerformed(ActionEvent e)
 643       {
 644         boolean newState = sortAnnByLabel.getState();
 645         sortAnnBySequence.setSelected(false);
 646         setAnnotationSortOrder(
 647                 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 648                         : SequenceAnnotationOrder.NONE);
 649         sortAnnotations_actionPerformed();
 650       }
 651     });
 652     colourTextMenuItem = new JCheckBoxMenuItem(
 653             MessageManager.getString("label.colour_text"));
 654     colourTextMenuItem.addActionListener(new ActionListener()
 655     {
 656       @Override
 657       public void actionPerformed(ActionEvent e)
 658       {
 659         colourTextMenuItem_actionPerformed(e);
 660       }
 661     });
 662     colourGapsMenuItem = new JCheckBoxMenuItem(
 663             MessageManager.getString("label.colour_gaps"));
 664     colourGapsMenuItem.addActionListener(new ActionListener()
 665     {
 666       @Override
 667       public void actionPerformed(ActionEvent e)
 668       {
 669         colourGapsMenuItem_actionPerformed(e);
 670       }
 671     });
 672     JMenuItem htmlMenuItem = new JMenuItem(
 673             MessageManager.getString("label.html"));
 674     htmlMenuItem.addActionListener(new ActionListener()
 675     {
 676       @Override
 677       public void actionPerformed(ActionEvent e)
 678       {
 679         htmlMenuItem_actionPerformed(e);
 680       }
 681     });
 682
 683     JMenuItem createBioJS = new JMenuItem(
 684             MessageManager.getString("label.biojs_html_export"));
 685     createBioJS.addActionListener(new java.awt.event.ActionListener()
 686     {
 687       @Override
 688       public void actionPerformed(ActionEvent e)
 689       {
 690         bioJSMenuItem_actionPerformed(e);
 691       }
 692     });
 693
 694     JMenuItem overviewMenuItem = new JMenuItem(
 695             MessageManager.getString("label.overview_window"));
 696     overviewMenuItem.addActionListener(new ActionListener()
 697     {
 698       @Override
 699       public void actionPerformed(ActionEvent e)
 700       {
 701         overviewMenuItem_actionPerformed(e);
 702       }
 703     });
 704
 705     undoMenuItem.setEnabled(false);
 706     undoMenuItem.setText(MessageManager.getString("action.undo"));
 707     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
 708             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 709     al = new ActionListener()
 710     {
 711       @Override
 712       public void actionPerformed(ActionEvent e)
 713       {
 714         undoMenuItem_actionPerformed(e);
 715       }
 716     };
 717     addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
 718
 719     redoMenuItem.setEnabled(false);
 720     redoMenuItem.setText(MessageManager.getString("action.redo"));
 721     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
 722             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 723     al = new ActionListener()
 724     {
 725       @Override
 726       public void actionPerformed(ActionEvent e)
 727       {
 728         redoMenuItem_actionPerformed(e);
 729       }
 730     };
 731     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
 732
 733     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
 734     wrapMenuItem.addActionListener(new ActionListener()
 735     {
 736       @Override
 737       public void actionPerformed(ActionEvent e)
 738       {
 739         wrapMenuItem_actionPerformed(e);
 740       }
 741     });
 742
 743     JMenuItem printMenuItem = new JMenuItem(
 744             MessageManager.getString("action.print"));
 745     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
 746             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 747     al = new ActionListener()
 748     {
 749       @Override
 750       public void actionPerformed(ActionEvent e)
 751       {
 752         printMenuItem_actionPerformed(e);
 753       }
 754     };
 755     addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
 756
 757     renderGapsMenuItem
 758             .setText(MessageManager.getString("action.show_gaps"));
 759     renderGapsMenuItem.setState(true);
 760     renderGapsMenuItem.addActionListener(new ActionListener()
 761     {
 762       @Override
 763       public void actionPerformed(ActionEvent e)
 764       {
 765         renderGapsMenuItem_actionPerformed(e);
 766       }
 767     });
 768
 769     JMenuItem findMenuItem = new JMenuItem(
 770             MessageManager.getString("action.find"));
 771     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
 772             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 773     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
 774             MessageManager.getString("label.find_tip")));
 775     al = new ActionListener()
 776     {
 777       @Override
 778       public void actionPerformed(ActionEvent e)
 779       {
 780         findMenuItem_actionPerformed(e);
 781       }
 782     };
 783     addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
 784
 785     showSeqFeatures.setText(
 786             MessageManager.getString("label.show_sequence_features"));
 787     showSeqFeatures.addActionListener(new ActionListener()
 788     {
 789       @Override
 790       public void actionPerformed(ActionEvent actionEvent)
 791       {
 792         showSeqFeatures_actionPerformed(actionEvent);
 793       }
 794     });
 795     /*
 796      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
 797      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
 798      * void actionPerformed(ActionEvent actionEvent) {
 799      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
 800      */
 801     showDbRefsMenuitem
 802             .setText(MessageManager.getString("label.show_database_refs"));
 803     showDbRefsMenuitem.addActionListener(new ActionListener()
 804     {
 805
 806       @Override
 807       public void actionPerformed(ActionEvent e)
 808       {
 809         showDbRefs_actionPerformed(e);
 810       }
 811
 812     });
 813     showNpFeatsMenuitem.setText(
 814             MessageManager.getString("label.show_non_positional_features"));
 815     showNpFeatsMenuitem.addActionListener(new ActionListener()
 816     {
 817
 818       @Override
 819       public void actionPerformed(ActionEvent e)
 820       {
 821         showNpFeats_actionPerformed(e);
 822       }
 823
 824     });
 825     showGroupConservation
 826             .setText(MessageManager.getString("label.group_conservation"));
 827     showGroupConservation.addActionListener(new ActionListener()
 828     {
 829
 830       @Override
 831       public void actionPerformed(ActionEvent e)
 832       {
 833         showGroupConservation_actionPerformed(e);
 834       }
 835
 836     });
 837
 838     showGroupConsensus
 839             .setText(MessageManager.getString("label.group_consensus"));
 840     showGroupConsensus.addActionListener(new ActionListener()
 841     {
 842
 843       @Override
 844       public void actionPerformed(ActionEvent e)
 845       {
 846         showGroupConsensus_actionPerformed(e);
 847       }
 848
 849     });
 850     showConsensusHistogram.setText(
 851             MessageManager.getString("label.show_consensus_histogram"));
 852     showConsensusHistogram.addActionListener(new ActionListener()
 853     {
 854
 855       @Override
 856       public void actionPerformed(ActionEvent e)
 857       {
 858         showConsensusHistogram_actionPerformed(e);
 859       }
 860
 861     });
 862     showSequenceLogo
 863             .setText(MessageManager.getString("label.show_consensus_logo"));
 864     showSequenceLogo.addActionListener(new ActionListener()
 865     {
 866
 867       @Override
 868       public void actionPerformed(ActionEvent e)
 869       {
 870         showSequenceLogo_actionPerformed(e);
 871       }
 872
 873     });
 874     normaliseSequenceLogo
 875             .setText(MessageManager.getString("label.norm_consensus_logo"));
 876     normaliseSequenceLogo.addActionListener(new ActionListener()
 877     {
 878
 879       @Override
 880       public void actionPerformed(ActionEvent e)
 881       {
 882         normaliseSequenceLogo_actionPerformed(e);
 883       }
 884
 885     });
 886     applyAutoAnnotationSettings
 887             .setText(MessageManager.getString("label.apply_all_groups"));
 888     applyAutoAnnotationSettings.setState(false);
 889     applyAutoAnnotationSettings.setVisible(true);
 890     applyAutoAnnotationSettings.addActionListener(new ActionListener()
 891     {
 892       @Override
 893       public void actionPerformed(ActionEvent e)
 894       {
 895         applyAutoAnnotationSettings_actionPerformed(e);
 896       }
 897     });
 898
 899     ButtonGroup buttonGroup = new ButtonGroup();
 900     final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
 901             MessageManager.getString("label.show_first"));
 902     final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
 903             MessageManager.getString("label.show_last"));
 904     buttonGroup.add(showAutoFirst);
 905     buttonGroup.add(showAutoLast);
 906     final boolean autoFirst = Cache
 907             .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
 908     showAutoFirst.setSelected(autoFirst);
 909     setShowAutoCalculatedAbove(autoFirst);
 910     showAutoFirst.addActionListener(new ActionListener()
 911     {
 912       @Override
 913       public void actionPerformed(ActionEvent e)
 914       {
 915         setShowAutoCalculatedAbove(showAutoFirst.isSelected());
 916         sortAnnotations_actionPerformed();
 917       }
 918     });
 919     showAutoLast.setSelected(!showAutoFirst.isSelected());
 920     showAutoLast.addActionListener(new ActionListener()
 921     {
 922       @Override
 923       public void actionPerformed(ActionEvent e)
 924       {
 925         setShowAutoCalculatedAbove(!showAutoLast.isSelected());
 926         sortAnnotations_actionPerformed();
 927       }
 928     });
 929
 930     JMenuItem deleteGroups = new JMenuItem(
 931             MessageManager.getString("action.undefine_groups"));
 932     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
 933             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 934     al = new ActionListener()
 935     {
 936       @Override
 937       public void actionPerformed(ActionEvent e)
 938       {
 939         deleteGroups_actionPerformed(e);
 940       }
 941     };
 942     addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
 943
 944     JMenuItem annotationColumn = new JMenuItem(
 945             MessageManager.getString("action.select_by_annotation"));
 946     annotationColumn.addActionListener(new ActionListener()
 947     {
 948       @Override
 949       public void actionPerformed(ActionEvent e)
 950       {
 951         annotationColumn_actionPerformed(e);
 952       }
 953     });
 954
 955     JMenuItem createGroup = new JMenuItem(
 956             MessageManager.getString("action.create_group"));
 957     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
 958             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 959     al = new ActionListener()
 960     {
 961       @Override
 962       public void actionPerformed(ActionEvent e)
 963       {
 964         createGroup_actionPerformed(e);
 965       }
 966     };
 967     addMenuActionAndAccelerator(keyStroke, createGroup, al);
 968
 969     JMenuItem unGroup = new JMenuItem(
 970             MessageManager.getString("action.remove_group"));
 971     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
 972             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
 973                     | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
 974             false);
 975     al = new ActionListener()
 976     {
 977       @Override
 978       public void actionPerformed(ActionEvent e)
 979       {
 980         unGroup_actionPerformed(e);
 981       }
 982     };
 983     addMenuActionAndAccelerator(keyStroke, unGroup, al);
 984
 985     copy.setText(MessageManager.getString("action.copy"));
 986     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
 987             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 988
 989     al = new ActionListener()
 990     {
 991       @Override
 992       public void actionPerformed(ActionEvent e)
 993       {
 994         copy_actionPerformed();
 995       }
 996     };
 997     addMenuActionAndAccelerator(keyStroke, copy, al);
 998
 999     cut.setText(MessageManager.getString("action.cut"));
1000     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
1001             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
1002     al = new ActionListener()
1003     {
1004       @Override
1005       public void actionPerformed(ActionEvent e)
1006       {
1007         cut_actionPerformed();
1008       }
1009     };
1010     addMenuActionAndAccelerator(keyStroke, cut, al);
1011
1012     JMenuItem delete = new JMenuItem(
1013             MessageManager.getString("action.delete"));
1014     delete.addActionListener(new ActionListener()
1015     {
1016       @Override
1017       public void actionPerformed(ActionEvent e)
1018       {
1019         delete_actionPerformed();
1020       }
1021     });
1022
1023     pasteMenu.setText(MessageManager.getString("action.paste"));
1024     JMenuItem pasteNew = new JMenuItem(
1025             MessageManager.getString("label.to_new_alignment"));
1026     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1027             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1028                     | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
1029             false);
1030     al = new ActionListener()
1031     {
1032       @Override
1033       public void actionPerformed(ActionEvent e)
1034       {
1035         pasteNew_actionPerformed(e);
1036       }
1037     };
1038     addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1039
1040     JMenuItem pasteThis = new JMenuItem(
1041             MessageManager.getString("label.to_this_alignment"));
1042     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1043             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
1044     al = new ActionListener()
1045     {
1046       @Override
1047       public void actionPerformed(ActionEvent e)
1048       {
1049         pasteThis_actionPerformed(e);
1050       }
1051     };
1052     addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1053
1054     JMenuItem createPNG = new JMenuItem("PNG");
1055     createPNG.addActionListener(new ActionListener()
1056     {
1057       @Override
1058       public void actionPerformed(ActionEvent e)
1059       {
1060         createPNG(null);
1061       }
1062     });
1063     createPNG.setActionCommand(
1064             MessageManager.getString("label.save_png_image"));
1065
1066     JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1067     font.addActionListener(new ActionListener()
1068     {
1069       @Override
1070       public void actionPerformed(ActionEvent e)
1071       {
1072         font_actionPerformed(e);
1073       }
1074     });
1075     seqLimits.setText(
1076             MessageManager.getString("label.show_sequence_limits"));
1077     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1078     seqLimits.addActionListener(new ActionListener()
1079     {
1080       @Override
1081       public void actionPerformed(ActionEvent e)
1082       {
1083         seqLimit_actionPerformed(e);
1084       }
1085     });
1086     JMenuItem epsFile = new JMenuItem("EPS");
1087     epsFile.addActionListener(new ActionListener()
1088     {
1089       @Override
1090       public void actionPerformed(ActionEvent e)
1091       {
1092         createEPS(null);
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
1253             .setText(MessageManager.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     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
1334     /*
1335      * add sub-menu of database we can fetch from
1336      */
1337     JMenuItem fetchSequence = new JMenuItem(
1338             MessageManager.getString("label.fetch_sequences"));
1339     fetchSequence.addActionListener(new ActionListener()
1340     {
1341       @Override
1342       public void actionPerformed(ActionEvent e)
1343       {
1344         fetchSequence_actionPerformed();
1345       }
1346     });
1347
1348     JMenuItem associatedData = new JMenuItem(
1349             MessageManager.getString("label.load_features_annotations"));
1350     associatedData.addActionListener(new ActionListener()
1351     {
1352       @Override
1353       public void actionPerformed(ActionEvent e)
1354       {
1355         associatedData_actionPerformed(e);
1356       }
1357     });
1358     loadVcf = new JMenuItem(
1359             MessageManager.getString("label.load_vcf_file"));
1360     loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
1361     loadVcf.addActionListener(new ActionListener()
1362     {
1363       @Override
1364       public void actionPerformed(ActionEvent e)
1365       {
1366         loadVcf_actionPerformed();
1367       }
1368     });
1369     autoCalculate.setText(
1370             MessageManager.getString("label.autocalculate_consensus"));
1371     autoCalculate.setState(
1372             jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1373     autoCalculate.addActionListener(new ActionListener()
1374     {
1375       @Override
1376       public void actionPerformed(ActionEvent e)
1377       {
1378         autoCalculate_actionPerformed(e);
1379       }
1380     });
1381     sortByTree.setText(
1382             MessageManager.getString("label.sort_alignment_new_tree"));
1383     sortByTree.setToolTipText("<html>" + MessageManager.getString(
1384             "label.enable_automatically_sort_alignment_when_open_new_tree"));
1385     sortByTree
1386             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1387     sortByTree.addActionListener(new ActionListener()
1388     {
1389       @Override
1390       public void actionPerformed(ActionEvent e)
1391       {
1392         sortByTreeOption_actionPerformed(e);
1393       }
1394     });
1395
1396     listenToViewSelections.setText(
1397             MessageManager.getString("label.listen_for_selections"));
1398     listenToViewSelections
1399             .setToolTipText("<html>" + MessageManager.getString(
1400                     "label.selections_mirror_selections_made_same_sequences_other_views"));
1401     listenToViewSelections.setState(false);
1402     listenToViewSelections.addActionListener(new ActionListener()
1403     {
1404       @Override
1405       public void actionPerformed(ActionEvent e)
1406       {
1407         listenToViewSelections_actionPerformed(e);
1408       }
1409     });
1410
1411     JMenu addSequenceMenu = new JMenu(
1412             MessageManager.getString("label.add_sequences"));
1413     JMenuItem addFromFile = new JMenuItem(
1414             MessageManager.getString("label.from_file"));
1415     addFromFile.addActionListener(new ActionListener()
1416     {
1417       @Override
1418       public void actionPerformed(ActionEvent e)
1419       {
1420         addFromFile_actionPerformed(e);
1421       }
1422     });
1423     JMenuItem addFromText = new JMenuItem(
1424             MessageManager.getString("label.from_textbox"));
1425     addFromText.addActionListener(new ActionListener()
1426     {
1427       @Override
1428       public void actionPerformed(ActionEvent e)
1429       {
1430         addFromText_actionPerformed(e);
1431       }
1432     });
1433     JMenuItem addFromURL = new JMenuItem(
1434             MessageManager.getString("label.from_url"));
1435     addFromURL.addActionListener(new ActionListener()
1436     {
1437       @Override
1438       public void actionPerformed(ActionEvent e)
1439       {
1440         addFromURL_actionPerformed(e);
1441       }
1442     });
1443     JMenuItem exportFeatures = new JMenuItem(
1444             MessageManager.getString("label.export_features"));
1445     exportFeatures.addActionListener(new ActionListener()
1446     {
1447       @Override
1448       public void actionPerformed(ActionEvent e)
1449       {
1450         exportFeatures_actionPerformed(e);
1451       }
1452     });
1453     JMenuItem exportAnnotations = new JMenuItem(
1454             MessageManager.getString("label.export_annotations"));
1455     exportAnnotations.addActionListener(new ActionListener()
1456     {
1457       @Override
1458       public void actionPerformed(ActionEvent e)
1459       {
1460         exportAnnotations_actionPerformed(e);
1461       }
1462     });
1463     statusPanel.setLayout(new GridLayout());
1464     JMenuItem showAllSeqs = new JMenuItem(
1465             MessageManager.getString("label.all_sequences"));
1466     showAllSeqs.setToolTipText(
1467             MessageManager.getString("label.toggle_sequence_visibility"));
1468     showAllSeqs.addActionListener(new ActionListener()
1469     {
1470       @Override
1471       public void actionPerformed(ActionEvent e)
1472       {
1473         showAllSeqs_actionPerformed(e);
1474       }
1475     });
1476     JMenuItem showAllColumns = new JMenuItem(
1477             MessageManager.getString("label.all_columns"));
1478     showAllColumns.setToolTipText(
1479             MessageManager.getString("label.toggle_columns_visibility"));
1480     showAllColumns.addActionListener(new ActionListener()
1481     {
1482       @Override
1483       public void actionPerformed(ActionEvent e)
1484       {
1485         showAllColumns_actionPerformed(e);
1486       }
1487     });
1488     JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1489     JMenuItem hideSelSequences = new JMenuItem(
1490             MessageManager.getString("label.selected_sequences"));
1491     hideSelSequences.setToolTipText(
1492             MessageManager.getString("label.toggle_sequence_visibility"));
1493     hideSelSequences.addActionListener(new ActionListener()
1494     {
1495       @Override
1496       public void actionPerformed(ActionEvent e)
1497       {
1498         hideSelSequences_actionPerformed(e);
1499       }
1500     });
1501     JMenuItem hideSelColumns = new JMenuItem(
1502             MessageManager.getString("label.selected_columns"));
1503     hideSelColumns.setToolTipText(
1504             MessageManager.getString("label.toggle_columns_visibility"));
1505     hideSelColumns.addActionListener(new ActionListener()
1506     {
1507       @Override
1508       public void actionPerformed(ActionEvent e)
1509       {
1510         hideSelColumns_actionPerformed(e);
1511       }
1512     });
1513     JMenuItem hideAllSelection = new JMenuItem(
1514             MessageManager.getString("label.selected_region"));
1515     hideAllSelection.addActionListener(new ActionListener()
1516     {
1517       @Override
1518       public void actionPerformed(ActionEvent e)
1519       {
1520         hideAllSelection_actionPerformed(e);
1521       }
1522     });
1523     // TODO: should be hidden if no selection exists.
1524     JMenuItem hideAllButSelection = new JMenuItem(
1525             MessageManager.getString("label.all_but_selected_region"));
1526     hideAllButSelection.addActionListener(new ActionListener()
1527     {
1528       @Override
1529       public void actionPerformed(ActionEvent e)
1530       {
1531         hideAllButSelection_actionPerformed(e);
1532       }
1533     });
1534     JMenuItem showAllhidden = new JMenuItem(
1535             MessageManager.getString("label.all_sequences_columns"));
1536     showAllhidden.setToolTipText(MessageManager
1537             .getString("label.toggles_visibility_hidden_selected_regions"));
1538     showAllhidden.addActionListener(new ActionListener()
1539     {
1540       @Override
1541       public void actionPerformed(ActionEvent e)
1542       {
1543         showAllhidden_actionPerformed(e);
1544       }
1545     });
1546     hiddenMarkers.setText(
1547             MessageManager.getString("action.show_hidden_markers"));
1548     hiddenMarkers.addActionListener(new ActionListener()
1549     {
1550       @Override
1551       public void actionPerformed(ActionEvent e)
1552       {
1553         hiddenMarkers_actionPerformed(e);
1554       }
1555     });
1556
1557     JMenuItem invertColSel = new JMenuItem(
1558             MessageManager.getString("action.invert_column_selection"));
1559     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1560             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1561                     | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
1562             false);
1563     al = new ActionListener()
1564     {
1565       @Override
1566       public void actionPerformed(ActionEvent e)
1567       {
1568         invertColSel_actionPerformed(e);
1569       }
1570     };
1571     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1572
1573     showComplementMenuItem.setVisible(false);
1574     showComplementMenuItem.addActionListener(new ActionListener()
1575     {
1576       @Override
1577       public void actionPerformed(ActionEvent e)
1578       {
1579         showComplement_actionPerformed(showComplementMenuItem.getState());
1580       }
1581     });
1582
1583     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1584     {
1585       @Override
1586       public void stateChanged(ChangeEvent evt)
1587       {
1588         JTabbedPane pane = (JTabbedPane) evt.getSource();
1589         int sel = pane.getSelectedIndex();
1590         tabSelectionChanged(sel);
1591       }
1592     });
1593     tabbedPane.addMouseListener(new MouseAdapter()
1594     {
1595       @Override
1596       public void mousePressed(MouseEvent e)
1597       {
1598         if (e.isPopupTrigger()) // Mac
1599         {
1600           tabbedPane_mousePressed(e);
1601         }
1602       }
1603
1604       @Override
1605       public void mouseReleased(MouseEvent e)
1606       {
1607         if (e.isPopupTrigger()) // Windows
1608         {
1609           tabbedPane_mousePressed(e);
1610         }
1611       }
1612     });
1613     tabbedPane.addFocusListener(new FocusAdapter()
1614     {
1615       @Override
1616       public void focusGained(FocusEvent e)
1617       {
1618         tabbedPane_focusGained(e);
1619       }
1620     });
1621
1622     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1623     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1624             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
1625     al = new ActionListener()
1626     {
1627       @Override
1628       public void actionPerformed(ActionEvent e)
1629       {
1630         save_actionPerformed(e);
1631       }
1632     };
1633     addMenuActionAndAccelerator(keyStroke, save, al);
1634
1635     reload.setEnabled(false);
1636     reload.setText(MessageManager.getString("action.reload"));
1637     reload.addActionListener(new ActionListener()
1638     {
1639       @Override
1640       public void actionPerformed(ActionEvent e)
1641       {
1642         reload_actionPerformed(e);
1643       }
1644     });
1645
1646     JMenuItem newView = new JMenuItem(
1647             MessageManager.getString("action.new_view"));
1648     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1649             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
1650     al = new ActionListener()
1651     {
1652       @Override
1653       public void actionPerformed(ActionEvent e)
1654       {
1655         newView_actionPerformed(e);
1656       }
1657     };
1658     addMenuActionAndAccelerator(keyStroke, newView, al);
1659
1660     tabbedPane.setToolTipText("<html><i>"
1661             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1662             + "</i></html>");
1663
1664     formatMenu.setText(MessageManager.getString("action.format"));
1665     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1666
1667     idRightAlign.setText(
1668             MessageManager.getString("label.right_align_sequence_id"));
1669     idRightAlign.addActionListener(new ActionListener()
1670     {
1671       @Override
1672       public void actionPerformed(ActionEvent e)
1673       {
1674         idRightAlign_actionPerformed(e);
1675       }
1676     });
1677
1678     gatherViews.setEnabled(false);
1679     gatherViews.setText(MessageManager.getString("action.gather_views"));
1680     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1681     al = new ActionListener()
1682     {
1683       @Override
1684       public void actionPerformed(ActionEvent e)
1685       {
1686         gatherViews_actionPerformed(e);
1687       }
1688     };
1689     addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1690
1691     expandViews.setEnabled(false);
1692     expandViews.setText(MessageManager.getString("action.expand_views"));
1693     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1694     al = new ActionListener()
1695     {
1696       @Override
1697       public void actionPerformed(ActionEvent e)
1698       {
1699         expandViews_actionPerformed(e);
1700       }
1701     };
1702     addMenuActionAndAccelerator(keyStroke, expandViews, al);
1703
1704     JMenuItem pageSetup = new JMenuItem(
1705             MessageManager.getString("action.page_setup"));
1706     pageSetup.addActionListener(new ActionListener()
1707     {
1708       @Override
1709       public void actionPerformed(ActionEvent e)
1710       {
1711         pageSetup_actionPerformed(e);
1712       }
1713     });
1714     JMenuItem alignmentProperties = new JMenuItem(
1715             MessageManager.getString("label.alignment_props"));
1716     alignmentProperties.addActionListener(new ActionListener()
1717     {
1718       @Override
1719       public void actionPerformed(ActionEvent actionEvent)
1720       {
1721         alignmentProperties();
1722       }
1723     });
1724     JMenuItem selectHighlighted = new JMenuItem(
1725             MessageManager.getString("action.select_highlighted_columns"));
1726     selectHighlighted.setToolTipText(
1727             MessageManager.getString("tooltip.select_highlighted_columns"));
1728     al = new ActionListener()
1729     {
1730       @Override
1731       public void actionPerformed(ActionEvent actionEvent)
1732       {
1733         selectHighlightedColumns_actionPerformed(actionEvent);
1734       }
1735     };
1736     selectHighlighted.addActionListener(al);
1737     JMenu tooltipSettingsMenu = new JMenu(
1738             MessageManager.getString("label.sequence_id_tooltip"));
1739     JMenu autoAnnMenu = new JMenu(
1740             MessageManager.getString("label.autocalculated_annotation"));
1741
1742     JMenu exportImageMenu = new JMenu(
1743             MessageManager.getString("label.export_image"));
1744     JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1745     alignFrameMenuBar.add(fileMenu);
1746     alignFrameMenuBar.add(editMenu);
1747     alignFrameMenuBar.add(selectMenu);
1748     alignFrameMenuBar.add(viewMenu);
1749     alignFrameMenuBar.add(annotationsMenu);
1750     alignFrameMenuBar.add(formatMenu);
1751     alignFrameMenuBar.add(colourMenu);
1752     alignFrameMenuBar.add(calculateMenu);
1753     if (!Platform.isJS())
1754     {
1755       alignFrameMenuBar.add(webService);
1756     }
1757
1758     fileMenu.add(fetchSequence);
1759     fileMenu.add(addSequenceMenu);
1760     fileMenu.add(reload);
1761     fileMenu.addSeparator();
1762     fileMenu.add(vamsasStore);
1763     fileMenu.add(save);
1764     fileMenu.add(saveAs);
1765     fileMenu.add(outputTextboxMenu);
1766     fileMenu.add(pageSetup);
1767     fileMenu.add(printMenuItem);
1768     fileMenu.addSeparator();
1769     fileMenu.add(exportImageMenu);
1770     fileMenu.add(exportFeatures);
1771     fileMenu.add(exportAnnotations);
1772     fileMenu.add(loadTreeMenuItem);
1773     fileMenu.add(associatedData);
1774     if (!Platform.isJS())
1775     {
1776       fileMenu.add(loadVcf);
1777     }
1778     fileMenu.addSeparator();
1779     fileMenu.add(closeMenuItem);
1780
1781     pasteMenu.add(pasteNew);
1782     pasteMenu.add(pasteThis);
1783     editMenu.add(undoMenuItem);
1784     editMenu.add(redoMenuItem);
1785     editMenu.add(cut);
1786     editMenu.add(copy);
1787     editMenu.add(pasteMenu);
1788     editMenu.add(delete);
1789     editMenu.addSeparator();
1790     editMenu.add(remove2LeftMenuItem);
1791     editMenu.add(remove2RightMenuItem);
1792     editMenu.add(removeGappedColumnMenuItem);
1793     editMenu.add(removeAllGapsMenuItem);
1794     editMenu.add(removeRedundancyMenuItem);
1795     editMenu.addSeparator();
1796     // dont add these yet in the CVS build - they cannot be undone!
1797     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1798     // editMenu.add(justifyLeftMenuItem);
1799     // editMenu.add(justifyRightMenuItem);
1800     // editMenu.addSeparator();
1801     editMenu.add(padGapsMenuitem);
1802
1803     showMenu.add(showAllColumns);
1804     showMenu.add(showAllSeqs);
1805     showMenu.add(showAllhidden);
1806     hideMenu.add(hideSelColumns);
1807     hideMenu.add(hideSelSequences);
1808     hideMenu.add(hideAllSelection);
1809     hideMenu.add(hideAllButSelection);
1810     viewMenu.add(newView);
1811     viewMenu.add(expandViews);
1812     viewMenu.add(gatherViews);
1813     viewMenu.addSeparator();
1814     viewMenu.add(showMenu);
1815     viewMenu.add(hideMenu);
1816     viewMenu.add(showComplementMenuItem);
1817     viewMenu.addSeparator();
1818     viewMenu.add(followHighlightMenuItem);
1819     viewMenu.addSeparator();
1820     viewMenu.add(showSeqFeatures);
1821     // viewMenu.add(showSeqFeaturesHeight);
1822     viewMenu.add(openFeatureSettings);
1823     tooltipSettingsMenu.add(showDbRefsMenuitem);
1824     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1825     viewMenu.add(tooltipSettingsMenu);
1826     viewMenu.addSeparator();
1827     viewMenu.add(alignmentProperties);
1828     viewMenu.addSeparator();
1829     viewMenu.add(overviewMenuItem);
1830
1831     annotationsMenu.add(annotationPanelMenuItem);
1832     annotationsMenu.addSeparator();
1833     annotationsMenu.add(showAllAlAnnotations);
1834     annotationsMenu.add(hideAllAlAnnotations);
1835     annotationsMenu.addSeparator();
1836     annotationsMenu.add(showAllSeqAnnotations);
1837     annotationsMenu.add(hideAllSeqAnnotations);
1838     annotationsMenu.add(sortAnnBySequence);
1839     annotationsMenu.add(sortAnnByLabel);
1840     annotationsMenu.addSeparator();
1841     autoAnnMenu.add(showAutoFirst);
1842     autoAnnMenu.add(showAutoLast);
1843     autoAnnMenu.addSeparator();
1844     autoAnnMenu.add(applyAutoAnnotationSettings);
1845     autoAnnMenu.add(showConsensusHistogram);
1846     autoAnnMenu.add(showSequenceLogo);
1847     autoAnnMenu.add(normaliseSequenceLogo);
1848     autoAnnMenu.addSeparator();
1849     autoAnnMenu.add(showGroupConservation);
1850     autoAnnMenu.add(showGroupConsensus);
1851     annotationsMenu.add(autoAnnMenu);
1852
1853     sort.add(sortIDMenuItem);
1854     sort.add(sortLengthMenuItem);
1855     sort.add(sortGroupMenuItem);
1856     sort.add(sortPairwiseMenuItem);
1857     sort.add(sortByTreeMenu);
1858     calculateMenu.add(sort);
1859     calculateMenu.add(calculateTree);
1860     calculateMenu.addSeparator();
1861     calculateMenu.add(pairwiseAlignmentMenuItem);
1862     calculateMenu.addSeparator();
1863     calculateMenu.add(showTranslation);
1864     calculateMenu.add(showReverse);
1865     calculateMenu.add(showReverseComplement);
1866     calculateMenu.add(showProducts);
1867     calculateMenu.add(autoCalculate);
1868     calculateMenu.add(sortByTree);
1869     calculateMenu.addSeparator();
1870     calculateMenu.add(expandAlignment);
1871     calculateMenu.add(extractScores);
1872     if (!Platform.isJS())
1873     {
1874       calculateMenu.addSeparator();
1875       calculateMenu.add(runGroovy);
1876     }
1877
1878     webServiceNoServices = new JMenuItem(
1879             MessageManager.getString("label.no_services"));
1880     webService.add(webServiceNoServices);
1881     if (!Platform.isJS())
1882     {
1883       exportImageMenu.add(htmlMenuItem);
1884     }
1885     exportImageMenu.add(epsFile);
1886     exportImageMenu.add(createPNG);
1887     if (!Platform.isJS())
1888     {
1889       exportImageMenu.add(createBioJS);
1890       exportImageMenu.add(createSVG);
1891     }
1892     addSequenceMenu.add(addFromFile);
1893     addSequenceMenu.add(addFromText);
1894     addSequenceMenu.add(addFromURL);
1895     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1896     statusPanel.add(statusBar, null);
1897     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1898
1899     formatMenu.add(font);
1900     formatMenu.addSeparator();
1901     formatMenu.add(wrapMenuItem);
1902     formatMenu.add(scaleAbove);
1903     formatMenu.add(scaleLeft);
1904     formatMenu.add(scaleRight);
1905     formatMenu.add(seqLimits);
1906     formatMenu.add(idRightAlign);
1907     formatMenu.add(hiddenMarkers);
1908     formatMenu.add(viewBoxesMenuItem);
1909     formatMenu.add(viewTextMenuItem);
1910     formatMenu.add(colourTextMenuItem);
1911     formatMenu.add(renderGapsMenuItem);
1912     formatMenu.add(colourGapsMenuItem);
1913     formatMenu.add(centreColumnLabelsMenuItem);
1914     formatMenu.add(showNonconservedMenuItem);
1915     selectMenu.add(findMenuItem);
1916     selectMenu.addSeparator();
1917     selectMenu.add(selectAllSequenceMenuItem);
1918     selectMenu.add(deselectAllSequenceMenuItem);
1919     selectMenu.add(invertSequenceMenuItem);
1920     selectMenu.add(invertColSel);
1921     selectMenu.add(createGroup);
1922     selectMenu.add(unGroup);
1923     selectMenu.add(grpsFromSelection);
1924     selectMenu.add(deleteGroups);
1925     selectMenu.add(annotationColumn);
1926     selectMenu.add(selectHighlighted);
1927     // TODO - determine if the listenToViewSelections button is needed : see bug
1928     // JAL-574
1929     // selectMenu.addSeparator();
1930     // selectMenu.add(listenToViewSelections);
1931   }
1932
1933   protected void colourGapsMenuItem_actionPerformed(ActionEvent e)
1934   {
1935     // TODO Auto-generated method stub
1936
1937   }
1938
1939   protected void loadVcf_actionPerformed()
1940   {
1941   }
1942
1943   /**
1944    * Constructs the entries on the Colour menu (but does not add them to the
1945    * menu).
1946    */
1947   protected void initColourMenu()
1948   {
1949     applyToAllGroups = new JCheckBoxMenuItem(
1950             MessageManager.getString("label.apply_colour_to_all_groups"));
1951     applyToAllGroups.addActionListener(new ActionListener()
1952     {
1953       @Override
1954       public void actionPerformed(ActionEvent e)
1955       {
1956         applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1957       }
1958     });
1959
1960     textColour = new JMenuItem(
1961             MessageManager.getString("label.text_colour"));
1962     textColour.addActionListener(new ActionListener()
1963     {
1964       @Override
1965       public void actionPerformed(ActionEvent e)
1966       {
1967         textColour_actionPerformed();
1968       }
1969     });
1970
1971     conservationMenuItem = new JCheckBoxMenuItem(
1972             MessageManager.getString("action.by_conservation"));
1973     conservationMenuItem.addActionListener(new ActionListener()
1974     {
1975       @Override
1976       public void actionPerformed(ActionEvent e)
1977       {
1978         conservationMenuItem_actionPerformed(
1979                 conservationMenuItem.isSelected());
1980       }
1981     });
1982
1983     abovePIDThreshold = new JCheckBoxMenuItem(
1984             MessageManager.getString("label.above_identity_threshold"));
1985     abovePIDThreshold.addActionListener(new ActionListener()
1986     {
1987       @Override
1988       public void actionPerformed(ActionEvent e)
1989       {
1990         abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
1991       }
1992     });
1993     modifyPID = new JMenuItem(
1994             MessageManager.getString("label.modify_identity_threshold"));
1995     modifyPID.addActionListener(new ActionListener()
1996     {
1997       @Override
1998       public void actionPerformed(ActionEvent e)
1999       {
2000         modifyPID_actionPerformed();
2001       }
2002     });
2003     modifyConservation = new JMenuItem(MessageManager
2004             .getString("label.modify_conservation_threshold"));
2005     modifyConservation.addActionListener(new ActionListener()
2006     {
2007       @Override
2008       public void actionPerformed(ActionEvent e)
2009       {
2010         modifyConservation_actionPerformed();
2011       }
2012     });
2013
2014     annotationColour = new JRadioButtonMenuItem(
2015             MessageManager.getString("action.by_annotation"));
2016     annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
2017     annotationColour.addActionListener(new ActionListener()
2018     {
2019       @Override
2020       public void actionPerformed(ActionEvent e)
2021       {
2022         annotationColour_actionPerformed();
2023       }
2024     });
2025   }
2026
2027   protected void selectHighlightedColumns_actionPerformed(
2028           ActionEvent actionEvent)
2029   {
2030     // TODO Auto-generated method stub
2031
2032   }
2033
2034   /**
2035    * Generate the reverse sequence (or reverse complement if the flag is true)
2036    * and add it to the alignment
2037    *
2038    * @param complement
2039    */
2040   protected void showReverse_actionPerformed(boolean complement)
2041   {
2042   }
2043
2044   /**
2045    * Try to run script in a Groovy console, having first ensured that this
2046    * alignframe is set as currentAlignFrame in Desktop
2047    */
2048   protected void runGroovy_actionPerformed()
2049   {
2050
2051   }
2052
2053   /**
2054    * Adds the given action listener and key accelerator to the given menu item.
2055    * Also saves in a lookup table to support lookup of action by key stroke.
2056    *
2057    * @param keyStroke
2058    * @param menuItem
2059    * @param actionListener
2060    */
2061   protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2062           JMenuItem menuItem, ActionListener actionListener)
2063   {
2064     menuItem.setAccelerator(keyStroke);
2065     accelerators.put(keyStroke, menuItem);
2066     menuItem.addActionListener(actionListener);
2067   }
2068
2069   /**
2070    * Action on clicking sort annotations by type.
2071    *
2072    * @param sortOrder
2073    */
2074   protected void sortAnnotations_actionPerformed()
2075   {
2076   }
2077
2078   /**
2079    * Action on clicking Show all annotations.
2080    *
2081    * @param forSequences
2082    *          update sequence-related annotations
2083    * @param forAlignment
2084    *          update non-sequence-related annotations
2085    */
2086   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2087           boolean forAlignment)
2088   {
2089     setAnnotationsVisibility(true, forSequences, forAlignment);
2090   }
2091
2092   /**
2093    * Action on clicking Hide all annotations.
2094    *
2095    * @param forSequences
2096    *          update sequence-related annotations
2097    * @param forAlignment
2098    *          update non-sequence-related annotations
2099    */
2100   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2101           boolean forAlignment)
2102   {
2103     setAnnotationsVisibility(false, forSequences, forAlignment);
2104   }
2105
2106   /**
2107    * Set the visibility of annotations to true or false. Can act on
2108    * sequence-related annotations, or alignment-related, or both.
2109    *
2110    * @param visible
2111    * @param forSequences
2112    *          update sequence-related annotations
2113    * @param forAlignment
2114    *          update non-sequence-related annotations
2115    */
2116   protected void setAnnotationsVisibility(boolean visible,
2117           boolean forSequences, boolean forAlignment)
2118   {
2119
2120   }
2121
2122   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2123   {
2124     // TODO Auto-generated method stub
2125
2126   }
2127
2128   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2129   {
2130     // TODO Auto-generated method stub
2131
2132   }
2133
2134   protected void showAllhidden_actionPerformed(ActionEvent e)
2135   {
2136     // TODO Auto-generated method stub
2137
2138   }
2139
2140   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2141   {
2142     // TODO Auto-generated method stub
2143
2144   }
2145
2146   protected void hideAllSelection_actionPerformed(ActionEvent e)
2147   {
2148     // TODO Auto-generated method stub
2149
2150   }
2151
2152   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2153   {
2154     // TODO Auto-generated method stub
2155
2156   }
2157
2158   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2159   {
2160     // TODO Auto-generated method stub
2161
2162   }
2163
2164   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2165   {
2166     // TODO Auto-generated method stub
2167
2168   }
2169
2170   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2171   {
2172     // TODO Auto-generated method stub
2173
2174   }
2175
2176   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2177   {
2178     // TODO Auto-generated method stub
2179
2180   }
2181
2182   protected void showGroupConservation_actionPerformed(ActionEvent e)
2183   {
2184     // TODO Auto-generated method stub
2185
2186   }
2187
2188   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2189   {
2190     // TODO Auto-generated method stub
2191
2192   }
2193
2194   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2195   {
2196     // TODO Auto-generated method stub
2197
2198   }
2199
2200   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2201   {
2202     // TODO Auto-generated method stub
2203
2204   }
2205
2206   protected void followHighlight_actionPerformed()
2207   {
2208     // TODO Auto-generated method stub
2209
2210   }
2211
2212   protected void showNpFeats_actionPerformed(ActionEvent e)
2213   {
2214     // TODO Auto-generated method stub
2215
2216   }
2217
2218   protected void showDbRefs_actionPerformed(ActionEvent e)
2219   {
2220     // TODO Auto-generated method stub
2221
2222   }
2223
2224   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2225   {
2226   }
2227
2228   protected void buildSortByAnnotationScoresMenu()
2229   {
2230   }
2231
2232   protected void extractScores_actionPerformed(ActionEvent e)
2233   {
2234   }
2235
2236   protected void outputText_actionPerformed(String formatName)
2237   {
2238   }
2239
2240   public void addFromFile_actionPerformed(ActionEvent e)
2241   {
2242
2243   }
2244
2245   public void addFromText_actionPerformed(ActionEvent e)
2246   {
2247
2248   }
2249
2250   public void addFromURL_actionPerformed(ActionEvent e)
2251   {
2252
2253   }
2254
2255   public void exportFeatures_actionPerformed(ActionEvent e)
2256   {
2257
2258   }
2259
2260   public void exportAnnotations_actionPerformed(ActionEvent e)
2261   {
2262
2263   }
2264
2265   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2266   {
2267   }
2268
2269   protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2270   {
2271
2272   }
2273
2274   protected void closeMenuItem_actionPerformed(boolean b)
2275   {
2276   }
2277
2278   protected void redoMenuItem_actionPerformed(ActionEvent e)
2279   {
2280   }
2281
2282   protected void undoMenuItem_actionPerformed(ActionEvent e)
2283   {
2284   }
2285
2286   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2287   {
2288   }
2289
2290   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2291   {
2292   }
2293
2294   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2295   {
2296   }
2297
2298   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2299   {
2300   }
2301
2302   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2303   {
2304   }
2305
2306   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2307   {
2308   }
2309
2310   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2311   {
2312   }
2313
2314   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2315   {
2316   }
2317
2318   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2319   {
2320   }
2321
2322   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2323   {
2324   }
2325
2326   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2327   {
2328   }
2329
2330   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2331   {
2332   }
2333
2334   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2335   {
2336   }
2337
2338   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2339   {
2340   }
2341
2342   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2343   {
2344   }
2345
2346   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2347   {
2348   }
2349
2350   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2351   {
2352   }
2353
2354   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2355   {
2356   }
2357
2358   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2359   {
2360   }
2361
2362   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2363   {
2364   }
2365
2366   protected void conservationMenuItem_actionPerformed(boolean selected)
2367   {
2368   }
2369
2370   protected void printMenuItem_actionPerformed(ActionEvent e)
2371   {
2372   }
2373
2374   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2375   {
2376   }
2377
2378   protected void findMenuItem_actionPerformed(ActionEvent e)
2379   {
2380   }
2381
2382   protected void abovePIDThreshold_actionPerformed(boolean selected)
2383   {
2384   }
2385
2386   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2387   {
2388   }
2389
2390   protected void deleteGroups_actionPerformed(ActionEvent e)
2391   {
2392   }
2393
2394   protected void createGroup_actionPerformed(ActionEvent e)
2395   {
2396   }
2397
2398   protected void unGroup_actionPerformed(ActionEvent e)
2399   {
2400   }
2401
2402   protected void copy_actionPerformed()
2403   {
2404   }
2405
2406   protected void cut_actionPerformed()
2407   {
2408   }
2409
2410   protected void delete_actionPerformed()
2411   {
2412   }
2413
2414   protected void pasteNew_actionPerformed(ActionEvent e)
2415   {
2416   }
2417
2418   protected void pasteThis_actionPerformed(ActionEvent e)
2419   {
2420   }
2421
2422   protected void applyToAllGroups_actionPerformed(boolean selected)
2423   {
2424   }
2425
2426   public void createPNG(java.io.File f)
2427   {
2428   }
2429
2430   protected void font_actionPerformed(ActionEvent e)
2431   {
2432   }
2433
2434   protected void seqLimit_actionPerformed(ActionEvent e)
2435   {
2436   }
2437
2438   public void seqDBRef_actionPerformed(ActionEvent e)
2439   {
2440
2441   }
2442
2443   public void createEPS(java.io.File f)
2444   {
2445   }
2446
2447   public void createSVG(java.io.File f)
2448   {
2449
2450   }
2451
2452   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2453   {
2454
2455   }
2456
2457   /**
2458    * Template method to handle the 'load T-Coffee scores' menu event.
2459    * <p>
2460    * Subclasses override this method to provide a custom action.
2461    *
2462    * @param event
2463    *          The raised event
2464    */
2465   protected void loadScores_actionPerformed(ActionEvent event)
2466   {
2467
2468   }
2469
2470   protected void jpred_actionPerformed(ActionEvent e)
2471   {
2472   }
2473
2474   protected void scaleAbove_actionPerformed(ActionEvent e)
2475   {
2476   }
2477
2478   protected void scaleLeft_actionPerformed(ActionEvent e)
2479   {
2480   }
2481
2482   protected void scaleRight_actionPerformed(ActionEvent e)
2483   {
2484   }
2485
2486   protected void modifyPID_actionPerformed()
2487   {
2488   }
2489
2490   protected void modifyConservation_actionPerformed()
2491   {
2492   }
2493
2494   protected void saveAs_actionPerformed()
2495   {
2496   }
2497
2498   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2499   {
2500   }
2501
2502   public void vamsasStore_actionPerformed(ActionEvent e)
2503   {
2504
2505   }
2506
2507   public void vamsasLoad_actionPerformed(ActionEvent e)
2508   {
2509
2510   }
2511
2512   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
2513   {
2514
2515   }
2516
2517   public void featureSettings_actionPerformed(ActionEvent e)
2518   {
2519
2520   }
2521
2522   public void fetchSequence_actionPerformed()
2523   {
2524
2525   }
2526
2527   public void smoothFont_actionPerformed(ActionEvent e)
2528   {
2529
2530   }
2531
2532   public void annotationColour_actionPerformed()
2533   {
2534   }
2535
2536   public void annotationColumn_actionPerformed(ActionEvent e)
2537   {
2538   }
2539
2540   public void associatedData_actionPerformed(ActionEvent e)
2541   {
2542
2543   }
2544
2545   public void autoCalculate_actionPerformed(ActionEvent e)
2546   {
2547
2548   }
2549
2550   public void sortByTreeOption_actionPerformed(ActionEvent e)
2551   {
2552
2553   }
2554
2555   public void showAllSeqs_actionPerformed(ActionEvent e)
2556   {
2557
2558   }
2559
2560   public void showAllColumns_actionPerformed(ActionEvent e)
2561   {
2562
2563   }
2564
2565   public void hideSelSequences_actionPerformed(ActionEvent e)
2566   {
2567
2568   }
2569
2570   public void hideSelColumns_actionPerformed(ActionEvent e)
2571   {
2572
2573   }
2574
2575   public void hiddenMarkers_actionPerformed(ActionEvent e)
2576   {
2577
2578   }
2579
2580   public void findPdbId_actionPerformed(ActionEvent e)
2581   {
2582
2583   }
2584
2585   public void enterPdbId_actionPerformed(ActionEvent e)
2586   {
2587
2588   }
2589
2590   public void pdbFile_actionPerformed(ActionEvent e)
2591   {
2592
2593   }
2594
2595   public void invertColSel_actionPerformed(ActionEvent e)
2596   {
2597
2598   }
2599
2600   public void tabSelectionChanged(int sel)
2601   {
2602
2603   }
2604
2605   public void tabbedPane_mousePressed(MouseEvent e)
2606   {
2607
2608   }
2609
2610   public void tabbedPane_focusGained(FocusEvent e)
2611   {
2612     requestFocus();
2613   }
2614
2615   public void save_actionPerformed(ActionEvent e)
2616   {
2617
2618   }
2619
2620   public void reload_actionPerformed(ActionEvent e)
2621   {
2622
2623   }
2624
2625   public void newView_actionPerformed(ActionEvent e)
2626   {
2627
2628   }
2629
2630   public void textColour_actionPerformed()
2631   {
2632
2633   }
2634
2635   public void idRightAlign_actionPerformed(ActionEvent e)
2636   {
2637
2638   }
2639
2640   public void expandViews_actionPerformed(ActionEvent e)
2641   {
2642
2643   }
2644
2645   public void gatherViews_actionPerformed(ActionEvent e)
2646   {
2647
2648   }
2649
2650   public void buildTreeSortMenu()
2651   {
2652
2653   }
2654
2655   public void pageSetup_actionPerformed(ActionEvent e)
2656   {
2657
2658   }
2659
2660   public void alignmentProperties()
2661   {
2662
2663   }
2664
2665   protected void expand_newalign(ActionEvent e)
2666   {
2667     // TODO Auto-generated method stub
2668
2669   }
2670
2671   protected boolean isShowAutoCalculatedAbove()
2672   {
2673     return showAutoCalculatedAbove;
2674   }
2675
2676   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2677   {
2678     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2679   }
2680
2681   protected SequenceAnnotationOrder getAnnotationSortOrder()
2682   {
2683     return annotationSortOrder;
2684   }
2685
2686   protected void setAnnotationSortOrder(
2687           SequenceAnnotationOrder annotationSortOrder)
2688   {
2689     this.annotationSortOrder = annotationSortOrder;
2690   }
2691
2692   public Map<KeyStroke, JMenuItem> getAccelerators()
2693   {
2694     return this.accelerators;
2695   }
2696
2697   /**
2698    * Returns the selected index of the tabbed pane, or -1 if none selected
2699    * (including the case where the tabbed pane has not been made visible).
2700    *
2701    * @return
2702    */
2703   public int getTabIndex()
2704   {
2705     return tabbedPane.getSelectedIndex();
2706   }
2707
2708   public JPanel getStatusPanel()
2709   {
2710     return statusPanel;
2711   }
2712
2713   /**
2714    * Sets a reference to the containing split frame. Also makes the 'toggle
2715    * split view' menu item visible and checked.
2716    *
2717    * @param sf
2718    */
2719   public void setSplitFrame(SplitContainerI sf)
2720   {
2721     this.splitFrame = sf;
2722     if (sf != null)
2723     {
2724       this.showComplementMenuItem.setVisible(true);
2725       this.showComplementMenuItem.setState(true);
2726     }
2727   }
2728
2729   public SplitContainerI getSplitViewContainer()
2730   {
2731     return this.splitFrame;
2732   }
2733
2734   protected void showComplement_actionPerformed(boolean complement)
2735   {
2736   }
2737 }