src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.jbgui;
  22
  23 import java.awt.BorderLayout;
  24 import java.awt.Color;
  25 import java.awt.GridLayout;
  26 import java.awt.event.ActionEvent;
  27 import java.awt.event.ActionListener;
  28 import java.awt.event.FocusAdapter;
  29 import java.awt.event.FocusEvent;
  30 import java.awt.event.KeyEvent;
  31 import java.awt.event.MouseAdapter;
  32 import java.awt.event.MouseEvent;
  33 import java.util.HashMap;
  34 import java.util.Map;
  35
  36 import javax.swing.BorderFactory;
  37 import javax.swing.ButtonGroup;
  38 import javax.swing.JCheckBoxMenuItem;
  39 import javax.swing.JInternalFrame;
  40 import javax.swing.JLabel;
  41 import javax.swing.JMenu;
  42 import javax.swing.JMenuBar;
  43 import javax.swing.JMenuItem;
  44 import javax.swing.JPanel;
  45 import javax.swing.JRadioButtonMenuItem;
  46 import javax.swing.JTabbedPane;
  47 import javax.swing.KeyStroke;
  48 import javax.swing.event.ChangeEvent;
  49 import javax.swing.event.MenuEvent;
  50 import javax.swing.event.MenuListener;
  51
  52 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  53 import jalview.analysis.GeneticCodeI;
  54 import jalview.analysis.GeneticCodes;
  55 import jalview.api.SplitContainerI;
  56 import jalview.bin.Cache;
  57 import jalview.gui.JvSwingUtils;
  58 import jalview.gui.Preferences;
  59 import jalview.io.FileFormats;
  60 import jalview.schemes.ResidueColourScheme;
  61 import jalview.util.MessageManager;
  62 import jalview.util.Platform;
  63
  64 @SuppressWarnings("serial")
  65 public class GAlignFrame extends JInternalFrame
  66 {
  67   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  68
  69   protected JMenuItem closeMenuItem = new JMenuItem();
  70
  71   public JMenu webService = new JMenu();// BH 2019 was protected, but not
  72                                         // sufficient for AlignFrame thread run
  73
  74   public JMenuItem webServiceNoServices;// BH 2019 was protected, but not
  75                                         // sufficient for AlignFrame thread run
  76
  77   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  78
  79   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  80
  81   protected JMenu sortByAnnotScore = new JMenu();
  82
  83   public JLabel statusBar = new JLabel(); // BH 2019 was protected, but not
  84                                           // sufficient for
  85                                           // AlignFrame.printWriter
  86
  87   protected JMenu outputTextboxMenu = new JMenu();
  88
  89   protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
  90
  91   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
  92
  93   protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
  94
  95   protected JMenuItem undoMenuItem = new JMenuItem();
  96
  97   protected JMenuItem redoMenuItem = new JMenuItem();
  98
  99   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 100
 101   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 102
 103   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 104
 105   JMenuItem copy = new JMenuItem();
 106
 107   JMenuItem copyHighlighted = new JMenuItem();
 108
 109   JMenuItem cut = new JMenuItem();
 110
 111   JMenu pasteMenu = new JMenu();
 112
 113   protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 114
 115   protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 116
 117   protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 118
 119   protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 120
 121   protected JCheckBoxMenuItem applyToAllGroups;
 122
 123   protected JMenu colourMenu = new JMenu();
 124
 125   protected JMenuItem textColour;
 126
 127   protected JCheckBoxMenuItem conservationMenuItem;
 128
 129   protected JMenuItem modifyConservation;
 130
 131   protected JCheckBoxMenuItem abovePIDThreshold;
 132
 133   protected JMenuItem modifyPID;
 134
 135   protected JRadioButtonMenuItem annotationColour;
 136
 137   protected JMenu sortByTreeMenu = new JMenu();
 138
 139   protected JMenu sort = new JMenu();
 140
 141   protected JMenuItem calculateTree = new JMenuItem();
 142
 143   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 144
 145   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 146
 147   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 148
 149   protected JMenu showTranslation = new JMenu();
 150
 151   protected JMenuItem showReverse = new JMenuItem();
 152
 153   protected JMenuItem showReverseComplement = new JMenuItem();
 154
 155   protected JMenu showProducts = new JMenu();
 156
 157   protected JMenuItem runGroovy = new JMenuItem();
 158
 159   protected JMenuItem loadVcf;
 160
 161   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 162
 163   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 164
 165   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 166
 167   protected JPanel statusPanel = new JPanel();
 168
 169   protected JMenuItem showAllSeqAnnotations = new JMenuItem();
 170
 171   protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
 172
 173   protected JMenuItem showAllAlAnnotations = new JMenuItem();
 174
 175   protected JMenuItem hideAllAlAnnotations = new JMenuItem();
 176
 177   protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
 178
 179   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 180
 181   protected JTabbedPane tabbedPane = new JTabbedPane();
 182
 183   protected JMenuItem reload = new JMenuItem();
 184
 185   protected JMenu formatMenu = new JMenu();
 186
 187   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 188
 189   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 190
 191   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 192
 193   protected JMenuItem gatherViews = new JMenuItem();
 194
 195   protected JMenuItem expandViews = new JMenuItem();
 196
 197   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 198
 199   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 200
 201   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 202
 203   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 204
 205   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 206
 207   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 208
 209   protected JMenuItem openFeatureSettings;
 210
 211   private SequenceAnnotationOrder annotationSortOrder;
 212
 213   private boolean showAutoCalculatedAbove = false;
 214
 215   private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
 216
 217   private SplitContainerI splitFrame;
 218
 219   public GAlignFrame()
 220   {
 221     try
 222     {
 223       setFrameIcon(null);
 224
 225       // for Web-page embedding using id=align-frame-div
 226       setName("jalview-alignment");
 227
 228       jbInit();
 229       setJMenuBar(alignFrameMenuBar);
 230
 231       // dynamically fill save as menu with available formats
 232       for (String ff : FileFormats.getInstance().getWritableFormats(true))
 233       {
 234         JMenuItem item = new JMenuItem(ff);
 235
 236         item.addActionListener(new ActionListener()
 237         {
 238           @Override
 239           public void actionPerformed(ActionEvent e)
 240           {
 241             outputText_actionPerformed(e.getActionCommand());
 242           }
 243         });
 244
 245         outputTextboxMenu.add(item);
 246       }
 247     } catch (Exception e)
 248     {
 249       jalview.bin.Console.errPrintln(e.toString());
 250     }
 251
 252     if (Platform.allowMnemonics()) // was "not mac and not JS"
 253     {
 254       closeMenuItem.setMnemonic('C');
 255       outputTextboxMenu.setMnemonic('T');
 256       undoMenuItem.setMnemonic('Z');
 257       redoMenuItem.setMnemonic('0');
 258       copy.setMnemonic('C');
 259       cut.setMnemonic('U');
 260       pasteMenu.setMnemonic('P');
 261       reload.setMnemonic('R');
 262     }
 263   }
 264
 265   private void jbInit() throws Exception
 266   {
 267     setFrameIcon(null);
 268     initColourMenu();
 269
 270     JMenuItem saveAs = new JMenuItem(
 271             MessageManager.getString("action.save_as"));
 272     ActionListener al = new ActionListener()
 273     {
 274       @Override
 275       public void actionPerformed(ActionEvent e)
 276       {
 277         saveAs_actionPerformed();
 278       }
 279     };
 280
 281     // FIXME getDefaultToolkit throws an exception in Headless mode
 282     KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
 283             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
 284                     | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
 285             false);
 286     addMenuActionAndAccelerator(keyStroke, saveAs, al);
 287
 288     closeMenuItem.setText(MessageManager.getString("action.close"));
 289     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
 290             jalview.util.ShortcutKeyMaskExWrapper
 291                     .getMenuShortcutKeyMaskEx(),
 292             false);
 293     al = new ActionListener()
 294     {
 295       @Override
 296       public void actionPerformed(ActionEvent e)
 297       {
 298         closeMenuItem_actionPerformed(false);
 299       }
 300     };
 301     addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
 302
 303     JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
 304     JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
 305     JMenu annotationsMenu = new JMenu(
 306             MessageManager.getString("action.annotations"));
 307     JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
 308     colourMenu.setText(MessageManager.getString("action.colour"));
 309     JMenu calculateMenu = new JMenu(
 310             MessageManager.getString("action.calculate"));
 311     webService.setText(MessageManager.getString("action.web_service"));
 312     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
 313             MessageManager.getString("action.select_all"));
 314     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
 315             jalview.util.ShortcutKeyMaskExWrapper
 316                     .getMenuShortcutKeyMaskEx(),
 317             false);
 318     al = new ActionListener()
 319     {
 320       @Override
 321       public void actionPerformed(ActionEvent e)
 322       {
 323         selectAllSequenceMenuItem_actionPerformed(e);
 324       }
 325     };
 326     addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
 327
 328     JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
 329             MessageManager.getString("action.deselect_all"));
 330     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
 331     al = new ActionListener()
 332     {
 333       @Override
 334       public void actionPerformed(ActionEvent e)
 335       {
 336         deselectAllSequenceMenuItem_actionPerformed(e);
 337       }
 338     };
 339     addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
 340
 341     JMenuItem invertSequenceMenuItem = new JMenuItem(
 342             MessageManager.getString("action.invert_sequence_selection"));
 343     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
 344             jalview.util.ShortcutKeyMaskExWrapper
 345                     .getMenuShortcutKeyMaskEx(),
 346             false);
 347     al = new ActionListener()
 348     {
 349       @Override
 350       public void actionPerformed(ActionEvent e)
 351       {
 352         invertSequenceMenuItem_actionPerformed(e);
 353       }
 354     };
 355     addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
 356
 357     JMenuItem grpsFromSelection = new JMenuItem(
 358             MessageManager.getString("action.make_groups_selection"));
 359     grpsFromSelection.addActionListener(new ActionListener()
 360     {
 361       @Override
 362       public void actionPerformed(ActionEvent e)
 363       {
 364         makeGrpsFromSelection_actionPerformed(e);
 365       }
 366     });
 367     JMenuItem expandAlignment = new JMenuItem(
 368             MessageManager.getString("action.view_flanking_regions"));
 369     expandAlignment.setToolTipText(
 370             MessageManager.getString("label.view_flanking_regions"));
 371     expandAlignment.addActionListener(new ActionListener()
 372     {
 373       @Override
 374       public void actionPerformed(ActionEvent e)
 375       {
 376         expand_newalign(e);
 377       }
 378     });
 379     JMenuItem remove2LeftMenuItem = new JMenuItem(
 380             MessageManager.getString("action.remove_left"));
 381     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
 382             jalview.util.ShortcutKeyMaskExWrapper
 383                     .getMenuShortcutKeyMaskEx(),
 384             false);
 385     al = new ActionListener()
 386     {
 387       @Override
 388       public void actionPerformed(ActionEvent e)
 389       {
 390         remove2LeftMenuItem_actionPerformed(e);
 391       }
 392     };
 393     addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
 394
 395     JMenuItem remove2RightMenuItem = new JMenuItem(
 396             MessageManager.getString("action.remove_right"));
 397     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
 398             jalview.util.ShortcutKeyMaskExWrapper
 399                     .getMenuShortcutKeyMaskEx(),
 400             false);
 401     al = new ActionListener()
 402     {
 403       @Override
 404       public void actionPerformed(ActionEvent e)
 405       {
 406         remove2RightMenuItem_actionPerformed(e);
 407       }
 408     };
 409     addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
 410
 411     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
 412             MessageManager.getString("action.remove_empty_columns"));
 413     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
 414             jalview.util.ShortcutKeyMaskExWrapper
 415                     .getMenuShortcutKeyMaskEx(),
 416             false);
 417     al = new ActionListener()
 418     {
 419       @Override
 420       public void actionPerformed(ActionEvent e)
 421       {
 422         removeGappedColumnMenuItem_actionPerformed(e);
 423       }
 424     };
 425     addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
 426
 427     JMenuItem removeAllGapsMenuItem = new JMenuItem(
 428             MessageManager.getString("action.remove_all_gaps"));
 429     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
 430             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
 431                     | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
 432             false);
 433     al = new ActionListener()
 434     {
 435       @Override
 436       public void actionPerformed(ActionEvent e)
 437       {
 438         removeAllGapsMenuItem_actionPerformed(e);
 439       }
 440     };
 441     addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
 442
 443     JMenuItem justifyLeftMenuItem = new JMenuItem(
 444             MessageManager.getString("action.left_justify"));
 445     justifyLeftMenuItem.setToolTipText(
 446             MessageManager.getString("tooltip.left_justify"));
 447     justifyLeftMenuItem.addActionListener(new ActionListener()
 448     {
 449       @Override
 450       public void actionPerformed(ActionEvent e)
 451       {
 452         justifyLeftMenuItem_actionPerformed(e);
 453       }
 454     });
 455     JMenuItem justifyRightMenuItem = new JMenuItem(
 456             MessageManager.getString("action.right_justify"));
 457     justifyRightMenuItem.setToolTipText(
 458             MessageManager.getString("action.left_justify"));
 459
 460     justifyRightMenuItem.addActionListener(new ActionListener()
 461     {
 462       @Override
 463       public void actionPerformed(ActionEvent e)
 464       {
 465         justifyRightMenuItem_actionPerformed(e);
 466       }
 467     });
 468     viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
 469     viewBoxesMenuItem.setState(true);
 470     viewBoxesMenuItem.addActionListener(new ActionListener()
 471     {
 472       @Override
 473       public void actionPerformed(ActionEvent e)
 474       {
 475         viewBoxesMenuItem_actionPerformed(e);
 476       }
 477     });
 478     viewTextMenuItem.setText(MessageManager.getString("action.text"));
 479     viewTextMenuItem.setState(true);
 480     viewTextMenuItem.addActionListener(new ActionListener()
 481     {
 482       @Override
 483       public void actionPerformed(ActionEvent e)
 484       {
 485         viewTextMenuItem_actionPerformed(e);
 486       }
 487     });
 488     showNonconservedMenuItem
 489             .setText(MessageManager.getString("label.show_non_conserved"));
 490     showNonconservedMenuItem.setState(false);
 491     showNonconservedMenuItem.addActionListener(new ActionListener()
 492     {
 493       @Override
 494       public void actionPerformed(ActionEvent e)
 495       {
 496         showUnconservedMenuItem_actionPerformed(e);
 497       }
 498     });
 499     JMenuItem sortPairwiseMenuItem = new JMenuItem(
 500             MessageManager.getString("action.by_pairwise_id"));
 501     sortPairwiseMenuItem.addActionListener(new ActionListener()
 502     {
 503       @Override
 504       public void actionPerformed(ActionEvent e)
 505       {
 506         sortPairwiseMenuItem_actionPerformed(e);
 507       }
 508     });
 509     JMenuItem sortIDMenuItem = new JMenuItem(
 510             MessageManager.getString("action.by_id"));
 511     sortIDMenuItem.addActionListener(new ActionListener()
 512     {
 513       @Override
 514       public void actionPerformed(ActionEvent e)
 515       {
 516         sortIDMenuItem_actionPerformed(e);
 517       }
 518     });
 519     JMenuItem sortLengthMenuItem = new JMenuItem(
 520             MessageManager.getString("action.by_length"));
 521     sortLengthMenuItem.addActionListener(new ActionListener()
 522     {
 523       @Override
 524       public void actionPerformed(ActionEvent e)
 525       {
 526         sortLengthMenuItem_actionPerformed(e);
 527       }
 528     });
 529     JMenuItem sortGroupMenuItem = new JMenuItem(
 530             MessageManager.getString("action.by_group"));
 531     sortGroupMenuItem.addActionListener(new ActionListener()
 532     {
 533       @Override
 534       public void actionPerformed(ActionEvent e)
 535       {
 536         sortGroupMenuItem_actionPerformed(e);
 537       }
 538     });
 539
 540     JMenuItem removeRedundancyMenuItem = new JMenuItem(
 541             MessageManager.getString("action.remove_redundancy"));
 542     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
 543             jalview.util.ShortcutKeyMaskExWrapper
 544                     .getMenuShortcutKeyMaskEx(),
 545             false);
 546     al = new ActionListener()
 547     {
 548       @Override
 549       public void actionPerformed(ActionEvent e)
 550       {
 551         removeRedundancyMenuItem_actionPerformed(e);
 552       }
 553     };
 554     addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
 555
 556     JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
 557             MessageManager.getString("action.pairwise_alignment"));
 558     pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
 559     {
 560       @Override
 561       public void actionPerformed(ActionEvent e)
 562       {
 563         pairwiseAlignmentMenuItem_actionPerformed(e);
 564       }
 565     });
 566
 567     this.getContentPane().setLayout(new BorderLayout());
 568     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 569     statusBar.setBackground(Color.white);
 570     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 571     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 572     statusBar.setText(MessageManager.getString("label.status_bar"));
 573     outputTextboxMenu
 574             .setText(MessageManager.getString("label.out_to_textbox"));
 575
 576     annotationPanelMenuItem.setActionCommand("");
 577     annotationPanelMenuItem
 578             .setText(MessageManager.getString("label.show_annotations"));
 579     annotationPanelMenuItem
 580             .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
 581     annotationPanelMenuItem.addActionListener(new ActionListener()
 582     {
 583       @Override
 584       public void actionPerformed(ActionEvent e)
 585       {
 586         annotationPanelMenuItem_actionPerformed(e);
 587       }
 588     });
 589     showAllAlAnnotations.setText(
 590             MessageManager.getString("label.show_all_al_annotations"));
 591     final boolean isAnnotationPanelShown = annotationPanelMenuItem
 592             .getState();
 593     showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 594     showAllAlAnnotations.addActionListener(new ActionListener()
 595     {
 596       @Override
 597       public void actionPerformed(ActionEvent e)
 598       {
 599         showAllAnnotations_actionPerformed(false, true);
 600       }
 601     });
 602     hideAllAlAnnotations.setText(
 603             MessageManager.getString("label.hide_all_al_annotations"));
 604     hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 605     hideAllAlAnnotations.addActionListener(new ActionListener()
 606     {
 607       @Override
 608       public void actionPerformed(ActionEvent e)
 609       {
 610         hideAllAnnotations_actionPerformed(false, true);
 611       }
 612     });
 613     showAllSeqAnnotations.setText(
 614             MessageManager.getString("label.show_all_seq_annotations"));
 615     showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 616     showAllSeqAnnotations.addActionListener(new ActionListener()
 617     {
 618       @Override
 619       public void actionPerformed(ActionEvent e)
 620       {
 621         showAllAnnotations_actionPerformed(true, false);
 622       }
 623     });
 624     hideAllSeqAnnotations.setText(
 625             MessageManager.getString("label.hide_all_seq_annotations"));
 626     hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 627     hideAllSeqAnnotations.addActionListener(new ActionListener()
 628     {
 629       @Override
 630       public void actionPerformed(ActionEvent e)
 631       {
 632         hideAllAnnotations_actionPerformed(true, false);
 633       }
 634     });
 635     SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
 636             .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
 637                     SequenceAnnotationOrder.NONE.name()));
 638     final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
 639             MessageManager.getString("label.sort_annotations_by_sequence"));
 640     final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
 641             MessageManager.getString("label.sort_annotations_by_label"));
 642
 643     sortAnnBySequence.setSelected(
 644             sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
 645     sortAnnBySequence.addActionListener(new ActionListener()
 646     {
 647       @Override
 648       public void actionPerformed(ActionEvent e)
 649       {
 650         boolean newState = sortAnnBySequence.getState();
 651         sortAnnByLabel.setSelected(false);
 652         setAnnotationSortOrder(
 653                 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 654                         : SequenceAnnotationOrder.NONE);
 655         sortAnnotations_actionPerformed();
 656       }
 657     });
 658     sortAnnByLabel.setSelected(
 659             sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
 660     sortAnnByLabel.addActionListener(new ActionListener()
 661     {
 662       @Override
 663       public void actionPerformed(ActionEvent e)
 664       {
 665         boolean newState = sortAnnByLabel.getState();
 666         sortAnnBySequence.setSelected(false);
 667         setAnnotationSortOrder(
 668                 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 669                         : SequenceAnnotationOrder.NONE);
 670         sortAnnotations_actionPerformed();
 671       }
 672     });
 673     colourTextMenuItem = new JCheckBoxMenuItem(
 674             MessageManager.getString("label.colour_text"));
 675     colourTextMenuItem.addActionListener(new ActionListener()
 676     {
 677       @Override
 678       public void actionPerformed(ActionEvent e)
 679       {
 680         colourTextMenuItem_actionPerformed(e);
 681       }
 682     });
 683
 684     JMenuItem htmlMenuItem = new JMenuItem(
 685             MessageManager.getString("label.html"));
 686     htmlMenuItem.addActionListener(new ActionListener()
 687     {
 688       @Override
 689       public void actionPerformed(ActionEvent e)
 690       {
 691         htmlMenuItem_actionPerformed(e);
 692       }
 693     });
 694
 695     JMenuItem createBioJS = new JMenuItem(
 696             MessageManager.getString("label.biojs_html_export"));
 697     createBioJS.addActionListener(new java.awt.event.ActionListener()
 698     {
 699       @Override
 700       public void actionPerformed(ActionEvent e)
 701       {
 702         bioJSMenuItem_actionPerformed(e);
 703       }
 704     });
 705
 706     JMenuItem overviewMenuItem = new JMenuItem(
 707             MessageManager.getString("label.overview_window"));
 708     overviewMenuItem.addActionListener(new ActionListener()
 709     {
 710       @Override
 711       public void actionPerformed(ActionEvent e)
 712       {
 713         overviewMenuItem_actionPerformed(e);
 714       }
 715     });
 716
 717     undoMenuItem.setEnabled(false);
 718     undoMenuItem.setText(MessageManager.getString("action.undo"));
 719     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
 720             jalview.util.ShortcutKeyMaskExWrapper
 721                     .getMenuShortcutKeyMaskEx(),
 722             false);
 723     al = new ActionListener()
 724     {
 725       @Override
 726       public void actionPerformed(ActionEvent e)
 727       {
 728         undoMenuItem_actionPerformed(e);
 729       }
 730     };
 731     addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
 732
 733     redoMenuItem.setEnabled(false);
 734     redoMenuItem.setText(MessageManager.getString("action.redo"));
 735     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
 736             jalview.util.ShortcutKeyMaskExWrapper
 737                     .getMenuShortcutKeyMaskEx(),
 738             false);
 739     al = new ActionListener()
 740     {
 741       @Override
 742       public void actionPerformed(ActionEvent e)
 743       {
 744         redoMenuItem_actionPerformed(e);
 745       }
 746     };
 747     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
 748
 749     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
 750     wrapMenuItem.addActionListener(new ActionListener()
 751     {
 752       @Override
 753       public void actionPerformed(ActionEvent e)
 754       {
 755         wrapMenuItem_actionPerformed(e);
 756       }
 757     });
 758
 759     JMenuItem printMenuItem = new JMenuItem(
 760             MessageManager.getString("action.print"));
 761     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
 762             jalview.util.ShortcutKeyMaskExWrapper
 763                     .getMenuShortcutKeyMaskEx(),
 764             false);
 765     al = new ActionListener()
 766     {
 767       @Override
 768       public void actionPerformed(ActionEvent e)
 769       {
 770         printMenuItem_actionPerformed(e);
 771       }
 772     };
 773     addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
 774
 775     renderGapsMenuItem
 776             .setText(MessageManager.getString("action.show_gaps"));
 777     renderGapsMenuItem.setState(true);
 778     renderGapsMenuItem.addActionListener(new ActionListener()
 779     {
 780       @Override
 781       public void actionPerformed(ActionEvent e)
 782       {
 783         renderGapsMenuItem_actionPerformed(e);
 784       }
 785     });
 786
 787     JMenuItem findMenuItem = new JMenuItem(
 788             MessageManager.getString("action.find"));
 789     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
 790             jalview.util.ShortcutKeyMaskExWrapper
 791                     .getMenuShortcutKeyMaskEx(),
 792             false);
 793     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
 794             MessageManager.getString("label.find_tip")));
 795     al = new ActionListener()
 796     {
 797       @Override
 798       public void actionPerformed(ActionEvent e)
 799       {
 800         findMenuItem_actionPerformed(e);
 801       }
 802     };
 803     addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
 804
 805     showSeqFeatures.setText(
 806             MessageManager.getString("label.show_sequence_features"));
 807     showSeqFeatures.addActionListener(new ActionListener()
 808     {
 809       @Override
 810       public void actionPerformed(ActionEvent actionEvent)
 811       {
 812         showSeqFeatures_actionPerformed(actionEvent);
 813       }
 814     });
 815     /*
 816      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
 817      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
 818      * void actionPerformed(ActionEvent actionEvent) {
 819      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
 820      */
 821     showDbRefsMenuitem
 822             .setText(MessageManager.getString("label.show_database_refs"));
 823     showDbRefsMenuitem.addActionListener(new ActionListener()
 824     {
 825
 826       @Override
 827       public void actionPerformed(ActionEvent e)
 828       {
 829         showDbRefs_actionPerformed(e);
 830       }
 831
 832     });
 833     showNpFeatsMenuitem.setText(
 834             MessageManager.getString("label.show_non_positional_features"));
 835     showNpFeatsMenuitem.addActionListener(new ActionListener()
 836     {
 837
 838       @Override
 839       public void actionPerformed(ActionEvent e)
 840       {
 841         showNpFeats_actionPerformed(e);
 842       }
 843
 844     });
 845     showGroupConservation
 846             .setText(MessageManager.getString("label.group_conservation"));
 847     showGroupConservation.addActionListener(new ActionListener()
 848     {
 849
 850       @Override
 851       public void actionPerformed(ActionEvent e)
 852       {
 853         showGroupConservation_actionPerformed(e);
 854       }
 855
 856     });
 857
 858     showGroupConsensus
 859             .setText(MessageManager.getString("label.group_consensus"));
 860     showGroupConsensus.addActionListener(new ActionListener()
 861     {
 862
 863       @Override
 864       public void actionPerformed(ActionEvent e)
 865       {
 866         showGroupConsensus_actionPerformed(e);
 867       }
 868
 869     });
 870     showConsensusHistogram.setText(
 871             MessageManager.getString("label.show_consensus_histogram"));
 872     showConsensusHistogram.addActionListener(new ActionListener()
 873     {
 874
 875       @Override
 876       public void actionPerformed(ActionEvent e)
 877       {
 878         showConsensusHistogram_actionPerformed(e);
 879       }
 880
 881     });
 882     showSequenceLogo
 883             .setText(MessageManager.getString("label.show_consensus_logo"));
 884     showSequenceLogo.addActionListener(new ActionListener()
 885     {
 886
 887       @Override
 888       public void actionPerformed(ActionEvent e)
 889       {
 890         showSequenceLogo_actionPerformed(e);
 891       }
 892
 893     });
 894     normaliseSequenceLogo
 895             .setText(MessageManager.getString("label.norm_consensus_logo"));
 896     normaliseSequenceLogo.addActionListener(new ActionListener()
 897     {
 898
 899       @Override
 900       public void actionPerformed(ActionEvent e)
 901       {
 902         normaliseSequenceLogo_actionPerformed(e);
 903       }
 904
 905     });
 906     applyAutoAnnotationSettings
 907             .setText(MessageManager.getString("label.apply_all_groups"));
 908     applyAutoAnnotationSettings.setState(false);
 909     applyAutoAnnotationSettings.setVisible(true);
 910     applyAutoAnnotationSettings.addActionListener(new ActionListener()
 911     {
 912       @Override
 913       public void actionPerformed(ActionEvent e)
 914       {
 915         applyAutoAnnotationSettings_actionPerformed(e);
 916       }
 917     });
 918
 919     ButtonGroup buttonGroup = new ButtonGroup();
 920     final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
 921             MessageManager.getString("label.show_first"));
 922     final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
 923             MessageManager.getString("label.show_last"));
 924     buttonGroup.add(showAutoFirst);
 925     buttonGroup.add(showAutoLast);
 926     final boolean autoFirst = Cache
 927             .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
 928     showAutoFirst.setSelected(autoFirst);
 929     setShowAutoCalculatedAbove(autoFirst);
 930     showAutoFirst.addActionListener(new ActionListener()
 931     {
 932       @Override
 933       public void actionPerformed(ActionEvent e)
 934       {
 935         setShowAutoCalculatedAbove(showAutoFirst.isSelected());
 936         sortAnnotations_actionPerformed();
 937       }
 938     });
 939     showAutoLast.setSelected(!showAutoFirst.isSelected());
 940     showAutoLast.addActionListener(new ActionListener()
 941     {
 942       @Override
 943       public void actionPerformed(ActionEvent e)
 944       {
 945         setShowAutoCalculatedAbove(!showAutoLast.isSelected());
 946         sortAnnotations_actionPerformed();
 947       }
 948     });
 949
 950     JMenuItem deleteGroups = new JMenuItem(
 951             MessageManager.getString("action.undefine_groups"));
 952     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
 953             jalview.util.ShortcutKeyMaskExWrapper
 954                     .getMenuShortcutKeyMaskEx(),
 955             false);
 956     al = new ActionListener()
 957     {
 958       @Override
 959       public void actionPerformed(ActionEvent e)
 960       {
 961         deleteGroups_actionPerformed(e);
 962       }
 963     };
 964     addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
 965
 966     JMenuItem annotationColumn = new JMenuItem(
 967             MessageManager.getString("action.select_by_annotation"));
 968     annotationColumn.addActionListener(new ActionListener()
 969     {
 970       @Override
 971       public void actionPerformed(ActionEvent e)
 972       {
 973         annotationColumn_actionPerformed(e);
 974       }
 975     });
 976
 977     JMenuItem createGroup = new JMenuItem(
 978             MessageManager.getString("action.create_group"));
 979     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
 980             jalview.util.ShortcutKeyMaskExWrapper
 981                     .getMenuShortcutKeyMaskEx(),
 982             false);
 983     al = new ActionListener()
 984     {
 985       @Override
 986       public void actionPerformed(ActionEvent e)
 987       {
 988         createGroup_actionPerformed(e);
 989       }
 990     };
 991     addMenuActionAndAccelerator(keyStroke, createGroup, al);
 992
 993     JMenuItem unGroup = new JMenuItem(
 994             MessageManager.getString("action.remove_group"));
 995     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
 996             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
 997                     | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
 998             false);
 999     al = new ActionListener()
1000     {
1001       @Override
1002       public void actionPerformed(ActionEvent e)
1003       {
1004         unGroup_actionPerformed(e);
1005       }
1006     };
1007     addMenuActionAndAccelerator(keyStroke, unGroup, al);
1008
1009     copy.setText(MessageManager.getString("action.copy"));
1010     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
1011             jalview.util.ShortcutKeyMaskExWrapper
1012                     .getMenuShortcutKeyMaskEx(),
1013             false);
1014
1015     al = new ActionListener()
1016     {
1017       @Override
1018       public void actionPerformed(ActionEvent e)
1019       {
1020         copy_actionPerformed();
1021       }
1022     };
1023     addMenuActionAndAccelerator(keyStroke, copy, al);
1024
1025     cut.setText(MessageManager.getString("action.cut"));
1026     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
1027             jalview.util.ShortcutKeyMaskExWrapper
1028                     .getMenuShortcutKeyMaskEx(),
1029             false);
1030     al = new ActionListener()
1031     {
1032       @Override
1033       public void actionPerformed(ActionEvent e)
1034       {
1035         cut_actionPerformed();
1036       }
1037     };
1038     addMenuActionAndAccelerator(keyStroke, cut, al);
1039
1040     JMenuItem delete = new JMenuItem(
1041             MessageManager.getString("action.delete"));
1042     delete.addActionListener(new ActionListener()
1043     {
1044       @Override
1045       public void actionPerformed(ActionEvent e)
1046       {
1047         delete_actionPerformed();
1048       }
1049     });
1050
1051     pasteMenu.setText(MessageManager.getString("action.paste"));
1052     JMenuItem pasteNew = new JMenuItem(
1053             MessageManager.getString("label.to_new_alignment"));
1054     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1055             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1056                     | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
1057             false);
1058     al = new ActionListener()
1059     {
1060       @Override
1061       public void actionPerformed(ActionEvent e)
1062       {
1063         pasteNew_actionPerformed(e);
1064       }
1065     };
1066     addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1067
1068     JMenuItem pasteThis = new JMenuItem(
1069             MessageManager.getString("label.to_this_alignment"));
1070     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1071             jalview.util.ShortcutKeyMaskExWrapper
1072                     .getMenuShortcutKeyMaskEx(),
1073             false);
1074     al = new ActionListener()
1075     {
1076       @Override
1077       public void actionPerformed(ActionEvent e)
1078       {
1079         pasteThis_actionPerformed(e);
1080       }
1081     };
1082     addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1083
1084     JMenuItem createPNG = new JMenuItem("PNG");
1085     createPNG.addActionListener(new ActionListener()
1086     {
1087       @Override
1088       public void actionPerformed(ActionEvent e)
1089       {
1090         createPNG_actionPerformed(e);
1091       }
1092     });
1093     createPNG.setActionCommand(
1094             MessageManager.getString("label.save_png_image"));
1095
1096     JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1097     font.addActionListener(new ActionListener()
1098     {
1099       @Override
1100       public void actionPerformed(ActionEvent e)
1101       {
1102         font_actionPerformed(e);
1103       }
1104     });
1105     seqLimits.setText(
1106             MessageManager.getString("label.show_sequence_limits"));
1107     seqLimits.setState(Cache.getDefault("SHOW_JVSUFFIX", true));
1108     seqLimits.addActionListener(new ActionListener()
1109     {
1110       @Override
1111       public void actionPerformed(ActionEvent e)
1112       {
1113         seqLimit_actionPerformed(e);
1114       }
1115     });
1116     JMenuItem epsFile = new JMenuItem("EPS");
1117     epsFile.addActionListener(new ActionListener()
1118     {
1119       @Override
1120       public void actionPerformed(ActionEvent e)
1121       {
1122         createEPS_actionPerformed(e);
1123       }
1124     });
1125
1126     JMenuItem createSVG = new JMenuItem("SVG");
1127     createSVG.addActionListener(new ActionListener()
1128     {
1129       @Override
1130       public void actionPerformed(ActionEvent e)
1131       {
1132         createSVG_actionPerformed(e);
1133       }
1134     });
1135
1136     JMenuItem loadTreeMenuItem = new JMenuItem(
1137             MessageManager.getString("label.load_associated_tree"));
1138     loadTreeMenuItem.setActionCommand(
1139             MessageManager.getString("label.load_tree_for_sequence_set"));
1140     loadTreeMenuItem.addActionListener(new ActionListener()
1141     {
1142       @Override
1143       public void actionPerformed(ActionEvent e)
1144       {
1145         loadTreeMenuItem_actionPerformed(e);
1146       }
1147     });
1148
1149     scaleAbove.setVisible(false);
1150     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1151     scaleAbove.addActionListener(new ActionListener()
1152     {
1153       @Override
1154       public void actionPerformed(ActionEvent e)
1155       {
1156         scaleAbove_actionPerformed(e);
1157       }
1158     });
1159     scaleLeft.setVisible(false);
1160     scaleLeft.setSelected(true);
1161     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1162     scaleLeft.addActionListener(new ActionListener()
1163     {
1164       @Override
1165       public void actionPerformed(ActionEvent e)
1166       {
1167         scaleLeft_actionPerformed(e);
1168       }
1169     });
1170     scaleRight.setVisible(false);
1171     scaleRight.setSelected(true);
1172     scaleRight.setText(MessageManager.getString("action.scale_right"));
1173     scaleRight.addActionListener(new ActionListener()
1174     {
1175       @Override
1176       public void actionPerformed(ActionEvent e)
1177       {
1178         scaleRight_actionPerformed(e);
1179       }
1180     });
1181     centreColumnLabelsMenuItem.setVisible(true);
1182     centreColumnLabelsMenuItem.setState(false);
1183     centreColumnLabelsMenuItem.setText(
1184             MessageManager.getString("label.centre_column_labels"));
1185     centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1186     {
1187       @Override
1188       public void actionPerformed(ActionEvent e)
1189       {
1190         centreColumnLabels_actionPerformed(e);
1191       }
1192     });
1193     followHighlightMenuItem.setVisible(true);
1194     followHighlightMenuItem.setState(true);
1195     followHighlightMenuItem
1196             .setText(MessageManager.getString("label.automatic_scrolling"));
1197     followHighlightMenuItem.addActionListener(new ActionListener()
1198     {
1199
1200       @Override
1201       public void actionPerformed(ActionEvent e)
1202       {
1203         followHighlight_actionPerformed();
1204       }
1205
1206     });
1207
1208     sortByTreeMenu
1209             .setText(MessageManager.getString("action.by_tree_order"));
1210     sort.setText(MessageManager.getString("action.sort"));
1211     sort.addMenuListener(new MenuListener()
1212     {
1213       @Override
1214       public void menuSelected(MenuEvent e)
1215       {
1216         buildTreeSortMenu();
1217       }
1218
1219       @Override
1220       public void menuDeselected(MenuEvent e)
1221       {
1222       }
1223
1224       @Override
1225       public void menuCanceled(MenuEvent e)
1226       {
1227       }
1228     });
1229     sortByAnnotScore
1230             .setText(MessageManager.getString("label.sort_by_score"));
1231     sort.add(sortByAnnotScore);
1232     sort.addMenuListener(new javax.swing.event.MenuListener()
1233     {
1234
1235       @Override
1236       public void menuCanceled(MenuEvent e)
1237       {
1238       }
1239
1240       @Override
1241       public void menuDeselected(MenuEvent e)
1242       {
1243       }
1244
1245       @Override
1246       public void menuSelected(MenuEvent e)
1247       {
1248         buildSortByAnnotationScoresMenu();
1249       }
1250     });
1251     sortByAnnotScore.setVisible(false);
1252
1253     calculateTree
1254             .setText(MessageManager.getString("action.calculate_tree_pca"));
1255
1256     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1257     padGapsMenuitem.setState(Cache.getDefault("PAD_GAPS", false));
1258     padGapsMenuitem.addActionListener(new ActionListener()
1259     {
1260       @Override
1261       public void actionPerformed(ActionEvent e)
1262       {
1263         padGapsMenuitem_actionPerformed(e);
1264       }
1265     });
1266     JMenuItem vamsasStore = new JMenuItem(
1267             MessageManager.getString("label.vamsas_store"));
1268     vamsasStore.setVisible(false);
1269     vamsasStore.addActionListener(new ActionListener()
1270     {
1271       @Override
1272       public void actionPerformed(ActionEvent e)
1273       {
1274         vamsasStore_actionPerformed(e);
1275       }
1276     });
1277
1278     /*
1279      * Translate as cDNA with sub-menu of translation tables
1280      */
1281     showTranslation
1282             .setText(MessageManager.getString("label.translate_cDNA"));
1283     boolean first = true;
1284     for (final GeneticCodeI table : GeneticCodes.getInstance()
1285             .getCodeTables())
1286     {
1287       JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
1288       showTranslation.add(item);
1289       item.addActionListener(new ActionListener()
1290       {
1291         @Override
1292         public void actionPerformed(ActionEvent e)
1293         {
1294           showTranslation_actionPerformed(table);
1295         }
1296       });
1297       if (first)
1298       {
1299         showTranslation.addSeparator();
1300       }
1301       first = false;
1302     }
1303
1304     showReverse.setText(MessageManager.getString("label.reverse"));
1305     showReverse.addActionListener(new ActionListener()
1306     {
1307       @Override
1308       public void actionPerformed(ActionEvent e)
1309       {
1310         showReverse_actionPerformed(false);
1311       }
1312     });
1313     showReverseComplement
1314             .setText(MessageManager.getString("label.reverse_complement"));
1315     showReverseComplement.addActionListener(new ActionListener()
1316     {
1317       @Override
1318       public void actionPerformed(ActionEvent e)
1319       {
1320         showReverse_actionPerformed(true);
1321       }
1322     });
1323
1324     JMenuItem extractScores = new JMenuItem(
1325             MessageManager.getString("label.extract_scores"));
1326     extractScores.addActionListener(new ActionListener()
1327     {
1328       @Override
1329       public void actionPerformed(ActionEvent e)
1330       {
1331         extractScores_actionPerformed(e);
1332       }
1333     });
1334     extractScores.setVisible(true);
1335     // JBPNote: TODO: make gui for regex based score extraction
1336
1337     // for show products actions see AlignFrame.canShowProducts
1338     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1339
1340     runGroovy.setText(MessageManager.getString("label.run_groovy"));
1341     runGroovy.setToolTipText(
1342             MessageManager.getString("label.run_groovy_tip"));
1343     runGroovy.addActionListener(new ActionListener()
1344     {
1345       @Override
1346       public void actionPerformed(ActionEvent e)
1347       {
1348         runGroovy_actionPerformed();
1349       }
1350     });
1351
1352     openFeatureSettings = new JMenuItem(
1353             MessageManager.getString("action.feature_settings"));
1354     openFeatureSettings.addActionListener(new ActionListener()
1355     {
1356       @Override
1357       public void actionPerformed(ActionEvent e)
1358       {
1359         featureSettings_actionPerformed(e);
1360       }
1361     });
1362
1363     /*
1364      * add sub-menu of database we can fetch from
1365      */
1366     JMenuItem fetchSequence = new JMenuItem(
1367             MessageManager.getString("label.fetch_sequences"));
1368     fetchSequence.addActionListener(new ActionListener()
1369     {
1370       @Override
1371       public void actionPerformed(ActionEvent e)
1372       {
1373         fetchSequence_actionPerformed();
1374       }
1375     });
1376
1377     JMenuItem associatedData = new JMenuItem(
1378             MessageManager.getString("label.load_features_annotations"));
1379     associatedData.addActionListener(new ActionListener()
1380     {
1381       @Override
1382       public void actionPerformed(ActionEvent e)
1383       {
1384         associatedData_actionPerformed(e);
1385       }
1386     });
1387     loadVcf = new JMenuItem(
1388             MessageManager.getString("label.load_vcf_file"));
1389     loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
1390     loadVcf.addActionListener(new ActionListener()
1391     {
1392       @Override
1393       public void actionPerformed(ActionEvent e)
1394       {
1395         loadVcf_actionPerformed();
1396       }
1397     });
1398     autoCalculate.setText(
1399             MessageManager.getString("label.autocalculate_consensus"));
1400     autoCalculate.setState(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1401     autoCalculate.addActionListener(new ActionListener()
1402     {
1403       @Override
1404       public void actionPerformed(ActionEvent e)
1405       {
1406         autoCalculate_actionPerformed(e);
1407       }
1408     });
1409     sortByTree.setText(
1410             MessageManager.getString("label.sort_alignment_new_tree"));
1411     sortByTree.setToolTipText("<html>" + MessageManager.getString(
1412             "label.enable_automatically_sort_alignment_when_open_new_tree"));
1413     sortByTree.setState(Cache.getDefault("SORT_BY_TREE", false));
1414     sortByTree.addActionListener(new ActionListener()
1415     {
1416       @Override
1417       public void actionPerformed(ActionEvent e)
1418       {
1419         sortByTreeOption_actionPerformed(e);
1420       }
1421     });
1422
1423     listenToViewSelections.setText(
1424             MessageManager.getString("label.listen_for_selections"));
1425     listenToViewSelections
1426             .setToolTipText("<html>" + MessageManager.getString(
1427                     "label.selections_mirror_selections_made_same_sequences_other_views"));
1428     listenToViewSelections.setState(false);
1429     listenToViewSelections.addActionListener(new ActionListener()
1430     {
1431       @Override
1432       public void actionPerformed(ActionEvent e)
1433       {
1434         listenToViewSelections_actionPerformed(e);
1435       }
1436     });
1437
1438     JMenu addSequenceMenu = new JMenu(
1439             MessageManager.getString("label.add_sequences"));
1440     JMenuItem addFromFile = new JMenuItem(
1441             MessageManager.getString("label.from_file"));
1442     addFromFile.addActionListener(new ActionListener()
1443     {
1444       @Override
1445       public void actionPerformed(ActionEvent e)
1446       {
1447         addFromFile_actionPerformed(e);
1448       }
1449     });
1450     JMenuItem addFromText = new JMenuItem(
1451             MessageManager.getString("label.from_textbox"));
1452     addFromText.addActionListener(new ActionListener()
1453     {
1454       @Override
1455       public void actionPerformed(ActionEvent e)
1456       {
1457         addFromText_actionPerformed(e);
1458       }
1459     });
1460     JMenuItem addFromURL = new JMenuItem(
1461             MessageManager.getString("label.from_url"));
1462     addFromURL.addActionListener(new ActionListener()
1463     {
1464       @Override
1465       public void actionPerformed(ActionEvent e)
1466       {
1467         addFromURL_actionPerformed(e);
1468       }
1469     });
1470     JMenuItem exportFeatures = new JMenuItem(
1471             MessageManager.getString("label.export_features"));
1472     exportFeatures.addActionListener(new ActionListener()
1473     {
1474       @Override
1475       public void actionPerformed(ActionEvent e)
1476       {
1477         exportFeatures_actionPerformed(e);
1478       }
1479     });
1480     JMenuItem exportAnnotations = new JMenuItem(
1481             MessageManager.getString("label.export_annotations"));
1482     exportAnnotations.addActionListener(new ActionListener()
1483     {
1484       @Override
1485       public void actionPerformed(ActionEvent e)
1486       {
1487         exportAnnotations_actionPerformed(e);
1488       }
1489     });
1490     statusPanel.setLayout(new GridLayout());
1491     JMenuItem showAllSeqs = new JMenuItem(
1492             MessageManager.getString("label.all_sequences"));
1493     showAllSeqs.setToolTipText(
1494             MessageManager.getString("label.toggle_sequence_visibility"));
1495     showAllSeqs.addActionListener(new ActionListener()
1496     {
1497       @Override
1498       public void actionPerformed(ActionEvent e)
1499       {
1500         showAllSeqs_actionPerformed(e);
1501       }
1502     });
1503     JMenuItem showAllColumns = new JMenuItem(
1504             MessageManager.getString("label.all_columns"));
1505     showAllColumns.setToolTipText(
1506             MessageManager.getString("label.toggle_columns_visibility"));
1507     showAllColumns.addActionListener(new ActionListener()
1508     {
1509       @Override
1510       public void actionPerformed(ActionEvent e)
1511       {
1512         showAllColumns_actionPerformed(e);
1513       }
1514     });
1515     JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1516     JMenuItem hideSelSequences = new JMenuItem(
1517             MessageManager.getString("label.selected_sequences"));
1518     hideSelSequences.setToolTipText(
1519             MessageManager.getString("label.toggle_sequence_visibility"));
1520     hideSelSequences.addActionListener(new ActionListener()
1521     {
1522       @Override
1523       public void actionPerformed(ActionEvent e)
1524       {
1525         hideSelSequences_actionPerformed(e);
1526       }
1527     });
1528     JMenuItem hideSelColumns = new JMenuItem(
1529             MessageManager.getString("label.selected_columns"));
1530     hideSelColumns.setToolTipText(
1531             MessageManager.getString("label.toggle_columns_visibility"));
1532     hideSelColumns.addActionListener(new ActionListener()
1533     {
1534       @Override
1535       public void actionPerformed(ActionEvent e)
1536       {
1537         hideSelColumns_actionPerformed(e);
1538       }
1539     });
1540     JMenuItem hideAllSelection = new JMenuItem(
1541             MessageManager.getString("label.selected_region"));
1542     hideAllSelection.addActionListener(new ActionListener()
1543     {
1544       @Override
1545       public void actionPerformed(ActionEvent e)
1546       {
1547         hideAllSelection_actionPerformed(e);
1548       }
1549     });
1550     // TODO: should be hidden if no selection exists.
1551     JMenuItem hideAllButSelection = new JMenuItem(
1552             MessageManager.getString("label.all_but_selected_region"));
1553     hideAllButSelection.addActionListener(new ActionListener()
1554     {
1555       @Override
1556       public void actionPerformed(ActionEvent e)
1557       {
1558         hideAllButSelection_actionPerformed(e);
1559       }
1560     });
1561     JMenuItem showAllhidden = new JMenuItem(
1562             MessageManager.getString("label.all_sequences_columns"));
1563     showAllhidden.setToolTipText(MessageManager
1564             .getString("label.toggles_visibility_hidden_selected_regions"));
1565     showAllhidden.addActionListener(new ActionListener()
1566     {
1567       @Override
1568       public void actionPerformed(ActionEvent e)
1569       {
1570         showAllhidden_actionPerformed(e);
1571       }
1572     });
1573     hiddenMarkers.setText(
1574             MessageManager.getString("action.show_hidden_markers"));
1575     hiddenMarkers.addActionListener(new ActionListener()
1576     {
1577       @Override
1578       public void actionPerformed(ActionEvent e)
1579       {
1580         hiddenMarkers_actionPerformed(e);
1581       }
1582     });
1583
1584     JMenuItem invertColSel = new JMenuItem(
1585             MessageManager.getString("action.invert_column_selection"));
1586     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1587             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1588                     | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
1589             false);
1590     al = new ActionListener()
1591     {
1592       @Override
1593       public void actionPerformed(ActionEvent e)
1594       {
1595         invertColSel_actionPerformed(e);
1596       }
1597     };
1598     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1599
1600     showComplementMenuItem.setVisible(false);
1601     showComplementMenuItem.addActionListener(new ActionListener()
1602     {
1603       @Override
1604       public void actionPerformed(ActionEvent e)
1605       {
1606         showComplement_actionPerformed(showComplementMenuItem.getState());
1607       }
1608     });
1609
1610     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1611     {
1612       @Override
1613       public void stateChanged(ChangeEvent evt)
1614       {
1615         JTabbedPane pane = (JTabbedPane) evt.getSource();
1616         int sel = pane.getSelectedIndex();
1617         tabSelectionChanged(sel);
1618       }
1619     });
1620     tabbedPane.addMouseListener(new MouseAdapter()
1621     {
1622       @Override
1623       public void mousePressed(MouseEvent e)
1624       {
1625         if (e.isPopupTrigger()) // Mac
1626         {
1627           tabbedPane_mousePressed(e);
1628         }
1629       }
1630
1631       @Override
1632       public void mouseReleased(MouseEvent e)
1633       {
1634         if (e.isPopupTrigger()) // Windows
1635         {
1636           tabbedPane_mousePressed(e);
1637         }
1638       }
1639     });
1640     tabbedPane.addFocusListener(new FocusAdapter()
1641     {
1642       @Override
1643       public void focusGained(FocusEvent e)
1644       {
1645         tabbedPane_focusGained(e);
1646       }
1647     });
1648
1649     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1650     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1651             jalview.util.ShortcutKeyMaskExWrapper
1652                     .getMenuShortcutKeyMaskEx(),
1653             false);
1654     al = new ActionListener()
1655     {
1656       @Override
1657       public void actionPerformed(ActionEvent e)
1658       {
1659         save_actionPerformed(e);
1660       }
1661     };
1662     addMenuActionAndAccelerator(keyStroke, save, al);
1663
1664     reload.setEnabled(false);
1665     reload.setText(MessageManager.getString("action.reload"));
1666     reload.addActionListener(new ActionListener()
1667     {
1668       @Override
1669       public void actionPerformed(ActionEvent e)
1670       {
1671         reload_actionPerformed(e);
1672       }
1673     });
1674
1675     JMenuItem newView = new JMenuItem(
1676             MessageManager.getString("action.new_view"));
1677     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1678             jalview.util.ShortcutKeyMaskExWrapper
1679                     .getMenuShortcutKeyMaskEx(),
1680             false);
1681     al = new ActionListener()
1682     {
1683       @Override
1684       public void actionPerformed(ActionEvent e)
1685       {
1686         newView_actionPerformed(e);
1687       }
1688     };
1689     addMenuActionAndAccelerator(keyStroke, newView, al);
1690
1691     tabbedPane.setToolTipText("<html><i>"
1692             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1693             + "</i></html>");
1694
1695     formatMenu.setText(MessageManager.getString("action.format"));
1696     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1697
1698     idRightAlign.setText(
1699             MessageManager.getString("label.right_align_sequence_id"));
1700     idRightAlign.addActionListener(new ActionListener()
1701     {
1702       @Override
1703       public void actionPerformed(ActionEvent e)
1704       {
1705         idRightAlign_actionPerformed(e);
1706       }
1707     });
1708
1709     gatherViews.setEnabled(false);
1710     gatherViews.setText(MessageManager.getString("action.gather_views"));
1711     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1712     al = new ActionListener()
1713     {
1714       @Override
1715       public void actionPerformed(ActionEvent e)
1716       {
1717         gatherViews_actionPerformed(e);
1718       }
1719     };
1720     addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1721
1722     expandViews.setEnabled(false);
1723     expandViews.setText(MessageManager.getString("action.expand_views"));
1724     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1725     al = new ActionListener()
1726     {
1727       @Override
1728       public void actionPerformed(ActionEvent e)
1729       {
1730         expandViews_actionPerformed(e);
1731       }
1732     };
1733     addMenuActionAndAccelerator(keyStroke, expandViews, al);
1734
1735     JMenuItem pageSetup = new JMenuItem(
1736             MessageManager.getString("action.page_setup"));
1737     pageSetup.addActionListener(new ActionListener()
1738     {
1739       @Override
1740       public void actionPerformed(ActionEvent e)
1741       {
1742         pageSetup_actionPerformed(e);
1743       }
1744     });
1745     JMenuItem alignmentProperties = new JMenuItem(
1746             MessageManager.getString("label.alignment_props"));
1747     alignmentProperties.addActionListener(new ActionListener()
1748     {
1749       @Override
1750       public void actionPerformed(ActionEvent actionEvent)
1751       {
1752         alignmentProperties();
1753       }
1754     });
1755     JMenuItem selectHighlighted = new JMenuItem(
1756             MessageManager.getString("action.select_highlighted_columns"));
1757     selectHighlighted.setToolTipText(
1758             MessageManager.getString("tooltip.select_highlighted_columns"));
1759     al = new ActionListener()
1760     {
1761       @Override
1762       public void actionPerformed(ActionEvent actionEvent)
1763       {
1764         selectHighlightedColumns_actionPerformed(actionEvent);
1765       }
1766     };
1767     selectHighlighted.addActionListener(al);
1768
1769     copyHighlighted = new JMenuItem(
1770             MessageManager.getString("action.copy_highlighted_regions"));
1771     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
1772             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1773                     + jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
1774             false);
1775     copyHighlighted.setToolTipText(
1776             MessageManager.getString("tooltip.copy_highlighted_regions"));
1777     al = new ActionListener()
1778     {
1779       @Override
1780       public void actionPerformed(ActionEvent actionEvent)
1781       {
1782         copyHighlightedColumns_actionPerformed(actionEvent);
1783       }
1784     };
1785     addMenuActionAndAccelerator(keyStroke, copyHighlighted, al);
1786     copyHighlighted.addActionListener(al);
1787
1788     JMenu tooltipSettingsMenu = new JMenu(
1789             MessageManager.getString("label.sequence_id_tooltip"));
1790     JMenu autoAnnMenu = new JMenu(
1791             MessageManager.getString("label.autocalculated_annotation"));
1792
1793     JMenu exportImageMenu = new JMenu(
1794             MessageManager.getString("label.export_image"));
1795     JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1796     alignFrameMenuBar.add(fileMenu);
1797     alignFrameMenuBar.add(editMenu);
1798     alignFrameMenuBar.add(selectMenu);
1799     alignFrameMenuBar.add(viewMenu);
1800     alignFrameMenuBar.add(annotationsMenu);
1801     alignFrameMenuBar.add(formatMenu);
1802     alignFrameMenuBar.add(colourMenu);
1803     alignFrameMenuBar.add(calculateMenu);
1804     if (!Platform.isJS())
1805     {
1806       alignFrameMenuBar.add(webService);
1807     }
1808
1809     fileMenu.add(fetchSequence);
1810     fileMenu.add(addSequenceMenu);
1811     fileMenu.add(reload);
1812     fileMenu.addSeparator();
1813     fileMenu.add(vamsasStore);
1814     fileMenu.add(save);
1815     fileMenu.add(saveAs);
1816     fileMenu.add(outputTextboxMenu);
1817     fileMenu.add(pageSetup);
1818     fileMenu.add(printMenuItem);
1819     fileMenu.addSeparator();
1820     fileMenu.add(exportImageMenu);
1821     fileMenu.add(exportFeatures);
1822     fileMenu.add(exportAnnotations);
1823     fileMenu.add(loadTreeMenuItem);
1824     fileMenu.add(associatedData);
1825     if (!Platform.isJS())
1826     {
1827       fileMenu.add(loadVcf);
1828     }
1829     fileMenu.addSeparator();
1830     fileMenu.add(closeMenuItem);
1831
1832     pasteMenu.add(pasteNew);
1833     pasteMenu.add(pasteThis);
1834     editMenu.add(undoMenuItem);
1835     editMenu.add(redoMenuItem);
1836     editMenu.add(cut);
1837     editMenu.add(copy);
1838     editMenu.add(copyHighlighted);
1839     editMenu.add(pasteMenu);
1840     editMenu.add(delete);
1841     editMenu.addSeparator();
1842     editMenu.add(remove2LeftMenuItem);
1843     editMenu.add(remove2RightMenuItem);
1844     editMenu.add(removeGappedColumnMenuItem);
1845     editMenu.add(removeAllGapsMenuItem);
1846     editMenu.add(removeRedundancyMenuItem);
1847     editMenu.addSeparator();
1848
1849     editMenu.add(justifyLeftMenuItem);
1850     editMenu.add(justifyRightMenuItem);
1851
1852     editMenu.addSeparator();
1853     editMenu.add(padGapsMenuitem);
1854
1855     showMenu.add(showAllColumns);
1856     showMenu.add(showAllSeqs);
1857     showMenu.add(showAllhidden);
1858     hideMenu.add(hideSelColumns);
1859     hideMenu.add(hideSelSequences);
1860     hideMenu.add(hideAllSelection);
1861     hideMenu.add(hideAllButSelection);
1862     viewMenu.add(newView);
1863     viewMenu.add(expandViews);
1864     viewMenu.add(gatherViews);
1865     viewMenu.addSeparator();
1866     viewMenu.add(showMenu);
1867     viewMenu.add(hideMenu);
1868     viewMenu.add(showComplementMenuItem);
1869     viewMenu.addSeparator();
1870     viewMenu.add(followHighlightMenuItem);
1871     viewMenu.addSeparator();
1872     viewMenu.add(showSeqFeatures);
1873     // viewMenu.add(showSeqFeaturesHeight);
1874     viewMenu.add(openFeatureSettings);
1875     tooltipSettingsMenu.add(showDbRefsMenuitem);
1876     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1877     viewMenu.add(tooltipSettingsMenu);
1878     viewMenu.addSeparator();
1879     viewMenu.add(alignmentProperties);
1880     viewMenu.addSeparator();
1881     viewMenu.add(overviewMenuItem);
1882
1883     annotationsMenu.add(annotationPanelMenuItem);
1884     annotationsMenu.addSeparator();
1885     annotationsMenu.add(showAllAlAnnotations);
1886     annotationsMenu.add(hideAllAlAnnotations);
1887     annotationsMenu.addSeparator();
1888     annotationsMenu.add(showAllSeqAnnotations);
1889     annotationsMenu.add(hideAllSeqAnnotations);
1890     annotationsMenu.add(sortAnnBySequence);
1891     annotationsMenu.add(sortAnnByLabel);
1892     annotationsMenu.addSeparator();
1893     autoAnnMenu.add(showAutoFirst);
1894     autoAnnMenu.add(showAutoLast);
1895     autoAnnMenu.addSeparator();
1896     autoAnnMenu.add(applyAutoAnnotationSettings);
1897     autoAnnMenu.add(showConsensusHistogram);
1898     autoAnnMenu.add(showSequenceLogo);
1899     autoAnnMenu.add(normaliseSequenceLogo);
1900     autoAnnMenu.addSeparator();
1901     autoAnnMenu.add(showGroupConservation);
1902     autoAnnMenu.add(showGroupConsensus);
1903     annotationsMenu.add(autoAnnMenu);
1904
1905     sort.add(sortIDMenuItem);
1906     sort.add(sortLengthMenuItem);
1907     sort.add(sortGroupMenuItem);
1908     sort.add(sortPairwiseMenuItem);
1909     sort.add(sortByTreeMenu);
1910     calculateMenu.add(sort);
1911     calculateMenu.add(calculateTree);
1912     calculateMenu.addSeparator();
1913     calculateMenu.add(pairwiseAlignmentMenuItem);
1914     calculateMenu.addSeparator();
1915     calculateMenu.add(showTranslation);
1916     calculateMenu.add(showReverse);
1917     calculateMenu.add(showReverseComplement);
1918     calculateMenu.add(showProducts);
1919     calculateMenu.add(autoCalculate);
1920     calculateMenu.add(sortByTree);
1921     calculateMenu.addSeparator();
1922     calculateMenu.add(expandAlignment);
1923     calculateMenu.add(extractScores);
1924     if (!Platform.isJS())
1925     {
1926       calculateMenu.addSeparator();
1927       calculateMenu.add(runGroovy);
1928     }
1929
1930     webServiceNoServices = new JMenuItem(
1931             MessageManager.getString("label.no_services"));
1932     webService.add(webServiceNoServices);
1933     if (!Platform.isJS())
1934     {
1935       exportImageMenu.add(htmlMenuItem);
1936     }
1937     exportImageMenu.add(epsFile);
1938     exportImageMenu.add(createPNG);
1939     if (!Platform.isJS())
1940     {
1941       exportImageMenu.add(createBioJS);
1942       exportImageMenu.add(createSVG);
1943     }
1944     addSequenceMenu.add(addFromFile);
1945     addSequenceMenu.add(addFromText);
1946     addSequenceMenu.add(addFromURL);
1947     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1948     statusPanel.add(statusBar, null);
1949     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1950
1951     formatMenu.add(font);
1952     formatMenu.addSeparator();
1953     formatMenu.add(wrapMenuItem);
1954     formatMenu.add(scaleAbove);
1955     formatMenu.add(scaleLeft);
1956     formatMenu.add(scaleRight);
1957     formatMenu.add(seqLimits);
1958     formatMenu.add(idRightAlign);
1959     formatMenu.add(hiddenMarkers);
1960     formatMenu.add(viewBoxesMenuItem);
1961     formatMenu.add(viewTextMenuItem);
1962     formatMenu.add(colourTextMenuItem);
1963     formatMenu.add(renderGapsMenuItem);
1964     formatMenu.add(centreColumnLabelsMenuItem);
1965     formatMenu.add(showNonconservedMenuItem);
1966     selectMenu.add(findMenuItem);
1967     selectMenu.addSeparator();
1968     selectMenu.add(selectAllSequenceMenuItem);
1969     selectMenu.add(deselectAllSequenceMenuItem);
1970     selectMenu.add(invertSequenceMenuItem);
1971     selectMenu.add(invertColSel);
1972     selectMenu.add(createGroup);
1973     selectMenu.add(unGroup);
1974     selectMenu.add(grpsFromSelection);
1975     selectMenu.add(deleteGroups);
1976     selectMenu.add(annotationColumn);
1977     selectMenu.add(selectHighlighted);
1978     // TODO - determine if the listenToViewSelections button is needed : see bug
1979     // JAL-574
1980     // selectMenu.addSeparator();
1981     // selectMenu.add(listenToViewSelections);
1982   }
1983
1984   protected void createPNG_actionPerformed(ActionEvent object)
1985   {
1986     // TODO Auto-generated method stub
1987
1988   }
1989
1990   protected void createEPS_actionPerformed(ActionEvent object)
1991   {
1992     // TODO Auto-generated method stub
1993
1994   }
1995
1996   protected void createSVG_actionPerformed(ActionEvent object)
1997   {
1998     // TODO Auto-generated method stub
1999
2000   }
2001
2002   protected void copyHighlightedColumns_actionPerformed(
2003           ActionEvent actionEvent)
2004   {
2005
2006   }
2007
2008   protected void loadVcf_actionPerformed()
2009   {
2010   }
2011
2012   /**
2013    * Constructs the entries on the Colour menu (but does not add them to the
2014    * menu).
2015    */
2016   protected void initColourMenu()
2017   {
2018     applyToAllGroups = new JCheckBoxMenuItem(
2019             MessageManager.getString("label.apply_colour_to_all_groups"));
2020     applyToAllGroups.addActionListener(new ActionListener()
2021     {
2022       @Override
2023       public void actionPerformed(ActionEvent e)
2024       {
2025         applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
2026       }
2027     });
2028
2029     textColour = new JMenuItem(
2030             MessageManager.getString("label.text_colour"));
2031     textColour.addActionListener(new ActionListener()
2032     {
2033       @Override
2034       public void actionPerformed(ActionEvent e)
2035       {
2036         textColour_actionPerformed();
2037       }
2038     });
2039
2040     conservationMenuItem = new JCheckBoxMenuItem(
2041             MessageManager.getString("action.by_conservation"));
2042     conservationMenuItem.addActionListener(new ActionListener()
2043     {
2044       @Override
2045       public void actionPerformed(ActionEvent e)
2046       {
2047         conservationMenuItem_actionPerformed(
2048                 conservationMenuItem.isSelected());
2049       }
2050     });
2051
2052     abovePIDThreshold = new JCheckBoxMenuItem(
2053             MessageManager.getString("label.above_identity_threshold"));
2054     abovePIDThreshold.addActionListener(new ActionListener()
2055     {
2056       @Override
2057       public void actionPerformed(ActionEvent e)
2058       {
2059         abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
2060       }
2061     });
2062     modifyPID = new JMenuItem(
2063             MessageManager.getString("label.modify_identity_threshold"));
2064     modifyPID.addActionListener(new ActionListener()
2065     {
2066       @Override
2067       public void actionPerformed(ActionEvent e)
2068       {
2069         modifyPID_actionPerformed();
2070       }
2071     });
2072     modifyConservation = new JMenuItem(MessageManager
2073             .getString("label.modify_conservation_threshold"));
2074     modifyConservation.addActionListener(new ActionListener()
2075     {
2076       @Override
2077       public void actionPerformed(ActionEvent e)
2078       {
2079         modifyConservation_actionPerformed();
2080       }
2081     });
2082
2083     annotationColour = new JRadioButtonMenuItem(
2084             MessageManager.getString("action.by_annotation"));
2085     annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
2086     annotationColour.addActionListener(new ActionListener()
2087     {
2088       @Override
2089       public void actionPerformed(ActionEvent e)
2090       {
2091         annotationColour_actionPerformed();
2092       }
2093     });
2094   }
2095
2096   protected void selectHighlightedColumns_actionPerformed(
2097           ActionEvent actionEvent)
2098   {
2099     // TODO Auto-generated method stub
2100
2101   }
2102
2103   /**
2104    * Generate the reverse sequence (or reverse complement if the flag is true)
2105    * and add it to the alignment
2106    *
2107    * @param complement
2108    */
2109   protected void showReverse_actionPerformed(boolean complement)
2110   {
2111   }
2112
2113   /**
2114    * Try to run script in a Groovy console, having first ensured that this
2115    * alignframe is set as currentAlignFrame in Desktop
2116    */
2117   protected void runGroovy_actionPerformed()
2118   {
2119
2120   }
2121
2122   /**
2123    * Adds the given action listener and key accelerator to the given menu item.
2124    * Also saves in a lookup table to support lookup of action by key stroke.
2125    *
2126    * @param keyStroke
2127    * @param menuItem
2128    * @param actionListener
2129    */
2130   protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2131           JMenuItem menuItem, ActionListener actionListener)
2132   {
2133     menuItem.setAccelerator(keyStroke);
2134     accelerators.put(keyStroke, menuItem);
2135     menuItem.addActionListener(actionListener);
2136   }
2137
2138   /**
2139    * Action on clicking sort annotations by type.
2140    *
2141    * @param sortOrder
2142    */
2143   protected void sortAnnotations_actionPerformed()
2144   {
2145   }
2146
2147   /**
2148    * Action on clicking Show all annotations.
2149    *
2150    * @param forSequences
2151    *          update sequence-related annotations
2152    * @param forAlignment
2153    *          update non-sequence-related annotations
2154    */
2155   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2156           boolean forAlignment)
2157   {
2158     setAnnotationsVisibility(true, forSequences, forAlignment);
2159   }
2160
2161   /**
2162    * Action on clicking Hide all annotations.
2163    *
2164    * @param forSequences
2165    *          update sequence-related annotations
2166    * @param forAlignment
2167    *          update non-sequence-related annotations
2168    */
2169   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2170           boolean forAlignment)
2171   {
2172     setAnnotationsVisibility(false, forSequences, forAlignment);
2173   }
2174
2175   /**
2176    * Set the visibility of annotations to true or false. Can act on
2177    * sequence-related annotations, or alignment-related, or both.
2178    *
2179    * @param visible
2180    * @param forSequences
2181    *          update sequence-related annotations
2182    * @param forAlignment
2183    *          update non-sequence-related annotations
2184    */
2185   public void setAnnotationsVisibility(boolean visible,
2186           boolean forSequences, boolean forAlignment)
2187   {
2188
2189   }
2190
2191   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2192   {
2193     // TODO Auto-generated method stub
2194
2195   }
2196
2197   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2198   {
2199     // TODO Auto-generated method stub
2200
2201   }
2202
2203   protected void showAllhidden_actionPerformed(ActionEvent e)
2204   {
2205     // TODO Auto-generated method stub
2206
2207   }
2208
2209   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2210   {
2211     // TODO Auto-generated method stub
2212
2213   }
2214
2215   protected void hideAllSelection_actionPerformed(ActionEvent e)
2216   {
2217     // TODO Auto-generated method stub
2218
2219   }
2220
2221   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2222   {
2223     // TODO Auto-generated method stub
2224
2225   }
2226
2227   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2228   {
2229     // TODO Auto-generated method stub
2230
2231   }
2232
2233   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2234   {
2235     // TODO Auto-generated method stub
2236
2237   }
2238
2239   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2240   {
2241     // TODO Auto-generated method stub
2242
2243   }
2244
2245   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2246   {
2247     // TODO Auto-generated method stub
2248
2249   }
2250
2251   protected void showGroupConservation_actionPerformed(ActionEvent e)
2252   {
2253     // TODO Auto-generated method stub
2254
2255   }
2256
2257   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2258   {
2259     // TODO Auto-generated method stub
2260
2261   }
2262
2263   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2264   {
2265     // TODO Auto-generated method stub
2266
2267   }
2268
2269   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2270   {
2271     // TODO Auto-generated method stub
2272
2273   }
2274
2275   protected void followHighlight_actionPerformed()
2276   {
2277     // TODO Auto-generated method stub
2278
2279   }
2280
2281   protected void showNpFeats_actionPerformed(ActionEvent e)
2282   {
2283     // TODO Auto-generated method stub
2284
2285   }
2286
2287   protected void showDbRefs_actionPerformed(ActionEvent e)
2288   {
2289     // TODO Auto-generated method stub
2290
2291   }
2292
2293   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2294   {
2295   }
2296
2297   protected void buildSortByAnnotationScoresMenu()
2298   {
2299   }
2300
2301   protected void extractScores_actionPerformed(ActionEvent e)
2302   {
2303   }
2304
2305   protected void outputText_actionPerformed(String formatName)
2306   {
2307   }
2308
2309   public void addFromFile_actionPerformed(ActionEvent e)
2310   {
2311
2312   }
2313
2314   public void addFromText_actionPerformed(ActionEvent e)
2315   {
2316
2317   }
2318
2319   public void addFromURL_actionPerformed(ActionEvent e)
2320   {
2321
2322   }
2323
2324   public void exportFeatures_actionPerformed(ActionEvent e)
2325   {
2326
2327   }
2328
2329   public void exportAnnotations_actionPerformed(ActionEvent e)
2330   {
2331
2332   }
2333
2334   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2335   {
2336   }
2337
2338   protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2339   {
2340
2341   }
2342
2343   protected void closeMenuItem_actionPerformed(boolean b)
2344   {
2345   }
2346
2347   protected void redoMenuItem_actionPerformed(ActionEvent e)
2348   {
2349   }
2350
2351   protected void undoMenuItem_actionPerformed(ActionEvent e)
2352   {
2353   }
2354
2355   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2356   {
2357   }
2358
2359   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2360   {
2361   }
2362
2363   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2364   {
2365   }
2366
2367   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2368   {
2369   }
2370
2371   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2372   {
2373   }
2374
2375   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2376   {
2377   }
2378
2379   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2380   {
2381   }
2382
2383   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2384   {
2385   }
2386
2387   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2388   {
2389   }
2390
2391   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2392   {
2393   }
2394
2395   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2396   {
2397   }
2398
2399   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2400   {
2401   }
2402
2403   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2404   {
2405   }
2406
2407   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2408   {
2409   }
2410
2411   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2412   {
2413   }
2414
2415   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2416   {
2417   }
2418
2419   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2420   {
2421   }
2422
2423   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2424   {
2425   }
2426
2427   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2428   {
2429   }
2430
2431   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2432   {
2433   }
2434
2435   protected void conservationMenuItem_actionPerformed(boolean selected)
2436   {
2437   }
2438
2439   protected void printMenuItem_actionPerformed(ActionEvent e)
2440   {
2441   }
2442
2443   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2444   {
2445   }
2446
2447   protected void findMenuItem_actionPerformed(ActionEvent e)
2448   {
2449   }
2450
2451   protected void abovePIDThreshold_actionPerformed(boolean selected)
2452   {
2453   }
2454
2455   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2456   {
2457   }
2458
2459   protected void deleteGroups_actionPerformed(ActionEvent e)
2460   {
2461   }
2462
2463   protected void createGroup_actionPerformed(ActionEvent e)
2464   {
2465   }
2466
2467   protected void unGroup_actionPerformed(ActionEvent e)
2468   {
2469   }
2470
2471   protected void copy_actionPerformed()
2472   {
2473   }
2474
2475   protected void cut_actionPerformed()
2476   {
2477   }
2478
2479   protected void delete_actionPerformed()
2480   {
2481   }
2482
2483   protected void pasteNew_actionPerformed(ActionEvent e)
2484   {
2485   }
2486
2487   protected void pasteThis_actionPerformed(ActionEvent e)
2488   {
2489   }
2490
2491   protected void applyToAllGroups_actionPerformed(boolean selected)
2492   {
2493   }
2494
2495   protected void font_actionPerformed(ActionEvent e)
2496   {
2497   }
2498
2499   protected void seqLimit_actionPerformed(ActionEvent e)
2500   {
2501   }
2502
2503   public void seqDBRef_actionPerformed(ActionEvent e)
2504   {
2505
2506   }
2507
2508   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2509   {
2510
2511   }
2512
2513   /**
2514    * Template method to handle the 'load T-Coffee scores' menu event.
2515    * <p>
2516    * Subclasses override this method to provide a custom action.
2517    *
2518    * @param event
2519    *          The raised event
2520    */
2521   protected void loadScores_actionPerformed(ActionEvent event)
2522   {
2523
2524   }
2525
2526   protected void jpred_actionPerformed(ActionEvent e)
2527   {
2528   }
2529
2530   protected void scaleAbove_actionPerformed(ActionEvent e)
2531   {
2532   }
2533
2534   protected void scaleLeft_actionPerformed(ActionEvent e)
2535   {
2536   }
2537
2538   protected void scaleRight_actionPerformed(ActionEvent e)
2539   {
2540   }
2541
2542   protected void modifyPID_actionPerformed()
2543   {
2544   }
2545
2546   protected void modifyConservation_actionPerformed()
2547   {
2548   }
2549
2550   protected void saveAs_actionPerformed()
2551   {
2552   }
2553
2554   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2555   {
2556   }
2557
2558   public void vamsasStore_actionPerformed(ActionEvent e)
2559   {
2560
2561   }
2562
2563   public void vamsasLoad_actionPerformed(ActionEvent e)
2564   {
2565
2566   }
2567
2568   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
2569   {
2570
2571   }
2572
2573   public void featureSettings_actionPerformed(ActionEvent e)
2574   {
2575
2576   }
2577
2578   public void fetchSequence_actionPerformed()
2579   {
2580
2581   }
2582
2583   public void smoothFont_actionPerformed(ActionEvent e)
2584   {
2585
2586   }
2587
2588   public void annotationColour_actionPerformed()
2589   {
2590   }
2591
2592   public void annotationColumn_actionPerformed(ActionEvent e)
2593   {
2594   }
2595
2596   public void associatedData_actionPerformed(ActionEvent e)
2597   {
2598
2599   }
2600
2601   public void autoCalculate_actionPerformed(ActionEvent e)
2602   {
2603
2604   }
2605
2606   public void sortByTreeOption_actionPerformed(ActionEvent e)
2607   {
2608
2609   }
2610
2611   public void showAllSeqs_actionPerformed(ActionEvent e)
2612   {
2613
2614   }
2615
2616   public void showAllColumns_actionPerformed(ActionEvent e)
2617   {
2618
2619   }
2620
2621   public void hideSelSequences_actionPerformed(ActionEvent e)
2622   {
2623
2624   }
2625
2626   public void hideSelColumns_actionPerformed(ActionEvent e)
2627   {
2628
2629   }
2630
2631   public void hiddenMarkers_actionPerformed(ActionEvent e)
2632   {
2633
2634   }
2635
2636   public void findPdbId_actionPerformed(ActionEvent e)
2637   {
2638
2639   }
2640
2641   public void enterPdbId_actionPerformed(ActionEvent e)
2642   {
2643
2644   }
2645
2646   public void pdbFile_actionPerformed(ActionEvent e)
2647   {
2648
2649   }
2650
2651   public void invertColSel_actionPerformed(ActionEvent e)
2652   {
2653
2654   }
2655
2656   public void tabSelectionChanged(int sel)
2657   {
2658
2659   }
2660
2661   public void tabbedPane_mousePressed(MouseEvent e)
2662   {
2663
2664   }
2665
2666   public void tabbedPane_focusGained(FocusEvent e)
2667   {
2668     requestFocus();
2669   }
2670
2671   public void save_actionPerformed(ActionEvent e)
2672   {
2673
2674   }
2675
2676   public void reload_actionPerformed(ActionEvent e)
2677   {
2678
2679   }
2680
2681   public void newView_actionPerformed(ActionEvent e)
2682   {
2683
2684   }
2685
2686   public void textColour_actionPerformed()
2687   {
2688
2689   }
2690
2691   public void idRightAlign_actionPerformed(ActionEvent e)
2692   {
2693
2694   }
2695
2696   public void expandViews_actionPerformed(ActionEvent e)
2697   {
2698
2699   }
2700
2701   public void gatherViews_actionPerformed(ActionEvent e)
2702   {
2703
2704   }
2705
2706   public void buildTreeSortMenu()
2707   {
2708
2709   }
2710
2711   public void pageSetup_actionPerformed(ActionEvent e)
2712   {
2713
2714   }
2715
2716   public void alignmentProperties()
2717   {
2718
2719   }
2720
2721   protected void expand_newalign(ActionEvent e)
2722   {
2723     // TODO Auto-generated method stub
2724
2725   }
2726
2727   protected boolean isShowAutoCalculatedAbove()
2728   {
2729     return showAutoCalculatedAbove;
2730   }
2731
2732   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2733   {
2734     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2735   }
2736
2737   protected SequenceAnnotationOrder getAnnotationSortOrder()
2738   {
2739     return annotationSortOrder;
2740   }
2741
2742   protected void setAnnotationSortOrder(
2743           SequenceAnnotationOrder annotationSortOrder)
2744   {
2745     this.annotationSortOrder = annotationSortOrder;
2746   }
2747
2748   public Map<KeyStroke, JMenuItem> getAccelerators()
2749   {
2750     return this.accelerators;
2751   }
2752
2753   /**
2754    * Returns the selected index of the tabbed pane, or -1 if none selected
2755    * (including the case where the tabbed pane has not been made visible).
2756    *
2757    * @return
2758    */
2759   public int getTabIndex()
2760   {
2761     return tabbedPane.getSelectedIndex();
2762   }
2763
2764   public JPanel getStatusPanel()
2765   {
2766     return statusPanel;
2767   }
2768
2769   /**
2770    * Sets a reference to the containing split frame. Also makes the 'toggle
2771    * split view' menu item visible and checked.
2772    *
2773    * @param sf
2774    */
2775   public void setSplitFrame(SplitContainerI sf)
2776   {
2777     this.splitFrame = sf;
2778     if (sf != null)
2779     {
2780       this.showComplementMenuItem.setVisible(true);
2781       this.showComplementMenuItem.setState(true);
2782     }
2783   }
2784
2785   public SplitContainerI getSplitViewContainer()
2786   {
2787     return this.splitFrame;
2788   }
2789
2790   protected void showComplement_actionPerformed(boolean complement)
2791   {
2792   }
2793 }