src/jalview/jbgui/GAlignFrame.java

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