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