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