src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.jbgui;
  22
  23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  24 import jalview.analysis.GeneticCodeI;
  25 import jalview.analysis.GeneticCodes;
  26 import jalview.api.SplitContainerI;
  27 import jalview.bin.Cache;
  28 import jalview.gui.JvSwingUtils;
  29 import jalview.gui.Preferences;
  30 import jalview.io.FileFormats;
  31 import jalview.schemes.ResidueColourScheme;
  32 import jalview.util.MessageManager;
  33 import jalview.util.Platform;
  34
  35 import java.awt.BorderLayout;
  36 import java.awt.Color;
  37 import java.awt.GridLayout;
  38 import java.awt.Toolkit;
  39 import java.awt.event.ActionEvent;
  40 import java.awt.event.ActionListener;
  41 import java.awt.event.FocusAdapter;
  42 import java.awt.event.FocusEvent;
  43 import java.awt.event.KeyEvent;
  44 import java.awt.event.MouseAdapter;
  45 import java.awt.event.MouseEvent;
  46 import java.util.HashMap;
  47 import java.util.Map;
  48
  49 import javax.swing.BorderFactory;
  50 import javax.swing.ButtonGroup;
  51 import javax.swing.JCheckBoxMenuItem;
  52 import javax.swing.JInternalFrame;
  53 import javax.swing.JLabel;
  54 import javax.swing.JMenu;
  55 import javax.swing.JMenuBar;
  56 import javax.swing.JMenuItem;
  57 import javax.swing.JPanel;
  58 import javax.swing.JRadioButtonMenuItem;
  59 import javax.swing.JTabbedPane;
  60 import javax.swing.KeyStroke;
  61 import javax.swing.event.ChangeEvent;
  62 import javax.swing.event.MenuEvent;
  63 import javax.swing.event.MenuListener;
  64
  65 public class GAlignFrame extends JInternalFrame
  66 {
  67   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  68
  69   protected JMenuItem closeMenuItem = new JMenuItem();
  70
  71   protected JMenu webService = new JMenu();
  72
  73   protected JMenuItem webServiceNoServices;
  74
  75   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  76
  77   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  78
  79   protected JMenu sortByAnnotScore = new JMenu();
  80
  81   protected JLabel statusBar = new JLabel();
  82
  83   protected JMenu outputTextboxMenu = new JMenu();
  84
  85   protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
  86
  87   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
  88
  89   protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
  90
  91   protected JMenuItem undoMenuItem = new JMenuItem();
  92
  93   protected JMenuItem redoMenuItem = new JMenuItem();
  94
  95   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
  96
  97   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
  98
  99   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 100
 101   JMenuItem copy = new JMenuItem();
 102
 103   JMenuItem cut = new JMenuItem();
 104
 105   JMenu pasteMenu = new JMenu();
 106
 107   protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 108
 109   protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 110
 111   protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 112
 113   protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 114
 115   protected JCheckBoxMenuItem applyToAllGroups;
 116
 117   protected JMenu colourMenu = new JMenu();
 118
 119   protected JMenuItem textColour;
 120
 121   protected JCheckBoxMenuItem conservationMenuItem;
 122
 123   protected JMenuItem modifyConservation;
 124
 125   protected JCheckBoxMenuItem abovePIDThreshold;
 126
 127   protected JMenuItem modifyPID;
 128
 129   protected JRadioButtonMenuItem annotationColour;
 130
 131   protected JMenu sortByTreeMenu = new JMenu();
 132
 133   protected JMenu sort = new JMenu();
 134
 135   protected JMenuItem calculateTree = new JMenuItem();
 136
 137   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 138
 139   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 140
 141   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 142
 143   protected JMenu showTranslation = new JMenu();
 144
 145   protected JMenuItem showReverse = new JMenuItem();
 146
 147   protected JMenuItem showReverseComplement = new JMenuItem();
 148
 149   protected JMenu showProducts = new JMenu();
 150
 151   protected JMenuItem runGroovy = new JMenuItem();
 152
 153   protected JMenuItem loadVcf;
 154
 155   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 156
 157   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 158
 159   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 160
 161   protected JPanel statusPanel = new JPanel();
 162
 163   protected JMenuItem showAllSeqAnnotations = new JMenuItem();
 164
 165   protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
 166
 167   protected JMenuItem showAllAlAnnotations = new JMenuItem();
 168
 169   protected JMenuItem hideAllAlAnnotations = new JMenuItem();
 170
 171   protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
 172
 173   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 174
 175   protected JTabbedPane tabbedPane = jalview.jbgui.GDesktop.createTabbedPane();
 176
 177   protected JMenuItem reload = new JMenuItem();
 178
 179   protected JMenu formatMenu = new JMenu();
 180
 181   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 182
 183   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 184
 185   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 186
 187   protected JMenuItem gatherViews = new JMenuItem();
 188
 189   protected JMenuItem expandViews = new JMenuItem();
 190
 191   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 192
 193   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 194
 195   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 196
 197   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 198
 199   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 200
 201   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 202
 203   protected JMenuItem openFeatureSettings;
 204
 205   private SequenceAnnotationOrder annotationSortOrder;
 206
 207   private boolean showAutoCalculatedAbove = false;
 208
 209   private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
 210
 211   private SplitContainerI splitFrame;
 212
 213   public GAlignFrame()
 214   {
 215     try
 216     {
 217       jbInit();
 218       setJMenuBar(alignFrameMenuBar);
 219
 220       // dynamically fill save as menu with available formats
 221       for (String ff : FileFormats.getInstance().getWritableFormats(true))
 222       {
 223         JMenuItem item = new JMenuItem(ff);
 224
 225         item.addActionListener(new ActionListener()
 226         {
 227           @Override
 228           public void actionPerformed(ActionEvent e)
 229           {
 230             outputText_actionPerformed(e.getActionCommand());
 231           }
 232         });
 233
 234         outputTextboxMenu.add(item);
 235       }
 236     } catch (Exception e)
 237     {
 238       System.err.println(e.toString());
 239     }
 240
 241     if (Platform.allowMnemonics()) // was "not mac and not JS"
 242     {
 243       closeMenuItem.setMnemonic('C');
 244       outputTextboxMenu.setMnemonic('T');
 245       undoMenuItem.setMnemonic('Z');
 246       redoMenuItem.setMnemonic('0');
 247       copy.setMnemonic('C');
 248       cut.setMnemonic('U');
 249       pasteMenu.setMnemonic('P');
 250       reload.setMnemonic('R');
 251     }
 252   }
 253
 254   private void jbInit() throws Exception
 255   {
 256     initColourMenu();
 257
 258     JMenuItem saveAs = new JMenuItem(
 259             MessageManager.getString("action.save_as"));
 260     ActionListener al = new ActionListener()
 261     {
 262       @Override
 263       public void actionPerformed(ActionEvent e)
 264       {
 265         saveAs_actionPerformed();
 266       }
 267     };
 268
 269     // FIXME getDefaultToolkit throws an exception in Headless mode
 270     KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
 271             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
 272                     | KeyEvent.SHIFT_MASK,
 273             false);
 274     addMenuActionAndAccelerator(keyStroke, saveAs, al);
 275
 276     closeMenuItem.setText(MessageManager.getString("action.close"));
 277     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
 278             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 279     al = new ActionListener()
 280     {
 281       @Override
 282       public void actionPerformed(ActionEvent e)
 283       {
 284         closeMenuItem_actionPerformed(false);
 285       }
 286     };
 287     addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
 288
 289     JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
 290     JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
 291     JMenu annotationsMenu = new JMenu(
 292             MessageManager.getString("action.annotations"));
 293     JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
 294     colourMenu.setText(MessageManager.getString("action.colour"));
 295     JMenu calculateMenu = new JMenu(
 296             MessageManager.getString("action.calculate"));
 297     webService.setText(MessageManager.getString("action.web_service"));
 298     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
 299             MessageManager.getString("action.select_all"));
 300     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
 301             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 302     al = new ActionListener()
 303     {
 304       @Override
 305       public void actionPerformed(ActionEvent e)
 306       {
 307         selectAllSequenceMenuItem_actionPerformed(e);
 308       }
 309     };
 310     addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
 311
 312     JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
 313             MessageManager.getString("action.deselect_all"));
 314     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
 315     al = new ActionListener()
 316     {
 317       @Override
 318       public void actionPerformed(ActionEvent e)
 319       {
 320         deselectAllSequenceMenuItem_actionPerformed(e);
 321       }
 322     };
 323     addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
 324
 325     JMenuItem invertSequenceMenuItem = new JMenuItem(
 326             MessageManager.getString("action.invert_sequence_selection"));
 327     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
 328             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 329     al = new ActionListener()
 330     {
 331       @Override
 332       public void actionPerformed(ActionEvent e)
 333       {
 334         invertSequenceMenuItem_actionPerformed(e);
 335       }
 336     };
 337     addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
 338
 339     JMenuItem grpsFromSelection = new JMenuItem(
 340             MessageManager.getString("action.make_groups_selection"));
 341     grpsFromSelection.addActionListener(new ActionListener()
 342     {
 343       @Override
 344       public void actionPerformed(ActionEvent e)
 345       {
 346         makeGrpsFromSelection_actionPerformed(e);
 347       }
 348     });
 349     JMenuItem expandAlignment = new JMenuItem(
 350             MessageManager.getString("action.view_flanking_regions"));
 351     expandAlignment.setToolTipText(
 352             MessageManager.getString("label.view_flanking_regions"));
 353     expandAlignment.addActionListener(new ActionListener()
 354     {
 355       @Override
 356       public void actionPerformed(ActionEvent e)
 357       {
 358         expand_newalign(e);
 359       }
 360     });
 361     JMenuItem remove2LeftMenuItem = new JMenuItem(
 362             MessageManager.getString("action.remove_left"));
 363     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
 364             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 365     al = new ActionListener()
 366     {
 367       @Override
 368       public void actionPerformed(ActionEvent e)
 369       {
 370         remove2LeftMenuItem_actionPerformed(e);
 371       }
 372     };
 373     addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
 374
 375     JMenuItem remove2RightMenuItem = new JMenuItem(
 376             MessageManager.getString("action.remove_right"));
 377     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
 378             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 379     al = new ActionListener()
 380     {
 381       @Override
 382       public void actionPerformed(ActionEvent e)
 383       {
 384         remove2RightMenuItem_actionPerformed(e);
 385       }
 386     };
 387     addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
 388
 389     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
 390             MessageManager.getString("action.remove_empty_columns"));
 391     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
 392             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 393     al = new ActionListener()
 394     {
 395       @Override
 396       public void actionPerformed(ActionEvent e)
 397       {
 398         removeGappedColumnMenuItem_actionPerformed(e);
 399       }
 400     };
 401     addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
 402
 403     JMenuItem removeAllGapsMenuItem = new JMenuItem(
 404             MessageManager.getString("action.remove_all_gaps"));
 405     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
 406             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
 407                     | KeyEvent.SHIFT_MASK,
 408             false);
 409     al = new ActionListener()
 410     {
 411       @Override
 412       public void actionPerformed(ActionEvent e)
 413       {
 414         removeAllGapsMenuItem_actionPerformed(e);
 415       }
 416     };
 417     addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
 418
 419     JMenuItem justifyLeftMenuItem = new JMenuItem(
 420             MessageManager.getString("action.left_justify_alignment"));
 421     justifyLeftMenuItem.addActionListener(new ActionListener()
 422     {
 423       @Override
 424       public void actionPerformed(ActionEvent e)
 425       {
 426         justifyLeftMenuItem_actionPerformed(e);
 427       }
 428     });
 429     JMenuItem justifyRightMenuItem = new JMenuItem(
 430             MessageManager.getString("action.right_justify_alignment"));
 431     justifyRightMenuItem.addActionListener(new ActionListener()
 432     {
 433       @Override
 434       public void actionPerformed(ActionEvent e)
 435       {
 436         justifyRightMenuItem_actionPerformed(e);
 437       }
 438     });
 439     viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
 440     viewBoxesMenuItem.setState(true);
 441     viewBoxesMenuItem.addActionListener(new ActionListener()
 442     {
 443       @Override
 444       public void actionPerformed(ActionEvent e)
 445       {
 446         viewBoxesMenuItem_actionPerformed(e);
 447       }
 448     });
 449     viewTextMenuItem.setText(MessageManager.getString("action.text"));
 450     viewTextMenuItem.setState(true);
 451     viewTextMenuItem.addActionListener(new ActionListener()
 452     {
 453       @Override
 454       public void actionPerformed(ActionEvent e)
 455       {
 456         viewTextMenuItem_actionPerformed(e);
 457       }
 458     });
 459     showNonconservedMenuItem
 460             .setText(MessageManager.getString("label.show_non_conserved"));
 461     showNonconservedMenuItem.setState(false);
 462     showNonconservedMenuItem.addActionListener(new ActionListener()
 463     {
 464       @Override
 465       public void actionPerformed(ActionEvent e)
 466       {
 467         showUnconservedMenuItem_actionPerformed(e);
 468       }
 469     });
 470     JMenuItem sortPairwiseMenuItem = new JMenuItem(
 471             MessageManager.getString("action.by_pairwise_id"));
 472     sortPairwiseMenuItem.addActionListener(new ActionListener()
 473     {
 474       @Override
 475       public void actionPerformed(ActionEvent e)
 476       {
 477         sortPairwiseMenuItem_actionPerformed(e);
 478       }
 479     });
 480     JMenuItem sortIDMenuItem = new JMenuItem(
 481             MessageManager.getString("action.by_id"));
 482     sortIDMenuItem.addActionListener(new ActionListener()
 483     {
 484       @Override
 485       public void actionPerformed(ActionEvent e)
 486       {
 487         sortIDMenuItem_actionPerformed(e);
 488       }
 489     });
 490     JMenuItem sortLengthMenuItem = new JMenuItem(
 491             MessageManager.getString("action.by_length"));
 492     sortLengthMenuItem.addActionListener(new ActionListener()
 493     {
 494       @Override
 495       public void actionPerformed(ActionEvent e)
 496       {
 497         sortLengthMenuItem_actionPerformed(e);
 498       }
 499     });
 500     JMenuItem sortGroupMenuItem = new JMenuItem(
 501             MessageManager.getString("action.by_group"));
 502     sortGroupMenuItem.addActionListener(new ActionListener()
 503     {
 504       @Override
 505       public void actionPerformed(ActionEvent e)
 506       {
 507         sortGroupMenuItem_actionPerformed(e);
 508       }
 509     });
 510
 511     JMenuItem removeRedundancyMenuItem = new JMenuItem(
 512             MessageManager.getString("action.remove_redundancy"));
 513     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
 514             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 515     al = new ActionListener()
 516     {
 517       @Override
 518       public void actionPerformed(ActionEvent e)
 519       {
 520         removeRedundancyMenuItem_actionPerformed(e);
 521       }
 522     };
 523     addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
 524
 525     JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
 526             MessageManager.getString("action.pairwise_alignment"));
 527     pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
 528     {
 529       @Override
 530       public void actionPerformed(ActionEvent e)
 531       {
 532         pairwiseAlignmentMenuItem_actionPerformed(e);
 533       }
 534     });
 535
 536     this.getContentPane().setLayout(new BorderLayout());
 537     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 538     statusBar.setBackground(Color.white);
 539     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 540     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 541     statusBar.setText(MessageManager.getString("label.status_bar"));
 542     outputTextboxMenu
 543             .setText(MessageManager.getString("label.out_to_textbox"));
 544
 545     annotationPanelMenuItem.setActionCommand("");
 546     annotationPanelMenuItem
 547             .setText(MessageManager.getString("label.show_annotations"));
 548     annotationPanelMenuItem
 549             .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
 550     annotationPanelMenuItem.addActionListener(new ActionListener()
 551     {
 552       @Override
 553       public void actionPerformed(ActionEvent e)
 554       {
 555         annotationPanelMenuItem_actionPerformed(e);
 556       }
 557     });
 558     showAllAlAnnotations.setText(
 559             MessageManager.getString("label.show_all_al_annotations"));
 560     final boolean isAnnotationPanelShown = annotationPanelMenuItem
 561             .getState();
 562     showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 563     showAllAlAnnotations.addActionListener(new ActionListener()
 564     {
 565       @Override
 566       public void actionPerformed(ActionEvent e)
 567       {
 568         showAllAnnotations_actionPerformed(false, true);
 569       }
 570     });
 571     hideAllAlAnnotations.setText(
 572             MessageManager.getString("label.hide_all_al_annotations"));
 573     hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 574     hideAllAlAnnotations.addActionListener(new ActionListener()
 575     {
 576       @Override
 577       public void actionPerformed(ActionEvent e)
 578       {
 579         hideAllAnnotations_actionPerformed(false, true);
 580       }
 581     });
 582     showAllSeqAnnotations.setText(
 583             MessageManager.getString("label.show_all_seq_annotations"));
 584     showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 585     showAllSeqAnnotations.addActionListener(new ActionListener()
 586     {
 587       @Override
 588       public void actionPerformed(ActionEvent e)
 589       {
 590         showAllAnnotations_actionPerformed(true, false);
 591       }
 592     });
 593     hideAllSeqAnnotations.setText(
 594             MessageManager.getString("label.hide_all_seq_annotations"));
 595     hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 596     hideAllSeqAnnotations.addActionListener(new ActionListener()
 597     {
 598       @Override
 599       public void actionPerformed(ActionEvent e)
 600       {
 601         hideAllAnnotations_actionPerformed(true, false);
 602       }
 603     });
 604     SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
 605             .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
 606                     SequenceAnnotationOrder.NONE.name()));
 607     final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
 608             MessageManager.getString("label.sort_annotations_by_sequence"));
 609     final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
 610             MessageManager.getString("label.sort_annotations_by_label"));
 611
 612     sortAnnBySequence.setSelected(
 613             sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
 614     sortAnnBySequence.addActionListener(new ActionListener()
 615     {
 616       @Override
 617       public void actionPerformed(ActionEvent e)
 618       {
 619         boolean newState = sortAnnBySequence.getState();
 620         sortAnnByLabel.setSelected(false);
 621         setAnnotationSortOrder(
 622                 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 623                         : SequenceAnnotationOrder.NONE);
 624         sortAnnotations_actionPerformed();
 625       }
 626     });
 627     sortAnnByLabel.setSelected(
 628             sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
 629     sortAnnByLabel.addActionListener(new ActionListener()
 630     {
 631       @Override
 632       public void actionPerformed(ActionEvent e)
 633       {
 634         boolean newState = sortAnnByLabel.getState();
 635         sortAnnBySequence.setSelected(false);
 636         setAnnotationSortOrder(
 637                 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 638                         : SequenceAnnotationOrder.NONE);
 639         sortAnnotations_actionPerformed();
 640       }
 641     });
 642     colourTextMenuItem = new JCheckBoxMenuItem(
 643             MessageManager.getString("label.colour_text"));
 644     colourTextMenuItem.addActionListener(new ActionListener()
 645     {
 646       @Override
 647       public void actionPerformed(ActionEvent e)
 648       {
 649         colourTextMenuItem_actionPerformed(e);
 650       }
 651     });
 652
 653     JMenuItem htmlMenuItem = new JMenuItem(
 654             MessageManager.getString("label.html"));
 655     htmlMenuItem.addActionListener(new ActionListener()
 656     {
 657       @Override
 658       public void actionPerformed(ActionEvent e)
 659       {
 660         htmlMenuItem_actionPerformed(e);
 661       }
 662     });
 663
 664     JMenuItem createBioJS = new JMenuItem(
 665             MessageManager.getString("label.biojs_html_export"));
 666     createBioJS.addActionListener(new java.awt.event.ActionListener()
 667     {
 668       @Override
 669       public void actionPerformed(ActionEvent e)
 670       {
 671         bioJSMenuItem_actionPerformed(e);
 672       }
 673     });
 674
 675     JMenuItem overviewMenuItem = new JMenuItem(
 676             MessageManager.getString("label.overview_window"));
 677     overviewMenuItem.addActionListener(new ActionListener()
 678     {
 679       @Override
 680       public void actionPerformed(ActionEvent e)
 681       {
 682         overviewMenuItem_actionPerformed(e);
 683       }
 684     });
 685
 686     undoMenuItem.setEnabled(false);
 687     undoMenuItem.setText(MessageManager.getString("action.undo"));
 688     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
 689             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 690     al = new ActionListener()
 691     {
 692       @Override
 693       public void actionPerformed(ActionEvent e)
 694       {
 695         undoMenuItem_actionPerformed(e);
 696       }
 697     };
 698     addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
 699
 700     redoMenuItem.setEnabled(false);
 701     redoMenuItem.setText(MessageManager.getString("action.redo"));
 702     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
 703             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 704     al = new ActionListener()
 705     {
 706       @Override
 707       public void actionPerformed(ActionEvent e)
 708       {
 709         redoMenuItem_actionPerformed(e);
 710       }
 711     };
 712     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
 713
 714     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
 715     wrapMenuItem.addActionListener(new ActionListener()
 716     {
 717       @Override
 718       public void actionPerformed(ActionEvent e)
 719       {
 720         wrapMenuItem_actionPerformed(e);
 721       }
 722     });
 723
 724     JMenuItem printMenuItem = new JMenuItem(
 725             MessageManager.getString("action.print"));
 726     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
 727             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 728     al = new ActionListener()
 729     {
 730       @Override
 731       public void actionPerformed(ActionEvent e)
 732       {
 733         printMenuItem_actionPerformed(e);
 734       }
 735     };
 736     addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
 737
 738     renderGapsMenuItem
 739             .setText(MessageManager.getString("action.show_gaps"));
 740     renderGapsMenuItem.setState(true);
 741     renderGapsMenuItem.addActionListener(new ActionListener()
 742     {
 743       @Override
 744       public void actionPerformed(ActionEvent e)
 745       {
 746         renderGapsMenuItem_actionPerformed(e);
 747       }
 748     });
 749
 750     JMenuItem findMenuItem = new JMenuItem(
 751             MessageManager.getString("action.find"));
 752     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
 753             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 754     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
 755             MessageManager.getString("label.find_tip")));
 756     al = new ActionListener()
 757     {
 758       @Override
 759       public void actionPerformed(ActionEvent e)
 760       {
 761         findMenuItem_actionPerformed(e);
 762       }
 763     };
 764     addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
 765
 766     showSeqFeatures.setText(
 767             MessageManager.getString("label.show_sequence_features"));
 768     showSeqFeatures.addActionListener(new ActionListener()
 769     {
 770       @Override
 771       public void actionPerformed(ActionEvent actionEvent)
 772       {
 773         showSeqFeatures_actionPerformed(actionEvent);
 774       }
 775     });
 776     /*
 777      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
 778      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
 779      * void actionPerformed(ActionEvent actionEvent) {
 780      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
 781      */
 782     showDbRefsMenuitem
 783             .setText(MessageManager.getString("label.show_database_refs"));
 784     showDbRefsMenuitem.addActionListener(new ActionListener()
 785     {
 786
 787       @Override
 788       public void actionPerformed(ActionEvent e)
 789       {
 790         showDbRefs_actionPerformed(e);
 791       }
 792
 793     });
 794     showNpFeatsMenuitem.setText(
 795             MessageManager.getString("label.show_non_positional_features"));
 796     showNpFeatsMenuitem.addActionListener(new ActionListener()
 797     {
 798
 799       @Override
 800       public void actionPerformed(ActionEvent e)
 801       {
 802         showNpFeats_actionPerformed(e);
 803       }
 804
 805     });
 806     showGroupConservation
 807             .setText(MessageManager.getString("label.group_conservation"));
 808     showGroupConservation.addActionListener(new ActionListener()
 809     {
 810
 811       @Override
 812       public void actionPerformed(ActionEvent e)
 813       {
 814         showGroupConservation_actionPerformed(e);
 815       }
 816
 817     });
 818
 819     showGroupConsensus
 820             .setText(MessageManager.getString("label.group_consensus"));
 821     showGroupConsensus.addActionListener(new ActionListener()
 822     {
 823
 824       @Override
 825       public void actionPerformed(ActionEvent e)
 826       {
 827         showGroupConsensus_actionPerformed(e);
 828       }
 829
 830     });
 831     showConsensusHistogram.setText(
 832             MessageManager.getString("label.show_consensus_histogram"));
 833     showConsensusHistogram.addActionListener(new ActionListener()
 834     {
 835
 836       @Override
 837       public void actionPerformed(ActionEvent e)
 838       {
 839         showConsensusHistogram_actionPerformed(e);
 840       }
 841
 842     });
 843     showSequenceLogo
 844             .setText(MessageManager.getString("label.show_consensus_logo"));
 845     showSequenceLogo.addActionListener(new ActionListener()
 846     {
 847
 848       @Override
 849       public void actionPerformed(ActionEvent e)
 850       {
 851         showSequenceLogo_actionPerformed(e);
 852       }
 853
 854     });
 855     normaliseSequenceLogo
 856             .setText(MessageManager.getString("label.norm_consensus_logo"));
 857     normaliseSequenceLogo.addActionListener(new ActionListener()
 858     {
 859
 860       @Override
 861       public void actionPerformed(ActionEvent e)
 862       {
 863         normaliseSequenceLogo_actionPerformed(e);
 864       }
 865
 866     });
 867     applyAutoAnnotationSettings
 868             .setText(MessageManager.getString("label.apply_all_groups"));
 869     applyAutoAnnotationSettings.setState(false);
 870     applyAutoAnnotationSettings.setVisible(true);
 871     applyAutoAnnotationSettings.addActionListener(new ActionListener()
 872     {
 873       @Override
 874       public void actionPerformed(ActionEvent e)
 875       {
 876         applyAutoAnnotationSettings_actionPerformed(e);
 877       }
 878     });
 879
 880     ButtonGroup buttonGroup = new ButtonGroup();
 881     final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
 882             MessageManager.getString("label.show_first"));
 883     final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
 884             MessageManager.getString("label.show_last"));
 885     buttonGroup.add(showAutoFirst);
 886     buttonGroup.add(showAutoLast);
 887     final boolean autoFirst = Cache
 888             .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
 889     showAutoFirst.setSelected(autoFirst);
 890     setShowAutoCalculatedAbove(autoFirst);
 891     showAutoFirst.addActionListener(new ActionListener()
 892     {
 893       @Override
 894       public void actionPerformed(ActionEvent e)
 895       {
 896         setShowAutoCalculatedAbove(showAutoFirst.isSelected());
 897         sortAnnotations_actionPerformed();
 898       }
 899     });
 900     showAutoLast.setSelected(!showAutoFirst.isSelected());
 901     showAutoLast.addActionListener(new ActionListener()
 902     {
 903       @Override
 904       public void actionPerformed(ActionEvent e)
 905       {
 906         setShowAutoCalculatedAbove(!showAutoLast.isSelected());
 907         sortAnnotations_actionPerformed();
 908       }
 909     });
 910
 911     JMenuItem deleteGroups = new JMenuItem(
 912             MessageManager.getString("action.undefine_groups"));
 913     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
 914             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 915     al = new ActionListener()
 916     {
 917       @Override
 918       public void actionPerformed(ActionEvent e)
 919       {
 920         deleteGroups_actionPerformed(e);
 921       }
 922     };
 923     addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
 924
 925     JMenuItem annotationColumn = new JMenuItem(
 926             MessageManager.getString("action.select_by_annotation"));
 927     annotationColumn.addActionListener(new ActionListener()
 928     {
 929       @Override
 930       public void actionPerformed(ActionEvent e)
 931       {
 932         annotationColumn_actionPerformed(e);
 933       }
 934     });
 935
 936     JMenuItem createGroup = new JMenuItem(
 937             MessageManager.getString("action.create_group"));
 938     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
 939             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 940     al = new ActionListener()
 941     {
 942       @Override
 943       public void actionPerformed(ActionEvent e)
 944       {
 945         createGroup_actionPerformed(e);
 946       }
 947     };
 948     addMenuActionAndAccelerator(keyStroke, createGroup, al);
 949
 950     JMenuItem unGroup = new JMenuItem(
 951             MessageManager.getString("action.remove_group"));
 952     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
 953             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
 954                     | KeyEvent.SHIFT_MASK,
 955             false);
 956     al = new ActionListener()
 957     {
 958       @Override
 959       public void actionPerformed(ActionEvent e)
 960       {
 961         unGroup_actionPerformed(e);
 962       }
 963     };
 964     addMenuActionAndAccelerator(keyStroke, unGroup, al);
 965
 966     copy.setText(MessageManager.getString("action.copy"));
 967     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
 968             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 969
 970     al = new ActionListener()
 971     {
 972       @Override
 973       public void actionPerformed(ActionEvent e)
 974       {
 975         copy_actionPerformed();
 976       }
 977     };
 978     addMenuActionAndAccelerator(keyStroke, copy, al);
 979
 980     cut.setText(MessageManager.getString("action.cut"));
 981     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
 982             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 983     al = new ActionListener()
 984     {
 985       @Override
 986       public void actionPerformed(ActionEvent e)
 987       {
 988         cut_actionPerformed();
 989       }
 990     };
 991     addMenuActionAndAccelerator(keyStroke, cut, al);
 992
 993     JMenuItem delete = new JMenuItem(
 994             MessageManager.getString("action.delete"));
 995     delete.addActionListener(new ActionListener()
 996     {
 997       @Override
 998       public void actionPerformed(ActionEvent e)
 999       {
1000         delete_actionPerformed();
1001       }
1002     });
1003
1004     pasteMenu.setText(MessageManager.getString("action.paste"));
1005     JMenuItem pasteNew = new JMenuItem(
1006             MessageManager.getString("label.to_new_alignment"));
1007     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1008             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1009                     | KeyEvent.SHIFT_MASK,
1010             false);
1011     al = new ActionListener()
1012     {
1013       @Override
1014       public void actionPerformed(ActionEvent e)
1015       {
1016         pasteNew_actionPerformed(e);
1017       }
1018     };
1019     addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1020
1021     JMenuItem pasteThis = new JMenuItem(
1022             MessageManager.getString("label.to_this_alignment"));
1023     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1024             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1025     al = new ActionListener()
1026     {
1027       @Override
1028       public void actionPerformed(ActionEvent e)
1029       {
1030         pasteThis_actionPerformed(e);
1031       }
1032     };
1033     addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1034
1035     JMenuItem createPNG = new JMenuItem("PNG");
1036     createPNG.addActionListener(new ActionListener()
1037     {
1038       @Override
1039       public void actionPerformed(ActionEvent e)
1040       {
1041         createPNG(null);
1042       }
1043     });
1044     createPNG.setActionCommand(
1045             MessageManager.getString("label.save_png_image"));
1046
1047     JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1048     font.addActionListener(new ActionListener()
1049     {
1050       @Override
1051       public void actionPerformed(ActionEvent e)
1052       {
1053         font_actionPerformed(e);
1054       }
1055     });
1056     seqLimits.setText(
1057             MessageManager.getString("label.show_sequence_limits"));
1058     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1059     seqLimits.addActionListener(new ActionListener()
1060     {
1061       @Override
1062       public void actionPerformed(ActionEvent e)
1063       {
1064         seqLimit_actionPerformed(e);
1065       }
1066     });
1067     JMenuItem epsFile = new JMenuItem("EPS");
1068     epsFile.addActionListener(new ActionListener()
1069     {
1070       @Override
1071       public void actionPerformed(ActionEvent e)
1072       {
1073         createEPS(null);
1074       }
1075     });
1076
1077     JMenuItem createSVG = new JMenuItem("SVG");
1078     createSVG.addActionListener(new ActionListener()
1079     {
1080       @Override
1081       public void actionPerformed(ActionEvent e)
1082       {
1083         createSVG(null);
1084       }
1085     });
1086
1087     JMenuItem loadTreeMenuItem = new JMenuItem(
1088             MessageManager.getString("label.load_associated_tree"));
1089     loadTreeMenuItem.setActionCommand(
1090             MessageManager.getString("label.load_tree_for_sequence_set"));
1091     loadTreeMenuItem.addActionListener(new ActionListener()
1092     {
1093       @Override
1094       public void actionPerformed(ActionEvent e)
1095       {
1096         loadTreeMenuItem_actionPerformed(e);
1097       }
1098     });
1099
1100     scaleAbove.setVisible(false);
1101     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1102     scaleAbove.addActionListener(new ActionListener()
1103     {
1104       @Override
1105       public void actionPerformed(ActionEvent e)
1106       {
1107         scaleAbove_actionPerformed(e);
1108       }
1109     });
1110     scaleLeft.setVisible(false);
1111     scaleLeft.setSelected(true);
1112     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1113     scaleLeft.addActionListener(new ActionListener()
1114     {
1115       @Override
1116       public void actionPerformed(ActionEvent e)
1117       {
1118         scaleLeft_actionPerformed(e);
1119       }
1120     });
1121     scaleRight.setVisible(false);
1122     scaleRight.setSelected(true);
1123     scaleRight.setText(MessageManager.getString("action.scale_right"));
1124     scaleRight.addActionListener(new ActionListener()
1125     {
1126       @Override
1127       public void actionPerformed(ActionEvent e)
1128       {
1129         scaleRight_actionPerformed(e);
1130       }
1131     });
1132     centreColumnLabelsMenuItem.setVisible(true);
1133     centreColumnLabelsMenuItem.setState(false);
1134     centreColumnLabelsMenuItem.setText(
1135             MessageManager.getString("label.centre_column_labels"));
1136     centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1137     {
1138       @Override
1139       public void actionPerformed(ActionEvent e)
1140       {
1141         centreColumnLabels_actionPerformed(e);
1142       }
1143     });
1144     followHighlightMenuItem.setVisible(true);
1145     followHighlightMenuItem.setState(true);
1146     followHighlightMenuItem
1147             .setText(MessageManager.getString("label.automatic_scrolling"));
1148     followHighlightMenuItem.addActionListener(new ActionListener()
1149     {
1150
1151       @Override
1152       public void actionPerformed(ActionEvent e)
1153       {
1154         followHighlight_actionPerformed();
1155       }
1156
1157     });
1158
1159     sortByTreeMenu
1160             .setText(MessageManager.getString("action.by_tree_order"));
1161     sort.setText(MessageManager.getString("action.sort"));
1162     sort.addMenuListener(new MenuListener()
1163     {
1164       @Override
1165       public void menuSelected(MenuEvent e)
1166       {
1167         buildTreeSortMenu();
1168       }
1169
1170       @Override
1171       public void menuDeselected(MenuEvent e)
1172       {
1173       }
1174
1175       @Override
1176       public void menuCanceled(MenuEvent e)
1177       {
1178       }
1179     });
1180     sortByAnnotScore
1181             .setText(MessageManager.getString("label.sort_by_score"));
1182     sort.add(sortByAnnotScore);
1183     sort.addMenuListener(new javax.swing.event.MenuListener()
1184     {
1185
1186       @Override
1187       public void menuCanceled(MenuEvent e)
1188       {
1189       }
1190
1191       @Override
1192       public void menuDeselected(MenuEvent e)
1193       {
1194       }
1195
1196       @Override
1197       public void menuSelected(MenuEvent e)
1198       {
1199         buildSortByAnnotationScoresMenu();
1200       }
1201     });
1202     sortByAnnotScore.setVisible(false);
1203
1204     calculateTree
1205             .setText(MessageManager.getString("action.calculate_tree_pca"));
1206
1207     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1208     padGapsMenuitem
1209             .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
1210     padGapsMenuitem.addActionListener(new ActionListener()
1211     {
1212       @Override
1213       public void actionPerformed(ActionEvent e)
1214       {
1215         padGapsMenuitem_actionPerformed(e);
1216       }
1217     });
1218     JMenuItem vamsasStore = new JMenuItem(
1219             MessageManager.getString("label.vamsas_store"));
1220     vamsasStore.setVisible(false);
1221     vamsasStore.addActionListener(new ActionListener()
1222     {
1223       @Override
1224       public void actionPerformed(ActionEvent e)
1225       {
1226         vamsasStore_actionPerformed(e);
1227       }
1228     });
1229
1230     /*
1231      * Translate as cDNA with sub-menu of translation tables
1232      */
1233     showTranslation.setText(MessageManager
1234             .getString("label.translate_cDNA"));
1235     boolean first = true;
1236     for (final GeneticCodeI table : GeneticCodes.getInstance()
1237             .getCodeTables())
1238     {
1239       JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
1240       showTranslation.add(item);
1241       item.addActionListener(new ActionListener()
1242       {
1243         @Override
1244         public void actionPerformed(ActionEvent e)
1245         {
1246           showTranslation_actionPerformed(table);
1247         }
1248       });
1249       if (first)
1250       {
1251         showTranslation.addSeparator();
1252       }
1253       first = false;
1254     }
1255
1256     showReverse.setText(MessageManager.getString("label.reverse"));
1257     showReverse.addActionListener(new ActionListener()
1258     {
1259       @Override
1260       public void actionPerformed(ActionEvent e)
1261       {
1262         showReverse_actionPerformed(false);
1263       }
1264     });
1265     showReverseComplement
1266             .setText(MessageManager.getString("label.reverse_complement"));
1267     showReverseComplement.addActionListener(new ActionListener()
1268     {
1269       @Override
1270       public void actionPerformed(ActionEvent e)
1271       {
1272         showReverse_actionPerformed(true);
1273       }
1274     });
1275
1276     JMenuItem extractScores = new JMenuItem(
1277             MessageManager.getString("label.extract_scores"));
1278     extractScores.addActionListener(new ActionListener()
1279     {
1280       @Override
1281       public void actionPerformed(ActionEvent e)
1282       {
1283         extractScores_actionPerformed(e);
1284       }
1285     });
1286     extractScores.setVisible(true);
1287     // JBPNote: TODO: make gui for regex based score extraction
1288
1289     // for show products actions see AlignFrame.canShowProducts
1290     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1291
1292     runGroovy.setText(MessageManager.getString("label.run_groovy"));
1293     runGroovy.setToolTipText(
1294             MessageManager.getString("label.run_groovy_tip"));
1295     runGroovy.addActionListener(new ActionListener()
1296     {
1297       @Override
1298       public void actionPerformed(ActionEvent e)
1299       {
1300         runGroovy_actionPerformed();
1301       }
1302     });
1303
1304     openFeatureSettings = new JMenuItem(
1305             MessageManager.getString("action.feature_settings"));
1306     openFeatureSettings.addActionListener(new ActionListener()
1307     {
1308       @Override
1309       public void actionPerformed(ActionEvent e)
1310       {
1311         featureSettings_actionPerformed(e);
1312       }
1313     });
1314
1315     /*
1316      * add sub-menu of database we can fetch from
1317      */
1318     JMenuItem fetchSequence = new JMenuItem(
1319             MessageManager.getString("label.fetch_sequences"));
1320     fetchSequence.addActionListener(new ActionListener()
1321     {
1322       @Override
1323       public void actionPerformed(ActionEvent e)
1324       {
1325         fetchSequence_actionPerformed();
1326       }
1327     });
1328
1329     JMenuItem associatedData = new JMenuItem(
1330             MessageManager.getString("label.load_features_annotations"));
1331     associatedData.addActionListener(new ActionListener()
1332     {
1333       @Override
1334       public void actionPerformed(ActionEvent e)
1335       {
1336         associatedData_actionPerformed(e);
1337       }
1338     });
1339     loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
1340     loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
1341     loadVcf.addActionListener(new ActionListener()
1342     {
1343       @Override
1344       public void actionPerformed(ActionEvent e)
1345       {
1346         loadVcf_actionPerformed();
1347       }
1348     });
1349     autoCalculate.setText(
1350             MessageManager.getString("label.autocalculate_consensus"));
1351     autoCalculate.setState(
1352             jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1353     autoCalculate.addActionListener(new ActionListener()
1354     {
1355       @Override
1356       public void actionPerformed(ActionEvent e)
1357       {
1358         autoCalculate_actionPerformed(e);
1359       }
1360     });
1361     sortByTree.setText(
1362             MessageManager.getString("label.sort_alignment_new_tree"));
1363     sortByTree.setToolTipText("<html>" + MessageManager.getString(
1364             "label.enable_automatically_sort_alignment_when_open_new_tree"));
1365     sortByTree
1366             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1367     sortByTree.addActionListener(new ActionListener()
1368     {
1369       @Override
1370       public void actionPerformed(ActionEvent e)
1371       {
1372         sortByTreeOption_actionPerformed(e);
1373       }
1374     });
1375
1376     listenToViewSelections.setText(
1377             MessageManager.getString("label.listen_for_selections"));
1378     listenToViewSelections
1379             .setToolTipText("<html>" + MessageManager.getString(
1380                     "label.selections_mirror_selections_made_same_sequences_other_views"));
1381     listenToViewSelections.setState(false);
1382     listenToViewSelections.addActionListener(new ActionListener()
1383     {
1384       @Override
1385       public void actionPerformed(ActionEvent e)
1386       {
1387         listenToViewSelections_actionPerformed(e);
1388       }
1389     });
1390
1391     JMenu addSequenceMenu = new JMenu(
1392             MessageManager.getString("label.add_sequences"));
1393     JMenuItem addFromFile = new JMenuItem(
1394             MessageManager.getString("label.from_file"));
1395     addFromFile.addActionListener(new ActionListener()
1396     {
1397       @Override
1398       public void actionPerformed(ActionEvent e)
1399       {
1400         addFromFile_actionPerformed(e);
1401       }
1402     });
1403     JMenuItem addFromText = new JMenuItem(
1404             MessageManager.getString("label.from_textbox"));
1405     addFromText.addActionListener(new ActionListener()
1406     {
1407       @Override
1408       public void actionPerformed(ActionEvent e)
1409       {
1410         addFromText_actionPerformed(e);
1411       }
1412     });
1413     JMenuItem addFromURL = new JMenuItem(
1414             MessageManager.getString("label.from_url"));
1415     addFromURL.addActionListener(new ActionListener()
1416     {
1417       @Override
1418       public void actionPerformed(ActionEvent e)
1419       {
1420         addFromURL_actionPerformed(e);
1421       }
1422     });
1423     JMenuItem exportFeatures = new JMenuItem(
1424             MessageManager.getString("label.export_features"));
1425     exportFeatures.addActionListener(new ActionListener()
1426     {
1427       @Override
1428       public void actionPerformed(ActionEvent e)
1429       {
1430         exportFeatures_actionPerformed(e);
1431       }
1432     });
1433     JMenuItem exportAnnotations = new JMenuItem(
1434             MessageManager.getString("label.export_annotations"));
1435     exportAnnotations.addActionListener(new ActionListener()
1436     {
1437       @Override
1438       public void actionPerformed(ActionEvent e)
1439       {
1440         exportAnnotations_actionPerformed(e);
1441       }
1442     });
1443     statusPanel.setLayout(new GridLayout());
1444     JMenuItem showAllSeqs = new JMenuItem(
1445             MessageManager.getString("label.all_sequences"));
1446     showAllSeqs.setToolTipText(
1447             MessageManager.getString("label.toggle_sequence_visibility"));
1448     showAllSeqs.addActionListener(new ActionListener()
1449     {
1450       @Override
1451       public void actionPerformed(ActionEvent e)
1452       {
1453         showAllSeqs_actionPerformed(e);
1454       }
1455     });
1456     JMenuItem showAllColumns = new JMenuItem(
1457             MessageManager.getString("label.all_columns"));
1458     showAllColumns.setToolTipText(
1459             MessageManager.getString("label.toggle_columns_visibility"));
1460     showAllColumns.addActionListener(new ActionListener()
1461     {
1462       @Override
1463       public void actionPerformed(ActionEvent e)
1464       {
1465         showAllColumns_actionPerformed(e);
1466       }
1467     });
1468     JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1469     JMenuItem hideSelSequences = new JMenuItem(
1470             MessageManager.getString("label.selected_sequences"));
1471     hideSelSequences.setToolTipText(
1472             MessageManager.getString("label.toggle_sequence_visibility"));
1473     hideSelSequences.addActionListener(new ActionListener()
1474     {
1475       @Override
1476       public void actionPerformed(ActionEvent e)
1477       {
1478         hideSelSequences_actionPerformed(e);
1479       }
1480     });
1481     JMenuItem hideSelColumns = new JMenuItem(
1482             MessageManager.getString("label.selected_columns"));
1483     hideSelColumns.setToolTipText(
1484             MessageManager.getString("label.toggle_columns_visibility"));
1485     hideSelColumns.addActionListener(new ActionListener()
1486     {
1487       @Override
1488       public void actionPerformed(ActionEvent e)
1489       {
1490         hideSelColumns_actionPerformed(e);
1491       }
1492     });
1493     JMenuItem hideAllSelection = new JMenuItem(
1494             MessageManager.getString("label.selected_region"));
1495     hideAllSelection.addActionListener(new ActionListener()
1496     {
1497       @Override
1498       public void actionPerformed(ActionEvent e)
1499       {
1500         hideAllSelection_actionPerformed(e);
1501       }
1502     });
1503     // TODO: should be hidden if no selection exists.
1504     JMenuItem hideAllButSelection = new JMenuItem(
1505             MessageManager.getString("label.all_but_selected_region"));
1506     hideAllButSelection.addActionListener(new ActionListener()
1507     {
1508       @Override
1509       public void actionPerformed(ActionEvent e)
1510       {
1511         hideAllButSelection_actionPerformed(e);
1512       }
1513     });
1514     JMenuItem showAllhidden = new JMenuItem(
1515             MessageManager.getString("label.all_sequences_columns"));
1516     showAllhidden.setToolTipText(MessageManager
1517             .getString("label.toggles_visibility_hidden_selected_regions"));
1518     showAllhidden.addActionListener(new ActionListener()
1519     {
1520       @Override
1521       public void actionPerformed(ActionEvent e)
1522       {
1523         showAllhidden_actionPerformed(e);
1524       }
1525     });
1526     hiddenMarkers.setText(
1527             MessageManager.getString("action.show_hidden_markers"));
1528     hiddenMarkers.addActionListener(new ActionListener()
1529     {
1530       @Override
1531       public void actionPerformed(ActionEvent e)
1532       {
1533         hiddenMarkers_actionPerformed(e);
1534       }
1535     });
1536
1537     JMenuItem invertColSel = new JMenuItem(
1538             MessageManager.getString("action.invert_column_selection"));
1539     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1540             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1541                     | KeyEvent.ALT_MASK,
1542             false);
1543     al = new ActionListener()
1544     {
1545       @Override
1546       public void actionPerformed(ActionEvent e)
1547       {
1548         invertColSel_actionPerformed(e);
1549       }
1550     };
1551     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1552
1553     showComplementMenuItem.setVisible(false);
1554     showComplementMenuItem.addActionListener(new ActionListener()
1555     {
1556       @Override
1557       public void actionPerformed(ActionEvent e)
1558       {
1559         showComplement_actionPerformed(showComplementMenuItem.getState());
1560       }
1561     });
1562
1563     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1564     {
1565       @Override
1566       public void stateChanged(ChangeEvent evt)
1567       {
1568         JTabbedPane pane = (JTabbedPane) evt.getSource();
1569         int sel = pane.getSelectedIndex();
1570         tabSelectionChanged(sel);
1571       }
1572     });
1573     tabbedPane.addMouseListener(new MouseAdapter()
1574     {
1575       @Override
1576       public void mousePressed(MouseEvent e)
1577       {
1578         if (e.isPopupTrigger()) // Mac
1579         {
1580           tabbedPane_mousePressed(e);
1581         }
1582       }
1583
1584       @Override
1585       public void mouseReleased(MouseEvent e)
1586       {
1587         if (e.isPopupTrigger()) // Windows
1588         {
1589           tabbedPane_mousePressed(e);
1590         }
1591       }
1592     });
1593     tabbedPane.addFocusListener(new FocusAdapter()
1594     {
1595       @Override
1596       public void focusGained(FocusEvent e)
1597       {
1598         tabbedPane_focusGained(e);
1599       }
1600     });
1601
1602     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1603     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1604             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1605     al = new ActionListener()
1606     {
1607       @Override
1608       public void actionPerformed(ActionEvent e)
1609       {
1610         save_actionPerformed(e);
1611       }
1612     };
1613     addMenuActionAndAccelerator(keyStroke, save, al);
1614
1615     reload.setEnabled(false);
1616     reload.setText(MessageManager.getString("action.reload"));
1617     reload.addActionListener(new ActionListener()
1618     {
1619       @Override
1620       public void actionPerformed(ActionEvent e)
1621       {
1622         reload_actionPerformed(e);
1623       }
1624     });
1625
1626     JMenuItem newView = new JMenuItem(
1627             MessageManager.getString("action.new_view"));
1628     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1629             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1630     al = new ActionListener()
1631     {
1632       @Override
1633       public void actionPerformed(ActionEvent e)
1634       {
1635         newView_actionPerformed(e);
1636       }
1637     };
1638     addMenuActionAndAccelerator(keyStroke, newView, al);
1639
1640     tabbedPane.setToolTipText("<html><i>"
1641             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1642             + "</i></html>");
1643
1644     formatMenu.setText(MessageManager.getString("action.format"));
1645     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1646
1647     idRightAlign.setText(
1648             MessageManager.getString("label.right_align_sequence_id"));
1649     idRightAlign.addActionListener(new ActionListener()
1650     {
1651       @Override
1652       public void actionPerformed(ActionEvent e)
1653       {
1654         idRightAlign_actionPerformed(e);
1655       }
1656     });
1657
1658     gatherViews.setEnabled(false);
1659     gatherViews.setText(MessageManager.getString("action.gather_views"));
1660     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1661     al = new ActionListener()
1662     {
1663       @Override
1664       public void actionPerformed(ActionEvent e)
1665       {
1666         gatherViews_actionPerformed(e);
1667       }
1668     };
1669     addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1670
1671     expandViews.setEnabled(false);
1672     expandViews.setText(MessageManager.getString("action.expand_views"));
1673     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1674     al = new ActionListener()
1675     {
1676       @Override
1677       public void actionPerformed(ActionEvent e)
1678       {
1679         expandViews_actionPerformed(e);
1680       }
1681     };
1682     addMenuActionAndAccelerator(keyStroke, expandViews, al);
1683
1684     JMenuItem pageSetup = new JMenuItem(
1685             MessageManager.getString("action.page_setup"));
1686     pageSetup.addActionListener(new ActionListener()
1687     {
1688       @Override
1689       public void actionPerformed(ActionEvent e)
1690       {
1691         pageSetup_actionPerformed(e);
1692       }
1693     });
1694     JMenuItem alignmentProperties = new JMenuItem(
1695             MessageManager.getString("label.alignment_props"));
1696     alignmentProperties.addActionListener(new ActionListener()
1697     {
1698       @Override
1699       public void actionPerformed(ActionEvent actionEvent)
1700       {
1701         alignmentProperties();
1702       }
1703     });
1704     JMenuItem selectHighlighted = new JMenuItem(
1705             MessageManager.getString("action.select_highlighted_columns"));
1706     selectHighlighted.setToolTipText(
1707             MessageManager.getString("tooltip.select_highlighted_columns"));
1708     al = new ActionListener()
1709     {
1710       @Override
1711       public void actionPerformed(ActionEvent actionEvent)
1712       {
1713         selectHighlightedColumns_actionPerformed(actionEvent);
1714       }
1715     };
1716     selectHighlighted.addActionListener(al);
1717     JMenu tooltipSettingsMenu = new JMenu(
1718             MessageManager.getString("label.sequence_id_tooltip"));
1719     JMenu autoAnnMenu = new JMenu(
1720             MessageManager.getString("label.autocalculated_annotation"));
1721
1722     JMenu exportImageMenu = new JMenu(
1723             MessageManager.getString("label.export_image"));
1724     JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1725     alignFrameMenuBar.add(fileMenu);
1726     alignFrameMenuBar.add(editMenu);
1727     alignFrameMenuBar.add(selectMenu);
1728     alignFrameMenuBar.add(viewMenu);
1729     alignFrameMenuBar.add(annotationsMenu);
1730     alignFrameMenuBar.add(formatMenu);
1731     alignFrameMenuBar.add(colourMenu);
1732     alignFrameMenuBar.add(calculateMenu);
1733     if (!Platform.isJS())
1734     {
1735       alignFrameMenuBar.add(webService);
1736     }
1737
1738     fileMenu.add(fetchSequence);
1739     fileMenu.add(addSequenceMenu);
1740     fileMenu.add(reload);
1741     fileMenu.addSeparator();
1742     fileMenu.add(vamsasStore);
1743     fileMenu.add(save);
1744     fileMenu.add(saveAs);
1745     fileMenu.add(outputTextboxMenu);
1746     fileMenu.add(pageSetup);
1747     fileMenu.add(printMenuItem);
1748     fileMenu.addSeparator();
1749     fileMenu.add(exportImageMenu);
1750     fileMenu.add(exportFeatures);
1751     fileMenu.add(exportAnnotations);
1752     fileMenu.add(loadTreeMenuItem);
1753     fileMenu.add(associatedData);
1754     if (!Platform.isJS())
1755     {
1756       fileMenu.add(loadVcf);
1757     }
1758     fileMenu.addSeparator();
1759     fileMenu.add(closeMenuItem);
1760
1761     pasteMenu.add(pasteNew);
1762     pasteMenu.add(pasteThis);
1763     editMenu.add(undoMenuItem);
1764     editMenu.add(redoMenuItem);
1765     editMenu.add(cut);
1766     editMenu.add(copy);
1767     editMenu.add(pasteMenu);
1768     editMenu.add(delete);
1769     editMenu.addSeparator();
1770     editMenu.add(remove2LeftMenuItem);
1771     editMenu.add(remove2RightMenuItem);
1772     editMenu.add(removeGappedColumnMenuItem);
1773     editMenu.add(removeAllGapsMenuItem);
1774     editMenu.add(removeRedundancyMenuItem);
1775     editMenu.addSeparator();
1776     // dont add these yet in the CVS build - they cannot be undone!
1777     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1778     // editMenu.add(justifyLeftMenuItem);
1779     // editMenu.add(justifyRightMenuItem);
1780     // editMenu.addSeparator();
1781     editMenu.add(padGapsMenuitem);
1782
1783     showMenu.add(showAllColumns);
1784     showMenu.add(showAllSeqs);
1785     showMenu.add(showAllhidden);
1786     hideMenu.add(hideSelColumns);
1787     hideMenu.add(hideSelSequences);
1788     hideMenu.add(hideAllSelection);
1789     hideMenu.add(hideAllButSelection);
1790     viewMenu.add(newView);
1791     viewMenu.add(expandViews);
1792     viewMenu.add(gatherViews);
1793     viewMenu.addSeparator();
1794     viewMenu.add(showMenu);
1795     viewMenu.add(hideMenu);
1796     viewMenu.add(showComplementMenuItem);
1797     viewMenu.addSeparator();
1798     viewMenu.add(followHighlightMenuItem);
1799     viewMenu.addSeparator();
1800     viewMenu.add(showSeqFeatures);
1801     // viewMenu.add(showSeqFeaturesHeight);
1802     viewMenu.add(openFeatureSettings);
1803     tooltipSettingsMenu.add(showDbRefsMenuitem);
1804     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1805     viewMenu.add(tooltipSettingsMenu);
1806     viewMenu.addSeparator();
1807     viewMenu.add(alignmentProperties);
1808     viewMenu.addSeparator();
1809     viewMenu.add(overviewMenuItem);
1810
1811     annotationsMenu.add(annotationPanelMenuItem);
1812     annotationsMenu.addSeparator();
1813     annotationsMenu.add(showAllAlAnnotations);
1814     annotationsMenu.add(hideAllAlAnnotations);
1815     annotationsMenu.addSeparator();
1816     annotationsMenu.add(showAllSeqAnnotations);
1817     annotationsMenu.add(hideAllSeqAnnotations);
1818     annotationsMenu.add(sortAnnBySequence);
1819     annotationsMenu.add(sortAnnByLabel);
1820     annotationsMenu.addSeparator();
1821     autoAnnMenu.add(showAutoFirst);
1822     autoAnnMenu.add(showAutoLast);
1823     autoAnnMenu.addSeparator();
1824     autoAnnMenu.add(applyAutoAnnotationSettings);
1825     autoAnnMenu.add(showConsensusHistogram);
1826     autoAnnMenu.add(showSequenceLogo);
1827     autoAnnMenu.add(normaliseSequenceLogo);
1828     autoAnnMenu.addSeparator();
1829     autoAnnMenu.add(showGroupConservation);
1830     autoAnnMenu.add(showGroupConsensus);
1831     annotationsMenu.add(autoAnnMenu);
1832
1833     sort.add(sortIDMenuItem);
1834     sort.add(sortLengthMenuItem);
1835     sort.add(sortGroupMenuItem);
1836     sort.add(sortPairwiseMenuItem);
1837     sort.add(sortByTreeMenu);
1838     calculateMenu.add(sort);
1839     calculateMenu.add(calculateTree);
1840     calculateMenu.addSeparator();
1841     calculateMenu.add(pairwiseAlignmentMenuItem);
1842     calculateMenu.addSeparator();
1843     calculateMenu.add(showTranslation);
1844     calculateMenu.add(showReverse);
1845     calculateMenu.add(showReverseComplement);
1846     calculateMenu.add(showProducts);
1847     calculateMenu.add(autoCalculate);
1848     calculateMenu.add(sortByTree);
1849     calculateMenu.addSeparator();
1850     calculateMenu.add(expandAlignment);
1851     calculateMenu.add(extractScores);
1852     if (!Platform.isJS())
1853     {
1854       calculateMenu.addSeparator();
1855       calculateMenu.add(runGroovy);
1856     }
1857
1858     webServiceNoServices = new JMenuItem(
1859             MessageManager.getString("label.no_services"));
1860     webService.add(webServiceNoServices);
1861     if (!Platform.isJS())
1862     {
1863       exportImageMenu.add(htmlMenuItem);
1864     }
1865     exportImageMenu.add(epsFile);
1866     exportImageMenu.add(createPNG);
1867     if (!Platform.isJS())
1868     {
1869       exportImageMenu.add(createBioJS);
1870       exportImageMenu.add(createSVG);
1871     }
1872     addSequenceMenu.add(addFromFile);
1873     addSequenceMenu.add(addFromText);
1874     addSequenceMenu.add(addFromURL);
1875     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1876     statusPanel.add(statusBar, null);
1877     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1878
1879     formatMenu.add(font);
1880     formatMenu.addSeparator();
1881     formatMenu.add(wrapMenuItem);
1882     formatMenu.add(scaleAbove);
1883     formatMenu.add(scaleLeft);
1884     formatMenu.add(scaleRight);
1885     formatMenu.add(seqLimits);
1886     formatMenu.add(idRightAlign);
1887     formatMenu.add(hiddenMarkers);
1888     formatMenu.add(viewBoxesMenuItem);
1889     formatMenu.add(viewTextMenuItem);
1890     formatMenu.add(colourTextMenuItem);
1891     formatMenu.add(renderGapsMenuItem);
1892     formatMenu.add(centreColumnLabelsMenuItem);
1893     formatMenu.add(showNonconservedMenuItem);
1894     selectMenu.add(findMenuItem);
1895     selectMenu.addSeparator();
1896     selectMenu.add(selectAllSequenceMenuItem);
1897     selectMenu.add(deselectAllSequenceMenuItem);
1898     selectMenu.add(invertSequenceMenuItem);
1899     selectMenu.add(invertColSel);
1900     selectMenu.add(createGroup);
1901     selectMenu.add(unGroup);
1902     selectMenu.add(grpsFromSelection);
1903     selectMenu.add(deleteGroups);
1904     selectMenu.add(annotationColumn);
1905     selectMenu.add(selectHighlighted);
1906     // TODO - determine if the listenToViewSelections button is needed : see bug
1907     // JAL-574
1908     // selectMenu.addSeparator();
1909     // selectMenu.add(listenToViewSelections);
1910   }
1911
1912   protected void loadVcf_actionPerformed()
1913   {
1914   }
1915
1916   /**
1917    * Constructs the entries on the Colour menu (but does not add them to the
1918    * menu).
1919    */
1920   protected void initColourMenu()
1921   {
1922     applyToAllGroups = new JCheckBoxMenuItem(
1923             MessageManager.getString("label.apply_colour_to_all_groups"));
1924     applyToAllGroups.addActionListener(new ActionListener()
1925     {
1926       @Override
1927       public void actionPerformed(ActionEvent e)
1928       {
1929         applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1930       }
1931     });
1932
1933     textColour = new JMenuItem(
1934             MessageManager.getString("label.text_colour"));
1935     textColour.addActionListener(new ActionListener()
1936     {
1937       @Override
1938       public void actionPerformed(ActionEvent e)
1939       {
1940         textColour_actionPerformed();
1941       }
1942     });
1943
1944     conservationMenuItem = new JCheckBoxMenuItem(
1945             MessageManager.getString("action.by_conservation"));
1946     conservationMenuItem.addActionListener(new ActionListener()
1947     {
1948       @Override
1949       public void actionPerformed(ActionEvent e)
1950       {
1951         conservationMenuItem_actionPerformed(
1952                 conservationMenuItem.isSelected());
1953       }
1954     });
1955
1956     abovePIDThreshold = new JCheckBoxMenuItem(
1957             MessageManager.getString("label.above_identity_threshold"));
1958     abovePIDThreshold.addActionListener(new ActionListener()
1959     {
1960       @Override
1961       public void actionPerformed(ActionEvent e)
1962       {
1963         abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
1964       }
1965     });
1966     modifyPID = new JMenuItem(
1967             MessageManager.getString("label.modify_identity_threshold"));
1968     modifyPID.addActionListener(new ActionListener()
1969     {
1970       @Override
1971       public void actionPerformed(ActionEvent e)
1972       {
1973         modifyPID_actionPerformed();
1974       }
1975     });
1976     modifyConservation = new JMenuItem(MessageManager
1977             .getString("label.modify_conservation_threshold"));
1978     modifyConservation.addActionListener(new ActionListener()
1979     {
1980       @Override
1981       public void actionPerformed(ActionEvent e)
1982       {
1983         modifyConservation_actionPerformed();
1984       }
1985     });
1986
1987     annotationColour = new JRadioButtonMenuItem(
1988             MessageManager.getString("action.by_annotation"));
1989     annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
1990     annotationColour.addActionListener(new ActionListener()
1991     {
1992       @Override
1993       public void actionPerformed(ActionEvent e)
1994       {
1995         annotationColour_actionPerformed();
1996       }
1997     });
1998   }
1999
2000   protected void selectHighlightedColumns_actionPerformed(
2001           ActionEvent actionEvent)
2002   {
2003     // TODO Auto-generated method stub
2004
2005   }
2006
2007   /**
2008    * Generate the reverse sequence (or reverse complement if the flag is true)
2009    * and add it to the alignment
2010    *
2011    * @param complement
2012    */
2013   protected void showReverse_actionPerformed(boolean complement)
2014   {
2015   }
2016
2017   /**
2018    * Try to run script in a Groovy console, having first ensured that this
2019    * alignframe is set as currentAlignFrame in Desktop
2020    */
2021   protected void runGroovy_actionPerformed()
2022   {
2023
2024   }
2025
2026   /**
2027    * Adds the given action listener and key accelerator to the given menu item.
2028    * Also saves in a lookup table to support lookup of action by key stroke.
2029    *
2030    * @param keyStroke
2031    * @param menuItem
2032    * @param actionListener
2033    */
2034   protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2035           JMenuItem menuItem, ActionListener actionListener)
2036   {
2037     menuItem.setAccelerator(keyStroke);
2038     accelerators.put(keyStroke, menuItem);
2039     menuItem.addActionListener(actionListener);
2040   }
2041
2042   /**
2043    * Action on clicking sort annotations by type.
2044    *
2045    * @param sortOrder
2046    */
2047   protected void sortAnnotations_actionPerformed()
2048   {
2049   }
2050
2051   /**
2052    * Action on clicking Show all annotations.
2053    *
2054    * @param forSequences
2055    *          update sequence-related annotations
2056    * @param forAlignment
2057    *          update non-sequence-related annotations
2058    */
2059   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2060           boolean forAlignment)
2061   {
2062     setAnnotationsVisibility(true, forSequences, forAlignment);
2063   }
2064
2065   /**
2066    * Action on clicking Hide all annotations.
2067    *
2068    * @param forSequences
2069    *          update sequence-related annotations
2070    * @param forAlignment
2071    *          update non-sequence-related annotations
2072    */
2073   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2074           boolean forAlignment)
2075   {
2076     setAnnotationsVisibility(false, forSequences, forAlignment);
2077   }
2078
2079   /**
2080    * Set the visibility of annotations to true or false. Can act on
2081    * sequence-related annotations, or alignment-related, or both.
2082    *
2083    * @param visible
2084    * @param forSequences
2085    *          update sequence-related annotations
2086    * @param forAlignment
2087    *          update non-sequence-related annotations
2088    */
2089   protected void setAnnotationsVisibility(boolean visible,
2090           boolean forSequences, boolean forAlignment)
2091   {
2092
2093   }
2094
2095   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2096   {
2097     // TODO Auto-generated method stub
2098
2099   }
2100
2101   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2102   {
2103     // TODO Auto-generated method stub
2104
2105   }
2106
2107   protected void showAllhidden_actionPerformed(ActionEvent e)
2108   {
2109     // TODO Auto-generated method stub
2110
2111   }
2112
2113   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2114   {
2115     // TODO Auto-generated method stub
2116
2117   }
2118
2119   protected void hideAllSelection_actionPerformed(ActionEvent e)
2120   {
2121     // TODO Auto-generated method stub
2122
2123   }
2124
2125   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2126   {
2127     // TODO Auto-generated method stub
2128
2129   }
2130
2131   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2132   {
2133     // TODO Auto-generated method stub
2134
2135   }
2136
2137   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2138   {
2139     // TODO Auto-generated method stub
2140
2141   }
2142
2143   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2144   {
2145     // TODO Auto-generated method stub
2146
2147   }
2148
2149   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2150   {
2151     // TODO Auto-generated method stub
2152
2153   }
2154
2155   protected void showGroupConservation_actionPerformed(ActionEvent e)
2156   {
2157     // TODO Auto-generated method stub
2158
2159   }
2160
2161   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2162   {
2163     // TODO Auto-generated method stub
2164
2165   }
2166
2167   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2168   {
2169     // TODO Auto-generated method stub
2170
2171   }
2172
2173   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2174   {
2175     // TODO Auto-generated method stub
2176
2177   }
2178
2179   protected void followHighlight_actionPerformed()
2180   {
2181     // TODO Auto-generated method stub
2182
2183   }
2184
2185   protected void showNpFeats_actionPerformed(ActionEvent e)
2186   {
2187     // TODO Auto-generated method stub
2188
2189   }
2190
2191   protected void showDbRefs_actionPerformed(ActionEvent e)
2192   {
2193     // TODO Auto-generated method stub
2194
2195   }
2196
2197   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2198   {
2199   }
2200
2201   protected void buildSortByAnnotationScoresMenu()
2202   {
2203   }
2204
2205   protected void extractScores_actionPerformed(ActionEvent e)
2206   {
2207   }
2208
2209   protected void outputText_actionPerformed(String formatName)
2210   {
2211   }
2212
2213   public void addFromFile_actionPerformed(ActionEvent e)
2214   {
2215
2216   }
2217
2218   public void addFromText_actionPerformed(ActionEvent e)
2219   {
2220
2221   }
2222
2223   public void addFromURL_actionPerformed(ActionEvent e)
2224   {
2225
2226   }
2227
2228   public void exportFeatures_actionPerformed(ActionEvent e)
2229   {
2230
2231   }
2232
2233   public void exportAnnotations_actionPerformed(ActionEvent e)
2234   {
2235
2236   }
2237
2238   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2239   {
2240   }
2241
2242   protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2243   {
2244
2245   }
2246
2247   protected void closeMenuItem_actionPerformed(boolean b)
2248   {
2249   }
2250
2251   protected void redoMenuItem_actionPerformed(ActionEvent e)
2252   {
2253   }
2254
2255   protected void undoMenuItem_actionPerformed(ActionEvent e)
2256   {
2257   }
2258
2259   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2260   {
2261   }
2262
2263   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2264   {
2265   }
2266
2267   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2268   {
2269   }
2270
2271   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2272   {
2273   }
2274
2275   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2276   {
2277   }
2278
2279   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2280   {
2281   }
2282
2283   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2284   {
2285   }
2286
2287   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2288   {
2289   }
2290
2291   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2292   {
2293   }
2294
2295   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2296   {
2297   }
2298
2299   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2300   {
2301   }
2302
2303   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2304   {
2305   }
2306
2307   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2308   {
2309   }
2310
2311   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2312   {
2313   }
2314
2315   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2316   {
2317   }
2318
2319   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2320   {
2321   }
2322
2323   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2324   {
2325   }
2326
2327   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2328   {
2329   }
2330
2331   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2332   {
2333   }
2334
2335   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2336   {
2337   }
2338
2339   protected void conservationMenuItem_actionPerformed(boolean selected)
2340   {
2341   }
2342
2343   protected void printMenuItem_actionPerformed(ActionEvent e)
2344   {
2345   }
2346
2347   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2348   {
2349   }
2350
2351   protected void findMenuItem_actionPerformed(ActionEvent e)
2352   {
2353   }
2354
2355   protected void abovePIDThreshold_actionPerformed(boolean selected)
2356   {
2357   }
2358
2359   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2360   {
2361   }
2362
2363   protected void deleteGroups_actionPerformed(ActionEvent e)
2364   {
2365   }
2366
2367   protected void createGroup_actionPerformed(ActionEvent e)
2368   {
2369   }
2370
2371   protected void unGroup_actionPerformed(ActionEvent e)
2372   {
2373   }
2374
2375   protected void copy_actionPerformed()
2376   {
2377   }
2378
2379   protected void cut_actionPerformed()
2380   {
2381   }
2382
2383   protected void delete_actionPerformed()
2384   {
2385   }
2386
2387   protected void pasteNew_actionPerformed(ActionEvent e)
2388   {
2389   }
2390
2391   protected void pasteThis_actionPerformed(ActionEvent e)
2392   {
2393   }
2394
2395   protected void applyToAllGroups_actionPerformed(boolean selected)
2396   {
2397   }
2398
2399   public void createPNG(java.io.File f)
2400   {
2401   }
2402
2403   protected void font_actionPerformed(ActionEvent e)
2404   {
2405   }
2406
2407   protected void seqLimit_actionPerformed(ActionEvent e)
2408   {
2409   }
2410
2411   public void seqDBRef_actionPerformed(ActionEvent e)
2412   {
2413
2414   }
2415
2416   public void createEPS(java.io.File f)
2417   {
2418   }
2419
2420   public void createSVG(java.io.File f)
2421   {
2422
2423   }
2424
2425   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2426   {
2427
2428   }
2429
2430   /**
2431    * Template method to handle the 'load T-Coffee scores' menu event.
2432    * <p>
2433    * Subclasses override this method to provide a custom action.
2434    *
2435    * @param event
2436    *          The raised event
2437    */
2438   protected void loadScores_actionPerformed(ActionEvent event)
2439   {
2440
2441   }
2442
2443   protected void jpred_actionPerformed(ActionEvent e)
2444   {
2445   }
2446
2447   protected void scaleAbove_actionPerformed(ActionEvent e)
2448   {
2449   }
2450
2451   protected void scaleLeft_actionPerformed(ActionEvent e)
2452   {
2453   }
2454
2455   protected void scaleRight_actionPerformed(ActionEvent e)
2456   {
2457   }
2458
2459   protected void modifyPID_actionPerformed()
2460   {
2461   }
2462
2463   protected void modifyConservation_actionPerformed()
2464   {
2465   }
2466
2467   protected void saveAs_actionPerformed()
2468   {
2469   }
2470
2471   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2472   {
2473   }
2474
2475   public void vamsasStore_actionPerformed(ActionEvent e)
2476   {
2477
2478   }
2479
2480   public void vamsasLoad_actionPerformed(ActionEvent e)
2481   {
2482
2483   }
2484
2485   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
2486   {
2487
2488   }
2489
2490   public void featureSettings_actionPerformed(ActionEvent e)
2491   {
2492
2493   }
2494
2495   public void fetchSequence_actionPerformed()
2496   {
2497
2498   }
2499
2500   public void smoothFont_actionPerformed(ActionEvent e)
2501   {
2502
2503   }
2504
2505   public void annotationColour_actionPerformed()
2506   {
2507   }
2508
2509   public void annotationColumn_actionPerformed(ActionEvent e)
2510   {
2511   }
2512
2513   public void associatedData_actionPerformed(ActionEvent e)
2514   {
2515
2516   }
2517
2518   public void autoCalculate_actionPerformed(ActionEvent e)
2519   {
2520
2521   }
2522
2523   public void sortByTreeOption_actionPerformed(ActionEvent e)
2524   {
2525
2526   }
2527
2528   public void showAllSeqs_actionPerformed(ActionEvent e)
2529   {
2530
2531   }
2532
2533   public void showAllColumns_actionPerformed(ActionEvent e)
2534   {
2535
2536   }
2537
2538   public void hideSelSequences_actionPerformed(ActionEvent e)
2539   {
2540
2541   }
2542
2543   public void hideSelColumns_actionPerformed(ActionEvent e)
2544   {
2545
2546   }
2547
2548   public void hiddenMarkers_actionPerformed(ActionEvent e)
2549   {
2550
2551   }
2552
2553   public void findPdbId_actionPerformed(ActionEvent e)
2554   {
2555
2556   }
2557
2558   public void enterPdbId_actionPerformed(ActionEvent e)
2559   {
2560
2561   }
2562
2563   public void pdbFile_actionPerformed(ActionEvent e)
2564   {
2565
2566   }
2567
2568   public void invertColSel_actionPerformed(ActionEvent e)
2569   {
2570
2571   }
2572
2573   public void tabSelectionChanged(int sel)
2574   {
2575
2576   }
2577
2578   public void tabbedPane_mousePressed(MouseEvent e)
2579   {
2580
2581   }
2582
2583   public void tabbedPane_focusGained(FocusEvent e)
2584   {
2585     requestFocus();
2586   }
2587
2588   public void save_actionPerformed(ActionEvent e)
2589   {
2590
2591   }
2592
2593   public void reload_actionPerformed(ActionEvent e)
2594   {
2595
2596   }
2597
2598   public void newView_actionPerformed(ActionEvent e)
2599   {
2600
2601   }
2602
2603   public void textColour_actionPerformed()
2604   {
2605
2606   }
2607
2608   public void idRightAlign_actionPerformed(ActionEvent e)
2609   {
2610
2611   }
2612
2613   public void expandViews_actionPerformed(ActionEvent e)
2614   {
2615
2616   }
2617
2618   public void gatherViews_actionPerformed(ActionEvent e)
2619   {
2620
2621   }
2622
2623   public void buildTreeSortMenu()
2624   {
2625
2626   }
2627
2628   public void pageSetup_actionPerformed(ActionEvent e)
2629   {
2630
2631   }
2632
2633   public void alignmentProperties()
2634   {
2635
2636   }
2637
2638   protected void expand_newalign(ActionEvent e)
2639   {
2640     // TODO Auto-generated method stub
2641
2642   }
2643
2644   protected boolean isShowAutoCalculatedAbove()
2645   {
2646     return showAutoCalculatedAbove;
2647   }
2648
2649   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2650   {
2651     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2652   }
2653
2654   protected SequenceAnnotationOrder getAnnotationSortOrder()
2655   {
2656     return annotationSortOrder;
2657   }
2658
2659   protected void setAnnotationSortOrder(
2660           SequenceAnnotationOrder annotationSortOrder)
2661   {
2662     this.annotationSortOrder = annotationSortOrder;
2663   }
2664
2665   public Map<KeyStroke, JMenuItem> getAccelerators()
2666   {
2667     return this.accelerators;
2668   }
2669
2670   /**
2671    * Returns the selected index of the tabbed pane, or -1 if none selected
2672    * (including the case where the tabbed pane has not been made visible).
2673    *
2674    * @return
2675    */
2676   public int getTabIndex()
2677   {
2678     return tabbedPane.getSelectedIndex();
2679   }
2680
2681   public JPanel getStatusPanel()
2682   {
2683     return statusPanel;
2684   }
2685
2686   /**
2687    * Sets a reference to the containing split frame. Also makes the 'toggle
2688    * split view' menu item visible and checked.
2689    *
2690    * @param sf
2691    */
2692   public void setSplitFrame(SplitContainerI sf)
2693   {
2694     this.splitFrame = sf;
2695     if (sf != null)
2696     {
2697       this.showComplementMenuItem.setVisible(true);
2698       this.showComplementMenuItem.setState(true);
2699     }
2700   }
2701
2702   public SplitContainerI getSplitViewContainer()
2703   {
2704     return this.splitFrame;
2705   }
2706
2707   protected void showComplement_actionPerformed(boolean complement)
2708   {
2709   }
2710 }