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.bin.Jalview;
  29 import jalview.gui.JvSwingUtils;
  30 import jalview.gui.Preferences;
  31 import jalview.io.FileFormats;
  32 import jalview.schemes.ResidueColourScheme;
  33 import jalview.util.MessageManager;
  34 import jalview.util.Platform;
  35
  36 import java.awt.BorderLayout;
  37 import java.awt.Color;
  38 import java.awt.GridLayout;
  39 import java.awt.Toolkit;
  40 import java.awt.event.ActionEvent;
  41 import java.awt.event.ActionListener;
  42 import java.awt.event.FocusAdapter;
  43 import java.awt.event.FocusEvent;
  44 import java.awt.event.KeyEvent;
  45 import java.awt.event.MouseAdapter;
  46 import java.awt.event.MouseEvent;
  47 import java.util.HashMap;
  48 import java.util.Map;
  49
  50 import javax.swing.BorderFactory;
  51 import javax.swing.ButtonGroup;
  52 import javax.swing.JCheckBoxMenuItem;
  53 import javax.swing.JInternalFrame;
  54 import javax.swing.JLabel;
  55 import javax.swing.JMenu;
  56 import javax.swing.JMenuBar;
  57 import javax.swing.JMenuItem;
  58 import javax.swing.JPanel;
  59 import javax.swing.JRadioButtonMenuItem;
  60 import javax.swing.JTabbedPane;
  61 import javax.swing.KeyStroke;
  62 import javax.swing.event.ChangeEvent;
  63 import javax.swing.event.MenuEvent;
  64 import javax.swing.event.MenuListener;
  65
  66 @SuppressWarnings("serial")
  67 public class GAlignFrame extends JInternalFrame
  68 {
  69   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  70
  71   protected JMenuItem closeMenuItem = new JMenuItem();
  72
  73   public JMenu webService = new JMenu();// BH 2019 was protected, but not
  74                                         // sufficient for AlignFrame thread run
  75
  76   public JMenuItem webServiceNoServices;// BH 2019 was protected, but not
  77                                         // sufficient for AlignFrame thread run
  78
  79   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  80
  81   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  82
  83   protected JMenu sortByAnnotScore = new JMenu();
  84
  85   public JLabel statusBar = new JLabel(); // BH 2019 was protected, but not
  86                                           // sufficient for
  87                                           // AlignFrame.printWriter
  88
  89   protected JMenu outputTextboxMenu = new JMenu();
  90
  91   protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
  92
  93   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
  94
  95   protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
  96
  97   protected JMenuItem undoMenuItem = new JMenuItem();
  98
  99   protected JMenuItem redoMenuItem = new JMenuItem();
 100
 101   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 102
 103   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 104
 105   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 106
 107   JMenuItem copy = new JMenuItem();
 108
 109   JMenuItem cut = new JMenuItem();
 110
 111   JMenu pasteMenu = new JMenu();
 112
 113   protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 114
 115   protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 116
 117   protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 118
 119   protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 120
 121   protected JCheckBoxMenuItem applyToAllGroups;
 122
 123   protected JMenu colourMenu = new JMenu();
 124
 125   protected JMenuItem textColour;
 126
 127   protected JCheckBoxMenuItem conservationMenuItem;
 128
 129   protected JMenuItem modifyConservation;
 130
 131   protected JCheckBoxMenuItem abovePIDThreshold;
 132
 133   protected JMenuItem modifyPID;
 134
 135   protected JRadioButtonMenuItem annotationColour;
 136
 137   protected JMenu sortByTreeMenu = new JMenu();
 138
 139   protected JMenu sort = new JMenu();
 140
 141   protected JMenuItem calculateTree = new JMenuItem();
 142
 143   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 144
 145   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 146
 147   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 148
 149   protected JMenu showTranslation = new JMenu();
 150
 151   protected JMenuItem showReverse = new JMenuItem();
 152
 153   protected JMenuItem showReverseComplement = new JMenuItem();
 154
 155   protected JMenu showProducts = new JMenu();
 156
 157   protected JMenuItem runGroovy = new JMenuItem();
 158
 159   protected JMenuItem loadVcf;
 160
 161   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 162
 163   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 164
 165   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 166
 167   protected JPanel statusPanel = new JPanel();
 168
 169   protected JMenuItem showAllSeqAnnotations = new JMenuItem();
 170
 171   protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
 172
 173   protected JMenuItem showAllAlAnnotations = new JMenuItem();
 174
 175   protected JMenuItem hideAllAlAnnotations = new JMenuItem();
 176
 177   protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
 178
 179   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 180
 181   protected JTabbedPane tabbedPane = new JTabbedPane();
 182
 183   protected JMenuItem reload = new JMenuItem();
 184
 185   protected JMenu formatMenu = new JMenu();
 186
 187   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 188
 189   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 190
 191   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 192
 193   protected JMenuItem gatherViews = new JMenuItem();
 194
 195   protected JMenuItem expandViews = new JMenuItem();
 196
 197   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 198
 199   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 200
 201   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 202
 203   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 204
 205   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 206
 207   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 208
 209   protected JMenuItem openFeatureSettings;
 210
 211   private SequenceAnnotationOrder annotationSortOrder;
 212
 213   private boolean showAutoCalculatedAbove = false;
 214
 215   private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
 216
 217   private SplitContainerI splitFrame;
 218
 219   public GAlignFrame()
 220   {
 221     try
 222     {
 223
 224       // for Web-page embedding using id=align-frame-div
 225       setName(Jalview.getAppID("alignment"));
 226
 227       jbInit();
 228       setJMenuBar(alignFrameMenuBar);
 229
 230       // dynamically fill save as menu with available formats
 231       for (String ff : FileFormats.getInstance().getWritableFormats(true))
 232       {
 233         JMenuItem item = new JMenuItem(ff);
 234
 235         item.addActionListener(new ActionListener()
 236         {
 237           @Override
 238           public void actionPerformed(ActionEvent e)
 239           {
 240             outputText_actionPerformed(e.getActionCommand());
 241           }
 242         });
 243
 244         outputTextboxMenu.add(item);
 245       }
 246     } catch (Exception e)
 247     {
 248       System.err.println(e.toString());
 249     }
 250
 251     if (Platform.allowMnemonics()) // was "not mac and not JS"
 252     {
 253       closeMenuItem.setMnemonic('C');
 254       outputTextboxMenu.setMnemonic('T');
 255       undoMenuItem.setMnemonic('Z');
 256       redoMenuItem.setMnemonic('0');
 257       copy.setMnemonic('C');
 258       cut.setMnemonic('U');
 259       pasteMenu.setMnemonic('P');
 260       reload.setMnemonic('R');
 261     }
 262   }
 263
 264   private void jbInit() throws Exception
 265   {
 266     initColourMenu();
 267
 268     JMenuItem saveAs = new JMenuItem(
 269             MessageManager.getString("action.save_as"));
 270     ActionListener al = new ActionListener()
 271     {
 272       @Override
 273       public void actionPerformed(ActionEvent e)
 274       {
 275         saveAs_actionPerformed();
 276       }
 277     };
 278
 279     // FIXME getDefaultToolkit throws an exception in Headless mode
 280     KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
 281             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
 282                     | KeyEvent.SHIFT_MASK,
 283             false);
 284     addMenuActionAndAccelerator(keyStroke, saveAs, al);
 285
 286     closeMenuItem.setText(MessageManager.getString("action.close"));
 287     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
 288             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 289     al = new ActionListener()
 290     {
 291       @Override
 292       public void actionPerformed(ActionEvent e)
 293       {
 294         closeMenuItem_actionPerformed(false);
 295       }
 296     };
 297     addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
 298
 299     JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
 300     JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
 301     JMenu annotationsMenu = new JMenu(
 302             MessageManager.getString("action.annotations"));
 303     JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
 304     colourMenu.setText(MessageManager.getString("action.colour"));
 305     JMenu calculateMenu = new JMenu(
 306             MessageManager.getString("action.calculate"));
 307     webService.setText(MessageManager.getString("action.web_service"));
 308     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
 309             MessageManager.getString("action.select_all"));
 310     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
 311             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 312     al = new ActionListener()
 313     {
 314       @Override
 315       public void actionPerformed(ActionEvent e)
 316       {
 317         selectAllSequenceMenuItem_actionPerformed(e);
 318       }
 319     };
 320     addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
 321
 322     JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
 323             MessageManager.getString("action.deselect_all"));
 324     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
 325     al = new ActionListener()
 326     {
 327       @Override
 328       public void actionPerformed(ActionEvent e)
 329       {
 330         deselectAllSequenceMenuItem_actionPerformed(e);
 331       }
 332     };
 333     addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
 334
 335     JMenuItem invertSequenceMenuItem = new JMenuItem(
 336             MessageManager.getString("action.invert_sequence_selection"));
 337     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
 338             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 339     al = new ActionListener()
 340     {
 341       @Override
 342       public void actionPerformed(ActionEvent e)
 343       {
 344         invertSequenceMenuItem_actionPerformed(e);
 345       }
 346     };
 347     addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
 348
 349     JMenuItem grpsFromSelection = new JMenuItem(
 350             MessageManager.getString("action.make_groups_selection"));
 351     grpsFromSelection.addActionListener(new ActionListener()
 352     {
 353       @Override
 354       public void actionPerformed(ActionEvent e)
 355       {
 356         makeGrpsFromSelection_actionPerformed(e);
 357       }
 358     });
 359     JMenuItem expandAlignment = new JMenuItem(
 360             MessageManager.getString("action.view_flanking_regions"));
 361     expandAlignment.setToolTipText(
 362             MessageManager.getString("label.view_flanking_regions"));
 363     expandAlignment.addActionListener(new ActionListener()
 364     {
 365       @Override
 366       public void actionPerformed(ActionEvent e)
 367       {
 368         expand_newalign(e);
 369       }
 370     });
 371     JMenuItem remove2LeftMenuItem = new JMenuItem(
 372             MessageManager.getString("action.remove_left"));
 373     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
 374             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 375     al = new ActionListener()
 376     {
 377       @Override
 378       public void actionPerformed(ActionEvent e)
 379       {
 380         remove2LeftMenuItem_actionPerformed(e);
 381       }
 382     };
 383     addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
 384
 385     JMenuItem remove2RightMenuItem = new JMenuItem(
 386             MessageManager.getString("action.remove_right"));
 387     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
 388             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 389     al = new ActionListener()
 390     {
 391       @Override
 392       public void actionPerformed(ActionEvent e)
 393       {
 394         remove2RightMenuItem_actionPerformed(e);
 395       }
 396     };
 397     addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
 398
 399     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
 400             MessageManager.getString("action.remove_empty_columns"));
 401     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
 402             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 403     al = new ActionListener()
 404     {
 405       @Override
 406       public void actionPerformed(ActionEvent e)
 407       {
 408         removeGappedColumnMenuItem_actionPerformed(e);
 409       }
 410     };
 411     addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
 412
 413     JMenuItem removeAllGapsMenuItem = new JMenuItem(
 414             MessageManager.getString("action.remove_all_gaps"));
 415     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
 416             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
 417                     | KeyEvent.SHIFT_MASK,
 418             false);
 419     al = new ActionListener()
 420     {
 421       @Override
 422       public void actionPerformed(ActionEvent e)
 423       {
 424         removeAllGapsMenuItem_actionPerformed(e);
 425       }
 426     };
 427     addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
 428
 429     JMenuItem justifyLeftMenuItem = new JMenuItem(
 430             MessageManager.getString("action.left_justify_alignment"));
 431     justifyLeftMenuItem.addActionListener(new ActionListener()
 432     {
 433       @Override
 434       public void actionPerformed(ActionEvent e)
 435       {
 436         justifyLeftMenuItem_actionPerformed(e);
 437       }
 438     });
 439     JMenuItem justifyRightMenuItem = new JMenuItem(
 440             MessageManager.getString("action.right_justify_alignment"));
 441     justifyRightMenuItem.addActionListener(new ActionListener()
 442     {
 443       @Override
 444       public void actionPerformed(ActionEvent e)
 445       {
 446         justifyRightMenuItem_actionPerformed(e);
 447       }
 448     });
 449     viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
 450     viewBoxesMenuItem.setState(true);
 451     viewBoxesMenuItem.addActionListener(new ActionListener()
 452     {
 453       @Override
 454       public void actionPerformed(ActionEvent e)
 455       {
 456         viewBoxesMenuItem_actionPerformed(e);
 457       }
 458     });
 459     viewTextMenuItem.setText(MessageManager.getString("action.text"));
 460     viewTextMenuItem.setState(true);
 461     viewTextMenuItem.addActionListener(new ActionListener()
 462     {
 463       @Override
 464       public void actionPerformed(ActionEvent e)
 465       {
 466         viewTextMenuItem_actionPerformed(e);
 467       }
 468     });
 469     showNonconservedMenuItem
 470             .setText(MessageManager.getString("label.show_non_conserved"));
 471     showNonconservedMenuItem.setState(false);
 472     showNonconservedMenuItem.addActionListener(new ActionListener()
 473     {
 474       @Override
 475       public void actionPerformed(ActionEvent e)
 476       {
 477         showUnconservedMenuItem_actionPerformed(e);
 478       }
 479     });
 480     JMenuItem sortPairwiseMenuItem = new JMenuItem(
 481             MessageManager.getString("action.by_pairwise_id"));
 482     sortPairwiseMenuItem.addActionListener(new ActionListener()
 483     {
 484       @Override
 485       public void actionPerformed(ActionEvent e)
 486       {
 487         sortPairwiseMenuItem_actionPerformed(e);
 488       }
 489     });
 490     JMenuItem sortIDMenuItem = new JMenuItem(
 491             MessageManager.getString("action.by_id"));
 492     sortIDMenuItem.addActionListener(new ActionListener()
 493     {
 494       @Override
 495       public void actionPerformed(ActionEvent e)
 496       {
 497         sortIDMenuItem_actionPerformed(e);
 498       }
 499     });
 500     JMenuItem sortLengthMenuItem = new JMenuItem(
 501             MessageManager.getString("action.by_length"));
 502     sortLengthMenuItem.addActionListener(new ActionListener()
 503     {
 504       @Override
 505       public void actionPerformed(ActionEvent e)
 506       {
 507         sortLengthMenuItem_actionPerformed(e);
 508       }
 509     });
 510     JMenuItem sortGroupMenuItem = new JMenuItem(
 511             MessageManager.getString("action.by_group"));
 512     sortGroupMenuItem.addActionListener(new ActionListener()
 513     {
 514       @Override
 515       public void actionPerformed(ActionEvent e)
 516       {
 517         sortGroupMenuItem_actionPerformed(e);
 518       }
 519     });
 520
 521     JMenuItem removeRedundancyMenuItem = new JMenuItem(
 522             MessageManager.getString("action.remove_redundancy"));
 523     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
 524             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 525     al = new ActionListener()
 526     {
 527       @Override
 528       public void actionPerformed(ActionEvent e)
 529       {
 530         removeRedundancyMenuItem_actionPerformed(e);
 531       }
 532     };
 533     addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
 534
 535     JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
 536             MessageManager.getString("action.pairwise_alignment"));
 537     pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
 538     {
 539       @Override
 540       public void actionPerformed(ActionEvent e)
 541       {
 542         pairwiseAlignmentMenuItem_actionPerformed(e);
 543       }
 544     });
 545
 546     this.getContentPane().setLayout(new BorderLayout());
 547     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 548     statusBar.setBackground(Color.white);
 549     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 550     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 551     statusBar.setText(MessageManager.getString("label.status_bar"));
 552     outputTextboxMenu
 553             .setText(MessageManager.getString("label.out_to_textbox"));
 554
 555     annotationPanelMenuItem.setActionCommand("");
 556     annotationPanelMenuItem
 557             .setText(MessageManager.getString("label.show_annotations"));
 558     annotationPanelMenuItem
 559             .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
 560     annotationPanelMenuItem.addActionListener(new ActionListener()
 561     {
 562       @Override
 563       public void actionPerformed(ActionEvent e)
 564       {
 565         annotationPanelMenuItem_actionPerformed(e);
 566       }
 567     });
 568     showAllAlAnnotations.setText(
 569             MessageManager.getString("label.show_all_al_annotations"));
 570     final boolean isAnnotationPanelShown = annotationPanelMenuItem
 571             .getState();
 572     showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 573     showAllAlAnnotations.addActionListener(new ActionListener()
 574     {
 575       @Override
 576       public void actionPerformed(ActionEvent e)
 577       {
 578         showAllAnnotations_actionPerformed(false, true);
 579       }
 580     });
 581     hideAllAlAnnotations.setText(
 582             MessageManager.getString("label.hide_all_al_annotations"));
 583     hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 584     hideAllAlAnnotations.addActionListener(new ActionListener()
 585     {
 586       @Override
 587       public void actionPerformed(ActionEvent e)
 588       {
 589         hideAllAnnotations_actionPerformed(false, true);
 590       }
 591     });
 592     showAllSeqAnnotations.setText(
 593             MessageManager.getString("label.show_all_seq_annotations"));
 594     showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 595     showAllSeqAnnotations.addActionListener(new ActionListener()
 596     {
 597       @Override
 598       public void actionPerformed(ActionEvent e)
 599       {
 600         showAllAnnotations_actionPerformed(true, false);
 601       }
 602     });
 603     hideAllSeqAnnotations.setText(
 604             MessageManager.getString("label.hide_all_seq_annotations"));
 605     hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 606     hideAllSeqAnnotations.addActionListener(new ActionListener()
 607     {
 608       @Override
 609       public void actionPerformed(ActionEvent e)
 610       {
 611         hideAllAnnotations_actionPerformed(true, false);
 612       }
 613     });
 614     SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
 615             .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
 616                     SequenceAnnotationOrder.NONE.name()));
 617     final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
 618             MessageManager.getString("label.sort_annotations_by_sequence"));
 619     final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
 620             MessageManager.getString("label.sort_annotations_by_label"));
 621
 622     sortAnnBySequence.setSelected(
 623             sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
 624     sortAnnBySequence.addActionListener(new ActionListener()
 625     {
 626       @Override
 627       public void actionPerformed(ActionEvent e)
 628       {
 629         boolean newState = sortAnnBySequence.getState();
 630         sortAnnByLabel.setSelected(false);
 631         setAnnotationSortOrder(
 632                 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 633                         : SequenceAnnotationOrder.NONE);
 634         sortAnnotations_actionPerformed();
 635       }
 636     });
 637     sortAnnByLabel.setSelected(
 638             sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
 639     sortAnnByLabel.addActionListener(new ActionListener()
 640     {
 641       @Override
 642       public void actionPerformed(ActionEvent e)
 643       {
 644         boolean newState = sortAnnByLabel.getState();
 645         sortAnnBySequence.setSelected(false);
 646         setAnnotationSortOrder(
 647                 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 648                         : SequenceAnnotationOrder.NONE);
 649         sortAnnotations_actionPerformed();
 650       }
 651     });
 652     colourTextMenuItem = new JCheckBoxMenuItem(
 653             MessageManager.getString("label.colour_text"));
 654     colourTextMenuItem.addActionListener(new ActionListener()
 655     {
 656       @Override
 657       public void actionPerformed(ActionEvent e)
 658       {
 659         colourTextMenuItem_actionPerformed(e);
 660       }
 661     });
 662
 663     JMenuItem htmlMenuItem = new JMenuItem(
 664             MessageManager.getString("label.html"));
 665     htmlMenuItem.addActionListener(new ActionListener()
 666     {
 667       @Override
 668       public void actionPerformed(ActionEvent e)
 669       {
 670         htmlMenuItem_actionPerformed(e);
 671       }
 672     });
 673
 674     JMenuItem createBioJS = new JMenuItem(
 675             MessageManager.getString("label.biojs_html_export"));
 676     createBioJS.addActionListener(new java.awt.event.ActionListener()
 677     {
 678       @Override
 679       public void actionPerformed(ActionEvent e)
 680       {
 681         bioJSMenuItem_actionPerformed(e);
 682       }
 683     });
 684
 685     JMenuItem overviewMenuItem = new JMenuItem(
 686             MessageManager.getString("label.overview_window"));
 687     overviewMenuItem.addActionListener(new ActionListener()
 688     {
 689       @Override
 690       public void actionPerformed(ActionEvent e)
 691       {
 692         overviewMenuItem_actionPerformed(e);
 693       }
 694     });
 695
 696     undoMenuItem.setEnabled(false);
 697     undoMenuItem.setText(MessageManager.getString("action.undo"));
 698     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
 699             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 700     al = new ActionListener()
 701     {
 702       @Override
 703       public void actionPerformed(ActionEvent e)
 704       {
 705         undoMenuItem_actionPerformed(e);
 706       }
 707     };
 708     addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
 709
 710     redoMenuItem.setEnabled(false);
 711     redoMenuItem.setText(MessageManager.getString("action.redo"));
 712     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
 713             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 714     al = new ActionListener()
 715     {
 716       @Override
 717       public void actionPerformed(ActionEvent e)
 718       {
 719         redoMenuItem_actionPerformed(e);
 720       }
 721     };
 722     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
 723
 724     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
 725     wrapMenuItem.addActionListener(new ActionListener()
 726     {
 727       @Override
 728       public void actionPerformed(ActionEvent e)
 729       {
 730         wrapMenuItem_actionPerformed(e);
 731       }
 732     });
 733
 734     JMenuItem printMenuItem = new JMenuItem(
 735             MessageManager.getString("action.print"));
 736     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
 737             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 738     al = new ActionListener()
 739     {
 740       @Override
 741       public void actionPerformed(ActionEvent e)
 742       {
 743         printMenuItem_actionPerformed(e);
 744       }
 745     };
 746     addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
 747
 748     renderGapsMenuItem
 749             .setText(MessageManager.getString("action.show_gaps"));
 750     renderGapsMenuItem.setState(true);
 751     renderGapsMenuItem.addActionListener(new ActionListener()
 752     {
 753       @Override
 754       public void actionPerformed(ActionEvent e)
 755       {
 756         renderGapsMenuItem_actionPerformed(e);
 757       }
 758     });
 759
 760     JMenuItem findMenuItem = new JMenuItem(
 761             MessageManager.getString("action.find"));
 762     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
 763             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 764     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
 765             MessageManager.getString("label.find_tip")));
 766     al = new ActionListener()
 767     {
 768       @Override
 769       public void actionPerformed(ActionEvent e)
 770       {
 771         findMenuItem_actionPerformed(e);
 772       }
 773     };
 774     addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
 775
 776     showSeqFeatures.setText(
 777             MessageManager.getString("label.show_sequence_features"));
 778     showSeqFeatures.addActionListener(new ActionListener()
 779     {
 780       @Override
 781       public void actionPerformed(ActionEvent actionEvent)
 782       {
 783         showSeqFeatures_actionPerformed(actionEvent);
 784       }
 785     });
 786     /*
 787      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
 788      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
 789      * void actionPerformed(ActionEvent actionEvent) {
 790      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
 791      */
 792     showDbRefsMenuitem
 793             .setText(MessageManager.getString("label.show_database_refs"));
 794     showDbRefsMenuitem.addActionListener(new ActionListener()
 795     {
 796
 797       @Override
 798       public void actionPerformed(ActionEvent e)
 799       {
 800         showDbRefs_actionPerformed(e);
 801       }
 802
 803     });
 804     showNpFeatsMenuitem.setText(
 805             MessageManager.getString("label.show_non_positional_features"));
 806     showNpFeatsMenuitem.addActionListener(new ActionListener()
 807     {
 808
 809       @Override
 810       public void actionPerformed(ActionEvent e)
 811       {
 812         showNpFeats_actionPerformed(e);
 813       }
 814
 815     });
 816     showGroupConservation
 817             .setText(MessageManager.getString("label.group_conservation"));
 818     showGroupConservation.addActionListener(new ActionListener()
 819     {
 820
 821       @Override
 822       public void actionPerformed(ActionEvent e)
 823       {
 824         showGroupConservation_actionPerformed(e);
 825       }
 826
 827     });
 828
 829     showGroupConsensus
 830             .setText(MessageManager.getString("label.group_consensus"));
 831     showGroupConsensus.addActionListener(new ActionListener()
 832     {
 833
 834       @Override
 835       public void actionPerformed(ActionEvent e)
 836       {
 837         showGroupConsensus_actionPerformed(e);
 838       }
 839
 840     });
 841     showConsensusHistogram.setText(
 842             MessageManager.getString("label.show_consensus_histogram"));
 843     showConsensusHistogram.addActionListener(new ActionListener()
 844     {
 845
 846       @Override
 847       public void actionPerformed(ActionEvent e)
 848       {
 849         showConsensusHistogram_actionPerformed(e);
 850       }
 851
 852     });
 853     showSequenceLogo
 854             .setText(MessageManager.getString("label.show_consensus_logo"));
 855     showSequenceLogo.addActionListener(new ActionListener()
 856     {
 857
 858       @Override
 859       public void actionPerformed(ActionEvent e)
 860       {
 861         showSequenceLogo_actionPerformed(e);
 862       }
 863
 864     });
 865     normaliseSequenceLogo
 866             .setText(MessageManager.getString("label.norm_consensus_logo"));
 867     normaliseSequenceLogo.addActionListener(new ActionListener()
 868     {
 869
 870       @Override
 871       public void actionPerformed(ActionEvent e)
 872       {
 873         normaliseSequenceLogo_actionPerformed(e);
 874       }
 875
 876     });
 877     applyAutoAnnotationSettings
 878             .setText(MessageManager.getString("label.apply_all_groups"));
 879     applyAutoAnnotationSettings.setState(false);
 880     applyAutoAnnotationSettings.setVisible(true);
 881     applyAutoAnnotationSettings.addActionListener(new ActionListener()
 882     {
 883       @Override
 884       public void actionPerformed(ActionEvent e)
 885       {
 886         applyAutoAnnotationSettings_actionPerformed(e);
 887       }
 888     });
 889
 890     ButtonGroup buttonGroup = new ButtonGroup();
 891     final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
 892             MessageManager.getString("label.show_first"));
 893     final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
 894             MessageManager.getString("label.show_last"));
 895     buttonGroup.add(showAutoFirst);
 896     buttonGroup.add(showAutoLast);
 897     final boolean autoFirst = Cache
 898             .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
 899     showAutoFirst.setSelected(autoFirst);
 900     setShowAutoCalculatedAbove(autoFirst);
 901     showAutoFirst.addActionListener(new ActionListener()
 902     {
 903       @Override
 904       public void actionPerformed(ActionEvent e)
 905       {
 906         setShowAutoCalculatedAbove(showAutoFirst.isSelected());
 907         sortAnnotations_actionPerformed();
 908       }
 909     });
 910     showAutoLast.setSelected(!showAutoFirst.isSelected());
 911     showAutoLast.addActionListener(new ActionListener()
 912     {
 913       @Override
 914       public void actionPerformed(ActionEvent e)
 915       {
 916         setShowAutoCalculatedAbove(!showAutoLast.isSelected());
 917         sortAnnotations_actionPerformed();
 918       }
 919     });
 920
 921     JMenuItem deleteGroups = new JMenuItem(
 922             MessageManager.getString("action.undefine_groups"));
 923     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
 924             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 925     al = new ActionListener()
 926     {
 927       @Override
 928       public void actionPerformed(ActionEvent e)
 929       {
 930         deleteGroups_actionPerformed(e);
 931       }
 932     };
 933     addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
 934
 935     JMenuItem annotationColumn = new JMenuItem(
 936             MessageManager.getString("action.select_by_annotation"));
 937     annotationColumn.addActionListener(new ActionListener()
 938     {
 939       @Override
 940       public void actionPerformed(ActionEvent e)
 941       {
 942         annotationColumn_actionPerformed(e);
 943       }
 944     });
 945
 946     JMenuItem createGroup = new JMenuItem(
 947             MessageManager.getString("action.create_group"));
 948     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
 949             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 950     al = new ActionListener()
 951     {
 952       @Override
 953       public void actionPerformed(ActionEvent e)
 954       {
 955         createGroup_actionPerformed(e);
 956       }
 957     };
 958     addMenuActionAndAccelerator(keyStroke, createGroup, al);
 959
 960     JMenuItem unGroup = new JMenuItem(
 961             MessageManager.getString("action.remove_group"));
 962     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
 963             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
 964                     | KeyEvent.SHIFT_MASK,
 965             false);
 966     al = new ActionListener()
 967     {
 968       @Override
 969       public void actionPerformed(ActionEvent e)
 970       {
 971         unGroup_actionPerformed(e);
 972       }
 973     };
 974     addMenuActionAndAccelerator(keyStroke, unGroup, al);
 975
 976     copy.setText(MessageManager.getString("action.copy"));
 977     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
 978             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 979
 980     al = new ActionListener()
 981     {
 982       @Override
 983       public void actionPerformed(ActionEvent e)
 984       {
 985         copy_actionPerformed();
 986       }
 987     };
 988     addMenuActionAndAccelerator(keyStroke, copy, al);
 989
 990     cut.setText(MessageManager.getString("action.cut"));
 991     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
 992             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 993     al = new ActionListener()
 994     {
 995       @Override
 996       public void actionPerformed(ActionEvent e)
 997       {
 998         cut_actionPerformed();
 999       }
1000     };
1001     addMenuActionAndAccelerator(keyStroke, cut, al);
1002
1003     JMenuItem delete = new JMenuItem(
1004             MessageManager.getString("action.delete"));
1005     delete.addActionListener(new ActionListener()
1006     {
1007       @Override
1008       public void actionPerformed(ActionEvent e)
1009       {
1010         delete_actionPerformed();
1011       }
1012     });
1013
1014     pasteMenu.setText(MessageManager.getString("action.paste"));
1015     JMenuItem pasteNew = new JMenuItem(
1016             MessageManager.getString("label.to_new_alignment"));
1017     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1018             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1019                     | KeyEvent.SHIFT_MASK,
1020             false);
1021     al = new ActionListener()
1022     {
1023       @Override
1024       public void actionPerformed(ActionEvent e)
1025       {
1026         pasteNew_actionPerformed(e);
1027       }
1028     };
1029     addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1030
1031     JMenuItem pasteThis = new JMenuItem(
1032             MessageManager.getString("label.to_this_alignment"));
1033     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1034             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1035     al = new ActionListener()
1036     {
1037       @Override
1038       public void actionPerformed(ActionEvent e)
1039       {
1040         pasteThis_actionPerformed(e);
1041       }
1042     };
1043     addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1044
1045     JMenuItem createPNG = new JMenuItem("PNG");
1046     createPNG.addActionListener(new ActionListener()
1047     {
1048       @Override
1049       public void actionPerformed(ActionEvent e)
1050       {
1051         createPNG(null);
1052       }
1053     });
1054     createPNG.setActionCommand(
1055             MessageManager.getString("label.save_png_image"));
1056
1057     JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1058     font.addActionListener(new ActionListener()
1059     {
1060       @Override
1061       public void actionPerformed(ActionEvent e)
1062       {
1063         font_actionPerformed(e);
1064       }
1065     });
1066     seqLimits.setText(
1067             MessageManager.getString("label.show_sequence_limits"));
1068     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1069     seqLimits.addActionListener(new ActionListener()
1070     {
1071       @Override
1072       public void actionPerformed(ActionEvent e)
1073       {
1074         seqLimit_actionPerformed(e);
1075       }
1076     });
1077     JMenuItem epsFile = new JMenuItem("EPS");
1078     epsFile.addActionListener(new ActionListener()
1079     {
1080       @Override
1081       public void actionPerformed(ActionEvent e)
1082       {
1083         createEPS(null);
1084       }
1085     });
1086
1087     JMenuItem createSVG = new JMenuItem("SVG");
1088     createSVG.addActionListener(new ActionListener()
1089     {
1090       @Override
1091       public void actionPerformed(ActionEvent e)
1092       {
1093         createSVG(null);
1094       }
1095     });
1096
1097     JMenuItem loadTreeMenuItem = new JMenuItem(
1098             MessageManager.getString("label.load_associated_tree"));
1099     loadTreeMenuItem.setActionCommand(
1100             MessageManager.getString("label.load_tree_for_sequence_set"));
1101     loadTreeMenuItem.addActionListener(new ActionListener()
1102     {
1103       @Override
1104       public void actionPerformed(ActionEvent e)
1105       {
1106         loadTreeMenuItem_actionPerformed(e);
1107       }
1108     });
1109
1110     scaleAbove.setVisible(false);
1111     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1112     scaleAbove.addActionListener(new ActionListener()
1113     {
1114       @Override
1115       public void actionPerformed(ActionEvent e)
1116       {
1117         scaleAbove_actionPerformed(e);
1118       }
1119     });
1120     scaleLeft.setVisible(false);
1121     scaleLeft.setSelected(true);
1122     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1123     scaleLeft.addActionListener(new ActionListener()
1124     {
1125       @Override
1126       public void actionPerformed(ActionEvent e)
1127       {
1128         scaleLeft_actionPerformed(e);
1129       }
1130     });
1131     scaleRight.setVisible(false);
1132     scaleRight.setSelected(true);
1133     scaleRight.setText(MessageManager.getString("action.scale_right"));
1134     scaleRight.addActionListener(new ActionListener()
1135     {
1136       @Override
1137       public void actionPerformed(ActionEvent e)
1138       {
1139         scaleRight_actionPerformed(e);
1140       }
1141     });
1142     centreColumnLabelsMenuItem.setVisible(true);
1143     centreColumnLabelsMenuItem.setState(false);
1144     centreColumnLabelsMenuItem.setText(
1145             MessageManager.getString("label.centre_column_labels"));
1146     centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1147     {
1148       @Override
1149       public void actionPerformed(ActionEvent e)
1150       {
1151         centreColumnLabels_actionPerformed(e);
1152       }
1153     });
1154     followHighlightMenuItem.setVisible(true);
1155     followHighlightMenuItem.setState(true);
1156     followHighlightMenuItem
1157             .setText(MessageManager.getString("label.automatic_scrolling"));
1158     followHighlightMenuItem.addActionListener(new ActionListener()
1159     {
1160
1161       @Override
1162       public void actionPerformed(ActionEvent e)
1163       {
1164         followHighlight_actionPerformed();
1165       }
1166
1167     });
1168
1169     sortByTreeMenu
1170             .setText(MessageManager.getString("action.by_tree_order"));
1171     sort.setText(MessageManager.getString("action.sort"));
1172     sort.addMenuListener(new MenuListener()
1173     {
1174       @Override
1175       public void menuSelected(MenuEvent e)
1176       {
1177         buildTreeSortMenu();
1178       }
1179
1180       @Override
1181       public void menuDeselected(MenuEvent e)
1182       {
1183       }
1184
1185       @Override
1186       public void menuCanceled(MenuEvent e)
1187       {
1188       }
1189     });
1190     sortByAnnotScore
1191             .setText(MessageManager.getString("label.sort_by_score"));
1192     sort.add(sortByAnnotScore);
1193     sort.addMenuListener(new javax.swing.event.MenuListener()
1194     {
1195
1196       @Override
1197       public void menuCanceled(MenuEvent e)
1198       {
1199       }
1200
1201       @Override
1202       public void menuDeselected(MenuEvent e)
1203       {
1204       }
1205
1206       @Override
1207       public void menuSelected(MenuEvent e)
1208       {
1209         buildSortByAnnotationScoresMenu();
1210       }
1211     });
1212     sortByAnnotScore.setVisible(false);
1213
1214     calculateTree
1215             .setText(MessageManager.getString("action.calculate_tree_pca"));
1216
1217     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1218     padGapsMenuitem
1219             .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
1220     padGapsMenuitem.addActionListener(new ActionListener()
1221     {
1222       @Override
1223       public void actionPerformed(ActionEvent e)
1224       {
1225         padGapsMenuitem_actionPerformed(e);
1226       }
1227     });
1228     JMenuItem vamsasStore = new JMenuItem(
1229             MessageManager.getString("label.vamsas_store"));
1230     vamsasStore.setVisible(false);
1231     vamsasStore.addActionListener(new ActionListener()
1232     {
1233       @Override
1234       public void actionPerformed(ActionEvent e)
1235       {
1236         vamsasStore_actionPerformed(e);
1237       }
1238     });
1239
1240     /*
1241      * Translate as cDNA with sub-menu of translation tables
1242      */
1243     showTranslation
1244             .setText(MessageManager.getString("label.translate_cDNA"));
1245     boolean first = true;
1246     for (final GeneticCodeI table : GeneticCodes.getCodeTables())
1247     {
1248       JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
1249       showTranslation.add(item);
1250       item.addActionListener(new ActionListener()
1251       {
1252         @Override
1253         public void actionPerformed(ActionEvent e)
1254         {
1255           showTranslation_actionPerformed(table);
1256         }
1257       });
1258       if (first)
1259       {
1260         showTranslation.addSeparator();
1261       }
1262       first = false;
1263     }
1264
1265     showReverse.setText(MessageManager.getString("label.reverse"));
1266     showReverse.addActionListener(new ActionListener()
1267     {
1268       @Override
1269       public void actionPerformed(ActionEvent e)
1270       {
1271         showReverse_actionPerformed(false);
1272       }
1273     });
1274     showReverseComplement
1275             .setText(MessageManager.getString("label.reverse_complement"));
1276     showReverseComplement.addActionListener(new ActionListener()
1277     {
1278       @Override
1279       public void actionPerformed(ActionEvent e)
1280       {
1281         showReverse_actionPerformed(true);
1282       }
1283     });
1284
1285     JMenuItem extractScores = new JMenuItem(
1286             MessageManager.getString("label.extract_scores"));
1287     extractScores.addActionListener(new ActionListener()
1288     {
1289       @Override
1290       public void actionPerformed(ActionEvent e)
1291       {
1292         extractScores_actionPerformed(e);
1293       }
1294     });
1295     extractScores.setVisible(true);
1296     // JBPNote: TODO: make gui for regex based score extraction
1297
1298     // for show products actions see AlignFrame.canShowProducts
1299     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1300
1301     runGroovy.setText(MessageManager.getString("label.run_groovy"));
1302     runGroovy.setToolTipText(
1303             MessageManager.getString("label.run_groovy_tip"));
1304     runGroovy.addActionListener(new ActionListener()
1305     {
1306       @Override
1307       public void actionPerformed(ActionEvent e)
1308       {
1309         runGroovy_actionPerformed();
1310       }
1311     });
1312
1313     openFeatureSettings = new JMenuItem(
1314             MessageManager.getString("action.feature_settings"));
1315     openFeatureSettings.addActionListener(new ActionListener()
1316     {
1317       @Override
1318       public void actionPerformed(ActionEvent e)
1319       {
1320         featureSettings_actionPerformed(e);
1321       }
1322     });
1323
1324     /*
1325      * add sub-menu of database we can fetch from
1326      */
1327     JMenuItem fetchSequence = new JMenuItem(
1328             MessageManager.getString("label.fetch_sequences"));
1329     fetchSequence.addActionListener(new ActionListener()
1330     {
1331       @Override
1332       public void actionPerformed(ActionEvent e)
1333       {
1334         fetchSequence_actionPerformed();
1335       }
1336     });
1337
1338     JMenuItem associatedData = new JMenuItem(
1339             MessageManager.getString("label.load_features_annotations"));
1340     associatedData.addActionListener(new ActionListener()
1341     {
1342       @Override
1343       public void actionPerformed(ActionEvent e)
1344       {
1345         associatedData_actionPerformed(e);
1346       }
1347     });
1348     loadVcf = new JMenuItem(
1349             MessageManager.getString("label.load_vcf_file"));
1350     loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
1351     loadVcf.addActionListener(new ActionListener()
1352     {
1353       @Override
1354       public void actionPerformed(ActionEvent e)
1355       {
1356         loadVcf_actionPerformed();
1357       }
1358     });
1359     autoCalculate.setText(
1360             MessageManager.getString("label.autocalculate_consensus"));
1361     autoCalculate.setState(
1362             jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1363     autoCalculate.addActionListener(new ActionListener()
1364     {
1365       @Override
1366       public void actionPerformed(ActionEvent e)
1367       {
1368         autoCalculate_actionPerformed(e);
1369       }
1370     });
1371     sortByTree.setText(
1372             MessageManager.getString("label.sort_alignment_new_tree"));
1373     sortByTree.setToolTipText("<html>" + MessageManager.getString(
1374             "label.enable_automatically_sort_alignment_when_open_new_tree"));
1375     sortByTree
1376             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1377     sortByTree.addActionListener(new ActionListener()
1378     {
1379       @Override
1380       public void actionPerformed(ActionEvent e)
1381       {
1382         sortByTreeOption_actionPerformed(e);
1383       }
1384     });
1385
1386     listenToViewSelections.setText(
1387             MessageManager.getString("label.listen_for_selections"));
1388     listenToViewSelections
1389             .setToolTipText("<html>" + MessageManager.getString(
1390                     "label.selections_mirror_selections_made_same_sequences_other_views"));
1391     listenToViewSelections.setState(false);
1392     listenToViewSelections.addActionListener(new ActionListener()
1393     {
1394       @Override
1395       public void actionPerformed(ActionEvent e)
1396       {
1397         listenToViewSelections_actionPerformed(e);
1398       }
1399     });
1400
1401     JMenu addSequenceMenu = new JMenu(
1402             MessageManager.getString("label.add_sequences"));
1403     JMenuItem addFromFile = new JMenuItem(
1404             MessageManager.getString("label.from_file"));
1405     addFromFile.addActionListener(new ActionListener()
1406     {
1407       @Override
1408       public void actionPerformed(ActionEvent e)
1409       {
1410         addFromFile_actionPerformed(e);
1411       }
1412     });
1413     JMenuItem addFromText = new JMenuItem(
1414             MessageManager.getString("label.from_textbox"));
1415     addFromText.addActionListener(new ActionListener()
1416     {
1417       @Override
1418       public void actionPerformed(ActionEvent e)
1419       {
1420         addFromText_actionPerformed(e);
1421       }
1422     });
1423     JMenuItem addFromURL = new JMenuItem(
1424             MessageManager.getString("label.from_url"));
1425     addFromURL.addActionListener(new ActionListener()
1426     {
1427       @Override
1428       public void actionPerformed(ActionEvent e)
1429       {
1430         addFromURL_actionPerformed(e);
1431       }
1432     });
1433     JMenuItem exportFeatures = new JMenuItem(
1434             MessageManager.getString("label.export_features"));
1435     exportFeatures.addActionListener(new ActionListener()
1436     {
1437       @Override
1438       public void actionPerformed(ActionEvent e)
1439       {
1440         exportFeatures_actionPerformed(e);
1441       }
1442     });
1443     JMenuItem exportAnnotations = new JMenuItem(
1444             MessageManager.getString("label.export_annotations"));
1445     exportAnnotations.addActionListener(new ActionListener()
1446     {
1447       @Override
1448       public void actionPerformed(ActionEvent e)
1449       {
1450         exportAnnotations_actionPerformed(e);
1451       }
1452     });
1453     statusPanel.setLayout(new GridLayout());
1454     JMenuItem showAllSeqs = new JMenuItem(
1455             MessageManager.getString("label.all_sequences"));
1456     showAllSeqs.setToolTipText(
1457             MessageManager.getString("label.toggle_sequence_visibility"));
1458     showAllSeqs.addActionListener(new ActionListener()
1459     {
1460       @Override
1461       public void actionPerformed(ActionEvent e)
1462       {
1463         showAllSeqs_actionPerformed(e);
1464       }
1465     });
1466     JMenuItem showAllColumns = new JMenuItem(
1467             MessageManager.getString("label.all_columns"));
1468     showAllColumns.setToolTipText(
1469             MessageManager.getString("label.toggle_columns_visibility"));
1470     showAllColumns.addActionListener(new ActionListener()
1471     {
1472       @Override
1473       public void actionPerformed(ActionEvent e)
1474       {
1475         showAllColumns_actionPerformed(e);
1476       }
1477     });
1478     JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1479     JMenuItem hideSelSequences = new JMenuItem(
1480             MessageManager.getString("label.selected_sequences"));
1481     hideSelSequences.setToolTipText(
1482             MessageManager.getString("label.toggle_sequence_visibility"));
1483     hideSelSequences.addActionListener(new ActionListener()
1484     {
1485       @Override
1486       public void actionPerformed(ActionEvent e)
1487       {
1488         hideSelSequences_actionPerformed(e);
1489       }
1490     });
1491     JMenuItem hideSelColumns = new JMenuItem(
1492             MessageManager.getString("label.selected_columns"));
1493     hideSelColumns.setToolTipText(
1494             MessageManager.getString("label.toggle_columns_visibility"));
1495     hideSelColumns.addActionListener(new ActionListener()
1496     {
1497       @Override
1498       public void actionPerformed(ActionEvent e)
1499       {
1500         hideSelColumns_actionPerformed(e);
1501       }
1502     });
1503     JMenuItem hideAllSelection = new JMenuItem(
1504             MessageManager.getString("label.selected_region"));
1505     hideAllSelection.addActionListener(new ActionListener()
1506     {
1507       @Override
1508       public void actionPerformed(ActionEvent e)
1509       {
1510         hideAllSelection_actionPerformed(e);
1511       }
1512     });
1513     // TODO: should be hidden if no selection exists.
1514     JMenuItem hideAllButSelection = new JMenuItem(
1515             MessageManager.getString("label.all_but_selected_region"));
1516     hideAllButSelection.addActionListener(new ActionListener()
1517     {
1518       @Override
1519       public void actionPerformed(ActionEvent e)
1520       {
1521         hideAllButSelection_actionPerformed(e);
1522       }
1523     });
1524     JMenuItem showAllhidden = new JMenuItem(
1525             MessageManager.getString("label.all_sequences_columns"));
1526     showAllhidden.setToolTipText(MessageManager
1527             .getString("label.toggles_visibility_hidden_selected_regions"));
1528     showAllhidden.addActionListener(new ActionListener()
1529     {
1530       @Override
1531       public void actionPerformed(ActionEvent e)
1532       {
1533         showAllhidden_actionPerformed(e);
1534       }
1535     });
1536     hiddenMarkers.setText(
1537             MessageManager.getString("action.show_hidden_markers"));
1538     hiddenMarkers.addActionListener(new ActionListener()
1539     {
1540       @Override
1541       public void actionPerformed(ActionEvent e)
1542       {
1543         hiddenMarkers_actionPerformed(e);
1544       }
1545     });
1546
1547     JMenuItem invertColSel = new JMenuItem(
1548             MessageManager.getString("action.invert_column_selection"));
1549     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1550             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1551                     | KeyEvent.ALT_MASK,
1552             false);
1553     al = new ActionListener()
1554     {
1555       @Override
1556       public void actionPerformed(ActionEvent e)
1557       {
1558         invertColSel_actionPerformed(e);
1559       }
1560     };
1561     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1562
1563     showComplementMenuItem.setVisible(false);
1564     showComplementMenuItem.addActionListener(new ActionListener()
1565     {
1566       @Override
1567       public void actionPerformed(ActionEvent e)
1568       {
1569         showComplement_actionPerformed(showComplementMenuItem.getState());
1570       }
1571     });
1572
1573     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1574     {
1575       @Override
1576       public void stateChanged(ChangeEvent evt)
1577       {
1578         JTabbedPane pane = (JTabbedPane) evt.getSource();
1579         int sel = pane.getSelectedIndex();
1580         tabSelectionChanged(sel);
1581       }
1582     });
1583     tabbedPane.addMouseListener(new MouseAdapter()
1584     {
1585       @Override
1586       public void mousePressed(MouseEvent e)
1587       {
1588         if (e.isPopupTrigger()) // Mac
1589         {
1590           tabbedPane_mousePressed(e);
1591         }
1592       }
1593
1594       @Override
1595       public void mouseReleased(MouseEvent e)
1596       {
1597         if (e.isPopupTrigger()) // Windows
1598         {
1599           tabbedPane_mousePressed(e);
1600         }
1601       }
1602     });
1603     tabbedPane.addFocusListener(new FocusAdapter()
1604     {
1605       @Override
1606       public void focusGained(FocusEvent e)
1607       {
1608         tabbedPane_focusGained(e);
1609       }
1610     });
1611
1612     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1613     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1614             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1615     al = new ActionListener()
1616     {
1617       @Override
1618       public void actionPerformed(ActionEvent e)
1619       {
1620         save_actionPerformed(e);
1621       }
1622     };
1623     addMenuActionAndAccelerator(keyStroke, save, al);
1624
1625     reload.setEnabled(false);
1626     reload.setText(MessageManager.getString("action.reload"));
1627     reload.addActionListener(new ActionListener()
1628     {
1629       @Override
1630       public void actionPerformed(ActionEvent e)
1631       {
1632         reload_actionPerformed(e);
1633       }
1634     });
1635
1636     JMenuItem newView = new JMenuItem(
1637             MessageManager.getString("action.new_view"));
1638     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1639             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1640     al = new ActionListener()
1641     {
1642       @Override
1643       public void actionPerformed(ActionEvent e)
1644       {
1645         newView_actionPerformed(e);
1646       }
1647     };
1648     addMenuActionAndAccelerator(keyStroke, newView, al);
1649
1650     tabbedPane.setToolTipText("<html><i>"
1651             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1652             + "</i></html>");
1653
1654     formatMenu.setText(MessageManager.getString("action.format"));
1655     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1656
1657     idRightAlign.setText(
1658             MessageManager.getString("label.right_align_sequence_id"));
1659     idRightAlign.addActionListener(new ActionListener()
1660     {
1661       @Override
1662       public void actionPerformed(ActionEvent e)
1663       {
1664         idRightAlign_actionPerformed(e);
1665       }
1666     });
1667
1668     gatherViews.setEnabled(false);
1669     gatherViews.setText(MessageManager.getString("action.gather_views"));
1670     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1671     al = new ActionListener()
1672     {
1673       @Override
1674       public void actionPerformed(ActionEvent e)
1675       {
1676         gatherViews_actionPerformed(e);
1677       }
1678     };
1679     addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1680
1681     expandViews.setEnabled(false);
1682     expandViews.setText(MessageManager.getString("action.expand_views"));
1683     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1684     al = new ActionListener()
1685     {
1686       @Override
1687       public void actionPerformed(ActionEvent e)
1688       {
1689         expandViews_actionPerformed(e);
1690       }
1691     };
1692     addMenuActionAndAccelerator(keyStroke, expandViews, al);
1693
1694     JMenuItem pageSetup = new JMenuItem(
1695             MessageManager.getString("action.page_setup"));
1696     pageSetup.addActionListener(new ActionListener()
1697     {
1698       @Override
1699       public void actionPerformed(ActionEvent e)
1700       {
1701         pageSetup_actionPerformed(e);
1702       }
1703     });
1704     JMenuItem alignmentProperties = new JMenuItem(
1705             MessageManager.getString("label.alignment_props"));
1706     alignmentProperties.addActionListener(new ActionListener()
1707     {
1708       @Override
1709       public void actionPerformed(ActionEvent actionEvent)
1710       {
1711         alignmentProperties();
1712       }
1713     });
1714     JMenuItem selectHighlighted = new JMenuItem(
1715             MessageManager.getString("action.select_highlighted_columns"));
1716     selectHighlighted.setToolTipText(
1717             MessageManager.getString("tooltip.select_highlighted_columns"));
1718     al = new ActionListener()
1719     {
1720       @Override
1721       public void actionPerformed(ActionEvent actionEvent)
1722       {
1723         selectHighlightedColumns_actionPerformed(actionEvent);
1724       }
1725     };
1726     selectHighlighted.addActionListener(al);
1727     JMenu tooltipSettingsMenu = new JMenu(
1728             MessageManager.getString("label.sequence_id_tooltip"));
1729     JMenu autoAnnMenu = new JMenu(
1730             MessageManager.getString("label.autocalculated_annotation"));
1731
1732     JMenu exportImageMenu = new JMenu(
1733             MessageManager.getString("label.export_image"));
1734     JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1735     alignFrameMenuBar.add(fileMenu);
1736     alignFrameMenuBar.add(editMenu);
1737     alignFrameMenuBar.add(selectMenu);
1738     alignFrameMenuBar.add(viewMenu);
1739     alignFrameMenuBar.add(annotationsMenu);
1740     alignFrameMenuBar.add(formatMenu);
1741     alignFrameMenuBar.add(colourMenu);
1742     alignFrameMenuBar.add(calculateMenu);
1743     if (!Platform.isJS())
1744     {
1745       alignFrameMenuBar.add(webService);
1746     }
1747
1748     fileMenu.add(fetchSequence);
1749     fileMenu.add(addSequenceMenu);
1750     fileMenu.add(reload);
1751     fileMenu.addSeparator();
1752     fileMenu.add(vamsasStore);
1753     fileMenu.add(save);
1754     fileMenu.add(saveAs);
1755     fileMenu.add(outputTextboxMenu);
1756     fileMenu.add(pageSetup);
1757     fileMenu.add(printMenuItem);
1758     fileMenu.addSeparator();
1759     fileMenu.add(exportImageMenu);
1760     fileMenu.add(exportFeatures);
1761     fileMenu.add(exportAnnotations);
1762     fileMenu.add(loadTreeMenuItem);
1763     fileMenu.add(associatedData);
1764     if (!Platform.isJS())
1765     {
1766       fileMenu.add(loadVcf);
1767     }
1768     fileMenu.addSeparator();
1769     fileMenu.add(closeMenuItem);
1770
1771     pasteMenu.add(pasteNew);
1772     pasteMenu.add(pasteThis);
1773     editMenu.add(undoMenuItem);
1774     editMenu.add(redoMenuItem);
1775     editMenu.add(cut);
1776     editMenu.add(copy);
1777     editMenu.add(pasteMenu);
1778     editMenu.add(delete);
1779     editMenu.addSeparator();
1780     editMenu.add(remove2LeftMenuItem);
1781     editMenu.add(remove2RightMenuItem);
1782     editMenu.add(removeGappedColumnMenuItem);
1783     editMenu.add(removeAllGapsMenuItem);
1784     editMenu.add(removeRedundancyMenuItem);
1785     editMenu.addSeparator();
1786     // dont add these yet in the CVS build - they cannot be undone!
1787     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1788     // editMenu.add(justifyLeftMenuItem);
1789     // editMenu.add(justifyRightMenuItem);
1790     // editMenu.addSeparator();
1791     editMenu.add(padGapsMenuitem);
1792
1793     showMenu.add(showAllColumns);
1794     showMenu.add(showAllSeqs);
1795     showMenu.add(showAllhidden);
1796     hideMenu.add(hideSelColumns);
1797     hideMenu.add(hideSelSequences);
1798     hideMenu.add(hideAllSelection);
1799     hideMenu.add(hideAllButSelection);
1800     viewMenu.add(newView);
1801     viewMenu.add(expandViews);
1802     viewMenu.add(gatherViews);
1803     viewMenu.addSeparator();
1804     viewMenu.add(showMenu);
1805     viewMenu.add(hideMenu);
1806     viewMenu.add(showComplementMenuItem);
1807     viewMenu.addSeparator();
1808     viewMenu.add(followHighlightMenuItem);
1809     viewMenu.addSeparator();
1810     viewMenu.add(showSeqFeatures);
1811     // viewMenu.add(showSeqFeaturesHeight);
1812     viewMenu.add(openFeatureSettings);
1813     tooltipSettingsMenu.add(showDbRefsMenuitem);
1814     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1815     viewMenu.add(tooltipSettingsMenu);
1816     viewMenu.addSeparator();
1817     viewMenu.add(alignmentProperties);
1818     viewMenu.addSeparator();
1819     viewMenu.add(overviewMenuItem);
1820
1821     annotationsMenu.add(annotationPanelMenuItem);
1822     annotationsMenu.addSeparator();
1823     annotationsMenu.add(showAllAlAnnotations);
1824     annotationsMenu.add(hideAllAlAnnotations);
1825     annotationsMenu.addSeparator();
1826     annotationsMenu.add(showAllSeqAnnotations);
1827     annotationsMenu.add(hideAllSeqAnnotations);
1828     annotationsMenu.add(sortAnnBySequence);
1829     annotationsMenu.add(sortAnnByLabel);
1830     annotationsMenu.addSeparator();
1831     autoAnnMenu.add(showAutoFirst);
1832     autoAnnMenu.add(showAutoLast);
1833     autoAnnMenu.addSeparator();
1834     autoAnnMenu.add(applyAutoAnnotationSettings);
1835     autoAnnMenu.add(showConsensusHistogram);
1836     autoAnnMenu.add(showSequenceLogo);
1837     autoAnnMenu.add(normaliseSequenceLogo);
1838     autoAnnMenu.addSeparator();
1839     autoAnnMenu.add(showGroupConservation);
1840     autoAnnMenu.add(showGroupConsensus);
1841     annotationsMenu.add(autoAnnMenu);
1842
1843     sort.add(sortIDMenuItem);
1844     sort.add(sortLengthMenuItem);
1845     sort.add(sortGroupMenuItem);
1846     sort.add(sortPairwiseMenuItem);
1847     sort.add(sortByTreeMenu);
1848     calculateMenu.add(sort);
1849     calculateMenu.add(calculateTree);
1850     calculateMenu.addSeparator();
1851     calculateMenu.add(pairwiseAlignmentMenuItem);
1852     calculateMenu.addSeparator();
1853     calculateMenu.add(showTranslation);
1854     calculateMenu.add(showReverse);
1855     calculateMenu.add(showReverseComplement);
1856     calculateMenu.add(showProducts);
1857     calculateMenu.add(autoCalculate);
1858     calculateMenu.add(sortByTree);
1859     calculateMenu.addSeparator();
1860     calculateMenu.add(expandAlignment);
1861     calculateMenu.add(extractScores);
1862     if (!Platform.isJS())
1863     {
1864       calculateMenu.addSeparator();
1865       calculateMenu.add(runGroovy);
1866     }
1867
1868     webServiceNoServices = new JMenuItem(
1869             MessageManager.getString("label.no_services"));
1870     webService.add(webServiceNoServices);
1871     if (!Platform.isJS())
1872     {
1873       exportImageMenu.add(htmlMenuItem);
1874     }
1875     exportImageMenu.add(epsFile);
1876     exportImageMenu.add(createPNG);
1877     if (!Platform.isJS())
1878     {
1879       exportImageMenu.add(createBioJS);
1880       exportImageMenu.add(createSVG);
1881     }
1882     addSequenceMenu.add(addFromFile);
1883     addSequenceMenu.add(addFromText);
1884     addSequenceMenu.add(addFromURL);
1885     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1886     statusPanel.add(statusBar, null);
1887     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1888
1889     formatMenu.add(font);
1890     formatMenu.addSeparator();
1891     formatMenu.add(wrapMenuItem);
1892     formatMenu.add(scaleAbove);
1893     formatMenu.add(scaleLeft);
1894     formatMenu.add(scaleRight);
1895     formatMenu.add(seqLimits);
1896     formatMenu.add(idRightAlign);
1897     formatMenu.add(hiddenMarkers);
1898     formatMenu.add(viewBoxesMenuItem);
1899     formatMenu.add(viewTextMenuItem);
1900     formatMenu.add(colourTextMenuItem);
1901     formatMenu.add(renderGapsMenuItem);
1902     formatMenu.add(centreColumnLabelsMenuItem);
1903     formatMenu.add(showNonconservedMenuItem);
1904     selectMenu.add(findMenuItem);
1905     selectMenu.addSeparator();
1906     selectMenu.add(selectAllSequenceMenuItem);
1907     selectMenu.add(deselectAllSequenceMenuItem);
1908     selectMenu.add(invertSequenceMenuItem);
1909     selectMenu.add(invertColSel);
1910     selectMenu.add(createGroup);
1911     selectMenu.add(unGroup);
1912     selectMenu.add(grpsFromSelection);
1913     selectMenu.add(deleteGroups);
1914     selectMenu.add(annotationColumn);
1915     selectMenu.add(selectHighlighted);
1916     // TODO - determine if the listenToViewSelections button is needed : see bug
1917     // JAL-574
1918     // selectMenu.addSeparator();
1919     // selectMenu.add(listenToViewSelections);
1920   }
1921
1922   protected void loadVcf_actionPerformed()
1923   {
1924   }
1925
1926   /**
1927    * Constructs the entries on the Colour menu (but does not add them to the
1928    * menu).
1929    */
1930   protected void initColourMenu()
1931   {
1932     applyToAllGroups = new JCheckBoxMenuItem(
1933             MessageManager.getString("label.apply_colour_to_all_groups"));
1934     applyToAllGroups.addActionListener(new ActionListener()
1935     {
1936       @Override
1937       public void actionPerformed(ActionEvent e)
1938       {
1939         applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1940       }
1941     });
1942
1943     textColour = new JMenuItem(
1944             MessageManager.getString("label.text_colour"));
1945     textColour.addActionListener(new ActionListener()
1946     {
1947       @Override
1948       public void actionPerformed(ActionEvent e)
1949       {
1950         textColour_actionPerformed();
1951       }
1952     });
1953
1954     conservationMenuItem = new JCheckBoxMenuItem(
1955             MessageManager.getString("action.by_conservation"));
1956     conservationMenuItem.addActionListener(new ActionListener()
1957     {
1958       @Override
1959       public void actionPerformed(ActionEvent e)
1960       {
1961         conservationMenuItem_actionPerformed(
1962                 conservationMenuItem.isSelected());
1963       }
1964     });
1965
1966     abovePIDThreshold = new JCheckBoxMenuItem(
1967             MessageManager.getString("label.above_identity_threshold"));
1968     abovePIDThreshold.addActionListener(new ActionListener()
1969     {
1970       @Override
1971       public void actionPerformed(ActionEvent e)
1972       {
1973         abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
1974       }
1975     });
1976     modifyPID = new JMenuItem(
1977             MessageManager.getString("label.modify_identity_threshold"));
1978     modifyPID.addActionListener(new ActionListener()
1979     {
1980       @Override
1981       public void actionPerformed(ActionEvent e)
1982       {
1983         modifyPID_actionPerformed();
1984       }
1985     });
1986     modifyConservation = new JMenuItem(MessageManager
1987             .getString("label.modify_conservation_threshold"));
1988     modifyConservation.addActionListener(new ActionListener()
1989     {
1990       @Override
1991       public void actionPerformed(ActionEvent e)
1992       {
1993         modifyConservation_actionPerformed();
1994       }
1995     });
1996
1997     annotationColour = new JRadioButtonMenuItem(
1998             MessageManager.getString("action.by_annotation"));
1999     annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
2000     annotationColour.addActionListener(new ActionListener()
2001     {
2002       @Override
2003       public void actionPerformed(ActionEvent e)
2004       {
2005         annotationColour_actionPerformed();
2006       }
2007     });
2008   }
2009
2010   protected void selectHighlightedColumns_actionPerformed(
2011           ActionEvent actionEvent)
2012   {
2013     // TODO Auto-generated method stub
2014
2015   }
2016
2017   /**
2018    * Generate the reverse sequence (or reverse complement if the flag is true)
2019    * and add it to the alignment
2020    *
2021    * @param complement
2022    */
2023   protected void showReverse_actionPerformed(boolean complement)
2024   {
2025   }
2026
2027   /**
2028    * Try to run script in a Groovy console, having first ensured that this
2029    * alignframe is set as currentAlignFrame in Desktop
2030    */
2031   protected void runGroovy_actionPerformed()
2032   {
2033
2034   }
2035
2036   /**
2037    * Adds the given action listener and key accelerator to the given menu item.
2038    * Also saves in a lookup table to support lookup of action by key stroke.
2039    *
2040    * @param keyStroke
2041    * @param menuItem
2042    * @param actionListener
2043    */
2044   protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2045           JMenuItem menuItem, ActionListener actionListener)
2046   {
2047     menuItem.setAccelerator(keyStroke);
2048     accelerators.put(keyStroke, menuItem);
2049     menuItem.addActionListener(actionListener);
2050   }
2051
2052   /**
2053    * Action on clicking sort annotations by type.
2054    *
2055    * @param sortOrder
2056    */
2057   protected void sortAnnotations_actionPerformed()
2058   {
2059   }
2060
2061   /**
2062    * Action on clicking Show all annotations.
2063    *
2064    * @param forSequences
2065    *          update sequence-related annotations
2066    * @param forAlignment
2067    *          update non-sequence-related annotations
2068    */
2069   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2070           boolean forAlignment)
2071   {
2072     setAnnotationsVisibility(true, forSequences, forAlignment);
2073   }
2074
2075   /**
2076    * Action on clicking Hide all annotations.
2077    *
2078    * @param forSequences
2079    *          update sequence-related annotations
2080    * @param forAlignment
2081    *          update non-sequence-related annotations
2082    */
2083   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2084           boolean forAlignment)
2085   {
2086     setAnnotationsVisibility(false, forSequences, forAlignment);
2087   }
2088
2089   /**
2090    * Set the visibility of annotations to true or false. Can act on
2091    * sequence-related annotations, or alignment-related, or both.
2092    *
2093    * @param visible
2094    * @param forSequences
2095    *          update sequence-related annotations
2096    * @param forAlignment
2097    *          update non-sequence-related annotations
2098    */
2099   protected void setAnnotationsVisibility(boolean visible,
2100           boolean forSequences, boolean forAlignment)
2101   {
2102
2103   }
2104
2105   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2106   {
2107     // TODO Auto-generated method stub
2108
2109   }
2110
2111   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2112   {
2113     // TODO Auto-generated method stub
2114
2115   }
2116
2117   protected void showAllhidden_actionPerformed(ActionEvent e)
2118   {
2119     // TODO Auto-generated method stub
2120
2121   }
2122
2123   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2124   {
2125     // TODO Auto-generated method stub
2126
2127   }
2128
2129   protected void hideAllSelection_actionPerformed(ActionEvent e)
2130   {
2131     // TODO Auto-generated method stub
2132
2133   }
2134
2135   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2136   {
2137     // TODO Auto-generated method stub
2138
2139   }
2140
2141   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2142   {
2143     // TODO Auto-generated method stub
2144
2145   }
2146
2147   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2148   {
2149     // TODO Auto-generated method stub
2150
2151   }
2152
2153   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2154   {
2155     // TODO Auto-generated method stub
2156
2157   }
2158
2159   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2160   {
2161     // TODO Auto-generated method stub
2162
2163   }
2164
2165   protected void showGroupConservation_actionPerformed(ActionEvent e)
2166   {
2167     // TODO Auto-generated method stub
2168
2169   }
2170
2171   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2172   {
2173     // TODO Auto-generated method stub
2174
2175   }
2176
2177   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2178   {
2179     // TODO Auto-generated method stub
2180
2181   }
2182
2183   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2184   {
2185     // TODO Auto-generated method stub
2186
2187   }
2188
2189   protected void followHighlight_actionPerformed()
2190   {
2191     // TODO Auto-generated method stub
2192
2193   }
2194
2195   protected void showNpFeats_actionPerformed(ActionEvent e)
2196   {
2197     // TODO Auto-generated method stub
2198
2199   }
2200
2201   protected void showDbRefs_actionPerformed(ActionEvent e)
2202   {
2203     // TODO Auto-generated method stub
2204
2205   }
2206
2207   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2208   {
2209   }
2210
2211   protected void buildSortByAnnotationScoresMenu()
2212   {
2213   }
2214
2215   protected void extractScores_actionPerformed(ActionEvent e)
2216   {
2217   }
2218
2219   protected void outputText_actionPerformed(String formatName)
2220   {
2221   }
2222
2223   public void addFromFile_actionPerformed(ActionEvent e)
2224   {
2225
2226   }
2227
2228   public void addFromText_actionPerformed(ActionEvent e)
2229   {
2230
2231   }
2232
2233   public void addFromURL_actionPerformed(ActionEvent e)
2234   {
2235
2236   }
2237
2238   public void exportFeatures_actionPerformed(ActionEvent e)
2239   {
2240
2241   }
2242
2243   public void exportAnnotations_actionPerformed(ActionEvent e)
2244   {
2245
2246   }
2247
2248   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2249   {
2250   }
2251
2252   protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2253   {
2254
2255   }
2256
2257   protected void closeMenuItem_actionPerformed(boolean b)
2258   {
2259   }
2260
2261   protected void redoMenuItem_actionPerformed(ActionEvent e)
2262   {
2263   }
2264
2265   protected void undoMenuItem_actionPerformed(ActionEvent e)
2266   {
2267   }
2268
2269   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2270   {
2271   }
2272
2273   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2274   {
2275   }
2276
2277   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2278   {
2279   }
2280
2281   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2282   {
2283   }
2284
2285   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2286   {
2287   }
2288
2289   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2290   {
2291   }
2292
2293   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2294   {
2295   }
2296
2297   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2298   {
2299   }
2300
2301   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2302   {
2303   }
2304
2305   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2306   {
2307   }
2308
2309   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2310   {
2311   }
2312
2313   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2314   {
2315   }
2316
2317   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2318   {
2319   }
2320
2321   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2322   {
2323   }
2324
2325   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2326   {
2327   }
2328
2329   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2330   {
2331   }
2332
2333   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2334   {
2335   }
2336
2337   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2338   {
2339   }
2340
2341   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2342   {
2343   }
2344
2345   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2346   {
2347   }
2348
2349   protected void conservationMenuItem_actionPerformed(boolean selected)
2350   {
2351   }
2352
2353   protected void printMenuItem_actionPerformed(ActionEvent e)
2354   {
2355   }
2356
2357   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2358   {
2359   }
2360
2361   protected void findMenuItem_actionPerformed(ActionEvent e)
2362   {
2363   }
2364
2365   protected void abovePIDThreshold_actionPerformed(boolean selected)
2366   {
2367   }
2368
2369   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2370   {
2371   }
2372
2373   protected void deleteGroups_actionPerformed(ActionEvent e)
2374   {
2375   }
2376
2377   protected void createGroup_actionPerformed(ActionEvent e)
2378   {
2379   }
2380
2381   protected void unGroup_actionPerformed(ActionEvent e)
2382   {
2383   }
2384
2385   protected void copy_actionPerformed()
2386   {
2387   }
2388
2389   protected void cut_actionPerformed()
2390   {
2391   }
2392
2393   protected void delete_actionPerformed()
2394   {
2395   }
2396
2397   protected void pasteNew_actionPerformed(ActionEvent e)
2398   {
2399   }
2400
2401   protected void pasteThis_actionPerformed(ActionEvent e)
2402   {
2403   }
2404
2405   protected void applyToAllGroups_actionPerformed(boolean selected)
2406   {
2407   }
2408
2409   public void createPNG(java.io.File f)
2410   {
2411   }
2412
2413   protected void font_actionPerformed(ActionEvent e)
2414   {
2415   }
2416
2417   protected void seqLimit_actionPerformed(ActionEvent e)
2418   {
2419   }
2420
2421   public void seqDBRef_actionPerformed(ActionEvent e)
2422   {
2423
2424   }
2425
2426   public void createEPS(java.io.File f)
2427   {
2428   }
2429
2430   public void createSVG(java.io.File f)
2431   {
2432
2433   }
2434
2435   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2436   {
2437
2438   }
2439
2440   /**
2441    * Template method to handle the 'load T-Coffee scores' menu event.
2442    * <p>
2443    * Subclasses override this method to provide a custom action.
2444    *
2445    * @param event
2446    *          The raised event
2447    */
2448   protected void loadScores_actionPerformed(ActionEvent event)
2449   {
2450
2451   }
2452
2453   protected void jpred_actionPerformed(ActionEvent e)
2454   {
2455   }
2456
2457   protected void scaleAbove_actionPerformed(ActionEvent e)
2458   {
2459   }
2460
2461   protected void scaleLeft_actionPerformed(ActionEvent e)
2462   {
2463   }
2464
2465   protected void scaleRight_actionPerformed(ActionEvent e)
2466   {
2467   }
2468
2469   protected void modifyPID_actionPerformed()
2470   {
2471   }
2472
2473   protected void modifyConservation_actionPerformed()
2474   {
2475   }
2476
2477   protected void saveAs_actionPerformed()
2478   {
2479   }
2480
2481   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2482   {
2483   }
2484
2485   public void vamsasStore_actionPerformed(ActionEvent e)
2486   {
2487
2488   }
2489
2490   public void vamsasLoad_actionPerformed(ActionEvent e)
2491   {
2492
2493   }
2494
2495   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
2496   {
2497
2498   }
2499
2500   public void featureSettings_actionPerformed(ActionEvent e)
2501   {
2502
2503   }
2504
2505   public void fetchSequence_actionPerformed()
2506   {
2507
2508   }
2509
2510   public void smoothFont_actionPerformed(ActionEvent e)
2511   {
2512
2513   }
2514
2515   public void annotationColour_actionPerformed()
2516   {
2517   }
2518
2519   public void annotationColumn_actionPerformed(ActionEvent e)
2520   {
2521   }
2522
2523   public void associatedData_actionPerformed(ActionEvent e)
2524   {
2525
2526   }
2527
2528   public void autoCalculate_actionPerformed(ActionEvent e)
2529   {
2530
2531   }
2532
2533   public void sortByTreeOption_actionPerformed(ActionEvent e)
2534   {
2535
2536   }
2537
2538   public void showAllSeqs_actionPerformed(ActionEvent e)
2539   {
2540
2541   }
2542
2543   public void showAllColumns_actionPerformed(ActionEvent e)
2544   {
2545
2546   }
2547
2548   public void hideSelSequences_actionPerformed(ActionEvent e)
2549   {
2550
2551   }
2552
2553   public void hideSelColumns_actionPerformed(ActionEvent e)
2554   {
2555
2556   }
2557
2558   public void hiddenMarkers_actionPerformed(ActionEvent e)
2559   {
2560
2561   }
2562
2563   public void findPdbId_actionPerformed(ActionEvent e)
2564   {
2565
2566   }
2567
2568   public void enterPdbId_actionPerformed(ActionEvent e)
2569   {
2570
2571   }
2572
2573   public void pdbFile_actionPerformed(ActionEvent e)
2574   {
2575
2576   }
2577
2578   public void invertColSel_actionPerformed(ActionEvent e)
2579   {
2580
2581   }
2582
2583   public void tabSelectionChanged(int sel)
2584   {
2585
2586   }
2587
2588   public void tabbedPane_mousePressed(MouseEvent e)
2589   {
2590
2591   }
2592
2593   public void tabbedPane_focusGained(FocusEvent e)
2594   {
2595     requestFocus();
2596   }
2597
2598   public void save_actionPerformed(ActionEvent e)
2599   {
2600
2601   }
2602
2603   public void reload_actionPerformed(ActionEvent e)
2604   {
2605
2606   }
2607
2608   public void newView_actionPerformed(ActionEvent e)
2609   {
2610
2611   }
2612
2613   public void textColour_actionPerformed()
2614   {
2615
2616   }
2617
2618   public void idRightAlign_actionPerformed(ActionEvent e)
2619   {
2620
2621   }
2622
2623   public void expandViews_actionPerformed(ActionEvent e)
2624   {
2625
2626   }
2627
2628   public void gatherViews_actionPerformed(ActionEvent e)
2629   {
2630
2631   }
2632
2633   public void buildTreeSortMenu()
2634   {
2635
2636   }
2637
2638   public void pageSetup_actionPerformed(ActionEvent e)
2639   {
2640
2641   }
2642
2643   public void alignmentProperties()
2644   {
2645
2646   }
2647
2648   protected void expand_newalign(ActionEvent e)
2649   {
2650     // TODO Auto-generated method stub
2651
2652   }
2653
2654   protected boolean isShowAutoCalculatedAbove()
2655   {
2656     return showAutoCalculatedAbove;
2657   }
2658
2659   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2660   {
2661     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2662   }
2663
2664   protected SequenceAnnotationOrder getAnnotationSortOrder()
2665   {
2666     return annotationSortOrder;
2667   }
2668
2669   protected void setAnnotationSortOrder(
2670           SequenceAnnotationOrder annotationSortOrder)
2671   {
2672     this.annotationSortOrder = annotationSortOrder;
2673   }
2674
2675   public Map<KeyStroke, JMenuItem> getAccelerators()
2676   {
2677     return this.accelerators;
2678   }
2679
2680   /**
2681    * Returns the selected index of the tabbed pane, or -1 if none selected
2682    * (including the case where the tabbed pane has not been made visible).
2683    *
2684    * @return
2685    */
2686   public int getTabIndex()
2687   {
2688     return tabbedPane.getSelectedIndex();
2689   }
2690
2691   public JPanel getStatusPanel()
2692   {
2693     return statusPanel;
2694   }
2695
2696   /**
2697    * Sets a reference to the containing split frame. Also makes the 'toggle
2698    * split view' menu item visible and checked.
2699    *
2700    * @param sf
2701    */
2702   public void setSplitFrame(SplitContainerI sf)
2703   {
2704     this.splitFrame = sf;
2705     if (sf != null)
2706     {
2707       this.showComplementMenuItem.setVisible(true);
2708       this.showComplementMenuItem.setState(true);
2709     }
2710   }
2711
2712   public SplitContainerI getSplitViewContainer()
2713   {
2714     return this.splitFrame;
2715   }
2716
2717   protected void showComplement_actionPerformed(boolean complement)
2718   {
2719   }
2720 }