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