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); BH 2019.08.01 -- this does nothing,
 549     // as the label is not opaque
 550     statusBar.setOpaque(true);// BH 2019.07.01 -- setting a label opaque avoids
 551                               // frame repaint in SwingJS and has no effect in
 552                               // Java
 553     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 554     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 555     statusBar.setText(MessageManager.getString("label.status_bar"));
 556     outputTextboxMenu
 557             .setText(MessageManager.getString("label.out_to_textbox"));
 558
 559     annotationPanelMenuItem.setActionCommand("");
 560     annotationPanelMenuItem
 561             .setText(MessageManager.getString("label.show_annotations"));
 562     annotationPanelMenuItem
 563             .setState(Cache.getDefault(Preferences.SHOW_ANNOTATIONS, true));
 564     annotationPanelMenuItem.addActionListener(new ActionListener()
 565     {
 566       @Override
 567       public void actionPerformed(ActionEvent e)
 568       {
 569         annotationPanelMenuItem_actionPerformed(e);
 570       }
 571     });
 572     showAllAlAnnotations.setText(
 573             MessageManager.getString("label.show_all_al_annotations"));
 574     final boolean isAnnotationPanelShown = annotationPanelMenuItem
 575             .getState();
 576     showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 577     showAllAlAnnotations.addActionListener(new ActionListener()
 578     {
 579       @Override
 580       public void actionPerformed(ActionEvent e)
 581       {
 582         showAllAnnotations_actionPerformed(false, true);
 583       }
 584     });
 585     hideAllAlAnnotations.setText(
 586             MessageManager.getString("label.hide_all_al_annotations"));
 587     hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 588     hideAllAlAnnotations.addActionListener(new ActionListener()
 589     {
 590       @Override
 591       public void actionPerformed(ActionEvent e)
 592       {
 593         hideAllAnnotations_actionPerformed(false, true);
 594       }
 595     });
 596     showAllSeqAnnotations.setText(
 597             MessageManager.getString("label.show_all_seq_annotations"));
 598     showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 599     showAllSeqAnnotations.addActionListener(new ActionListener()
 600     {
 601       @Override
 602       public void actionPerformed(ActionEvent e)
 603       {
 604         showAllAnnotations_actionPerformed(true, false);
 605       }
 606     });
 607     hideAllSeqAnnotations.setText(
 608             MessageManager.getString("label.hide_all_seq_annotations"));
 609     hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 610     hideAllSeqAnnotations.addActionListener(new ActionListener()
 611     {
 612       @Override
 613       public void actionPerformed(ActionEvent e)
 614       {
 615         hideAllAnnotations_actionPerformed(true, false);
 616       }
 617     });
 618     SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
 619             .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
 620                     SequenceAnnotationOrder.NONE.name()));
 621     final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
 622             MessageManager.getString("label.sort_annotations_by_sequence"));
 623     final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
 624             MessageManager.getString("label.sort_annotations_by_label"));
 625
 626     sortAnnBySequence.setSelected(
 627             sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
 628     sortAnnBySequence.addActionListener(new ActionListener()
 629     {
 630       @Override
 631       public void actionPerformed(ActionEvent e)
 632       {
 633         boolean newState = sortAnnBySequence.getState();
 634         sortAnnByLabel.setSelected(false);
 635         setAnnotationSortOrder(
 636                 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 637                         : SequenceAnnotationOrder.NONE);
 638         sortAnnotations_actionPerformed();
 639       }
 640     });
 641     sortAnnByLabel.setSelected(
 642             sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
 643     sortAnnByLabel.addActionListener(new ActionListener()
 644     {
 645       @Override
 646       public void actionPerformed(ActionEvent e)
 647       {
 648         boolean newState = sortAnnByLabel.getState();
 649         sortAnnBySequence.setSelected(false);
 650         setAnnotationSortOrder(
 651                 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 652                         : SequenceAnnotationOrder.NONE);
 653         sortAnnotations_actionPerformed();
 654       }
 655     });
 656     colourTextMenuItem = new JCheckBoxMenuItem(
 657             MessageManager.getString("label.colour_text"));
 658     colourTextMenuItem.addActionListener(new ActionListener()
 659     {
 660       @Override
 661       public void actionPerformed(ActionEvent e)
 662       {
 663         colourTextMenuItem_actionPerformed(e);
 664       }
 665     });
 666
 667     JMenuItem htmlMenuItem = new JMenuItem(
 668             MessageManager.getString("label.html"));
 669     htmlMenuItem.addActionListener(new ActionListener()
 670     {
 671       @Override
 672       public void actionPerformed(ActionEvent e)
 673       {
 674         htmlMenuItem_actionPerformed(e);
 675       }
 676     });
 677
 678     JMenuItem createBioJS = new JMenuItem(
 679             MessageManager.getString("label.biojs_html_export"));
 680     createBioJS.addActionListener(new java.awt.event.ActionListener()
 681     {
 682       @Override
 683       public void actionPerformed(ActionEvent e)
 684       {
 685         bioJSMenuItem_actionPerformed(e);
 686       }
 687     });
 688
 689     JMenuItem overviewMenuItem = new JMenuItem(
 690             MessageManager.getString("label.overview_window"));
 691     overviewMenuItem.addActionListener(new ActionListener()
 692     {
 693       @Override
 694       public void actionPerformed(ActionEvent e)
 695       {
 696         overviewMenuItem_actionPerformed(e);
 697       }
 698     });
 699
 700     undoMenuItem.setEnabled(false);
 701     undoMenuItem.setText(MessageManager.getString("action.undo"));
 702     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
 703             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 704     al = new ActionListener()
 705     {
 706       @Override
 707       public void actionPerformed(ActionEvent e)
 708       {
 709         undoMenuItem_actionPerformed(e);
 710       }
 711     };
 712     addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
 713
 714     redoMenuItem.setEnabled(false);
 715     redoMenuItem.setText(MessageManager.getString("action.redo"));
 716     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
 717             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 718     al = new ActionListener()
 719     {
 720       @Override
 721       public void actionPerformed(ActionEvent e)
 722       {
 723         redoMenuItem_actionPerformed(e);
 724       }
 725     };
 726     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
 727
 728     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
 729     wrapMenuItem.addActionListener(new ActionListener()
 730     {
 731       @Override
 732       public void actionPerformed(ActionEvent e)
 733       {
 734         wrapMenuItem_actionPerformed(e);
 735       }
 736     });
 737
 738     JMenuItem printMenuItem = new JMenuItem(
 739             MessageManager.getString("action.print"));
 740     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
 741             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 742     al = new ActionListener()
 743     {
 744       @Override
 745       public void actionPerformed(ActionEvent e)
 746       {
 747         printMenuItem_actionPerformed(e);
 748       }
 749     };
 750     addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
 751
 752     renderGapsMenuItem
 753             .setText(MessageManager.getString("action.show_gaps"));
 754     renderGapsMenuItem.setState(true);
 755     renderGapsMenuItem.addActionListener(new ActionListener()
 756     {
 757       @Override
 758       public void actionPerformed(ActionEvent e)
 759       {
 760         renderGapsMenuItem_actionPerformed(e);
 761       }
 762     });
 763
 764     JMenuItem findMenuItem = new JMenuItem(
 765             MessageManager.getString("action.find"));
 766     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
 767             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 768     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
 769             MessageManager.getString("label.find_tip")));
 770     al = new ActionListener()
 771     {
 772       @Override
 773       public void actionPerformed(ActionEvent e)
 774       {
 775         findMenuItem_actionPerformed(e);
 776       }
 777     };
 778     addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
 779
 780     showSeqFeatures.setText(
 781             MessageManager.getString("label.show_sequence_features"));
 782     showSeqFeatures.addActionListener(new ActionListener()
 783     {
 784       @Override
 785       public void actionPerformed(ActionEvent actionEvent)
 786       {
 787         showSeqFeatures_actionPerformed(actionEvent);
 788       }
 789     });
 790     /*
 791      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
 792      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
 793      * void actionPerformed(ActionEvent actionEvent) {
 794      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
 795      */
 796     showDbRefsMenuitem
 797             .setText(MessageManager.getString("label.show_database_refs"));
 798     showDbRefsMenuitem.addActionListener(new ActionListener()
 799     {
 800
 801       @Override
 802       public void actionPerformed(ActionEvent e)
 803       {
 804         showDbRefs_actionPerformed(e);
 805       }
 806
 807     });
 808     showNpFeatsMenuitem.setText(
 809             MessageManager.getString("label.show_non_positional_features"));
 810     showNpFeatsMenuitem.addActionListener(new ActionListener()
 811     {
 812
 813       @Override
 814       public void actionPerformed(ActionEvent e)
 815       {
 816         showNpFeats_actionPerformed(e);
 817       }
 818
 819     });
 820     showGroupConservation
 821             .setText(MessageManager.getString("label.group_conservation"));
 822     showGroupConservation.addActionListener(new ActionListener()
 823     {
 824
 825       @Override
 826       public void actionPerformed(ActionEvent e)
 827       {
 828         showGroupConservation_actionPerformed(e);
 829       }
 830
 831     });
 832
 833     showGroupConsensus
 834             .setText(MessageManager.getString("label.group_consensus"));
 835     showGroupConsensus.addActionListener(new ActionListener()
 836     {
 837
 838       @Override
 839       public void actionPerformed(ActionEvent e)
 840       {
 841         showGroupConsensus_actionPerformed(e);
 842       }
 843
 844     });
 845     showConsensusHistogram.setText(
 846             MessageManager.getString("label.show_consensus_histogram"));
 847     showConsensusHistogram.addActionListener(new ActionListener()
 848     {
 849
 850       @Override
 851       public void actionPerformed(ActionEvent e)
 852       {
 853         showConsensusHistogram_actionPerformed(e);
 854       }
 855
 856     });
 857     showSequenceLogo
 858             .setText(MessageManager.getString("label.show_consensus_logo"));
 859     showSequenceLogo.addActionListener(new ActionListener()
 860     {
 861
 862       @Override
 863       public void actionPerformed(ActionEvent e)
 864       {
 865         showSequenceLogo_actionPerformed(e);
 866       }
 867
 868     });
 869     normaliseSequenceLogo
 870             .setText(MessageManager.getString("label.norm_consensus_logo"));
 871     normaliseSequenceLogo.addActionListener(new ActionListener()
 872     {
 873
 874       @Override
 875       public void actionPerformed(ActionEvent e)
 876       {
 877         normaliseSequenceLogo_actionPerformed(e);
 878       }
 879
 880     });
 881     applyAutoAnnotationSettings
 882             .setText(MessageManager.getString("label.apply_all_groups"));
 883     applyAutoAnnotationSettings.setState(false);
 884     applyAutoAnnotationSettings.setVisible(true);
 885     applyAutoAnnotationSettings.addActionListener(new ActionListener()
 886     {
 887       @Override
 888       public void actionPerformed(ActionEvent e)
 889       {
 890         applyAutoAnnotationSettings_actionPerformed(e);
 891       }
 892     });
 893
 894     ButtonGroup buttonGroup = new ButtonGroup();
 895     final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
 896             MessageManager.getString("label.show_first"));
 897     final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
 898             MessageManager.getString("label.show_last"));
 899     buttonGroup.add(showAutoFirst);
 900     buttonGroup.add(showAutoLast);
 901     final boolean autoFirst = Cache
 902             .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
 903     showAutoFirst.setSelected(autoFirst);
 904     setShowAutoCalculatedAbove(autoFirst);
 905     showAutoFirst.addActionListener(new ActionListener()
 906     {
 907       @Override
 908       public void actionPerformed(ActionEvent e)
 909       {
 910         setShowAutoCalculatedAbove(showAutoFirst.isSelected());
 911         sortAnnotations_actionPerformed();
 912       }
 913     });
 914     showAutoLast.setSelected(!showAutoFirst.isSelected());
 915     showAutoLast.addActionListener(new ActionListener()
 916     {
 917       @Override
 918       public void actionPerformed(ActionEvent e)
 919       {
 920         setShowAutoCalculatedAbove(!showAutoLast.isSelected());
 921         sortAnnotations_actionPerformed();
 922       }
 923     });
 924
 925     JMenuItem deleteGroups = new JMenuItem(
 926             MessageManager.getString("action.undefine_groups"));
 927     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
 928             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 929     al = new ActionListener()
 930     {
 931       @Override
 932       public void actionPerformed(ActionEvent e)
 933       {
 934         deleteGroups_actionPerformed(e);
 935       }
 936     };
 937     addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
 938
 939     JMenuItem annotationColumn = new JMenuItem(
 940             MessageManager.getString("action.select_by_annotation"));
 941     annotationColumn.addActionListener(new ActionListener()
 942     {
 943       @Override
 944       public void actionPerformed(ActionEvent e)
 945       {
 946         annotationColumn_actionPerformed(e);
 947       }
 948     });
 949
 950     JMenuItem createGroup = new JMenuItem(
 951             MessageManager.getString("action.create_group"));
 952     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
 953             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 954     al = new ActionListener()
 955     {
 956       @Override
 957       public void actionPerformed(ActionEvent e)
 958       {
 959         createGroup_actionPerformed(e);
 960       }
 961     };
 962     addMenuActionAndAccelerator(keyStroke, createGroup, al);
 963
 964     JMenuItem unGroup = new JMenuItem(
 965             MessageManager.getString("action.remove_group"));
 966     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
 967             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
 968                     | KeyEvent.SHIFT_MASK,
 969             false);
 970     al = new ActionListener()
 971     {
 972       @Override
 973       public void actionPerformed(ActionEvent e)
 974       {
 975         unGroup_actionPerformed(e);
 976       }
 977     };
 978     addMenuActionAndAccelerator(keyStroke, unGroup, al);
 979
 980     copy.setText(MessageManager.getString("action.copy"));
 981     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
 982             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 983
 984     al = new ActionListener()
 985     {
 986       @Override
 987       public void actionPerformed(ActionEvent e)
 988       {
 989         copy_actionPerformed();
 990       }
 991     };
 992     addMenuActionAndAccelerator(keyStroke, copy, al);
 993
 994     cut.setText(MessageManager.getString("action.cut"));
 995     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
 996             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 997     al = new ActionListener()
 998     {
 999       @Override
1000       public void actionPerformed(ActionEvent e)
1001       {
1002         cut_actionPerformed();
1003       }
1004     };
1005     addMenuActionAndAccelerator(keyStroke, cut, al);
1006
1007     JMenuItem delete = new JMenuItem(
1008             MessageManager.getString("action.delete"));
1009     delete.addActionListener(new ActionListener()
1010     {
1011       @Override
1012       public void actionPerformed(ActionEvent e)
1013       {
1014         delete_actionPerformed();
1015       }
1016     });
1017
1018     pasteMenu.setText(MessageManager.getString("action.paste"));
1019     JMenuItem pasteNew = new JMenuItem(
1020             MessageManager.getString("label.to_new_alignment"));
1021     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1022             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1023                     | KeyEvent.SHIFT_MASK,
1024             false);
1025     al = new ActionListener()
1026     {
1027       @Override
1028       public void actionPerformed(ActionEvent e)
1029       {
1030         pasteNew_actionPerformed(e);
1031       }
1032     };
1033     addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1034
1035     JMenuItem pasteThis = new JMenuItem(
1036             MessageManager.getString("label.to_this_alignment"));
1037     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1038             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1039     al = new ActionListener()
1040     {
1041       @Override
1042       public void actionPerformed(ActionEvent e)
1043       {
1044         pasteThis_actionPerformed(e);
1045       }
1046     };
1047     addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1048
1049     JMenuItem createPNG = new JMenuItem("PNG");
1050     createPNG.addActionListener(new ActionListener()
1051     {
1052       @Override
1053       public void actionPerformed(ActionEvent e)
1054       {
1055         createPNG(null);
1056       }
1057     });
1058     createPNG.setActionCommand(
1059             MessageManager.getString("label.save_png_image"));
1060
1061     JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1062     font.addActionListener(new ActionListener()
1063     {
1064       @Override
1065       public void actionPerformed(ActionEvent e)
1066       {
1067         font_actionPerformed(e);
1068       }
1069     });
1070     seqLimits.setText(
1071             MessageManager.getString("label.show_sequence_limits"));
1072     seqLimits.setState(jalview.bin.Cache.getDefault(Preferences.SHOW_JVSUFFIX, true));
1073     seqLimits.addActionListener(new ActionListener()
1074     {
1075       @Override
1076       public void actionPerformed(ActionEvent e)
1077       {
1078         seqLimit_actionPerformed(e);
1079       }
1080     });
1081     JMenuItem epsFile = new JMenuItem("EPS");
1082     epsFile.addActionListener(new ActionListener()
1083     {
1084       @Override
1085       public void actionPerformed(ActionEvent e)
1086       {
1087         createEPS(null);
1088       }
1089     });
1090
1091     JMenuItem createSVG = new JMenuItem("SVG");
1092     createSVG.addActionListener(new ActionListener()
1093     {
1094       @Override
1095       public void actionPerformed(ActionEvent e)
1096       {
1097         createSVG(null);
1098       }
1099     });
1100
1101     JMenuItem loadTreeMenuItem = new JMenuItem(
1102             MessageManager.getString("label.load_associated_tree"));
1103     loadTreeMenuItem.setActionCommand(
1104             MessageManager.getString("label.load_tree_for_sequence_set"));
1105     loadTreeMenuItem.addActionListener(new ActionListener()
1106     {
1107       @Override
1108       public void actionPerformed(ActionEvent e)
1109       {
1110         loadTreeMenuItem_actionPerformed(e);
1111       }
1112     });
1113
1114     scaleAbove.setVisible(false);
1115     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1116     scaleAbove.addActionListener(new ActionListener()
1117     {
1118       @Override
1119       public void actionPerformed(ActionEvent e)
1120       {
1121         scaleAbove_actionPerformed(e);
1122       }
1123     });
1124     scaleLeft.setVisible(false);
1125     scaleLeft.setSelected(true);
1126     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1127     scaleLeft.addActionListener(new ActionListener()
1128     {
1129       @Override
1130       public void actionPerformed(ActionEvent e)
1131       {
1132         scaleLeft_actionPerformed(e);
1133       }
1134     });
1135     scaleRight.setVisible(false);
1136     scaleRight.setSelected(true);
1137     scaleRight.setText(MessageManager.getString("action.scale_right"));
1138     scaleRight.addActionListener(new ActionListener()
1139     {
1140       @Override
1141       public void actionPerformed(ActionEvent e)
1142       {
1143         scaleRight_actionPerformed(e);
1144       }
1145     });
1146     centreColumnLabelsMenuItem.setVisible(true);
1147     centreColumnLabelsMenuItem.setState(false);
1148     centreColumnLabelsMenuItem.setText(
1149             MessageManager.getString("label.centre_column_labels"));
1150     centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1151     {
1152       @Override
1153       public void actionPerformed(ActionEvent e)
1154       {
1155         centreColumnLabels_actionPerformed(e);
1156       }
1157     });
1158     followHighlightMenuItem.setVisible(true);
1159     followHighlightMenuItem.setState(true);
1160     followHighlightMenuItem
1161             .setText(MessageManager.getString("label.automatic_scrolling"));
1162     followHighlightMenuItem.addActionListener(new ActionListener()
1163     {
1164
1165       @Override
1166       public void actionPerformed(ActionEvent e)
1167       {
1168         followHighlight_actionPerformed();
1169       }
1170
1171     });
1172
1173     sortByTreeMenu
1174             .setText(MessageManager.getString("action.by_tree_order"));
1175     sort.setText(MessageManager.getString("action.sort"));
1176     sort.addMenuListener(new MenuListener()
1177     {
1178       @Override
1179       public void menuSelected(MenuEvent e)
1180       {
1181         buildTreeSortMenu();
1182       }
1183
1184       @Override
1185       public void menuDeselected(MenuEvent e)
1186       {
1187       }
1188
1189       @Override
1190       public void menuCanceled(MenuEvent e)
1191       {
1192       }
1193     });
1194     sortByAnnotScore
1195             .setText(MessageManager.getString("label.sort_by_score"));
1196     sort.add(sortByAnnotScore);
1197     sort.addMenuListener(new javax.swing.event.MenuListener()
1198     {
1199
1200       @Override
1201       public void menuCanceled(MenuEvent e)
1202       {
1203       }
1204
1205       @Override
1206       public void menuDeselected(MenuEvent e)
1207       {
1208       }
1209
1210       @Override
1211       public void menuSelected(MenuEvent e)
1212       {
1213         buildSortByAnnotationScoresMenu();
1214       }
1215     });
1216     sortByAnnotScore.setVisible(false);
1217
1218     calculateTree
1219             .setText(MessageManager.getString("action.calculate_tree_pca"));
1220
1221     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1222     padGapsMenuitem
1223             .setState(jalview.bin.Cache.getDefault(Preferences.PAD_GAPS, false));
1224     padGapsMenuitem.addActionListener(new ActionListener()
1225     {
1226       @Override
1227       public void actionPerformed(ActionEvent e)
1228       {
1229         padGapsMenuitem_actionPerformed(e);
1230       }
1231     });
1232     JMenuItem vamsasStore = new JMenuItem(
1233             MessageManager.getString("label.vamsas_store"));
1234     vamsasStore.setVisible(false);
1235     vamsasStore.addActionListener(new ActionListener()
1236     {
1237       @Override
1238       public void actionPerformed(ActionEvent e)
1239       {
1240         vamsasStore_actionPerformed(e);
1241       }
1242     });
1243
1244     /*
1245      * Translate as cDNA with sub-menu of translation tables
1246      */
1247     showTranslation
1248             .setText(MessageManager.getString("label.translate_cDNA"));
1249     boolean first = true;
1250     for (final GeneticCodeI table : GeneticCodes.getCodeTables())
1251     {
1252       JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
1253       showTranslation.add(item);
1254       item.addActionListener(new ActionListener()
1255       {
1256         @Override
1257         public void actionPerformed(ActionEvent e)
1258         {
1259           showTranslation_actionPerformed(table);
1260         }
1261       });
1262       if (first)
1263       {
1264         showTranslation.addSeparator();
1265       }
1266       first = false;
1267     }
1268
1269     showReverse.setText(MessageManager.getString("label.reverse"));
1270     showReverse.addActionListener(new ActionListener()
1271     {
1272       @Override
1273       public void actionPerformed(ActionEvent e)
1274       {
1275         showReverse_actionPerformed(false);
1276       }
1277     });
1278     showReverseComplement
1279             .setText(MessageManager.getString("label.reverse_complement"));
1280     showReverseComplement.addActionListener(new ActionListener()
1281     {
1282       @Override
1283       public void actionPerformed(ActionEvent e)
1284       {
1285         showReverse_actionPerformed(true);
1286       }
1287     });
1288
1289     JMenuItem extractScores = new JMenuItem(
1290             MessageManager.getString("label.extract_scores"));
1291     extractScores.addActionListener(new ActionListener()
1292     {
1293       @Override
1294       public void actionPerformed(ActionEvent e)
1295       {
1296         extractScores_actionPerformed(e);
1297       }
1298     });
1299     extractScores.setVisible(true);
1300     // JBPNote: TODO: make gui for regex based score extraction
1301
1302     // for show products actions see AlignFrame.canShowProducts
1303     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1304
1305     runGroovy.setText(MessageManager.getString("label.run_groovy"));
1306     runGroovy.setToolTipText(
1307             MessageManager.getString("label.run_groovy_tip"));
1308     runGroovy.addActionListener(new ActionListener()
1309     {
1310       @Override
1311       public void actionPerformed(ActionEvent e)
1312       {
1313         runGroovy_actionPerformed();
1314       }
1315     });
1316
1317     openFeatureSettings = new JMenuItem(
1318             MessageManager.getString("action.feature_settings"));
1319     openFeatureSettings.addActionListener(new ActionListener()
1320     {
1321       @Override
1322       public void actionPerformed(ActionEvent e)
1323       {
1324         featureSettings_actionPerformed(e);
1325       }
1326     });
1327
1328     /*
1329      * add sub-menu of database we can fetch from
1330      */
1331     JMenuItem fetchSequence = new JMenuItem(
1332             MessageManager.getString("label.fetch_sequences"));
1333     fetchSequence.addActionListener(new ActionListener()
1334     {
1335       @Override
1336       public void actionPerformed(ActionEvent e)
1337       {
1338         fetchSequence_actionPerformed();
1339       }
1340     });
1341
1342     JMenuItem associatedData = new JMenuItem(
1343             MessageManager.getString("label.load_features_annotations"));
1344     associatedData.addActionListener(new ActionListener()
1345     {
1346       @Override
1347       public void actionPerformed(ActionEvent e)
1348       {
1349         associatedData_actionPerformed(e);
1350       }
1351     });
1352     loadVcf = new JMenuItem(
1353             MessageManager.getString("label.load_vcf_file"));
1354     loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
1355     loadVcf.addActionListener(new ActionListener()
1356     {
1357       @Override
1358       public void actionPerformed(ActionEvent e)
1359       {
1360         loadVcf_actionPerformed();
1361       }
1362     });
1363     autoCalculate.setText(
1364             MessageManager.getString("label.autocalculate_consensus"));
1365     autoCalculate.setState(
1366             jalview.bin.Cache.getDefault(Preferences.AUTO_CALC_CONSENSUS, true));
1367     autoCalculate.addActionListener(new ActionListener()
1368     {
1369       @Override
1370       public void actionPerformed(ActionEvent e)
1371       {
1372         autoCalculate_actionPerformed(e);
1373       }
1374     });
1375     sortByTree.setText(
1376             MessageManager.getString("label.sort_alignment_new_tree"));
1377     sortByTree.setToolTipText("<html>" + MessageManager.getString(
1378             "label.enable_automatically_sort_alignment_when_open_new_tree"));
1379     sortByTree
1380             .setState(jalview.bin.Cache.getDefault(Preferences.SORT_BY_TREE,
1381                     false));
1382     sortByTree.addActionListener(new ActionListener()
1383     {
1384       @Override
1385       public void actionPerformed(ActionEvent e)
1386       {
1387         sortByTreeOption_actionPerformed(e);
1388       }
1389     });
1390
1391     listenToViewSelections.setText(
1392             MessageManager.getString("label.listen_for_selections"));
1393     listenToViewSelections
1394             .setToolTipText("<html>" + MessageManager.getString(
1395                     "label.selections_mirror_selections_made_same_sequences_other_views"));
1396     listenToViewSelections.setState(false);
1397     listenToViewSelections.addActionListener(new ActionListener()
1398     {
1399       @Override
1400       public void actionPerformed(ActionEvent e)
1401       {
1402         listenToViewSelections_actionPerformed(e);
1403       }
1404     });
1405
1406     JMenu addSequenceMenu = new JMenu(
1407             MessageManager.getString("label.add_sequences"));
1408     JMenuItem addFromFile = new JMenuItem(
1409             MessageManager.getString("label.from_file"));
1410     addFromFile.addActionListener(new ActionListener()
1411     {
1412       @Override
1413       public void actionPerformed(ActionEvent e)
1414       {
1415         addFromFile_actionPerformed(e);
1416       }
1417     });
1418     JMenuItem addFromText = new JMenuItem(
1419             MessageManager.getString("label.from_textbox"));
1420     addFromText.addActionListener(new ActionListener()
1421     {
1422       @Override
1423       public void actionPerformed(ActionEvent e)
1424       {
1425         addFromText_actionPerformed(e);
1426       }
1427     });
1428     JMenuItem addFromURL = new JMenuItem(
1429             MessageManager.getString("label.from_url"));
1430     addFromURL.addActionListener(new ActionListener()
1431     {
1432       @Override
1433       public void actionPerformed(ActionEvent e)
1434       {
1435         addFromURL_actionPerformed(e);
1436       }
1437     });
1438     JMenuItem exportFeatures = new JMenuItem(
1439             MessageManager.getString("label.export_features"));
1440     exportFeatures.addActionListener(new ActionListener()
1441     {
1442       @Override
1443       public void actionPerformed(ActionEvent e)
1444       {
1445         exportFeatures_actionPerformed(e);
1446       }
1447     });
1448     JMenuItem exportAnnotations = new JMenuItem(
1449             MessageManager.getString("label.export_annotations"));
1450     exportAnnotations.addActionListener(new ActionListener()
1451     {
1452       @Override
1453       public void actionPerformed(ActionEvent e)
1454       {
1455         exportAnnotations_actionPerformed(e);
1456       }
1457     });
1458     statusPanel.setLayout(new GridLayout());
1459     JMenuItem showAllSeqs = new JMenuItem(
1460             MessageManager.getString("label.all_sequences"));
1461     showAllSeqs.setToolTipText(
1462             MessageManager.getString("label.toggle_sequence_visibility"));
1463     showAllSeqs.addActionListener(new ActionListener()
1464     {
1465       @Override
1466       public void actionPerformed(ActionEvent e)
1467       {
1468         showAllSeqs_actionPerformed(e);
1469       }
1470     });
1471     JMenuItem showAllColumns = new JMenuItem(
1472             MessageManager.getString("label.all_columns"));
1473     showAllColumns.setToolTipText(
1474             MessageManager.getString("label.toggle_columns_visibility"));
1475     showAllColumns.addActionListener(new ActionListener()
1476     {
1477       @Override
1478       public void actionPerformed(ActionEvent e)
1479       {
1480         showAllColumns_actionPerformed(e);
1481       }
1482     });
1483     JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1484     JMenuItem hideSelSequences = new JMenuItem(
1485             MessageManager.getString("label.selected_sequences"));
1486     hideSelSequences.setToolTipText(
1487             MessageManager.getString("label.toggle_sequence_visibility"));
1488     hideSelSequences.addActionListener(new ActionListener()
1489     {
1490       @Override
1491       public void actionPerformed(ActionEvent e)
1492       {
1493         hideSelSequences_actionPerformed(e);
1494       }
1495     });
1496     JMenuItem hideSelColumns = new JMenuItem(
1497             MessageManager.getString("label.selected_columns"));
1498     hideSelColumns.setToolTipText(
1499             MessageManager.getString("label.toggle_columns_visibility"));
1500     hideSelColumns.addActionListener(new ActionListener()
1501     {
1502       @Override
1503       public void actionPerformed(ActionEvent e)
1504       {
1505         hideSelColumns_actionPerformed(e);
1506       }
1507     });
1508     JMenuItem hideAllSelection = new JMenuItem(
1509             MessageManager.getString("label.selected_region"));
1510     hideAllSelection.addActionListener(new ActionListener()
1511     {
1512       @Override
1513       public void actionPerformed(ActionEvent e)
1514       {
1515         hideAllSelection_actionPerformed(e);
1516       }
1517     });
1518     // TODO: should be hidden if no selection exists.
1519     JMenuItem hideAllButSelection = new JMenuItem(
1520             MessageManager.getString("label.all_but_selected_region"));
1521     hideAllButSelection.addActionListener(new ActionListener()
1522     {
1523       @Override
1524       public void actionPerformed(ActionEvent e)
1525       {
1526         hideAllButSelection_actionPerformed(e);
1527       }
1528     });
1529     JMenuItem showAllhidden = new JMenuItem(
1530             MessageManager.getString("label.all_sequences_columns"));
1531     showAllhidden.setToolTipText(MessageManager
1532             .getString("label.toggles_visibility_hidden_selected_regions"));
1533     showAllhidden.addActionListener(new ActionListener()
1534     {
1535       @Override
1536       public void actionPerformed(ActionEvent e)
1537       {
1538         showAllhidden_actionPerformed(e);
1539       }
1540     });
1541     hiddenMarkers.setText(
1542             MessageManager.getString("action.show_hidden_markers"));
1543     hiddenMarkers.addActionListener(new ActionListener()
1544     {
1545       @Override
1546       public void actionPerformed(ActionEvent e)
1547       {
1548         hiddenMarkers_actionPerformed(e);
1549       }
1550     });
1551
1552     JMenuItem invertColSel = new JMenuItem(
1553             MessageManager.getString("action.invert_column_selection"));
1554     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1555             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1556                     | KeyEvent.ALT_MASK,
1557             false);
1558     al = new ActionListener()
1559     {
1560       @Override
1561       public void actionPerformed(ActionEvent e)
1562       {
1563         invertColSel_actionPerformed(e);
1564       }
1565     };
1566     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1567
1568     showComplementMenuItem.setVisible(false);
1569     showComplementMenuItem.addActionListener(new ActionListener()
1570     {
1571       @Override
1572       public void actionPerformed(ActionEvent e)
1573       {
1574         showComplement_actionPerformed(showComplementMenuItem.getState());
1575       }
1576     });
1577
1578     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1579     {
1580       @Override
1581       public void stateChanged(ChangeEvent evt)
1582       {
1583         JTabbedPane pane = (JTabbedPane) evt.getSource();
1584         int sel = pane.getSelectedIndex();
1585         tabSelectionChanged(sel);
1586       }
1587     });
1588     tabbedPane.addMouseListener(new MouseAdapter()
1589     {
1590       @Override
1591       public void mousePressed(MouseEvent e)
1592       {
1593         if (e.isPopupTrigger()) // Mac
1594         {
1595           tabbedPane_mousePressed(e);
1596         }
1597       }
1598
1599       @Override
1600       public void mouseReleased(MouseEvent e)
1601       {
1602         if (e.isPopupTrigger()) // Windows
1603         {
1604           tabbedPane_mousePressed(e);
1605         }
1606       }
1607     });
1608     tabbedPane.addFocusListener(new FocusAdapter()
1609     {
1610       @Override
1611       public void focusGained(FocusEvent e)
1612       {
1613         tabbedPane_focusGained(e);
1614       }
1615     });
1616
1617     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1618     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1619             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1620     al = new ActionListener()
1621     {
1622       @Override
1623       public void actionPerformed(ActionEvent e)
1624       {
1625         save_actionPerformed(e);
1626       }
1627     };
1628     addMenuActionAndAccelerator(keyStroke, save, al);
1629
1630     reload.setEnabled(false);
1631     reload.setText(MessageManager.getString("action.reload"));
1632     reload.addActionListener(new ActionListener()
1633     {
1634       @Override
1635       public void actionPerformed(ActionEvent e)
1636       {
1637         reload_actionPerformed(e);
1638       }
1639     });
1640
1641     JMenuItem newView = new JMenuItem(
1642             MessageManager.getString("action.new_view"));
1643     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1644             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1645     al = new ActionListener()
1646     {
1647       @Override
1648       public void actionPerformed(ActionEvent e)
1649       {
1650         newView_actionPerformed(e);
1651       }
1652     };
1653     addMenuActionAndAccelerator(keyStroke, newView, al);
1654
1655     tabbedPane.setToolTipText("<html><i>"
1656             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1657             + "</i></html>");
1658
1659     formatMenu.setText(MessageManager.getString("action.format"));
1660     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1661
1662     idRightAlign.setText(
1663             MessageManager.getString("label.right_align_sequence_id"));
1664     idRightAlign.addActionListener(new ActionListener()
1665     {
1666       @Override
1667       public void actionPerformed(ActionEvent e)
1668       {
1669         idRightAlign_actionPerformed(e);
1670       }
1671     });
1672
1673     gatherViews.setEnabled(false);
1674     gatherViews.setText(MessageManager.getString("action.gather_views"));
1675     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1676     al = new ActionListener()
1677     {
1678       @Override
1679       public void actionPerformed(ActionEvent e)
1680       {
1681         gatherViews_actionPerformed(e);
1682       }
1683     };
1684     addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1685
1686     expandViews.setEnabled(false);
1687     expandViews.setText(MessageManager.getString("action.expand_views"));
1688     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1689     al = new ActionListener()
1690     {
1691       @Override
1692       public void actionPerformed(ActionEvent e)
1693       {
1694         expandViews_actionPerformed(e);
1695       }
1696     };
1697     addMenuActionAndAccelerator(keyStroke, expandViews, al);
1698
1699     JMenuItem pageSetup = new JMenuItem(
1700             MessageManager.getString("action.page_setup"));
1701     pageSetup.addActionListener(new ActionListener()
1702     {
1703       @Override
1704       public void actionPerformed(ActionEvent e)
1705       {
1706         pageSetup_actionPerformed(e);
1707       }
1708     });
1709     JMenuItem alignmentProperties = new JMenuItem(
1710             MessageManager.getString("label.alignment_props"));
1711     alignmentProperties.addActionListener(new ActionListener()
1712     {
1713       @Override
1714       public void actionPerformed(ActionEvent actionEvent)
1715       {
1716         alignmentProperties();
1717       }
1718     });
1719     JMenuItem selectHighlighted = new JMenuItem(
1720             MessageManager.getString("action.select_highlighted_columns"));
1721     selectHighlighted.setToolTipText(
1722             MessageManager.getString("tooltip.select_highlighted_columns"));
1723     al = new ActionListener()
1724     {
1725       @Override
1726       public void actionPerformed(ActionEvent actionEvent)
1727       {
1728         selectHighlightedColumns_actionPerformed(actionEvent);
1729       }
1730     };
1731     selectHighlighted.addActionListener(al);
1732     JMenu tooltipSettingsMenu = new JMenu(
1733             MessageManager.getString("label.sequence_id_tooltip"));
1734     JMenu autoAnnMenu = new JMenu(
1735             MessageManager.getString("label.autocalculated_annotation"));
1736
1737     JMenu exportImageMenu = new JMenu(
1738             MessageManager.getString("label.export_image"));
1739     JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1740     alignFrameMenuBar.add(fileMenu);
1741     alignFrameMenuBar.add(editMenu);
1742     alignFrameMenuBar.add(selectMenu);
1743     alignFrameMenuBar.add(viewMenu);
1744     alignFrameMenuBar.add(annotationsMenu);
1745     alignFrameMenuBar.add(formatMenu);
1746     alignFrameMenuBar.add(colourMenu);
1747     alignFrameMenuBar.add(calculateMenu);
1748     if (!Platform.isJS())
1749     {
1750       alignFrameMenuBar.add(webService);
1751     }
1752
1753     fileMenu.add(fetchSequence);
1754     fileMenu.add(addSequenceMenu);
1755     fileMenu.add(reload);
1756     fileMenu.addSeparator();
1757     fileMenu.add(vamsasStore);
1758     fileMenu.add(save);
1759     fileMenu.add(saveAs);
1760     fileMenu.add(outputTextboxMenu);
1761     fileMenu.add(pageSetup);
1762     fileMenu.add(printMenuItem);
1763     fileMenu.addSeparator();
1764     fileMenu.add(exportImageMenu);
1765     fileMenu.add(exportFeatures);
1766     fileMenu.add(exportAnnotations);
1767     fileMenu.add(loadTreeMenuItem);
1768     fileMenu.add(associatedData);
1769     if (!Platform.isJS())
1770     {
1771       fileMenu.add(loadVcf);
1772     }
1773     fileMenu.addSeparator();
1774     fileMenu.add(closeMenuItem);
1775
1776     pasteMenu.add(pasteNew);
1777     pasteMenu.add(pasteThis);
1778     editMenu.add(undoMenuItem);
1779     editMenu.add(redoMenuItem);
1780     editMenu.add(cut);
1781     editMenu.add(copy);
1782     editMenu.add(pasteMenu);
1783     editMenu.add(delete);
1784     editMenu.addSeparator();
1785     editMenu.add(remove2LeftMenuItem);
1786     editMenu.add(remove2RightMenuItem);
1787     editMenu.add(removeGappedColumnMenuItem);
1788     editMenu.add(removeAllGapsMenuItem);
1789     editMenu.add(removeRedundancyMenuItem);
1790     editMenu.addSeparator();
1791     // dont add these yet in the CVS build - they cannot be undone!
1792     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1793     // editMenu.add(justifyLeftMenuItem);
1794     // editMenu.add(justifyRightMenuItem);
1795     // editMenu.addSeparator();
1796     editMenu.add(padGapsMenuitem);
1797
1798     showMenu.add(showAllColumns);
1799     showMenu.add(showAllSeqs);
1800     showMenu.add(showAllhidden);
1801     hideMenu.add(hideSelColumns);
1802     hideMenu.add(hideSelSequences);
1803     hideMenu.add(hideAllSelection);
1804     hideMenu.add(hideAllButSelection);
1805     viewMenu.add(newView);
1806     viewMenu.add(expandViews);
1807     viewMenu.add(gatherViews);
1808     viewMenu.addSeparator();
1809     viewMenu.add(showMenu);
1810     viewMenu.add(hideMenu);
1811     viewMenu.add(showComplementMenuItem);
1812     viewMenu.addSeparator();
1813     viewMenu.add(followHighlightMenuItem);
1814     viewMenu.addSeparator();
1815     viewMenu.add(showSeqFeatures);
1816     // viewMenu.add(showSeqFeaturesHeight);
1817     viewMenu.add(openFeatureSettings);
1818     tooltipSettingsMenu.add(showDbRefsMenuitem);
1819     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1820     viewMenu.add(tooltipSettingsMenu);
1821     viewMenu.addSeparator();
1822     viewMenu.add(alignmentProperties);
1823     viewMenu.addSeparator();
1824     viewMenu.add(overviewMenuItem);
1825
1826     annotationsMenu.add(annotationPanelMenuItem);
1827     annotationsMenu.addSeparator();
1828     annotationsMenu.add(showAllAlAnnotations);
1829     annotationsMenu.add(hideAllAlAnnotations);
1830     annotationsMenu.addSeparator();
1831     annotationsMenu.add(showAllSeqAnnotations);
1832     annotationsMenu.add(hideAllSeqAnnotations);
1833     annotationsMenu.add(sortAnnBySequence);
1834     annotationsMenu.add(sortAnnByLabel);
1835     annotationsMenu.addSeparator();
1836     autoAnnMenu.add(showAutoFirst);
1837     autoAnnMenu.add(showAutoLast);
1838     autoAnnMenu.addSeparator();
1839     autoAnnMenu.add(applyAutoAnnotationSettings);
1840     autoAnnMenu.add(showConsensusHistogram);
1841     autoAnnMenu.add(showSequenceLogo);
1842     autoAnnMenu.add(normaliseSequenceLogo);
1843     autoAnnMenu.addSeparator();
1844     autoAnnMenu.add(showGroupConservation);
1845     autoAnnMenu.add(showGroupConsensus);
1846     annotationsMenu.add(autoAnnMenu);
1847
1848     sort.add(sortIDMenuItem);
1849     sort.add(sortLengthMenuItem);
1850     sort.add(sortGroupMenuItem);
1851     sort.add(sortPairwiseMenuItem);
1852     sort.add(sortByTreeMenu);
1853     calculateMenu.add(sort);
1854     calculateMenu.add(calculateTree);
1855     calculateMenu.addSeparator();
1856     calculateMenu.add(pairwiseAlignmentMenuItem);
1857     calculateMenu.addSeparator();
1858     calculateMenu.add(showTranslation);
1859     calculateMenu.add(showReverse);
1860     calculateMenu.add(showReverseComplement);
1861     calculateMenu.add(showProducts);
1862     calculateMenu.add(autoCalculate);
1863     calculateMenu.add(sortByTree);
1864     calculateMenu.addSeparator();
1865     calculateMenu.add(expandAlignment);
1866     calculateMenu.add(extractScores);
1867     if (!Platform.isJS())
1868     {
1869       calculateMenu.addSeparator();
1870       calculateMenu.add(runGroovy);
1871     }
1872
1873     webServiceNoServices = new JMenuItem(
1874             MessageManager.getString("label.no_services"));
1875     webService.add(webServiceNoServices);
1876     if (!Platform.isJS())
1877     {
1878       exportImageMenu.add(htmlMenuItem);
1879     }
1880     exportImageMenu.add(epsFile);
1881     exportImageMenu.add(createPNG);
1882     if (!Platform.isJS())
1883     {
1884       exportImageMenu.add(createBioJS);
1885       exportImageMenu.add(createSVG);
1886     }
1887     addSequenceMenu.add(addFromFile);
1888     addSequenceMenu.add(addFromText);
1889     addSequenceMenu.add(addFromURL);
1890     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1891     statusPanel.add(statusBar, null);
1892     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1893
1894     formatMenu.add(font);
1895     formatMenu.addSeparator();
1896     formatMenu.add(wrapMenuItem);
1897     formatMenu.add(scaleAbove);
1898     formatMenu.add(scaleLeft);
1899     formatMenu.add(scaleRight);
1900     formatMenu.add(seqLimits);
1901     formatMenu.add(idRightAlign);
1902     formatMenu.add(hiddenMarkers);
1903     formatMenu.add(viewBoxesMenuItem);
1904     formatMenu.add(viewTextMenuItem);
1905     formatMenu.add(colourTextMenuItem);
1906     formatMenu.add(renderGapsMenuItem);
1907     formatMenu.add(centreColumnLabelsMenuItem);
1908     formatMenu.add(showNonconservedMenuItem);
1909     selectMenu.add(findMenuItem);
1910     selectMenu.addSeparator();
1911     selectMenu.add(selectAllSequenceMenuItem);
1912     selectMenu.add(deselectAllSequenceMenuItem);
1913     selectMenu.add(invertSequenceMenuItem);
1914     selectMenu.add(invertColSel);
1915     selectMenu.add(createGroup);
1916     selectMenu.add(unGroup);
1917     selectMenu.add(grpsFromSelection);
1918     selectMenu.add(deleteGroups);
1919     selectMenu.add(annotationColumn);
1920     selectMenu.add(selectHighlighted);
1921     // TODO - determine if the listenToViewSelections button is needed : see bug
1922     // JAL-574
1923     // selectMenu.addSeparator();
1924     // selectMenu.add(listenToViewSelections);
1925   }
1926
1927   protected void loadVcf_actionPerformed()
1928   {
1929   }
1930
1931   /**
1932    * Constructs the entries on the Colour menu (but does not add them to the
1933    * menu).
1934    */
1935   protected void initColourMenu()
1936   {
1937     applyToAllGroups = new JCheckBoxMenuItem(
1938             MessageManager.getString("label.apply_colour_to_all_groups"));
1939     applyToAllGroups.addActionListener(new ActionListener()
1940     {
1941       @Override
1942       public void actionPerformed(ActionEvent e)
1943       {
1944         applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1945       }
1946     });
1947
1948     textColour = new JMenuItem(
1949             MessageManager.getString("label.text_colour"));
1950     textColour.addActionListener(new ActionListener()
1951     {
1952       @Override
1953       public void actionPerformed(ActionEvent e)
1954       {
1955         textColour_actionPerformed();
1956       }
1957     });
1958
1959     conservationMenuItem = new JCheckBoxMenuItem(
1960             MessageManager.getString("action.by_conservation"));
1961     conservationMenuItem.addActionListener(new ActionListener()
1962     {
1963       @Override
1964       public void actionPerformed(ActionEvent e)
1965       {
1966         conservationMenuItem_actionPerformed(
1967                 conservationMenuItem.isSelected());
1968       }
1969     });
1970
1971     abovePIDThreshold = new JCheckBoxMenuItem(
1972             MessageManager.getString("label.above_identity_threshold"));
1973     abovePIDThreshold.addActionListener(new ActionListener()
1974     {
1975       @Override
1976       public void actionPerformed(ActionEvent e)
1977       {
1978         abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
1979       }
1980     });
1981     modifyPID = new JMenuItem(
1982             MessageManager.getString("label.modify_identity_threshold"));
1983     modifyPID.addActionListener(new ActionListener()
1984     {
1985       @Override
1986       public void actionPerformed(ActionEvent e)
1987       {
1988         modifyPID_actionPerformed();
1989       }
1990     });
1991     modifyConservation = new JMenuItem(MessageManager
1992             .getString("label.modify_conservation_threshold"));
1993     modifyConservation.addActionListener(new ActionListener()
1994     {
1995       @Override
1996       public void actionPerformed(ActionEvent e)
1997       {
1998         modifyConservation_actionPerformed();
1999       }
2000     });
2001
2002     annotationColour = new JRadioButtonMenuItem(
2003             MessageManager.getString("action.by_annotation"));
2004     annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
2005     annotationColour.addActionListener(new ActionListener()
2006     {
2007       @Override
2008       public void actionPerformed(ActionEvent e)
2009       {
2010         annotationColour_actionPerformed();
2011       }
2012     });
2013   }
2014
2015   protected void selectHighlightedColumns_actionPerformed(
2016           ActionEvent actionEvent)
2017   {
2018     // TODO Auto-generated method stub
2019
2020   }
2021
2022   /**
2023    * Generate the reverse sequence (or reverse complement if the flag is true)
2024    * and add it to the alignment
2025    *
2026    * @param complement
2027    */
2028   protected void showReverse_actionPerformed(boolean complement)
2029   {
2030   }
2031
2032   /**
2033    * Try to run script in a Groovy console, having first ensured that this
2034    * alignframe is set as currentAlignFrame in Desktop
2035    */
2036   protected void runGroovy_actionPerformed()
2037   {
2038
2039   }
2040
2041   /**
2042    * Adds the given action listener and key accelerator to the given menu item.
2043    * Also saves in a lookup table to support lookup of action by key stroke.
2044    *
2045    * @param keyStroke
2046    * @param menuItem
2047    * @param actionListener
2048    */
2049   protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2050           JMenuItem menuItem, ActionListener actionListener)
2051   {
2052     menuItem.setAccelerator(keyStroke);
2053     accelerators.put(keyStroke, menuItem);
2054     menuItem.addActionListener(actionListener);
2055   }
2056
2057   /**
2058    * Action on clicking sort annotations by type.
2059    *
2060    * @param sortOrder
2061    */
2062   protected void sortAnnotations_actionPerformed()
2063   {
2064   }
2065
2066   /**
2067    * Action on clicking Show all annotations.
2068    *
2069    * @param forSequences
2070    *          update sequence-related annotations
2071    * @param forAlignment
2072    *          update non-sequence-related annotations
2073    */
2074   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2075           boolean forAlignment)
2076   {
2077     setAnnotationsVisibility(true, forSequences, forAlignment);
2078   }
2079
2080   /**
2081    * Action on clicking Hide all annotations.
2082    *
2083    * @param forSequences
2084    *          update sequence-related annotations
2085    * @param forAlignment
2086    *          update non-sequence-related annotations
2087    */
2088   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2089           boolean forAlignment)
2090   {
2091     setAnnotationsVisibility(false, forSequences, forAlignment);
2092   }
2093
2094   /**
2095    * Set the visibility of annotations to true or false. Can act on
2096    * sequence-related annotations, or alignment-related, or both.
2097    *
2098    * @param visible
2099    * @param forSequences
2100    *          update sequence-related annotations
2101    * @param forAlignment
2102    *          update non-sequence-related annotations
2103    */
2104   protected void setAnnotationsVisibility(boolean visible,
2105           boolean forSequences, boolean forAlignment)
2106   {
2107
2108   }
2109
2110   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2111   {
2112     // TODO Auto-generated method stub
2113
2114   }
2115
2116   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2117   {
2118     // TODO Auto-generated method stub
2119
2120   }
2121
2122   protected void showAllhidden_actionPerformed(ActionEvent e)
2123   {
2124     // TODO Auto-generated method stub
2125
2126   }
2127
2128   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2129   {
2130     // TODO Auto-generated method stub
2131
2132   }
2133
2134   protected void hideAllSelection_actionPerformed(ActionEvent e)
2135   {
2136     // TODO Auto-generated method stub
2137
2138   }
2139
2140   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2141   {
2142     // TODO Auto-generated method stub
2143
2144   }
2145
2146   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2147   {
2148     // TODO Auto-generated method stub
2149
2150   }
2151
2152   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2153   {
2154     // TODO Auto-generated method stub
2155
2156   }
2157
2158   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2159   {
2160     // TODO Auto-generated method stub
2161
2162   }
2163
2164   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2165   {
2166     // TODO Auto-generated method stub
2167
2168   }
2169
2170   protected void showGroupConservation_actionPerformed(ActionEvent e)
2171   {
2172     // TODO Auto-generated method stub
2173
2174   }
2175
2176   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2177   {
2178     // TODO Auto-generated method stub
2179
2180   }
2181
2182   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2183   {
2184     // TODO Auto-generated method stub
2185
2186   }
2187
2188   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2189   {
2190     // TODO Auto-generated method stub
2191
2192   }
2193
2194   protected void followHighlight_actionPerformed()
2195   {
2196     // TODO Auto-generated method stub
2197
2198   }
2199
2200   protected void showNpFeats_actionPerformed(ActionEvent e)
2201   {
2202     // TODO Auto-generated method stub
2203
2204   }
2205
2206   protected void showDbRefs_actionPerformed(ActionEvent e)
2207   {
2208     // TODO Auto-generated method stub
2209
2210   }
2211
2212   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2213   {
2214   }
2215
2216   protected void buildSortByAnnotationScoresMenu()
2217   {
2218   }
2219
2220   protected void extractScores_actionPerformed(ActionEvent e)
2221   {
2222   }
2223
2224   protected void outputText_actionPerformed(String formatName)
2225   {
2226   }
2227
2228   public void addFromFile_actionPerformed(ActionEvent e)
2229   {
2230
2231   }
2232
2233   public void addFromText_actionPerformed(ActionEvent e)
2234   {
2235
2236   }
2237
2238   public void addFromURL_actionPerformed(ActionEvent e)
2239   {
2240
2241   }
2242
2243   public void exportFeatures_actionPerformed(ActionEvent e)
2244   {
2245
2246   }
2247
2248   public void exportAnnotations_actionPerformed(ActionEvent e)
2249   {
2250
2251   }
2252
2253   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2254   {
2255   }
2256
2257   protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2258   {
2259
2260   }
2261
2262   protected void closeMenuItem_actionPerformed(boolean b)
2263   {
2264   }
2265
2266   protected void redoMenuItem_actionPerformed(ActionEvent e)
2267   {
2268   }
2269
2270   protected void undoMenuItem_actionPerformed(ActionEvent e)
2271   {
2272   }
2273
2274   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2275   {
2276   }
2277
2278   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2279   {
2280   }
2281
2282   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2283   {
2284   }
2285
2286   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2287   {
2288   }
2289
2290   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2291   {
2292   }
2293
2294   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2295   {
2296   }
2297
2298   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2299   {
2300   }
2301
2302   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2303   {
2304   }
2305
2306   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2307   {
2308   }
2309
2310   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2311   {
2312   }
2313
2314   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2315   {
2316   }
2317
2318   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2319   {
2320   }
2321
2322   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2323   {
2324   }
2325
2326   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2327   {
2328   }
2329
2330   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2331   {
2332   }
2333
2334   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2335   {
2336   }
2337
2338   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2339   {
2340   }
2341
2342   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2343   {
2344   }
2345
2346   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2347   {
2348   }
2349
2350   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2351   {
2352   }
2353
2354   protected void conservationMenuItem_actionPerformed(boolean selected)
2355   {
2356   }
2357
2358   protected void printMenuItem_actionPerformed(ActionEvent e)
2359   {
2360   }
2361
2362   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2363   {
2364   }
2365
2366   protected void findMenuItem_actionPerformed(ActionEvent e)
2367   {
2368   }
2369
2370   protected void abovePIDThreshold_actionPerformed(boolean selected)
2371   {
2372   }
2373
2374   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2375   {
2376   }
2377
2378   protected void deleteGroups_actionPerformed(ActionEvent e)
2379   {
2380   }
2381
2382   protected void createGroup_actionPerformed(ActionEvent e)
2383   {
2384   }
2385
2386   protected void unGroup_actionPerformed(ActionEvent e)
2387   {
2388   }
2389
2390   protected void copy_actionPerformed()
2391   {
2392   }
2393
2394   protected void cut_actionPerformed()
2395   {
2396   }
2397
2398   protected void delete_actionPerformed()
2399   {
2400   }
2401
2402   protected void pasteNew_actionPerformed(ActionEvent e)
2403   {
2404   }
2405
2406   protected void pasteThis_actionPerformed(ActionEvent e)
2407   {
2408   }
2409
2410   protected void applyToAllGroups_actionPerformed(boolean selected)
2411   {
2412   }
2413
2414   public void createPNG(java.io.File f)
2415   {
2416   }
2417
2418   protected void font_actionPerformed(ActionEvent e)
2419   {
2420   }
2421
2422   protected void seqLimit_actionPerformed(ActionEvent e)
2423   {
2424   }
2425
2426   public void seqDBRef_actionPerformed(ActionEvent e)
2427   {
2428
2429   }
2430
2431   public void createEPS(java.io.File f)
2432   {
2433   }
2434
2435   public void createSVG(java.io.File f)
2436   {
2437
2438   }
2439
2440   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2441   {
2442
2443   }
2444
2445   /**
2446    * Template method to handle the 'load T-Coffee scores' menu event.
2447    * <p>
2448    * Subclasses override this method to provide a custom action.
2449    *
2450    * @param event
2451    *          The raised event
2452    */
2453   protected void loadScores_actionPerformed(ActionEvent event)
2454   {
2455
2456   }
2457
2458   protected void jpred_actionPerformed(ActionEvent e)
2459   {
2460   }
2461
2462   protected void scaleAbove_actionPerformed(ActionEvent e)
2463   {
2464   }
2465
2466   protected void scaleLeft_actionPerformed(ActionEvent e)
2467   {
2468   }
2469
2470   protected void scaleRight_actionPerformed(ActionEvent e)
2471   {
2472   }
2473
2474   protected void modifyPID_actionPerformed()
2475   {
2476   }
2477
2478   protected void modifyConservation_actionPerformed()
2479   {
2480   }
2481
2482   protected void saveAs_actionPerformed()
2483   {
2484   }
2485
2486   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2487   {
2488   }
2489
2490   public void vamsasStore_actionPerformed(ActionEvent e)
2491   {
2492
2493   }
2494
2495   public void vamsasLoad_actionPerformed(ActionEvent e)
2496   {
2497
2498   }
2499
2500   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
2501   {
2502
2503   }
2504
2505   public void featureSettings_actionPerformed(ActionEvent e)
2506   {
2507
2508   }
2509
2510   public void fetchSequence_actionPerformed()
2511   {
2512
2513   }
2514
2515   public void smoothFont_actionPerformed(ActionEvent e)
2516   {
2517
2518   }
2519
2520   public void annotationColour_actionPerformed()
2521   {
2522   }
2523
2524   public void annotationColumn_actionPerformed(ActionEvent e)
2525   {
2526   }
2527
2528   public void associatedData_actionPerformed(ActionEvent e)
2529   {
2530
2531   }
2532
2533   public void autoCalculate_actionPerformed(ActionEvent e)
2534   {
2535
2536   }
2537
2538   public void sortByTreeOption_actionPerformed(ActionEvent e)
2539   {
2540
2541   }
2542
2543   public void showAllSeqs_actionPerformed(ActionEvent e)
2544   {
2545
2546   }
2547
2548   public void showAllColumns_actionPerformed(ActionEvent e)
2549   {
2550
2551   }
2552
2553   public void hideSelSequences_actionPerformed(ActionEvent e)
2554   {
2555
2556   }
2557
2558   public void hideSelColumns_actionPerformed(ActionEvent e)
2559   {
2560
2561   }
2562
2563   public void hiddenMarkers_actionPerformed(ActionEvent e)
2564   {
2565
2566   }
2567
2568   public void findPdbId_actionPerformed(ActionEvent e)
2569   {
2570
2571   }
2572
2573   public void enterPdbId_actionPerformed(ActionEvent e)
2574   {
2575
2576   }
2577
2578   public void pdbFile_actionPerformed(ActionEvent e)
2579   {
2580
2581   }
2582
2583   public void invertColSel_actionPerformed(ActionEvent e)
2584   {
2585
2586   }
2587
2588   public void tabSelectionChanged(int sel)
2589   {
2590
2591   }
2592
2593   public void tabbedPane_mousePressed(MouseEvent e)
2594   {
2595
2596   }
2597
2598   public void tabbedPane_focusGained(FocusEvent e)
2599   {
2600     requestFocus();
2601   }
2602
2603   public void save_actionPerformed(ActionEvent e)
2604   {
2605
2606   }
2607
2608   public void reload_actionPerformed(ActionEvent e)
2609   {
2610
2611   }
2612
2613   public void newView_actionPerformed(ActionEvent e)
2614   {
2615
2616   }
2617
2618   public void textColour_actionPerformed()
2619   {
2620
2621   }
2622
2623   public void idRightAlign_actionPerformed(ActionEvent e)
2624   {
2625
2626   }
2627
2628   public void expandViews_actionPerformed(ActionEvent e)
2629   {
2630
2631   }
2632
2633   public void gatherViews_actionPerformed(ActionEvent e)
2634   {
2635
2636   }
2637
2638   public void buildTreeSortMenu()
2639   {
2640
2641   }
2642
2643   public void pageSetup_actionPerformed(ActionEvent e)
2644   {
2645
2646   }
2647
2648   public void alignmentProperties()
2649   {
2650
2651   }
2652
2653   protected void expand_newalign(ActionEvent e)
2654   {
2655     // TODO Auto-generated method stub
2656
2657   }
2658
2659   protected boolean isShowAutoCalculatedAbove()
2660   {
2661     return showAutoCalculatedAbove;
2662   }
2663
2664   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2665   {
2666     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2667   }
2668
2669   protected SequenceAnnotationOrder getAnnotationSortOrder()
2670   {
2671     return annotationSortOrder;
2672   }
2673
2674   protected void setAnnotationSortOrder(
2675           SequenceAnnotationOrder annotationSortOrder)
2676   {
2677     this.annotationSortOrder = annotationSortOrder;
2678   }
2679
2680   public Map<KeyStroke, JMenuItem> getAccelerators()
2681   {
2682     return this.accelerators;
2683   }
2684
2685   /**
2686    * Returns the selected index of the tabbed pane, or -1 if none selected
2687    * (including the case where the tabbed pane has not been made visible).
2688    *
2689    * @return
2690    */
2691   public int getTabIndex()
2692   {
2693     return tabbedPane.getSelectedIndex();
2694   }
2695
2696   public JPanel getStatusPanel()
2697   {
2698     return statusPanel;
2699   }
2700
2701   /**
2702    * Sets a reference to the containing split frame. Also makes the 'toggle
2703    * split view' menu item visible and checked.
2704    *
2705    * @param sf
2706    */
2707   public void setSplitFrame(SplitContainerI sf)
2708   {
2709     this.splitFrame = sf;
2710     if (sf != null)
2711     {
2712       this.showComplementMenuItem.setVisible(true);
2713       this.showComplementMenuItem.setState(true);
2714     }
2715   }
2716
2717   public SplitContainerI getSplitViewContainer()
2718   {
2719     return this.splitFrame;
2720   }
2721
2722   protected void showComplement_actionPerformed(boolean complement)
2723   {
2724   }
2725 }