src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.jbgui;
  22
  23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  24 import jalview.api.SplitContainerI;
  25 import jalview.bin.Cache;
  26 import jalview.gui.JvSwingUtils;
  27 import jalview.gui.Preferences;
  28 import jalview.io.FileFormats;
  29 import jalview.util.MessageManager;
  30 import jalview.util.Platform;
  31
  32 import java.awt.BorderLayout;
  33 import java.awt.Color;
  34 import java.awt.GridLayout;
  35 import java.awt.Toolkit;
  36 import java.awt.event.ActionEvent;
  37 import java.awt.event.ActionListener;
  38 import java.awt.event.FocusAdapter;
  39 import java.awt.event.FocusEvent;
  40 import java.awt.event.KeyEvent;
  41 import java.awt.event.MouseAdapter;
  42 import java.awt.event.MouseEvent;
  43 import java.io.IOException;
  44 import java.util.HashMap;
  45 import java.util.Map;
  46
  47 import javax.swing.BorderFactory;
  48 import javax.swing.ButtonGroup;
  49 import javax.swing.JCheckBoxMenuItem;
  50 import javax.swing.JInternalFrame;
  51 import javax.swing.JLabel;
  52 import javax.swing.JMenu;
  53 import javax.swing.JMenuBar;
  54 import javax.swing.JMenuItem;
  55 import javax.swing.JPanel;
  56 import javax.swing.JRadioButtonMenuItem;
  57 import javax.swing.JTabbedPane;
  58 import javax.swing.KeyStroke;
  59 import javax.swing.event.ChangeEvent;
  60 import javax.swing.event.MenuEvent;
  61 import javax.swing.event.MenuListener;
  62
  63 public class GAlignFrame extends JInternalFrame
  64 {
  65   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  66
  67   protected JMenuItem closeMenuItem = new JMenuItem();
  68
  69   protected JMenu webService = new JMenu();
  70
  71   protected JMenu hmmerMenu = new JMenu();
  72
  73   protected JCheckBoxMenuItem autoAlignSeqs = new JCheckBoxMenuItem();
  74
  75   protected JMenuItem hmmAlign = new JMenuItem();
  76
  77   protected JMenuItem hmmSearch = new JMenuItem();
  78
  79   protected JMenuItem hmmBuild = new JCheckBoxMenuItem();
  80
  81   protected JMenuItem webServiceNoServices;
  82
  83   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  84
  85   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  86
  87   protected JMenu sortByAnnotScore = new JMenu();
  88
  89   public JLabel statusBar = new JLabel();
  90
  91   protected JMenu outputTextboxMenu = new JMenu();
  92
  93   protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
  94
  95   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
  96
  97   protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
  98
  99   protected JMenuItem undoMenuItem = new JMenuItem();
 100
 101   protected JMenuItem redoMenuItem = new JMenuItem();
 102
 103   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 104
 105   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 106
 107   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 108
 109   JMenuItem copy = new JMenuItem();
 110
 111   JMenuItem cut = new JMenuItem();
 112
 113   JMenu pasteMenu = new JMenu();
 114
 115   protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 116
 117   protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 118
 119   protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 120
 121   protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 122
 123   protected JCheckBoxMenuItem applyToAllGroups;
 124
 125   protected JMenu colourMenu = new JMenu();
 126
 127   protected JMenuItem textColour;
 128
 129   protected JCheckBoxMenuItem conservationMenuItem;
 130
 131   protected JMenuItem modifyConservation;
 132
 133   protected JCheckBoxMenuItem abovePIDThreshold;
 134
 135   protected JMenuItem modifyPID;
 136
 137   protected JMenuItem annotationColour;
 138
 139   protected JMenu sortByTreeMenu = new JMenu();
 140
 141   protected JMenu sort = new JMenu();
 142
 143   protected JMenuItem calculateTree = new JMenuItem();
 144
 145   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 146
 147   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 148
 149   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 150
 151   protected JMenuItem showTranslation = new JMenuItem();
 152
 153   protected JMenuItem showReverse = new JMenuItem();
 154
 155   protected JMenuItem showReverseComplement = new JMenuItem();
 156
 157   protected JMenu showProducts = new JMenu();
 158
 159   protected JMenuItem runGroovy = new JMenuItem();
 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 showInformationHistogram = new JCheckBoxMenuItem();
 208
 209   protected JCheckBoxMenuItem showHMMSequenceLogo = new JCheckBoxMenuItem();
 210
 211   protected JCheckBoxMenuItem normaliseHMMSequenceLogo = new JCheckBoxMenuItem();
 212
 213   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 214
 215   private SequenceAnnotationOrder annotationSortOrder;
 216
 217   private boolean showAutoCalculatedAbove = false;
 218
 219   private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
 220
 221   private SplitContainerI splitFrame;
 222
 223   public GAlignFrame()
 224   {
 225     try
 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);
 241           }
 242         });
 243
 244         outputTextboxMenu.add(item);
 245       }
 246     } catch (Exception e)
 247     {
 248       System.err.println(e.toString());
 249     }
 250
 251     if (!Platform.isAMac())
 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     initHMMERMenu();
 268
 269     JMenuItem saveAs = new JMenuItem(
 270             MessageManager.getString("action.save_as"));
 271     ActionListener al = new ActionListener()
 272     {
 273       @Override
 274       public void actionPerformed(ActionEvent e)
 275       {
 276         saveAs_actionPerformed(e);
 277       }
 278     };
 279
 280     // FIXME getDefaultToolkit throws an exception in Headless mode
 281     KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
 282             .getDefaultToolkit().getMenuShortcutKeyMask()
 283             | KeyEvent.SHIFT_MASK, false);
 284     addMenuActionAndAccelerator(keyStroke, saveAs, al);
 285
 286     closeMenuItem.setText(MessageManager.getString("action.close"));
 287     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
 288             .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     hmmerMenu.setText(MessageManager.getString("action.hmmer"));
 309     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
 310             MessageManager.getString("action.select_all"));
 311     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
 312             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 313     al = new ActionListener()
 314     {
 315       @Override
 316       public void actionPerformed(ActionEvent e)
 317       {
 318         selectAllSequenceMenuItem_actionPerformed(e);
 319       }
 320     };
 321     addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
 322
 323     JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
 324             MessageManager.getString("action.deselect_all"));
 325     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
 326     al = new ActionListener()
 327     {
 328       @Override
 329       public void actionPerformed(ActionEvent e)
 330       {
 331         deselectAllSequenceMenuItem_actionPerformed(e);
 332       }
 333     };
 334     addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
 335
 336     JMenuItem invertSequenceMenuItem = new JMenuItem(
 337             MessageManager.getString("action.invert_sequence_selection"));
 338     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
 339             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 340     al = new ActionListener()
 341     {
 342       @Override
 343       public void actionPerformed(ActionEvent e)
 344       {
 345         invertSequenceMenuItem_actionPerformed(e);
 346       }
 347     };
 348     addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
 349
 350     JMenuItem grpsFromSelection = new JMenuItem(
 351             MessageManager.getString("action.make_groups_selection"));
 352     grpsFromSelection.addActionListener(new ActionListener()
 353     {
 354       @Override
 355       public void actionPerformed(ActionEvent e)
 356       {
 357         makeGrpsFromSelection_actionPerformed(e);
 358       }
 359     });
 360     JMenuItem expandAlignment = new JMenuItem(
 361             MessageManager.getString("action.view_flanking_regions"));
 362     expandAlignment.setToolTipText(MessageManager
 363             .getString("label.view_flanking_regions"));
 364     expandAlignment.addActionListener(new ActionListener()
 365     {
 366       @Override
 367       public void actionPerformed(ActionEvent e)
 368       {
 369         expand_newalign(e);
 370       }
 371     });
 372     JMenuItem remove2LeftMenuItem = new JMenuItem(
 373             MessageManager.getString("action.remove_left"));
 374     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
 375             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 376     al = new ActionListener()
 377     {
 378       @Override
 379       public void actionPerformed(ActionEvent e)
 380       {
 381         remove2LeftMenuItem_actionPerformed(e);
 382       }
 383     };
 384     addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
 385
 386     JMenuItem remove2RightMenuItem = new JMenuItem(
 387             MessageManager.getString("action.remove_right"));
 388     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
 389             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 390     al = new ActionListener()
 391     {
 392       @Override
 393       public void actionPerformed(ActionEvent e)
 394       {
 395         remove2RightMenuItem_actionPerformed(e);
 396       }
 397     };
 398     addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
 399
 400     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
 401             MessageManager.getString("action.remove_empty_columns"));
 402     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
 403             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 404     al = new ActionListener()
 405     {
 406       @Override
 407       public void actionPerformed(ActionEvent e)
 408       {
 409         removeGappedColumnMenuItem_actionPerformed(e);
 410       }
 411     };
 412     addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
 413
 414     JMenuItem removeAllGapsMenuItem = new JMenuItem(
 415             MessageManager.getString("action.remove_all_gaps"));
 416     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
 417             .getDefaultToolkit().getMenuShortcutKeyMask()
 418             | KeyEvent.SHIFT_MASK, 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.setText(MessageManager
 470             .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, Toolkit
 524             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 525     al = new ActionListener()
 526     {
 527       @Override
 528       public void actionPerformed(ActionEvent e)
 529       {
 530         removeRedundancyMenuItem_actionPerformed(e);
 531       }
 532     };
 533     addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
 534
 535     JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
 536             MessageManager.getString("action.pairwise_alignment"));
 537     pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
 538     {
 539       @Override
 540       public void actionPerformed(ActionEvent e)
 541       {
 542         pairwiseAlignmentMenuItem_actionPerformed(e);
 543       }
 544     });
 545
 546     this.getContentPane().setLayout(new BorderLayout());
 547     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 548     statusBar.setBackground(Color.white);
 549     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 550     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 551     statusBar.setText(MessageManager.getString("label.status_bar"));
 552     outputTextboxMenu.setText(MessageManager
 553             .getString("label.out_to_textbox"));
 554
 555     annotationPanelMenuItem.setActionCommand("");
 556     annotationPanelMenuItem.setText(MessageManager
 557             .getString("label.show_annotations"));
 558     annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
 559             true));
 560     annotationPanelMenuItem.addActionListener(new ActionListener()
 561     {
 562       @Override
 563       public void actionPerformed(ActionEvent e)
 564       {
 565         annotationPanelMenuItem_actionPerformed(e);
 566       }
 567     });
 568     showAllAlAnnotations.setText(MessageManager
 569             .getString("label.show_all_al_annotations"));
 570     final boolean isAnnotationPanelShown = annotationPanelMenuItem
 571             .getState();
 572     showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 573     showAllAlAnnotations.addActionListener(new ActionListener()
 574     {
 575       @Override
 576       public void actionPerformed(ActionEvent e)
 577       {
 578         showAllAnnotations_actionPerformed(false, true);
 579       }
 580     });
 581     hideAllAlAnnotations.setText(MessageManager
 582             .getString("label.hide_all_al_annotations"));
 583     hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 584     hideAllAlAnnotations.addActionListener(new ActionListener()
 585     {
 586       @Override
 587       public void actionPerformed(ActionEvent e)
 588       {
 589         hideAllAnnotations_actionPerformed(false, true);
 590       }
 591     });
 592     showAllSeqAnnotations.setText(MessageManager
 593             .getString("label.show_all_seq_annotations"));
 594     showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 595     showAllSeqAnnotations.addActionListener(new ActionListener()
 596     {
 597       @Override
 598       public void actionPerformed(ActionEvent e)
 599       {
 600         showAllAnnotations_actionPerformed(true, false);
 601       }
 602     });
 603     hideAllSeqAnnotations.setText(MessageManager
 604             .getString("label.hide_all_seq_annotations"));
 605     hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 606     hideAllSeqAnnotations.addActionListener(new ActionListener()
 607     {
 608       @Override
 609       public void actionPerformed(ActionEvent e)
 610       {
 611         hideAllAnnotations_actionPerformed(true, false);
 612       }
 613     });
 614     SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
 615             .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
 616                     SequenceAnnotationOrder.NONE.name()));
 617     final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
 618             MessageManager.getString("label.sort_annotations_by_sequence"));
 619     final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
 620             MessageManager.getString("label.sort_annotations_by_label"));
 621
 622     sortAnnBySequence
 623             .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
 624     sortAnnBySequence.addActionListener(new ActionListener()
 625     {
 626       @Override
 627       public void actionPerformed(ActionEvent e)
 628       {
 629         boolean newState = sortAnnBySequence.getState();
 630         sortAnnByLabel.setSelected(false);
 631         setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 632                 : SequenceAnnotationOrder.NONE);
 633         sortAnnotations_actionPerformed();
 634       }
 635     });
 636     sortAnnByLabel
 637             .setSelected(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(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 646                 : SequenceAnnotationOrder.NONE);
 647         sortAnnotations_actionPerformed();
 648       }
 649     });
 650     colourTextMenuItem = new JCheckBoxMenuItem(
 651             MessageManager
 652             .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, Toolkit
 698             .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, Toolkit
 712             .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, Toolkit
 736             .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, Toolkit
 762             .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(MessageManager
 776             .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.setText(MessageManager
 792             .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(MessageManager
 804             .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.setText(MessageManager
 816             .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.setText(MessageManager
 829             .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(MessageManager
 841             .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.setText(MessageManager
 853             .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.setText(MessageManager
 865             .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.setText(MessageManager
 877             .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.getDefault(
 897             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, Toolkit
 923             .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, Toolkit
 948             .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, Toolkit
 962             .getDefaultToolkit().getMenuShortcutKeyMask()
 963             | KeyEvent.SHIFT_MASK, false);
 964     al = new ActionListener()
 965     {
 966       @Override
 967       public void actionPerformed(ActionEvent e)
 968       {
 969         unGroup_actionPerformed(e);
 970       }
 971     };
 972     addMenuActionAndAccelerator(keyStroke, unGroup, al);
 973
 974     copy.setText(MessageManager.getString("action.copy"));
 975     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
 976             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 977
 978     al = new ActionListener()
 979     {
 980       @Override
 981       public void actionPerformed(ActionEvent e)
 982       {
 983         copy_actionPerformed(e);
 984       }
 985     };
 986     addMenuActionAndAccelerator(keyStroke, copy, al);
 987
 988     cut.setText(MessageManager.getString("action.cut"));
 989     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
 990             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 991     al = new ActionListener()
 992     {
 993       @Override
 994       public void actionPerformed(ActionEvent e)
 995       {
 996         cut_actionPerformed(e);
 997       }
 998     };
 999     addMenuActionAndAccelerator(keyStroke, cut, al);
1000
1001     JMenuItem delete = new JMenuItem(
1002             MessageManager.getString("action.delete"));
1003     delete.addActionListener(new ActionListener()
1004     {
1005       @Override
1006       public void actionPerformed(ActionEvent e)
1007       {
1008         delete_actionPerformed(e);
1009       }
1010     });
1011
1012     pasteMenu.setText(MessageManager.getString("action.paste"));
1013     JMenuItem pasteNew = new JMenuItem(
1014             MessageManager.getString("label.to_new_alignment"));
1015     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1016             .getDefaultToolkit().getMenuShortcutKeyMask()
1017             | KeyEvent.SHIFT_MASK, false);
1018     al = new ActionListener()
1019     {
1020       @Override
1021       public void actionPerformed(ActionEvent e)
1022       {
1023         pasteNew_actionPerformed(e);
1024       }
1025     };
1026     addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1027
1028     JMenuItem pasteThis = new JMenuItem(
1029             MessageManager.getString("label.to_this_alignment"));
1030     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1031             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1032     al = new ActionListener()
1033     {
1034       @Override
1035       public void actionPerformed(ActionEvent e)
1036       {
1037         pasteThis_actionPerformed(e);
1038       }
1039     };
1040     addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1041
1042     JMenuItem createPNG = new JMenuItem("PNG");
1043     createPNG.addActionListener(new ActionListener()
1044     {
1045       @Override
1046       public void actionPerformed(ActionEvent e)
1047       {
1048         createPNG(null);
1049       }
1050     });
1051     createPNG.setActionCommand(MessageManager
1052             .getString("label.save_png_image"));
1053
1054     JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1055     font.addActionListener(new ActionListener()
1056     {
1057       @Override
1058       public void actionPerformed(ActionEvent e)
1059       {
1060         font_actionPerformed(e);
1061       }
1062     });
1063     seqLimits.setText(MessageManager
1064             .getString("label.show_sequence_limits"));
1065     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1066     seqLimits.addActionListener(new ActionListener()
1067     {
1068       @Override
1069       public void actionPerformed(ActionEvent e)
1070       {
1071         seqLimit_actionPerformed(e);
1072       }
1073     });
1074     JMenuItem epsFile = new JMenuItem("EPS");
1075     epsFile.addActionListener(new ActionListener()
1076     {
1077       @Override
1078       public void actionPerformed(ActionEvent e)
1079       {
1080         createEPS(null);
1081       }
1082     });
1083
1084     JMenuItem createSVG = new JMenuItem("SVG");
1085     createSVG.addActionListener(new ActionListener()
1086     {
1087       @Override
1088       public void actionPerformed(ActionEvent e)
1089       {
1090         createSVG(null);
1091       }
1092     });
1093
1094     JMenuItem loadTreeMenuItem = new JMenuItem(
1095             MessageManager.getString("label.load_associated_tree"));
1096     loadTreeMenuItem.setActionCommand(MessageManager
1097             .getString("label.load_tree_for_sequence_set"));
1098     loadTreeMenuItem.addActionListener(new ActionListener()
1099     {
1100       @Override
1101       public void actionPerformed(ActionEvent e)
1102       {
1103         loadTreeMenuItem_actionPerformed(e);
1104       }
1105     });
1106
1107     scaleAbove.setVisible(false);
1108     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1109     scaleAbove.addActionListener(new ActionListener()
1110     {
1111       @Override
1112       public void actionPerformed(ActionEvent e)
1113       {
1114         scaleAbove_actionPerformed(e);
1115       }
1116     });
1117     scaleLeft.setVisible(false);
1118     scaleLeft.setSelected(true);
1119     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1120     scaleLeft.addActionListener(new ActionListener()
1121     {
1122       @Override
1123       public void actionPerformed(ActionEvent e)
1124       {
1125         scaleLeft_actionPerformed(e);
1126       }
1127     });
1128     scaleRight.setVisible(false);
1129     scaleRight.setSelected(true);
1130     scaleRight.setText(MessageManager.getString("action.scale_right"));
1131     scaleRight.addActionListener(new ActionListener()
1132     {
1133       @Override
1134       public void actionPerformed(ActionEvent e)
1135       {
1136         scaleRight_actionPerformed(e);
1137       }
1138     });
1139     centreColumnLabelsMenuItem.setVisible(true);
1140     centreColumnLabelsMenuItem.setState(false);
1141     centreColumnLabelsMenuItem.setText(MessageManager
1142             .getString("label.centre_column_labels"));
1143     centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1144     {
1145       @Override
1146       public void actionPerformed(ActionEvent e)
1147       {
1148         centreColumnLabels_actionPerformed(e);
1149       }
1150     });
1151     followHighlightMenuItem.setVisible(true);
1152     followHighlightMenuItem.setState(true);
1153     followHighlightMenuItem.setText(MessageManager
1154             .getString("label.automatic_scrolling"));
1155     followHighlightMenuItem.addActionListener(new ActionListener()
1156     {
1157
1158       @Override
1159       public void actionPerformed(ActionEvent e)
1160       {
1161         followHighlight_actionPerformed();
1162       }
1163
1164     });
1165
1166     sortByTreeMenu
1167             .setText(MessageManager.getString("action.by_tree_order"));
1168     sort.setText(MessageManager.getString("action.sort"));
1169     sort.addMenuListener(new MenuListener()
1170     {
1171       @Override
1172       public void menuSelected(MenuEvent e)
1173       {
1174         buildTreeSortMenu();
1175       }
1176
1177       @Override
1178       public void menuDeselected(MenuEvent e)
1179       {
1180       }
1181
1182       @Override
1183       public void menuCanceled(MenuEvent e)
1184       {
1185       }
1186     });
1187     sortByAnnotScore.setText(MessageManager
1188             .getString("label.sort_by_score"));
1189     sort.add(sortByAnnotScore);
1190     sort.addMenuListener(new javax.swing.event.MenuListener()
1191     {
1192
1193       @Override
1194       public void menuCanceled(MenuEvent e)
1195       {
1196       }
1197
1198       @Override
1199       public void menuDeselected(MenuEvent e)
1200       {
1201       }
1202
1203       @Override
1204       public void menuSelected(MenuEvent e)
1205       {
1206         buildSortByAnnotationScoresMenu();
1207       }
1208     });
1209     sortByAnnotScore.setVisible(false);
1210
1211     calculateTree.setText(MessageManager
1212             .getString("action.calculate_tree_pca"));
1213
1214     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1215     padGapsMenuitem.setState(jalview.bin.Cache
1216             .getDefault("PAD_GAPS", false));
1217     padGapsMenuitem.addActionListener(new ActionListener()
1218     {
1219       @Override
1220       public void actionPerformed(ActionEvent e)
1221       {
1222         padGapsMenuitem_actionPerformed(e);
1223       }
1224     });
1225     JMenuItem vamsasStore = new JMenuItem(
1226             MessageManager.getString("label.vamsas_store"));
1227     vamsasStore.setVisible(false);
1228     vamsasStore.addActionListener(new ActionListener()
1229     {
1230       @Override
1231       public void actionPerformed(ActionEvent e)
1232       {
1233         vamsasStore_actionPerformed(e);
1234       }
1235     });
1236     showTranslation.setText(MessageManager
1237             .getString("label.translate_cDNA"));
1238     showTranslation.addActionListener(new ActionListener()
1239     {
1240       @Override
1241       public void actionPerformed(ActionEvent e)
1242       {
1243         showTranslation_actionPerformed(e);
1244       }
1245     });
1246     showReverse.setText(MessageManager.getString("label.reverse"));
1247     showReverse.addActionListener(new ActionListener()
1248     {
1249       @Override
1250       public void actionPerformed(ActionEvent e)
1251       {
1252         showReverse_actionPerformed(false);
1253       }
1254     });
1255     showReverseComplement.setText(MessageManager
1256             .getString("label.reverse_complement"));
1257     showReverseComplement.addActionListener(new ActionListener()
1258     {
1259       @Override
1260       public void actionPerformed(ActionEvent e)
1261       {
1262         showReverse_actionPerformed(true);
1263       }
1264     });
1265
1266     JMenuItem extractScores = new JMenuItem(
1267             MessageManager.getString("label.extract_scores"));
1268     extractScores.addActionListener(new ActionListener()
1269     {
1270       @Override
1271       public void actionPerformed(ActionEvent e)
1272       {
1273         extractScores_actionPerformed(e);
1274       }
1275     });
1276     extractScores.setVisible(true);
1277     // JBPNote: TODO: make gui for regex based score extraction
1278
1279     // for show products actions see AlignFrame.canShowProducts
1280     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1281
1282     runGroovy.setText(MessageManager.getString("label.run_groovy"));
1283     runGroovy.setToolTipText(MessageManager
1284             .getString("label.run_groovy_tip"));
1285     runGroovy.addActionListener(new ActionListener()
1286     {
1287       @Override
1288       public void actionPerformed(ActionEvent e)
1289       {
1290         runGroovy_actionPerformed();
1291       }
1292     });
1293
1294     JMenuItem openFeatureSettings = new JMenuItem(
1295             MessageManager.getString("action.feature_settings"));
1296     openFeatureSettings.addActionListener(new ActionListener()
1297     {
1298       @Override
1299       public void actionPerformed(ActionEvent e)
1300       {
1301         featureSettings_actionPerformed(e);
1302       }
1303     });
1304     JMenuItem fetchSequence = new JMenuItem(
1305             MessageManager.getString("label.fetch_sequences"));
1306     fetchSequence.addActionListener(new ActionListener()
1307     {
1308       @Override
1309       public void actionPerformed(ActionEvent e)
1310       {
1311         fetchSequence_actionPerformed(e);
1312       }
1313     });
1314
1315     JMenuItem associatedData = new JMenuItem(
1316             MessageManager.getString("label.load_features_annotations"));
1317     associatedData.addActionListener(new ActionListener()
1318     {
1319       @Override
1320       public void actionPerformed(ActionEvent e)
1321       {
1322         associatedData_actionPerformed(e);
1323       }
1324     });
1325     autoCalculate.setText(MessageManager
1326             .getString("label.autocalculate_consensus"));
1327     autoCalculate.setState(jalview.bin.Cache.getDefault(
1328             "AUTO_CALC_CONSENSUS", true));
1329     autoCalculate.addActionListener(new ActionListener()
1330     {
1331       @Override
1332       public void actionPerformed(ActionEvent e)
1333       {
1334         autoCalculate_actionPerformed(e);
1335       }
1336     });
1337     sortByTree.setText(MessageManager
1338             .getString("label.sort_alignment_new_tree"));
1339     sortByTree
1340             .setToolTipText("<html>"
1341                     + MessageManager
1342                             .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1343     sortByTree
1344             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1345     sortByTree.addActionListener(new ActionListener()
1346     {
1347       @Override
1348       public void actionPerformed(ActionEvent e)
1349       {
1350         sortByTreeOption_actionPerformed(e);
1351       }
1352     });
1353
1354     listenToViewSelections.setText(MessageManager
1355             .getString("label.listen_for_selections"));
1356     listenToViewSelections
1357             .setToolTipText("<html>"
1358                     + MessageManager
1359                             .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1360     listenToViewSelections.setState(false);
1361     listenToViewSelections.addActionListener(new ActionListener()
1362     {
1363       @Override
1364       public void actionPerformed(ActionEvent e)
1365       {
1366         listenToViewSelections_actionPerformed(e);
1367       }
1368     });
1369
1370     JMenu addSequenceMenu = new JMenu(
1371             MessageManager.getString("label.add_sequences"));
1372     JMenuItem addFromFile = new JMenuItem(
1373             MessageManager.getString("label.from_file"));
1374     addFromFile.addActionListener(new ActionListener()
1375     {
1376       @Override
1377       public void actionPerformed(ActionEvent e)
1378       {
1379         addFromFile_actionPerformed(e);
1380       }
1381     });
1382     JMenuItem addFromText = new JMenuItem(
1383             MessageManager.getString("label.from_textbox"));
1384     addFromText.addActionListener(new ActionListener()
1385     {
1386       @Override
1387       public void actionPerformed(ActionEvent e)
1388       {
1389         addFromText_actionPerformed(e);
1390       }
1391     });
1392     JMenuItem addFromURL = new JMenuItem(
1393             MessageManager.getString("label.from_url"));
1394     addFromURL.addActionListener(new ActionListener()
1395     {
1396       @Override
1397       public void actionPerformed(ActionEvent e)
1398       {
1399         addFromURL_actionPerformed(e);
1400       }
1401     });
1402     JMenuItem exportFeatures = new JMenuItem(
1403             MessageManager.getString("label.export_features"));
1404     exportFeatures.addActionListener(new ActionListener()
1405     {
1406       @Override
1407       public void actionPerformed(ActionEvent e)
1408       {
1409         exportFeatures_actionPerformed(e);
1410       }
1411     });
1412     JMenuItem exportAnnotations = new JMenuItem(
1413             MessageManager.getString("label.export_annotations"));
1414     exportAnnotations.addActionListener(new ActionListener()
1415     {
1416       @Override
1417       public void actionPerformed(ActionEvent e)
1418       {
1419         exportAnnotations_actionPerformed(e);
1420       }
1421     });
1422     statusPanel.setLayout(new GridLayout());
1423     JMenuItem showAllSeqs = new JMenuItem(
1424             MessageManager.getString("label.all_sequences"));
1425     showAllSeqs.setToolTipText(MessageManager
1426             .getString("label.toggle_sequence_visibility"));
1427     showAllSeqs.addActionListener(new ActionListener()
1428     {
1429       @Override
1430       public void actionPerformed(ActionEvent e)
1431       {
1432         showAllSeqs_actionPerformed(e);
1433       }
1434     });
1435     JMenuItem showAllColumns = new JMenuItem(
1436             MessageManager.getString("label.all_columns"));
1437     showAllColumns.setToolTipText(MessageManager
1438             .getString("label.toggle_columns_visibility"));
1439     showAllColumns.addActionListener(new ActionListener()
1440     {
1441       @Override
1442       public void actionPerformed(ActionEvent e)
1443       {
1444         showAllColumns_actionPerformed(e);
1445       }
1446     });
1447     JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1448     JMenuItem hideSelSequences = new JMenuItem(
1449             MessageManager.getString("label.selected_sequences"));
1450     hideSelSequences.setToolTipText(MessageManager
1451             .getString("label.toggle_sequence_visibility"));
1452     hideSelSequences.addActionListener(new ActionListener()
1453     {
1454       @Override
1455       public void actionPerformed(ActionEvent e)
1456       {
1457         hideSelSequences_actionPerformed(e);
1458       }
1459     });
1460     JMenuItem hideSelColumns = new JMenuItem(
1461             MessageManager.getString("label.selected_columns"));
1462     hideSelColumns.setToolTipText(MessageManager
1463             .getString("label.toggle_columns_visibility"));
1464     hideSelColumns.addActionListener(new ActionListener()
1465     {
1466       @Override
1467       public void actionPerformed(ActionEvent e)
1468       {
1469         hideSelColumns_actionPerformed(e);
1470       }
1471     });
1472     JMenuItem hideAllSelection = new JMenuItem(
1473             MessageManager.getString("label.selected_region"));
1474     hideAllSelection.addActionListener(new ActionListener()
1475     {
1476       @Override
1477       public void actionPerformed(ActionEvent e)
1478       {
1479         hideAllSelection_actionPerformed(e);
1480       }
1481     });
1482     // TODO: should be hidden if no selection exists.
1483     JMenuItem hideAllButSelection = new JMenuItem(
1484             MessageManager.getString("label.all_but_selected_region"));
1485     hideAllButSelection.addActionListener(new ActionListener()
1486     {
1487       @Override
1488       public void actionPerformed(ActionEvent e)
1489       {
1490         hideAllButSelection_actionPerformed(e);
1491       }
1492     });
1493     JMenuItem showAllhidden = new JMenuItem(
1494             MessageManager.getString("label.all_sequences_columns"));
1495     showAllhidden.setToolTipText(MessageManager
1496             .getString("label.toggles_visibility_hidden_selected_regions"));
1497     showAllhidden.addActionListener(new ActionListener()
1498     {
1499       @Override
1500       public void actionPerformed(ActionEvent e)
1501       {
1502         showAllhidden_actionPerformed(e);
1503       }
1504     });
1505     hiddenMarkers.setText(MessageManager
1506             .getString("action.show_hidden_markers"));
1507     hiddenMarkers.addActionListener(new ActionListener()
1508     {
1509       @Override
1510       public void actionPerformed(ActionEvent e)
1511       {
1512         hiddenMarkers_actionPerformed(e);
1513       }
1514     });
1515
1516     JMenuItem invertColSel = new JMenuItem(
1517             MessageManager.getString("action.invert_column_selection"));
1518     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
1519             .getDefaultToolkit().getMenuShortcutKeyMask()
1520             | KeyEvent.ALT_MASK, false);
1521     al = new ActionListener()
1522     {
1523       @Override
1524       public void actionPerformed(ActionEvent e)
1525       {
1526         invertColSel_actionPerformed(e);
1527       }
1528     };
1529     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1530
1531     showComplementMenuItem.setVisible(false);
1532     showComplementMenuItem.addActionListener(new ActionListener()
1533     {
1534       @Override
1535       public void actionPerformed(ActionEvent e)
1536       {
1537         showComplement_actionPerformed(showComplementMenuItem.getState());
1538       }
1539     });
1540
1541     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1542     {
1543       @Override
1544       public void stateChanged(ChangeEvent evt)
1545       {
1546         JTabbedPane pane = (JTabbedPane) evt.getSource();
1547         int sel = pane.getSelectedIndex();
1548         tabSelectionChanged(sel);
1549       }
1550     });
1551     tabbedPane.addMouseListener(new MouseAdapter()
1552     {
1553       @Override
1554       public void mousePressed(MouseEvent e)
1555       {
1556         if (e.isPopupTrigger()) // Mac
1557         {
1558           tabbedPane_mousePressed(e);
1559         }
1560       }
1561
1562       @Override
1563       public void mouseReleased(MouseEvent e)
1564       {
1565         if (e.isPopupTrigger()) // Windows
1566         {
1567           tabbedPane_mousePressed(e);
1568         }
1569       }
1570     });
1571     tabbedPane.addFocusListener(new FocusAdapter()
1572     {
1573       @Override
1574       public void focusGained(FocusEvent e)
1575       {
1576         tabbedPane_focusGained(e);
1577       }
1578     });
1579
1580     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1581     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
1582             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1583     al = new ActionListener()
1584     {
1585       @Override
1586       public void actionPerformed(ActionEvent e)
1587       {
1588         save_actionPerformed(e);
1589       }
1590     };
1591     addMenuActionAndAccelerator(keyStroke, save, al);
1592
1593     reload.setEnabled(false);
1594     reload.setText(MessageManager.getString("action.reload"));
1595     reload.addActionListener(new ActionListener()
1596     {
1597       @Override
1598       public void actionPerformed(ActionEvent e)
1599       {
1600         reload_actionPerformed(e);
1601       }
1602     });
1603
1604     JMenuItem newView = new JMenuItem(
1605             MessageManager.getString("action.new_view"));
1606     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
1607             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1608     al = new ActionListener()
1609     {
1610       @Override
1611       public void actionPerformed(ActionEvent e)
1612       {
1613         newView_actionPerformed(e);
1614       }
1615     };
1616     addMenuActionAndAccelerator(keyStroke, newView, al);
1617
1618     tabbedPane.setToolTipText("<html><i>"
1619             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1620             + "</i></html>");
1621
1622     formatMenu.setText(MessageManager.getString("action.format"));
1623     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1624
1625     idRightAlign.setText(MessageManager
1626             .getString("label.right_align_sequence_id"));
1627     idRightAlign.addActionListener(new ActionListener()
1628     {
1629       @Override
1630       public void actionPerformed(ActionEvent e)
1631       {
1632         idRightAlign_actionPerformed(e);
1633       }
1634     });
1635
1636     gatherViews.setEnabled(false);
1637     gatherViews.setText(MessageManager.getString("action.gather_views"));
1638     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1639     al = new ActionListener()
1640     {
1641       @Override
1642       public void actionPerformed(ActionEvent e)
1643       {
1644         gatherViews_actionPerformed(e);
1645       }
1646     };
1647     addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1648
1649     expandViews.setEnabled(false);
1650     expandViews.setText(MessageManager.getString("action.expand_views"));
1651     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1652     al = new ActionListener()
1653     {
1654       @Override
1655       public void actionPerformed(ActionEvent e)
1656       {
1657         expandViews_actionPerformed(e);
1658       }
1659     };
1660     addMenuActionAndAccelerator(keyStroke, expandViews, al);
1661
1662     JMenuItem pageSetup = new JMenuItem(
1663             MessageManager.getString("action.page_setup"));
1664     pageSetup.addActionListener(new ActionListener()
1665     {
1666       @Override
1667       public void actionPerformed(ActionEvent e)
1668       {
1669         pageSetup_actionPerformed(e);
1670       }
1671     });
1672     JMenuItem alignmentProperties = new JMenuItem(
1673             MessageManager.getString("label.alignment_props"));
1674     alignmentProperties.addActionListener(new ActionListener()
1675     {
1676       @Override
1677       public void actionPerformed(ActionEvent actionEvent)
1678       {
1679         alignmentProperties();
1680       }
1681     });
1682     JMenuItem selectHighlighted = new JMenuItem(
1683             MessageManager.getString("action.select_highlighted_columns"));
1684     selectHighlighted.setToolTipText(MessageManager
1685             .getString("tooltip.select_highlighted_columns"));
1686     al = new ActionListener()
1687     {
1688       @Override
1689       public void actionPerformed(ActionEvent actionEvent)
1690       {
1691         selectHighlightedColumns_actionPerformed(actionEvent);
1692       }
1693     };
1694     hmmBuild.setText(MessageManager.getString("label.hmmbuild"));
1695     hmmBuild.addActionListener(new ActionListener()
1696     {
1697
1698       @Override
1699       public void actionPerformed(ActionEvent e)
1700       {
1701         try
1702         {
1703           hmmBuild_actionPerformed(e);
1704         } catch (IOException e1)
1705         {
1706           // TODO Auto-generated catch block
1707           e1.printStackTrace();
1708         } catch (InterruptedException e1)
1709         {
1710           // TODO Auto-generated catch block
1711           e1.printStackTrace();
1712         }
1713       }
1714
1715     });
1716     selectHighlighted.addActionListener(al);
1717     JMenu tooltipSettingsMenu = new JMenu(
1718             MessageManager.getString("label.sequence_id_tooltip"));
1719     JMenu autoAnnMenu = new JMenu(
1720             MessageManager.getString("label.autocalculated_annotation"));
1721
1722     JMenu exportImageMenu = new JMenu(
1723             MessageManager.getString("label.export_image"));
1724     JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1725     alignFrameMenuBar.add(fileMenu);
1726     alignFrameMenuBar.add(editMenu);
1727     alignFrameMenuBar.add(selectMenu);
1728     alignFrameMenuBar.add(viewMenu);
1729     alignFrameMenuBar.add(annotationsMenu);
1730     alignFrameMenuBar.add(formatMenu);
1731     alignFrameMenuBar.add(colourMenu);
1732     alignFrameMenuBar.add(calculateMenu);
1733     alignFrameMenuBar.add(webService);
1734     alignFrameMenuBar.add(hmmerMenu);
1735
1736     fileMenu.add(fetchSequence);
1737     fileMenu.add(addSequenceMenu);
1738     fileMenu.add(reload);
1739     fileMenu.addSeparator();
1740     fileMenu.add(vamsasStore);
1741     fileMenu.add(save);
1742     fileMenu.add(saveAs);
1743     fileMenu.add(outputTextboxMenu);
1744     fileMenu.add(pageSetup);
1745     fileMenu.add(printMenuItem);
1746     fileMenu.addSeparator();
1747     fileMenu.add(exportImageMenu);
1748     fileMenu.add(exportFeatures);
1749     fileMenu.add(exportAnnotations);
1750     fileMenu.add(loadTreeMenuItem);
1751     fileMenu.add(associatedData);
1752     fileMenu.addSeparator();
1753     fileMenu.add(closeMenuItem);
1754
1755     pasteMenu.add(pasteNew);
1756     pasteMenu.add(pasteThis);
1757     editMenu.add(undoMenuItem);
1758     editMenu.add(redoMenuItem);
1759     editMenu.add(cut);
1760     editMenu.add(copy);
1761     editMenu.add(pasteMenu);
1762     editMenu.add(delete);
1763     editMenu.addSeparator();
1764     editMenu.add(remove2LeftMenuItem);
1765     editMenu.add(remove2RightMenuItem);
1766     editMenu.add(removeGappedColumnMenuItem);
1767     editMenu.add(removeAllGapsMenuItem);
1768     editMenu.add(removeRedundancyMenuItem);
1769     editMenu.addSeparator();
1770     // dont add these yet in the CVS build - they cannot be undone!
1771     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1772     // editMenu.add(justifyLeftMenuItem);
1773     // editMenu.add(justifyRightMenuItem);
1774     // editMenu.addSeparator();
1775     editMenu.add(padGapsMenuitem);
1776
1777     showMenu.add(showAllColumns);
1778     showMenu.add(showAllSeqs);
1779     showMenu.add(showAllhidden);
1780     hideMenu.add(hideSelColumns);
1781     hideMenu.add(hideSelSequences);
1782     hideMenu.add(hideAllSelection);
1783     hideMenu.add(hideAllButSelection);
1784     viewMenu.add(newView);
1785     viewMenu.add(expandViews);
1786     viewMenu.add(gatherViews);
1787     viewMenu.addSeparator();
1788     viewMenu.add(showMenu);
1789     viewMenu.add(hideMenu);
1790     viewMenu.add(showComplementMenuItem);
1791     viewMenu.addSeparator();
1792     viewMenu.add(followHighlightMenuItem);
1793     viewMenu.addSeparator();
1794     viewMenu.add(showSeqFeatures);
1795     // viewMenu.add(showSeqFeaturesHeight);
1796     viewMenu.add(openFeatureSettings);
1797     tooltipSettingsMenu.add(showDbRefsMenuitem);
1798     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1799     viewMenu.add(tooltipSettingsMenu);
1800     viewMenu.addSeparator();
1801     viewMenu.add(alignmentProperties);
1802     viewMenu.addSeparator();
1803     viewMenu.add(overviewMenuItem);
1804
1805     annotationsMenu.add(annotationPanelMenuItem);
1806     annotationsMenu.addSeparator();
1807     annotationsMenu.add(showAllAlAnnotations);
1808     annotationsMenu.add(hideAllAlAnnotations);
1809     annotationsMenu.addSeparator();
1810     annotationsMenu.add(showAllSeqAnnotations);
1811     annotationsMenu.add(hideAllSeqAnnotations);
1812     annotationsMenu.add(sortAnnBySequence);
1813     annotationsMenu.add(sortAnnByLabel);
1814     annotationsMenu.addSeparator();
1815     autoAnnMenu.add(showAutoFirst);
1816     autoAnnMenu.add(showAutoLast);
1817     autoAnnMenu.addSeparator();
1818     autoAnnMenu.add(applyAutoAnnotationSettings);
1819     autoAnnMenu.add(showConsensusHistogram);
1820     autoAnnMenu.add(showSequenceLogo);
1821     autoAnnMenu.add(normaliseSequenceLogo);
1822     autoAnnMenu.addSeparator();
1823     autoAnnMenu.add(showGroupConservation);
1824     autoAnnMenu.add(showGroupConsensus);
1825     annotationsMenu.add(autoAnnMenu);
1826
1827
1828     sort.add(sortIDMenuItem);
1829     sort.add(sortLengthMenuItem);
1830     sort.add(sortGroupMenuItem);
1831     sort.add(sortPairwiseMenuItem);
1832     sort.add(sortByTreeMenu);
1833     calculateMenu.add(sort);
1834     calculateMenu.add(calculateTree);
1835     calculateMenu.addSeparator();
1836     calculateMenu.add(pairwiseAlignmentMenuItem);
1837     calculateMenu.addSeparator();
1838     calculateMenu.add(showTranslation);
1839     calculateMenu.add(showReverse);
1840     calculateMenu.add(showReverseComplement);
1841     calculateMenu.add(showProducts);
1842     calculateMenu.add(autoCalculate);
1843     calculateMenu.add(sortByTree);
1844     calculateMenu.addSeparator();
1845     calculateMenu.add(expandAlignment);
1846     calculateMenu.add(extractScores);
1847     calculateMenu.addSeparator();
1848     calculateMenu.add(runGroovy);
1849
1850     webServiceNoServices = new JMenuItem(
1851             MessageManager.getString("label.no_services"));
1852     webService.add(webServiceNoServices);
1853     exportImageMenu.add(htmlMenuItem);
1854     exportImageMenu.add(epsFile);
1855     exportImageMenu.add(createPNG);
1856     exportImageMenu.add(createBioJS);
1857     exportImageMenu.add(createSVG);
1858     addSequenceMenu.add(addFromFile);
1859     addSequenceMenu.add(addFromText);
1860     addSequenceMenu.add(addFromURL);
1861     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1862     statusPanel.add(statusBar, null);
1863     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1864
1865     formatMenu.add(font);
1866     formatMenu.addSeparator();
1867     formatMenu.add(wrapMenuItem);
1868     formatMenu.add(scaleAbove);
1869     formatMenu.add(scaleLeft);
1870     formatMenu.add(scaleRight);
1871     formatMenu.add(seqLimits);
1872     formatMenu.add(idRightAlign);
1873     formatMenu.add(hiddenMarkers);
1874     formatMenu.add(viewBoxesMenuItem);
1875     formatMenu.add(viewTextMenuItem);
1876     formatMenu.add(colourTextMenuItem);
1877     formatMenu.add(renderGapsMenuItem);
1878     formatMenu.add(centreColumnLabelsMenuItem);
1879     formatMenu.add(showNonconservedMenuItem);
1880     selectMenu.add(findMenuItem);
1881     selectMenu.addSeparator();
1882     selectMenu.add(selectAllSequenceMenuItem);
1883     selectMenu.add(deselectAllSequenceMenuItem);
1884     selectMenu.add(invertSequenceMenuItem);
1885     selectMenu.add(invertColSel);
1886     selectMenu.add(createGroup);
1887     selectMenu.add(unGroup);
1888     selectMenu.add(grpsFromSelection);
1889     selectMenu.add(deleteGroups);
1890     selectMenu.add(annotationColumn);
1891     selectMenu.add(selectHighlighted);
1892     // TODO - determine if the listenToViewSelections button is needed : see bug
1893     // JAL-574
1894     // selectMenu.addSeparator();
1895     // selectMenu.add(listenToViewSelections);
1896   }
1897
1898   /**
1899    * Constructs the entries on the Colour menu (but does not add them to the
1900    * menu).
1901    */
1902   protected void initHMMERMenu()
1903   {
1904     autoAlignSeqs = new JCheckBoxMenuItem(
1905             MessageManager.getString("label.auto_align_seqs"));
1906     hmmAlign = new JMenuItem(MessageManager.getString("label.hmmalign"));
1907     hmmBuild = new JMenuItem(MessageManager.getString("label.hmmbuild"));
1908     hmmSearch = new JMenuItem(MessageManager.getString("label.hmmsearch"));
1909     autoAlignSeqs.addActionListener(new ActionListener()
1910     {
1911       @Override
1912       public void actionPerformed(ActionEvent e)
1913       {
1914         autoAlignSeqs_actionPerformed(autoAlignSeqs.isSelected());
1915       }
1916     });
1917
1918   }
1919   protected void initColourMenu()
1920   {
1921     applyToAllGroups = new JCheckBoxMenuItem(
1922             MessageManager.getString("label.apply_colour_to_all_groups"));
1923     applyToAllGroups.addActionListener(new ActionListener()
1924     {
1925       @Override
1926       public void actionPerformed(ActionEvent e)
1927       {
1928         applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1929       }
1930     });
1931
1932     textColour = new JMenuItem(
1933             MessageManager.getString("label.text_colour"));
1934     textColour.addActionListener(new ActionListener()
1935     {
1936       @Override
1937       public void actionPerformed(ActionEvent e)
1938       {
1939         textColour_actionPerformed();
1940       }
1941     });
1942
1943     conservationMenuItem = new JCheckBoxMenuItem(
1944             MessageManager.getString("action.by_conservation"));
1945     conservationMenuItem.addActionListener(new ActionListener()
1946     {
1947       @Override
1948       public void actionPerformed(ActionEvent e)
1949       {
1950         conservationMenuItem_actionPerformed(conservationMenuItem
1951                 .isSelected());
1952       }
1953     });
1954
1955     abovePIDThreshold = new JCheckBoxMenuItem(
1956             MessageManager.getString("label.above_identity_threshold"));
1957     abovePIDThreshold.addActionListener(new ActionListener()
1958     {
1959       @Override
1960       public void actionPerformed(ActionEvent e)
1961       {
1962         abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
1963       }
1964     });
1965     modifyPID = new JMenuItem(
1966             MessageManager.getString("label.modify_identity_threshold"));
1967     modifyPID.addActionListener(new ActionListener()
1968     {
1969       @Override
1970       public void actionPerformed(ActionEvent e)
1971       {
1972         modifyPID_actionPerformed();
1973       }
1974     });
1975     modifyConservation = new JMenuItem(
1976             MessageManager
1977             .getString("label.modify_conservation_threshold"));
1978     modifyConservation.addActionListener(new ActionListener()
1979     {
1980       @Override
1981       public void actionPerformed(ActionEvent e)
1982       {
1983         modifyConservation_actionPerformed();
1984       }
1985     });
1986
1987     annotationColour = new JMenuItem(
1988             MessageManager.getString("action.by_annotation"));
1989     annotationColour.addActionListener(new ActionListener()
1990     {
1991       @Override
1992       public void actionPerformed(ActionEvent e)
1993       {
1994         annotationColour_actionPerformed();
1995       }
1996     });
1997   }
1998
1999   protected void selectHighlightedColumns_actionPerformed(
2000           ActionEvent actionEvent)
2001   {
2002     // TODO Auto-generated method stub
2003
2004   }
2005
2006   /**
2007    * Generate the reverse sequence (or reverse complement if the flag is true)
2008    * and add it to the alignment
2009    *
2010    * @param complement
2011    */
2012   protected void showReverse_actionPerformed(boolean complement)
2013   {
2014   }
2015
2016   /**
2017    * Try to run script in a Groovy console, having first ensured that this
2018    * alignframe is set as currentAlignFrame in Desktop
2019    */
2020   protected void runGroovy_actionPerformed()
2021   {
2022
2023   }
2024
2025   /**
2026    * Adds the given action listener and key accelerator to the given menu item.
2027    * Also saves in a lookup table to support lookup of action by key stroke.
2028    *
2029    * @param keyStroke
2030    * @param menuItem
2031    * @param actionListener
2032    */
2033   protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2034           JMenuItem menuItem, ActionListener actionListener)
2035   {
2036     menuItem.setAccelerator(keyStroke);
2037     accelerators.put(keyStroke, menuItem);
2038     menuItem.addActionListener(actionListener);
2039   }
2040
2041   /**
2042    * Action on clicking sort annotations by type.
2043    *
2044    * @param sortOrder
2045    */
2046   protected void sortAnnotations_actionPerformed()
2047   {
2048   }
2049
2050   /**
2051    * Action on clicking Show all annotations.
2052    *
2053    * @param forSequences
2054    *          update sequence-related annotations
2055    * @param forAlignment
2056    *          update non-sequence-related annotations
2057    */
2058   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2059           boolean forAlignment)
2060   {
2061     setAnnotationsVisibility(true, forSequences, forAlignment);
2062   }
2063
2064   /**
2065    * Action on clicking Hide all annotations.
2066    *
2067    * @param forSequences
2068    *          update sequence-related annotations
2069    * @param forAlignment
2070    *          update non-sequence-related annotations
2071    */
2072   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2073           boolean forAlignment)
2074   {
2075     setAnnotationsVisibility(false, forSequences, forAlignment);
2076   }
2077
2078   /**
2079    * Set the visibility of annotations to true or false. Can act on
2080    * sequence-related annotations, or alignment-related, or both.
2081    *
2082    * @param visible
2083    * @param forSequences
2084    *          update sequence-related annotations
2085    * @param forAlignment
2086    *          update non-sequence-related annotations
2087    */
2088   protected void setAnnotationsVisibility(boolean visible,
2089           boolean forSequences, boolean forAlignment)
2090   {
2091
2092   }
2093
2094   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2095   {
2096     // TODO Auto-generated method stub
2097
2098   }
2099
2100   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2101   {
2102     // TODO Auto-generated method stub
2103
2104   }
2105
2106   protected void showAllhidden_actionPerformed(ActionEvent e)
2107   {
2108     // TODO Auto-generated method stub
2109
2110   }
2111
2112   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2113   {
2114     // TODO Auto-generated method stub
2115
2116   }
2117
2118   protected void hideAllSelection_actionPerformed(ActionEvent e)
2119   {
2120     // TODO Auto-generated method stub
2121
2122   }
2123
2124   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2125   {
2126     // TODO Auto-generated method stub
2127
2128   }
2129
2130   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2131   {
2132     // TODO Auto-generated method stub
2133
2134   }
2135
2136   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2137   {
2138     // TODO Auto-generated method stub
2139
2140   }
2141
2142   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2143   {
2144     // TODO Auto-generated method stub
2145
2146   }
2147
2148   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2149   {
2150     // TODO Auto-generated method stub
2151
2152   }
2153
2154   protected void showGroupConservation_actionPerformed(ActionEvent e)
2155   {
2156     // TODO Auto-generated method stub
2157
2158   }
2159
2160   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2161   {
2162     // TODO Auto-generated method stub
2163
2164   }
2165
2166   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2167   {
2168     // TODO Auto-generated method stub
2169
2170   }
2171
2172   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2173   {
2174     // TODO Auto-generated method stub
2175
2176   }
2177
2178   protected void followHighlight_actionPerformed()
2179   {
2180     // TODO Auto-generated method stub
2181
2182   }
2183
2184   protected void showNpFeats_actionPerformed(ActionEvent e)
2185   {
2186     // TODO Auto-generated method stub
2187
2188   }
2189
2190   protected void showDbRefs_actionPerformed(ActionEvent e)
2191   {
2192     // TODO Auto-generated method stub
2193
2194   }
2195
2196   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2197   {
2198   }
2199
2200   protected void buildSortByAnnotationScoresMenu()
2201   {
2202   }
2203
2204   protected void extractScores_actionPerformed(ActionEvent e)
2205   {
2206   }
2207
2208   protected void outputText_actionPerformed(ActionEvent e)
2209   {
2210   }
2211
2212   public void addFromFile_actionPerformed(ActionEvent e)
2213   {
2214
2215   }
2216
2217   public void addFromText_actionPerformed(ActionEvent e)
2218   {
2219
2220   }
2221
2222   public void addFromURL_actionPerformed(ActionEvent e)
2223   {
2224
2225   }
2226
2227   public void exportFeatures_actionPerformed(ActionEvent e)
2228   {
2229
2230   }
2231
2232   public void exportAnnotations_actionPerformed(ActionEvent e)
2233   {
2234
2235   }
2236
2237   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2238   {
2239   }
2240
2241   protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2242   {
2243
2244   }
2245
2246   protected void closeMenuItem_actionPerformed(boolean b)
2247   {
2248   }
2249
2250   protected void redoMenuItem_actionPerformed(ActionEvent e)
2251   {
2252   }
2253
2254   protected void undoMenuItem_actionPerformed(ActionEvent e)
2255   {
2256   }
2257
2258   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2259   {
2260   }
2261
2262   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2263   {
2264   }
2265
2266   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2267   {
2268   }
2269
2270   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2271   {
2272   }
2273
2274   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2275   {
2276   }
2277
2278   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2279   {
2280   }
2281
2282   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2283   {
2284   }
2285
2286   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2287   {
2288   }
2289
2290   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2291   {
2292   }
2293
2294   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2295   {
2296   }
2297
2298   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2299   {
2300   }
2301
2302   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2303   {
2304   }
2305
2306   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2307   {
2308   }
2309
2310   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2311   {
2312   }
2313
2314   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2315   {
2316   }
2317
2318   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2319   {
2320   }
2321
2322   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2323   {
2324   }
2325
2326   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2327   {
2328   }
2329
2330   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2331   {
2332   }
2333
2334   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2335   {
2336   }
2337
2338   protected void conservationMenuItem_actionPerformed(boolean selected)
2339   {
2340   }
2341
2342   protected void printMenuItem_actionPerformed(ActionEvent e)
2343   {
2344   }
2345
2346   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2347   {
2348   }
2349
2350   protected void findMenuItem_actionPerformed(ActionEvent e)
2351   {
2352   }
2353
2354   protected void abovePIDThreshold_actionPerformed(boolean selected)
2355   {
2356   }
2357
2358   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2359   {
2360   }
2361
2362   protected void deleteGroups_actionPerformed(ActionEvent e)
2363   {
2364   }
2365
2366   protected void createGroup_actionPerformed(ActionEvent e)
2367   {
2368   }
2369
2370   protected void unGroup_actionPerformed(ActionEvent e)
2371   {
2372   }
2373
2374   protected void copy_actionPerformed(ActionEvent e)
2375   {
2376   }
2377
2378   protected void cut_actionPerformed(ActionEvent e)
2379   {
2380   }
2381
2382   protected void delete_actionPerformed(ActionEvent e)
2383   {
2384   }
2385
2386   protected void pasteNew_actionPerformed(ActionEvent e)
2387   {
2388   }
2389
2390   protected void pasteThis_actionPerformed(ActionEvent e)
2391   {
2392   }
2393
2394   protected void applyToAllGroups_actionPerformed(boolean selected)
2395   {
2396   }
2397
2398   protected void autoAlignSeqs_actionPerformed(boolean selected)
2399   {
2400   }
2401
2402   protected void hmmAlign_actionPerformed(ActionEvent e)
2403   {
2404   }
2405
2406   protected void hmmBuild_actionPerformed(ActionEvent e)
2407           throws IOException, InterruptedException
2408   {
2409   }
2410
2411   protected void hmmSearch_actionPerformed(ActionEvent e)
2412   {
2413   }
2414
2415   public void createPNG(java.io.File f)
2416   {
2417   }
2418
2419   protected void font_actionPerformed(ActionEvent e)
2420   {
2421   }
2422
2423   protected void seqLimit_actionPerformed(ActionEvent e)
2424   {
2425   }
2426
2427   public void seqDBRef_actionPerformed(ActionEvent e)
2428   {
2429
2430   }
2431
2432   public void createEPS(java.io.File f)
2433   {
2434   }
2435
2436   public void createSVG(java.io.File f)
2437   {
2438
2439   }
2440
2441   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2442   {
2443
2444   }
2445
2446   /**
2447    * Template method to handle the 'load T-Coffee scores' menu event.
2448    * <p>
2449    * Subclasses override this method to provide a custom action.
2450    *
2451    * @param event
2452    *          The raised event
2453    */
2454   protected void loadScores_actionPerformed(ActionEvent event)
2455   {
2456
2457   }
2458
2459   protected void jpred_actionPerformed(ActionEvent e)
2460   {
2461   }
2462
2463   protected void scaleAbove_actionPerformed(ActionEvent e)
2464   {
2465   }
2466
2467   protected void scaleLeft_actionPerformed(ActionEvent e)
2468   {
2469   }
2470
2471   protected void scaleRight_actionPerformed(ActionEvent e)
2472   {
2473   }
2474
2475   protected void modifyPID_actionPerformed()
2476   {
2477   }
2478
2479   protected void modifyConservation_actionPerformed()
2480   {
2481   }
2482
2483   protected void saveAs_actionPerformed(ActionEvent e)
2484   {
2485   }
2486
2487   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2488   {
2489   }
2490
2491   public void vamsasStore_actionPerformed(ActionEvent e)
2492   {
2493
2494   }
2495
2496   public void vamsasLoad_actionPerformed(ActionEvent e)
2497   {
2498
2499   }
2500
2501   public void showTranslation_actionPerformed(ActionEvent e)
2502   {
2503
2504   }
2505
2506   public void featureSettings_actionPerformed(ActionEvent e)
2507   {
2508
2509   }
2510
2511   public void fetchSequence_actionPerformed(ActionEvent e)
2512   {
2513
2514   }
2515
2516   public void smoothFont_actionPerformed(ActionEvent e)
2517   {
2518
2519   }
2520
2521   public void annotationColour_actionPerformed()
2522   {
2523   }
2524
2525   public void annotationColumn_actionPerformed(ActionEvent e)
2526   {
2527   }
2528
2529   public void associatedData_actionPerformed(ActionEvent e)
2530   {
2531
2532   }
2533
2534   public void autoCalculate_actionPerformed(ActionEvent e)
2535   {
2536
2537   }
2538
2539   public void sortByTreeOption_actionPerformed(ActionEvent e)
2540   {
2541
2542   }
2543
2544   public void showAllSeqs_actionPerformed(ActionEvent e)
2545   {
2546
2547   }
2548
2549   public void showAllColumns_actionPerformed(ActionEvent e)
2550   {
2551
2552   }
2553
2554   public void hideSelSequences_actionPerformed(ActionEvent e)
2555   {
2556
2557   }
2558
2559   public void hideSelColumns_actionPerformed(ActionEvent e)
2560   {
2561
2562   }
2563
2564   public void hiddenMarkers_actionPerformed(ActionEvent e)
2565   {
2566
2567   }
2568
2569   public void findPdbId_actionPerformed(ActionEvent e)
2570   {
2571
2572   }
2573
2574   public void enterPdbId_actionPerformed(ActionEvent e)
2575   {
2576
2577   }
2578
2579   public void pdbFile_actionPerformed(ActionEvent e)
2580   {
2581
2582   }
2583
2584   public void invertColSel_actionPerformed(ActionEvent e)
2585   {
2586
2587   }
2588
2589   public void tabSelectionChanged(int sel)
2590   {
2591
2592   }
2593
2594   public void tabbedPane_mousePressed(MouseEvent e)
2595   {
2596
2597   }
2598
2599   public void tabbedPane_focusGained(FocusEvent e)
2600   {
2601     requestFocus();
2602   }
2603
2604   public void save_actionPerformed(ActionEvent e)
2605   {
2606
2607   }
2608
2609   public void reload_actionPerformed(ActionEvent e)
2610   {
2611
2612   }
2613
2614   public void newView_actionPerformed(ActionEvent e)
2615   {
2616
2617   }
2618
2619   public void textColour_actionPerformed()
2620   {
2621
2622   }
2623
2624   public void idRightAlign_actionPerformed(ActionEvent e)
2625   {
2626
2627   }
2628
2629   public void expandViews_actionPerformed(ActionEvent e)
2630   {
2631
2632   }
2633
2634   public void gatherViews_actionPerformed(ActionEvent e)
2635   {
2636
2637   }
2638
2639   public void buildTreeSortMenu()
2640   {
2641
2642   }
2643
2644   public void pageSetup_actionPerformed(ActionEvent e)
2645   {
2646
2647   }
2648
2649   public void alignmentProperties()
2650   {
2651
2652   }
2653
2654   protected void expand_newalign(ActionEvent e)
2655   {
2656     // TODO Auto-generated method stub
2657
2658   }
2659
2660   protected boolean isShowAutoCalculatedAbove()
2661   {
2662     return showAutoCalculatedAbove;
2663   }
2664
2665   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2666   {
2667     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2668   }
2669
2670   protected SequenceAnnotationOrder getAnnotationSortOrder()
2671   {
2672     return annotationSortOrder;
2673   }
2674
2675   protected void setAnnotationSortOrder(
2676           SequenceAnnotationOrder annotationSortOrder)
2677   {
2678     this.annotationSortOrder = annotationSortOrder;
2679   }
2680
2681   public Map<KeyStroke, JMenuItem> getAccelerators()
2682   {
2683     return this.accelerators;
2684   }
2685
2686   /**
2687    * Returns the selected index of the tabbed pane, or -1 if none selected
2688    * (including the case where the tabbed pane has not been made visible).
2689    *
2690    * @return
2691    */
2692   public int getTabIndex()
2693   {
2694     return tabbedPane.getSelectedIndex();
2695   }
2696
2697   public JPanel getStatusPanel()
2698   {
2699     return statusPanel;
2700   }
2701
2702   /**
2703    * Sets a reference to the containing split frame. Also makes the 'toggle
2704    * split view' menu item visible and checked.
2705    *
2706    * @param sf
2707    */
2708   public void setSplitFrame(SplitContainerI sf)
2709   {
2710     this.splitFrame = sf;
2711     if (sf != null)
2712     {
2713       this.showComplementMenuItem.setVisible(true);
2714       this.showComplementMenuItem.setState(true);
2715     }
2716   }
2717
2718   public SplitContainerI getSplitViewContainer()
2719   {
2720     return this.splitFrame;
2721   }
2722
2723   protected void showComplement_actionPerformed(boolean complement)
2724   {
2725   }
2726
2727   protected void showInformationHistogram_actionPerformed(ActionEvent e)
2728   {
2729     // TODO Auto-generated method stub
2730
2731   }
2732
2733   protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
2734   {
2735     // TODO Auto-generated method stub
2736
2737   }
2738
2739   protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
2740   {
2741     // TODO Auto-generated method stub
2742
2743   }
2744 }