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 java.awt.BorderLayout;
  24 import java.awt.Color;
  25 import java.awt.GridLayout;
  26 import java.awt.event.ActionEvent;
  27 import java.awt.event.ActionListener;
  28 import java.awt.event.FocusAdapter;
  29 import java.awt.event.FocusEvent;
  30 import java.awt.event.InputEvent;
  31 import java.awt.event.KeyEvent;
  32 import java.awt.event.MouseAdapter;
  33 import java.awt.event.MouseEvent;
  34 import java.io.IOException;
  35 import java.util.HashMap;
  36 import java.util.Map;
  37
  38 import javax.swing.BorderFactory;
  39 import javax.swing.ButtonGroup;
  40 import javax.swing.JCheckBoxMenuItem;
  41 import javax.swing.JInternalFrame;
  42 import javax.swing.JLabel;
  43 import javax.swing.JMenu;
  44 import javax.swing.JMenuBar;
  45 import javax.swing.JMenuItem;
  46 import javax.swing.JPanel;
  47 import javax.swing.JRadioButtonMenuItem;
  48 import javax.swing.JTabbedPane;
  49 import javax.swing.KeyStroke;
  50 import javax.swing.event.ChangeEvent;
  51 import javax.swing.event.MenuEvent;
  52 import javax.swing.event.MenuListener;
  53
  54 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  55 import jalview.analysis.GeneticCodeI;
  56 import jalview.analysis.GeneticCodes;
  57 import jalview.api.SplitContainerI;
  58 import jalview.bin.Cache;
  59 import jalview.gui.JvSwingUtils;
  60 import jalview.gui.Preferences;
  61 import jalview.hmmer.HmmerCommand;
  62 import jalview.io.FileFormatException;
  63 import jalview.io.FileFormats;
  64 import jalview.schemes.ResidueColourScheme;
  65 import jalview.util.MessageManager;
  66 import jalview.util.Platform;
  67
  68
  69 @SuppressWarnings("serial")
  70 public class GAlignFrame extends JInternalFrame
  71 {
  72   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  73
  74   protected JMenuItem closeMenuItem = new JMenuItem();
  75
  76   public JMenu webService = new JMenu();// BH 2019 was protected, but not
  77                                         // sufficient for AlignFrame thread run
  78     // JBP - followed suite for these other service related GUI elements.
  79     // TODO: check we really need these to be public
  80   public JMenu hmmerMenu = new JMenu();
  81
  82   public JMenuItem webServiceNoServices;
  83
  84   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  85
  86   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  87
  88   protected JMenu sortByAnnotScore = new JMenu();
  89
  90   public JLabel statusBar = new JLabel(); // BH 2019 was protected, but not
  91                                           // sufficient for
  92                                           // AlignFrame.printWriter
  93
  94   protected JMenu outputTextboxMenu = new JMenu();
  95
  96   protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
  97
  98   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
  99
 100   protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
 101
 102   protected JMenuItem undoMenuItem = new JMenuItem();
 103
 104   protected JMenuItem redoMenuItem = new JMenuItem();
 105
 106   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 107
 108   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 109
 110   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 111
 112   JMenuItem copy = new JMenuItem();
 113
 114   JMenuItem cut = new JMenuItem();
 115
 116   JMenu pasteMenu = new JMenu();
 117
 118   protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 119
 120   protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 121
 122   protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 123
 124   protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 125
 126   protected JCheckBoxMenuItem applyToAllGroups;
 127
 128   protected JMenu colourMenu = new JMenu();
 129
 130   protected JMenuItem textColour;
 131
 132   protected JCheckBoxMenuItem conservationMenuItem;
 133
 134   protected JMenuItem modifyConservation;
 135
 136   protected JCheckBoxMenuItem abovePIDThreshold;
 137
 138   protected JMenuItem modifyPID;
 139
 140   protected JRadioButtonMenuItem annotationColour;
 141
 142   protected JMenu sortByTreeMenu = new JMenu();
 143
 144   protected JMenu sort = new JMenu();
 145
 146   protected JMenuItem calculateTree = new JMenuItem();
 147
 148   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 149
 150   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 151
 152   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 153
 154   protected JMenu showTranslation = new JMenu();
 155
 156   protected JMenuItem showReverse = new JMenuItem();
 157
 158   protected JMenuItem showReverseComplement = new JMenuItem();
 159
 160   protected JMenu showProducts = new JMenu();
 161
 162   protected JMenuItem runGroovy = new JMenuItem();
 163
 164   protected JMenuItem loadVcf;
 165
 166   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 167
 168   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 169
 170   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 171
 172   protected JPanel statusPanel = new JPanel();
 173
 174   protected JMenuItem showAllSeqAnnotations = new JMenuItem();
 175
 176   protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
 177
 178   protected JMenuItem showAllAlAnnotations = new JMenuItem();
 179
 180   protected JMenuItem hideAllAlAnnotations = new JMenuItem();
 181
 182   protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
 183
 184   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 185
 186   protected JTabbedPane tabbedPane = new JTabbedPane();
 187
 188   protected JMenuItem reload = new JMenuItem();
 189
 190   protected JMenu formatMenu = new JMenu();
 191
 192   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 193
 194   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 195
 196   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 197
 198   protected JMenuItem gatherViews = new JMenuItem();
 199
 200   protected JMenuItem expandViews = new JMenuItem();
 201
 202   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 203
 204   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 205
 206   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 207
 208   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 209
 210   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 211
 212   protected JCheckBoxMenuItem showInformationHistogram = new JCheckBoxMenuItem();
 213
 214   protected JCheckBoxMenuItem showHMMSequenceLogo = new JCheckBoxMenuItem();
 215
 216   protected JCheckBoxMenuItem normaliseHMMSequenceLogo = new JCheckBoxMenuItem();
 217
 218   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 219
 220   protected JMenuItem openFeatureSettings;
 221
 222   private SequenceAnnotationOrder annotationSortOrder;
 223
 224   private boolean showAutoCalculatedAbove = false;
 225
 226   private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
 227
 228   private SplitContainerI splitFrame;
 229
 230   public GAlignFrame()
 231   {
 232     try
 233     {
 234
 235       // for Web-page embedding using id=align-frame-div
 236       setName(Platform.getAppID("alignment"));
 237
 238
 239       jbInit();
 240       setJMenuBar(alignFrameMenuBar);
 241
 242       // dynamically fill save as menu with available formats
 243       for (String ff : FileFormats.getInstance().getWritableFormats(true))
 244       {
 245         JMenuItem item = new JMenuItem(ff);
 246
 247         item.addActionListener(new ActionListener()
 248         {
 249           @Override
 250           public void actionPerformed(ActionEvent e)
 251           {
 252             outputText_actionPerformed(e.getActionCommand());
 253           }
 254         });
 255
 256         outputTextboxMenu.add(item);
 257       }
 258     } catch (Exception e)
 259     {
 260       System.err.println(e.toString());
 261     }
 262
 263     if (Platform.allowMnemonics()) // was "not mac and not JS"
 264     {
 265       closeMenuItem.setMnemonic('C');
 266       outputTextboxMenu.setMnemonic('T');
 267       undoMenuItem.setMnemonic('Z');
 268       redoMenuItem.setMnemonic('0');
 269       copy.setMnemonic('C');
 270       cut.setMnemonic('U');
 271       pasteMenu.setMnemonic('P');
 272       reload.setMnemonic('R');
 273     }
 274   }
 275
 276   private void jbInit() throws Exception
 277   {
 278     initColourMenu();
 279
 280     JMenuItem saveAs = new JMenuItem(
 281             MessageManager.getString("action.save_as"));
 282     ActionListener al = new ActionListener()
 283     {
 284       @Override
 285       public void actionPerformed(ActionEvent e)
 286       {
 287         saveAs_actionPerformed();
 288       }
 289     };
 290
 291     // FIXME getDefaultToolkit throws an exception in Headless mode
 292     KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Platform.SHORTCUT_KEY_MASK | InputEvent.SHIFT_DOWN_MASK,
 293             false);
 294     addMenuActionAndAccelerator(keyStroke, saveAs, al);
 295
 296     closeMenuItem.setText(MessageManager.getString("action.close"));
 297     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Platform.SHORTCUT_KEY_MASK, false);
 298     al = new ActionListener()
 299     {
 300       @Override
 301       public void actionPerformed(ActionEvent e)
 302       {
 303         closeMenuItem_actionPerformed(false);
 304       }
 305     };
 306     addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
 307
 308     JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
 309     JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
 310     JMenu annotationsMenu = new JMenu(
 311             MessageManager.getString("action.annotations"));
 312     JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
 313     colourMenu.setText(MessageManager.getString("action.colour"));
 314     JMenu calculateMenu = new JMenu(
 315             MessageManager.getString("action.calculate"));
 316     webService.setText(MessageManager.getString("action.web_service"));
 317
 318     initHMMERMenu();
 319
 320     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
 321             MessageManager.getString("action.select_all"));
 322     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
 323             Platform.SHORTCUT_KEY_MASK, false);
 324     al = new ActionListener()
 325     {
 326       @Override
 327       public void actionPerformed(ActionEvent e)
 328       {
 329         selectAllSequenceMenuItem_actionPerformed(e);
 330       }
 331     };
 332     addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
 333
 334     JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
 335             MessageManager.getString("action.deselect_all"));
 336     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
 337     al = new ActionListener()
 338     {
 339       @Override
 340       public void actionPerformed(ActionEvent e)
 341       {
 342         deselectAllSequenceMenuItem_actionPerformed(e);
 343       }
 344     };
 345     addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
 346
 347     JMenuItem invertSequenceMenuItem = new JMenuItem(
 348             MessageManager.getString("action.invert_sequence_selection"));
 349     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
 350             Platform.SHORTCUT_KEY_MASK, false);
 351     al = new ActionListener()
 352     {
 353       @Override
 354       public void actionPerformed(ActionEvent e)
 355       {
 356         invertSequenceMenuItem_actionPerformed(e);
 357       }
 358     };
 359     addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
 360
 361     JMenuItem grpsFromSelection = new JMenuItem(
 362             MessageManager.getString("action.make_groups_selection"));
 363     grpsFromSelection.addActionListener(new ActionListener()
 364     {
 365       @Override
 366       public void actionPerformed(ActionEvent e)
 367       {
 368         makeGrpsFromSelection_actionPerformed(e);
 369       }
 370     });
 371     JMenuItem expandAlignment = new JMenuItem(
 372             MessageManager.getString("action.view_flanking_regions"));
 373     expandAlignment.setToolTipText(
 374             MessageManager.getString("label.view_flanking_regions"));
 375     expandAlignment.addActionListener(new ActionListener()
 376     {
 377       @Override
 378       public void actionPerformed(ActionEvent e)
 379       {
 380         expand_newalign(e);
 381       }
 382     });
 383     JMenuItem remove2LeftMenuItem = new JMenuItem(
 384             MessageManager.getString("action.remove_left"));
 385     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
 386             Platform.SHORTCUT_KEY_MASK, false);
 387     al = new ActionListener()
 388     {
 389       @Override
 390       public void actionPerformed(ActionEvent e)
 391       {
 392         remove2LeftMenuItem_actionPerformed(e);
 393       }
 394     };
 395     addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
 396
 397     JMenuItem remove2RightMenuItem = new JMenuItem(
 398             MessageManager.getString("action.remove_right"));
 399     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
 400             Platform.SHORTCUT_KEY_MASK, false);
 401     al = new ActionListener()
 402     {
 403       @Override
 404       public void actionPerformed(ActionEvent e)
 405       {
 406         remove2RightMenuItem_actionPerformed(e);
 407       }
 408     };
 409     addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
 410
 411     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
 412             MessageManager.getString("action.remove_empty_columns"));
 413     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
 414             Platform.SHORTCUT_KEY_MASK, false);
 415     al = new ActionListener()
 416     {
 417       @Override
 418       public void actionPerformed(ActionEvent e)
 419       {
 420         removeGappedColumnMenuItem_actionPerformed(e);
 421       }
 422     };
 423     addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
 424
 425     JMenuItem removeAllGapsMenuItem = new JMenuItem(
 426             MessageManager.getString("action.remove_all_gaps"));
 427     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
 428             Platform.SHORTCUT_KEY_MASK
 429                     | InputEvent.SHIFT_DOWN_MASK,
 430             false);
 431     al = new ActionListener()
 432     {
 433       @Override
 434       public void actionPerformed(ActionEvent e)
 435       {
 436         removeAllGapsMenuItem_actionPerformed(e);
 437       }
 438     };
 439     addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
 440
 441     JMenuItem justifyLeftMenuItem = new JMenuItem(
 442             MessageManager.getString("action.left_justify_alignment"));
 443     justifyLeftMenuItem.addActionListener(new ActionListener()
 444     {
 445       @Override
 446       public void actionPerformed(ActionEvent e)
 447       {
 448         justifyLeftMenuItem_actionPerformed(e);
 449       }
 450     });
 451     JMenuItem justifyRightMenuItem = new JMenuItem(
 452             MessageManager.getString("action.right_justify_alignment"));
 453     justifyRightMenuItem.addActionListener(new ActionListener()
 454     {
 455       @Override
 456       public void actionPerformed(ActionEvent e)
 457       {
 458         justifyRightMenuItem_actionPerformed(e);
 459       }
 460     });
 461     viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
 462     viewBoxesMenuItem.setState(true);
 463     viewBoxesMenuItem.addActionListener(new ActionListener()
 464     {
 465       @Override
 466       public void actionPerformed(ActionEvent e)
 467       {
 468         viewBoxesMenuItem_actionPerformed(e);
 469       }
 470     });
 471     viewTextMenuItem.setText(MessageManager.getString("action.text"));
 472     viewTextMenuItem.setState(true);
 473     viewTextMenuItem.addActionListener(new ActionListener()
 474     {
 475       @Override
 476       public void actionPerformed(ActionEvent e)
 477       {
 478         viewTextMenuItem_actionPerformed(e);
 479       }
 480     });
 481     showNonconservedMenuItem
 482             .setText(MessageManager.getString("label.show_non_conserved"));
 483     showNonconservedMenuItem.setState(false);
 484     showNonconservedMenuItem.addActionListener(new ActionListener()
 485     {
 486       @Override
 487       public void actionPerformed(ActionEvent e)
 488       {
 489         showUnconservedMenuItem_actionPerformed(e);
 490       }
 491     });
 492     JMenuItem sortPairwiseMenuItem = new JMenuItem(
 493             MessageManager.getString("action.by_pairwise_id"));
 494     sortPairwiseMenuItem.addActionListener(new ActionListener()
 495     {
 496       @Override
 497       public void actionPerformed(ActionEvent e)
 498       {
 499         sortPairwiseMenuItem_actionPerformed(e);
 500       }
 501     });
 502     JMenuItem sortIDMenuItem = new JMenuItem(
 503             MessageManager.getString("action.by_id"));
 504     sortIDMenuItem.addActionListener(new ActionListener()
 505     {
 506       @Override
 507       public void actionPerformed(ActionEvent e)
 508       {
 509         sortIDMenuItem_actionPerformed(e);
 510       }
 511     });
 512     JMenuItem sortLengthMenuItem = new JMenuItem(
 513             MessageManager.getString("action.by_length"));
 514     sortLengthMenuItem.addActionListener(new ActionListener()
 515     {
 516       @Override
 517       public void actionPerformed(ActionEvent e)
 518       {
 519         sortLengthMenuItem_actionPerformed(e);
 520       }
 521     });
 522     JMenuItem sortGroupMenuItem = new JMenuItem(
 523             MessageManager.getString("action.by_group"));
 524     sortGroupMenuItem.addActionListener(new ActionListener()
 525     {
 526       @Override
 527       public void actionPerformed(ActionEvent e)
 528       {
 529         sortGroupMenuItem_actionPerformed(e);
 530       }
 531     });
 532     JMenuItem sortEValueMenuItem = new JMenuItem(
 533             MessageManager.getString("action.by_evalue"));
 534     sortEValueMenuItem.addActionListener(new ActionListener()
 535     {
 536       @Override
 537       public void actionPerformed(ActionEvent e)
 538       {
 539         sortEValueMenuItem_actionPerformed(e);
 540       }
 541     });
 542     JMenuItem sortBitScoreMenuItem = new JMenuItem(
 543             MessageManager.getString("action.by_bit_score"));
 544     sortBitScoreMenuItem.addActionListener(new ActionListener()
 545     {
 546       @Override
 547       public void actionPerformed(ActionEvent e)
 548       {
 549         sortBitScoreMenuItem_actionPerformed(e);
 550       }
 551     });
 552
 553     JMenuItem removeRedundancyMenuItem = new JMenuItem(
 554             MessageManager.getString("action.remove_redundancy"));
 555     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
 556             Platform.SHORTCUT_KEY_MASK, false);
 557     al = new ActionListener()
 558     {
 559       @Override
 560       public void actionPerformed(ActionEvent e)
 561       {
 562         removeRedundancyMenuItem_actionPerformed(e);
 563       }
 564     };
 565     addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
 566
 567     JMenuItem filterByEValue = new JMenuItem(
 568             MessageManager.getString("action.filter_by_evalue"));
 569     filterByEValue.addActionListener(new ActionListener()
 570     {
 571       @Override
 572       public void actionPerformed(ActionEvent e)
 573       {
 574         filterByEValue_actionPerformed();
 575       }
 576
 577     });
 578
 579     JMenuItem filterByScore = new JMenuItem(
 580             MessageManager.getString("action.filter_by_score"));
 581     filterByScore.addActionListener(new ActionListener()
 582     {
 583       @Override
 584       public void actionPerformed(ActionEvent e)
 585       {
 586         filterByScore_actionPerformed();
 587       }
 588
 589     });
 590
 591     JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
 592             MessageManager.getString("action.pairwise_alignment"));
 593     pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
 594     {
 595       @Override
 596       public void actionPerformed(ActionEvent e)
 597       {
 598         pairwiseAlignmentMenuItem_actionPerformed(e);
 599       }
 600     });
 601
 602     this.getContentPane().setLayout(new BorderLayout());
 603     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 604     statusBar.setBackground(Color.white);
 605     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 606     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 607     statusBar.setText(MessageManager.getString("label.status_bar"));
 608
 609     outputTextboxMenu
 610             .setText(MessageManager.getString("label.out_to_textbox"));
 611
 612
 613     annotationPanelMenuItem.setActionCommand("");
 614     annotationPanelMenuItem
 615             .setText(MessageManager.getString("label.show_annotations"));
 616     annotationPanelMenuItem
 617             .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
 618     annotationPanelMenuItem.addActionListener(new ActionListener()
 619     {
 620       @Override
 621       public void actionPerformed(ActionEvent e)
 622       {
 623         annotationPanelMenuItem_actionPerformed(e);
 624       }
 625     });
 626     showAllAlAnnotations.setText(
 627             MessageManager.getString("label.show_all_al_annotations"));
 628     final boolean isAnnotationPanelShown = annotationPanelMenuItem
 629             .getState();
 630     showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 631     showAllAlAnnotations.addActionListener(new ActionListener()
 632     {
 633       @Override
 634       public void actionPerformed(ActionEvent e)
 635       {
 636         showAllAnnotations_actionPerformed(false, true);
 637       }
 638     });
 639     hideAllAlAnnotations.setText(
 640             MessageManager.getString("label.hide_all_al_annotations"));
 641     hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 642     hideAllAlAnnotations.addActionListener(new ActionListener()
 643     {
 644       @Override
 645       public void actionPerformed(ActionEvent e)
 646       {
 647         hideAllAnnotations_actionPerformed(false, true);
 648       }
 649     });
 650     showAllSeqAnnotations.setText(
 651             MessageManager.getString("label.show_all_seq_annotations"));
 652     showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 653     showAllSeqAnnotations.addActionListener(new ActionListener()
 654     {
 655       @Override
 656       public void actionPerformed(ActionEvent e)
 657       {
 658         showAllAnnotations_actionPerformed(true, false);
 659       }
 660     });
 661     hideAllSeqAnnotations.setText(
 662             MessageManager.getString("label.hide_all_seq_annotations"));
 663     hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 664     hideAllSeqAnnotations.addActionListener(new ActionListener()
 665     {
 666       @Override
 667       public void actionPerformed(ActionEvent e)
 668       {
 669         hideAllAnnotations_actionPerformed(true, false);
 670       }
 671     });
 672     SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
 673             .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
 674                     SequenceAnnotationOrder.NONE.name()));
 675     final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
 676             MessageManager.getString("label.sort_annotations_by_sequence"));
 677     final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
 678             MessageManager.getString("label.sort_annotations_by_label"));
 679
 680
 681     sortAnnBySequence.setSelected(
 682             sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
 683     sortAnnBySequence.addActionListener(new ActionListener()
 684     {
 685       @Override
 686       public void actionPerformed(ActionEvent e)
 687       {
 688         boolean newState = sortAnnBySequence.getState();
 689         sortAnnByLabel.setSelected(false);
 690         setAnnotationSortOrder(
 691                 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 692                         : SequenceAnnotationOrder.NONE);
 693         sortAnnotations_actionPerformed();
 694       }
 695     });
 696     sortAnnByLabel.setSelected(
 697             sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
 698     sortAnnByLabel.addActionListener(new ActionListener()
 699     {
 700       @Override
 701       public void actionPerformed(ActionEvent e)
 702       {
 703         boolean newState = sortAnnByLabel.getState();
 704         sortAnnBySequence.setSelected(false);
 705         setAnnotationSortOrder(
 706                 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 707                         : SequenceAnnotationOrder.NONE);
 708         sortAnnotations_actionPerformed();
 709       }
 710     });
 711     colourTextMenuItem = new JCheckBoxMenuItem(
 712             MessageManager.getString("label.colour_text"));
 713     colourTextMenuItem.addActionListener(new ActionListener()
 714     {
 715       @Override
 716       public void actionPerformed(ActionEvent e)
 717       {
 718         colourTextMenuItem_actionPerformed(e);
 719       }
 720     });
 721
 722     JMenuItem htmlMenuItem = new JMenuItem(
 723             MessageManager.getString("label.html"));
 724     htmlMenuItem.addActionListener(new ActionListener()
 725     {
 726       @Override
 727       public void actionPerformed(ActionEvent e)
 728       {
 729         htmlMenuItem_actionPerformed(e);
 730       }
 731     });
 732
 733     JMenuItem createBioJS = new JMenuItem(
 734             MessageManager.getString("label.biojs_html_export"));
 735     createBioJS.addActionListener(new java.awt.event.ActionListener()
 736     {
 737       @Override
 738       public void actionPerformed(ActionEvent e)
 739       {
 740         bioJSMenuItem_actionPerformed(e);
 741       }
 742     });
 743
 744     JMenuItem overviewMenuItem = new JMenuItem(
 745             MessageManager.getString("label.overview_window"));
 746     overviewMenuItem.addActionListener(new ActionListener()
 747     {
 748       @Override
 749       public void actionPerformed(ActionEvent e)
 750       {
 751         overviewMenuItem_actionPerformed(e);
 752       }
 753     });
 754
 755     undoMenuItem.setEnabled(false);
 756     undoMenuItem.setText(MessageManager.getString("action.undo"));
 757     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
 758             Platform.SHORTCUT_KEY_MASK, false);
 759     al = new ActionListener()
 760     {
 761       @Override
 762       public void actionPerformed(ActionEvent e)
 763       {
 764         undoMenuItem_actionPerformed(e);
 765       }
 766     };
 767     addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
 768
 769     redoMenuItem.setEnabled(false);
 770     redoMenuItem.setText(MessageManager.getString("action.redo"));
 771     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
 772             Platform.SHORTCUT_KEY_MASK, false);
 773     al = new ActionListener()
 774     {
 775       @Override
 776       public void actionPerformed(ActionEvent e)
 777       {
 778         redoMenuItem_actionPerformed(e);
 779       }
 780     };
 781     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
 782
 783     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
 784     wrapMenuItem.addActionListener(new ActionListener()
 785     {
 786       @Override
 787       public void actionPerformed(ActionEvent e)
 788       {
 789         wrapMenuItem_actionPerformed(e);
 790       }
 791     });
 792
 793     JMenuItem printMenuItem = new JMenuItem(
 794             MessageManager.getString("action.print"));
 795     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
 796             Platform.SHORTCUT_KEY_MASK, false);
 797     al = new ActionListener()
 798     {
 799       @Override
 800       public void actionPerformed(ActionEvent e)
 801       {
 802         printMenuItem_actionPerformed(e);
 803       }
 804     };
 805     addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
 806
 807     renderGapsMenuItem
 808             .setText(MessageManager.getString("action.show_gaps"));
 809     renderGapsMenuItem.setState(true);
 810     renderGapsMenuItem.addActionListener(new ActionListener()
 811     {
 812       @Override
 813       public void actionPerformed(ActionEvent e)
 814       {
 815         renderGapsMenuItem_actionPerformed(e);
 816       }
 817     });
 818
 819     JMenuItem findMenuItem = new JMenuItem(
 820             MessageManager.getString("action.find"));
 821     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
 822             Platform.SHORTCUT_KEY_MASK, false);
 823     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
 824             MessageManager.getString("label.find_tip")));
 825     al = new ActionListener()
 826     {
 827       @Override
 828       public void actionPerformed(ActionEvent e)
 829       {
 830         findMenuItem_actionPerformed(e);
 831       }
 832     };
 833     addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
 834
 835     showSeqFeatures.setText(
 836             MessageManager.getString("label.show_sequence_features"));
 837
 838     showSeqFeatures.addActionListener(new ActionListener()
 839     {
 840       @Override
 841       public void actionPerformed(ActionEvent actionEvent)
 842       {
 843         showSeqFeatures_actionPerformed(actionEvent);
 844       }
 845     });
 846     /*
 847      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
 848      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
 849      * void actionPerformed(ActionEvent actionEvent) {
 850      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
 851      */
 852     showDbRefsMenuitem
 853             .setText(MessageManager.getString("label.show_database_refs"));
 854     showDbRefsMenuitem.addActionListener(new ActionListener()
 855     {
 856
 857       @Override
 858       public void actionPerformed(ActionEvent e)
 859       {
 860         showDbRefs_actionPerformed(e);
 861       }
 862
 863     });
 864     showNpFeatsMenuitem.setText(
 865             MessageManager.getString("label.show_non_positional_features"));
 866     showNpFeatsMenuitem.addActionListener(new ActionListener()
 867     {
 868
 869       @Override
 870       public void actionPerformed(ActionEvent e)
 871       {
 872         showNpFeats_actionPerformed(e);
 873       }
 874
 875     });
 876     showGroupConservation
 877             .setText(MessageManager.getString("label.group_conservation"));
 878     showGroupConservation.addActionListener(new ActionListener()
 879     {
 880
 881       @Override
 882       public void actionPerformed(ActionEvent e)
 883       {
 884         showGroupConservation_actionPerformed(e);
 885       }
 886
 887     });
 888
 889     showGroupConsensus
 890             .setText(MessageManager.getString("label.group_consensus"));
 891     showGroupConsensus.addActionListener(new ActionListener()
 892     {
 893
 894       @Override
 895       public void actionPerformed(ActionEvent e)
 896       {
 897         showGroupConsensus_actionPerformed(e);
 898       }
 899
 900     });
 901     showConsensusHistogram.setText(
 902             MessageManager.getString("label.show_consensus_histogram"));
 903     showConsensusHistogram.addActionListener(new ActionListener()
 904     {
 905
 906       @Override
 907       public void actionPerformed(ActionEvent e)
 908       {
 909         showConsensusHistogram_actionPerformed(e);
 910       }
 911
 912     });
 913     showSequenceLogo
 914             .setText(MessageManager.getString("label.show_consensus_logo"));
 915     showSequenceLogo.addActionListener(new ActionListener()
 916     {
 917
 918       @Override
 919       public void actionPerformed(ActionEvent e)
 920       {
 921         showSequenceLogo_actionPerformed(e);
 922       }
 923
 924     });
 925     normaliseSequenceLogo
 926             .setText(MessageManager.getString("label.norm_consensus_logo"));
 927     normaliseSequenceLogo.addActionListener(new ActionListener()
 928     {
 929
 930       @Override
 931       public void actionPerformed(ActionEvent e)
 932       {
 933         normaliseSequenceLogo_actionPerformed(e);
 934       }
 935
 936     });
 937     applyAutoAnnotationSettings
 938             .setText(MessageManager.getString("label.apply_all_groups"));
 939     applyAutoAnnotationSettings.setState(false);
 940     applyAutoAnnotationSettings.setVisible(true);
 941     applyAutoAnnotationSettings.addActionListener(new ActionListener()
 942     {
 943       @Override
 944       public void actionPerformed(ActionEvent e)
 945       {
 946         applyAutoAnnotationSettings_actionPerformed(e);
 947       }
 948     });
 949
 950     ButtonGroup buttonGroup = new ButtonGroup();
 951     final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
 952             MessageManager.getString("label.show_first"));
 953     final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
 954             MessageManager.getString("label.show_last"));
 955     buttonGroup.add(showAutoFirst);
 956     buttonGroup.add(showAutoLast);
 957     final boolean autoFirst = Cache
 958             .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
 959     showAutoFirst.setSelected(autoFirst);
 960     setShowAutoCalculatedAbove(autoFirst);
 961     showAutoFirst.addActionListener(new ActionListener()
 962     {
 963       @Override
 964       public void actionPerformed(ActionEvent e)
 965       {
 966         setShowAutoCalculatedAbove(showAutoFirst.isSelected());
 967         sortAnnotations_actionPerformed();
 968       }
 969     });
 970     showAutoLast.setSelected(!showAutoFirst.isSelected());
 971     showAutoLast.addActionListener(new ActionListener()
 972     {
 973       @Override
 974       public void actionPerformed(ActionEvent e)
 975       {
 976         setShowAutoCalculatedAbove(!showAutoLast.isSelected());
 977         sortAnnotations_actionPerformed();
 978       }
 979     });
 980
 981     JMenuItem deleteGroups = new JMenuItem(
 982             MessageManager.getString("action.undefine_groups"));
 983     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
 984             Platform.SHORTCUT_KEY_MASK, false);
 985     al = new ActionListener()
 986     {
 987       @Override
 988       public void actionPerformed(ActionEvent e)
 989       {
 990         deleteGroups_actionPerformed(e);
 991       }
 992     };
 993     addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
 994
 995     JMenuItem annotationColumn = new JMenuItem(
 996             MessageManager.getString("action.select_by_annotation"));
 997     annotationColumn.addActionListener(new ActionListener()
 998     {
 999       @Override
1000       public void actionPerformed(ActionEvent e)
1001       {
1002         annotationColumn_actionPerformed(e);
1003       }
1004     });
1005
1006     JMenuItem createGroup = new JMenuItem(
1007             MessageManager.getString("action.create_group"));
1008     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
1009             Platform.SHORTCUT_KEY_MASK, false);
1010     al = new ActionListener()
1011     {
1012       @Override
1013       public void actionPerformed(ActionEvent e)
1014       {
1015         createGroup_actionPerformed(e);
1016       }
1017     };
1018     addMenuActionAndAccelerator(keyStroke, createGroup, al);
1019
1020     JMenuItem unGroup = new JMenuItem(
1021             MessageManager.getString("action.remove_group"));
1022     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
1023             Platform.SHORTCUT_KEY_MASK
1024                     | InputEvent.SHIFT_DOWN_MASK,
1025             false);
1026     al = new ActionListener()
1027     {
1028       @Override
1029       public void actionPerformed(ActionEvent e)
1030       {
1031         unGroup_actionPerformed(e);
1032       }
1033     };
1034     addMenuActionAndAccelerator(keyStroke, unGroup, al);
1035
1036     copy.setText(MessageManager.getString("action.copy"));
1037     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
1038             Platform.SHORTCUT_KEY_MASK, false);
1039
1040     al = new ActionListener()
1041     {
1042       @Override
1043       public void actionPerformed(ActionEvent e)
1044       {
1045         copy_actionPerformed();
1046       }
1047     };
1048     addMenuActionAndAccelerator(keyStroke, copy, al);
1049
1050     cut.setText(MessageManager.getString("action.cut"));
1051     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
1052             Platform.SHORTCUT_KEY_MASK, false);
1053     al = new ActionListener()
1054     {
1055       @Override
1056       public void actionPerformed(ActionEvent e)
1057       {
1058         cut_actionPerformed();
1059       }
1060     };
1061     addMenuActionAndAccelerator(keyStroke, cut, al);
1062
1063     JMenuItem delete = new JMenuItem(
1064             MessageManager.getString("action.delete"));
1065     delete.addActionListener(new ActionListener()
1066     {
1067       @Override
1068       public void actionPerformed(ActionEvent e)
1069       {
1070         delete_actionPerformed();
1071       }
1072     });
1073
1074     pasteMenu.setText(MessageManager.getString("action.paste"));
1075     JMenuItem pasteNew = new JMenuItem(
1076             MessageManager.getString("label.to_new_alignment"));
1077     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1078             Platform.SHORTCUT_KEY_MASK
1079                     | InputEvent.SHIFT_DOWN_MASK,
1080             false);
1081     al = new ActionListener()
1082     {
1083       @Override
1084       public void actionPerformed(ActionEvent e)
1085       {
1086         try
1087         {
1088           pasteNew_actionPerformed(e);
1089         } catch (IOException | InterruptedException e1)
1090         {
1091           // TODO Auto-generated catch block
1092           e1.printStackTrace();
1093         }
1094       }
1095     };
1096     addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1097
1098     JMenuItem pasteThis = new JMenuItem(
1099             MessageManager.getString("label.to_this_alignment"));
1100     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1101             Platform.SHORTCUT_KEY_MASK, false);
1102     al = new ActionListener()
1103     {
1104       @Override
1105       public void actionPerformed(ActionEvent e)
1106       {
1107         try
1108         {
1109           pasteThis_actionPerformed(e);
1110         } catch (IOException | InterruptedException e1)
1111         {
1112           // TODO Auto-generated catch block
1113           e1.printStackTrace();
1114         }
1115       }
1116     };
1117     addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1118
1119     JMenuItem createPNG = new JMenuItem("PNG");
1120     createPNG.addActionListener(new ActionListener()
1121     {
1122       @Override
1123       public void actionPerformed(ActionEvent e)
1124       {
1125         createPNG(null);
1126       }
1127     });
1128     createPNG.setActionCommand(
1129             MessageManager.getString("label.save_png_image"));
1130     JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1131     font.addActionListener(new ActionListener()
1132     {
1133       @Override
1134       public void actionPerformed(ActionEvent e)
1135       {
1136         font_actionPerformed(e);
1137       }
1138     });
1139     seqLimits.setText(
1140             MessageManager.getString("label.show_sequence_limits"));
1141     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1142     seqLimits.addActionListener(new ActionListener()
1143     {
1144       @Override
1145       public void actionPerformed(ActionEvent e)
1146       {
1147         seqLimit_actionPerformed(e);
1148       }
1149     });
1150     JMenuItem epsFile = new JMenuItem("EPS");
1151     epsFile.addActionListener(new ActionListener()
1152     {
1153       @Override
1154       public void actionPerformed(ActionEvent e)
1155       {
1156         createEPS(null);
1157       }
1158     });
1159
1160     JMenuItem createSVG = new JMenuItem("SVG");
1161     createSVG.addActionListener(new ActionListener()
1162     {
1163       @Override
1164       public void actionPerformed(ActionEvent e)
1165       {
1166         createSVG(null);
1167       }
1168     });
1169
1170     JMenuItem loadTreeMenuItem = new JMenuItem(
1171             MessageManager.getString("label.load_associated_tree"));
1172     loadTreeMenuItem.setActionCommand(
1173             MessageManager.getString("label.load_tree_for_sequence_set"));
1174     loadTreeMenuItem.addActionListener(new ActionListener()
1175     {
1176       @Override
1177       public void actionPerformed(ActionEvent e)
1178       {
1179         loadTreeMenuItem_actionPerformed(e);
1180       }
1181     });
1182
1183     scaleAbove.setVisible(false);
1184     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1185     scaleAbove.addActionListener(new ActionListener()
1186     {
1187       @Override
1188       public void actionPerformed(ActionEvent e)
1189       {
1190         scaleAbove_actionPerformed(e);
1191       }
1192     });
1193     scaleLeft.setVisible(false);
1194     scaleLeft.setSelected(true);
1195     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1196     scaleLeft.addActionListener(new ActionListener()
1197     {
1198       @Override
1199       public void actionPerformed(ActionEvent e)
1200       {
1201         scaleLeft_actionPerformed(e);
1202       }
1203     });
1204     scaleRight.setVisible(false);
1205     scaleRight.setSelected(true);
1206     scaleRight.setText(MessageManager.getString("action.scale_right"));
1207     scaleRight.addActionListener(new ActionListener()
1208     {
1209       @Override
1210       public void actionPerformed(ActionEvent e)
1211       {
1212         scaleRight_actionPerformed(e);
1213       }
1214     });
1215     centreColumnLabelsMenuItem.setVisible(true);
1216     centreColumnLabelsMenuItem.setState(false);
1217     centreColumnLabelsMenuItem.setText(
1218             MessageManager.getString("label.centre_column_labels"));
1219     centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1220     {
1221       @Override
1222       public void actionPerformed(ActionEvent e)
1223       {
1224         centreColumnLabels_actionPerformed(e);
1225       }
1226     });
1227     followHighlightMenuItem.setVisible(true);
1228     followHighlightMenuItem.setState(true);
1229     followHighlightMenuItem
1230             .setText(MessageManager.getString("label.automatic_scrolling"));
1231     followHighlightMenuItem.addActionListener(new ActionListener()
1232     {
1233
1234       @Override
1235       public void actionPerformed(ActionEvent e)
1236       {
1237         followHighlight_actionPerformed();
1238       }
1239
1240     });
1241
1242     sortByTreeMenu
1243             .setText(MessageManager.getString("action.by_tree_order"));
1244     sort.setText(MessageManager.getString("action.sort"));
1245     sort.addMenuListener(new MenuListener()
1246     {
1247       @Override
1248       public void menuSelected(MenuEvent e)
1249       {
1250         enableSortMenuOptions();
1251       }
1252
1253       @Override
1254       public void menuDeselected(MenuEvent e)
1255       {
1256       }
1257
1258       @Override
1259       public void menuCanceled(MenuEvent e)
1260       {
1261       }
1262     });
1263     sortByTreeMenu.addMenuListener(new MenuListener()
1264     {
1265       @Override
1266       public void menuSelected(MenuEvent e)
1267       {
1268         buildTreeSortMenu();
1269       }
1270
1271       @Override
1272       public void menuDeselected(MenuEvent e)
1273       {
1274       }
1275
1276       @Override
1277       public void menuCanceled(MenuEvent e)
1278       {
1279       }
1280     });
1281     sortByAnnotScore
1282             .setText(MessageManager.getString("label.sort_by_score"));
1283     sort.add(sortByAnnotScore);
1284     sort.addMenuListener(new javax.swing.event.MenuListener()
1285     {
1286
1287       @Override
1288       public void menuCanceled(MenuEvent e)
1289       {
1290       }
1291
1292       @Override
1293       public void menuDeselected(MenuEvent e)
1294       {
1295       }
1296
1297       @Override
1298       public void menuSelected(MenuEvent e)
1299       {
1300         buildSortByAnnotationScoresMenu();
1301       }
1302     });
1303     sortByAnnotScore.setVisible(false);
1304
1305     calculateTree
1306             .setText(MessageManager.getString("action.calculate_tree_pca"));
1307
1308     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1309     padGapsMenuitem
1310             .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
1311     padGapsMenuitem.addActionListener(new ActionListener()
1312     {
1313       @Override
1314       public void actionPerformed(ActionEvent e)
1315       {
1316         padGapsMenuitem_actionPerformed(e);
1317       }
1318     });
1319     JMenuItem vamsasStore = new JMenuItem(
1320             MessageManager.getString("label.vamsas_store"));
1321     vamsasStore.setVisible(false);
1322     vamsasStore.addActionListener(new ActionListener()
1323     {
1324       @Override
1325       public void actionPerformed(ActionEvent e)
1326       {
1327         vamsasStore_actionPerformed(e);
1328       }
1329     });
1330
1331     /*
1332      * Translate as cDNA with sub-menu of translation tables
1333      */
1334     showTranslation
1335             .setText(MessageManager.getString("label.translate_cDNA"));
1336     boolean first = true;
1337     for (final GeneticCodeI table : GeneticCodes.getInstance()
1338             .getCodeTables())
1339     {
1340       JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
1341       showTranslation.add(item);
1342       item.addActionListener(new ActionListener()
1343       {
1344         @Override
1345         public void actionPerformed(ActionEvent e)
1346         {
1347           showTranslation_actionPerformed(table);
1348         }
1349       });
1350       if (first)
1351       {
1352         showTranslation.addSeparator();
1353       }
1354       first = false;
1355     }
1356
1357     showReverse.setText(MessageManager.getString("label.reverse"));
1358     showReverse.addActionListener(new ActionListener()
1359     {
1360       @Override
1361       public void actionPerformed(ActionEvent e)
1362       {
1363         showReverse_actionPerformed(false);
1364       }
1365     });
1366     showReverseComplement
1367             .setText(MessageManager.getString("label.reverse_complement"));
1368     showReverseComplement.addActionListener(new ActionListener()
1369     {
1370       @Override
1371       public void actionPerformed(ActionEvent e)
1372       {
1373         showReverse_actionPerformed(true);
1374       }
1375     });
1376
1377     JMenuItem extractScores = new JMenuItem(
1378             MessageManager.getString("label.extract_scores"));
1379     extractScores.addActionListener(new ActionListener()
1380     {
1381       @Override
1382       public void actionPerformed(ActionEvent e)
1383       {
1384         extractScores_actionPerformed(e);
1385       }
1386     });
1387     extractScores.setVisible(true);
1388     // JBPNote: TODO: make gui for regex based score extraction
1389
1390     // for show products actions see AlignFrame.canShowProducts
1391     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1392
1393     runGroovy.setText(MessageManager.getString("label.run_groovy"));
1394     runGroovy.setToolTipText(
1395             MessageManager.getString("label.run_groovy_tip"));
1396     runGroovy.addActionListener(new ActionListener()
1397     {
1398       @Override
1399       public void actionPerformed(ActionEvent e)
1400       {
1401         runGroovy_actionPerformed();
1402       }
1403     });
1404
1405     openFeatureSettings = new JMenuItem(
1406             MessageManager.getString("action.feature_settings"));
1407     openFeatureSettings.addActionListener(new ActionListener()
1408     {
1409       @Override
1410       public void actionPerformed(ActionEvent e)
1411       {
1412         featureSettings_actionPerformed(e);
1413       }
1414     });
1415
1416     /*
1417      * add sub-menu of database we can fetch from
1418      */
1419     JMenuItem fetchSequence = new JMenuItem(
1420             MessageManager.getString("label.fetch_sequences"));
1421     fetchSequence.addActionListener(new ActionListener()
1422     {
1423       @Override
1424       public void actionPerformed(ActionEvent e)
1425       {
1426         fetchSequence_actionPerformed();
1427       }
1428     });
1429
1430     JMenuItem associatedData = new JMenuItem(
1431             MessageManager.getString("label.load_features_annotations"));
1432     associatedData.addActionListener(new ActionListener()
1433     {
1434       @Override
1435       public void actionPerformed(ActionEvent e)
1436       {
1437         try
1438         {
1439           associatedData_actionPerformed(e);
1440         } catch (IOException | InterruptedException e1)
1441         {
1442           // TODO Auto-generated catch block
1443           e1.printStackTrace();
1444         }
1445       }
1446     });
1447     loadVcf = new JMenuItem(
1448             MessageManager.getString("label.load_vcf_file"));
1449     loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
1450     loadVcf.addActionListener(new ActionListener()
1451     {
1452       @Override
1453       public void actionPerformed(ActionEvent e)
1454       {
1455         loadVcf_actionPerformed();
1456       }
1457     });
1458     autoCalculate.setText(
1459             MessageManager.getString("label.autocalculate_consensus"));
1460     autoCalculate.setState(
1461             jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1462     autoCalculate.addActionListener(new ActionListener()
1463     {
1464       @Override
1465       public void actionPerformed(ActionEvent e)
1466       {
1467         autoCalculate_actionPerformed(e);
1468       }
1469     });
1470     sortByTree.setText(
1471             MessageManager.getString("label.sort_alignment_new_tree"));
1472     sortByTree.setToolTipText("<html>" + MessageManager.getString(
1473             "label.enable_automatically_sort_alignment_when_open_new_tree"));
1474     sortByTree
1475             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1476     sortByTree.addActionListener(new ActionListener()
1477     {
1478       @Override
1479       public void actionPerformed(ActionEvent e)
1480       {
1481         sortByTreeOption_actionPerformed(e);
1482       }
1483     });
1484
1485     listenToViewSelections.setText(
1486             MessageManager.getString("label.listen_for_selections"));
1487     listenToViewSelections
1488             .setToolTipText("<html>" + MessageManager.getString(
1489                     "label.selections_mirror_selections_made_same_sequences_other_views"));
1490     listenToViewSelections.setState(false);
1491     listenToViewSelections.addActionListener(new ActionListener()
1492     {
1493       @Override
1494       public void actionPerformed(ActionEvent e)
1495       {
1496         listenToViewSelections_actionPerformed(e);
1497       }
1498     });
1499
1500     JMenu addSequenceMenu = new JMenu(
1501             MessageManager.getString("label.add_sequences"));
1502     JMenuItem addFromFile = new JMenuItem(
1503             MessageManager.getString("label.from_file"));
1504     addFromFile.addActionListener(new ActionListener()
1505     {
1506       @Override
1507       public void actionPerformed(ActionEvent e)
1508       {
1509         addFromFile_actionPerformed(e);
1510       }
1511     });
1512     JMenuItem addFromText = new JMenuItem(
1513             MessageManager.getString("label.from_textbox"));
1514     addFromText.addActionListener(new ActionListener()
1515     {
1516       @Override
1517       public void actionPerformed(ActionEvent e)
1518       {
1519         addFromText_actionPerformed(e);
1520       }
1521     });
1522     JMenuItem addFromURL = new JMenuItem(
1523             MessageManager.getString("label.from_url"));
1524     addFromURL.addActionListener(new ActionListener()
1525     {
1526       @Override
1527       public void actionPerformed(ActionEvent e)
1528       {
1529         addFromURL_actionPerformed(e);
1530       }
1531     });
1532     JMenuItem exportFeatures = new JMenuItem(
1533             MessageManager.getString("label.export_features"));
1534     exportFeatures.addActionListener(new ActionListener()
1535     {
1536       @Override
1537       public void actionPerformed(ActionEvent e)
1538       {
1539         exportFeatures_actionPerformed(e);
1540       }
1541     });
1542     JMenuItem exportAnnotations = new JMenuItem(
1543             MessageManager.getString("label.export_annotations"));
1544     exportAnnotations.addActionListener(new ActionListener()
1545     {
1546       @Override
1547       public void actionPerformed(ActionEvent e)
1548       {
1549         exportAnnotations_actionPerformed(e);
1550       }
1551     });
1552     statusPanel.setLayout(new GridLayout());
1553     JMenuItem showAllSeqs = new JMenuItem(
1554             MessageManager.getString("label.all_sequences"));
1555     showAllSeqs.setToolTipText(
1556             MessageManager.getString("label.toggle_sequence_visibility"));
1557     showAllSeqs.addActionListener(new ActionListener()
1558     {
1559       @Override
1560       public void actionPerformed(ActionEvent e)
1561       {
1562         showAllSeqs_actionPerformed(e);
1563       }
1564     });
1565     JMenuItem showAllColumns = new JMenuItem(
1566             MessageManager.getString("label.all_columns"));
1567     showAllColumns.setToolTipText(
1568             MessageManager.getString("label.toggle_columns_visibility"));
1569     showAllColumns.addActionListener(new ActionListener()
1570     {
1571       @Override
1572       public void actionPerformed(ActionEvent e)
1573       {
1574         showAllColumns_actionPerformed(e);
1575       }
1576     });
1577     JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1578     JMenuItem hideSelSequences = new JMenuItem(
1579             MessageManager.getString("label.selected_sequences"));
1580     hideSelSequences.setToolTipText(
1581             MessageManager.getString("label.toggle_sequence_visibility"));
1582     hideSelSequences.addActionListener(new ActionListener()
1583     {
1584       @Override
1585       public void actionPerformed(ActionEvent e)
1586       {
1587         hideSelSequences_actionPerformed(e);
1588       }
1589     });
1590     JMenuItem hideSelColumns = new JMenuItem(
1591             MessageManager.getString("label.selected_columns"));
1592     hideSelColumns.setToolTipText(
1593             MessageManager.getString("label.toggle_columns_visibility"));
1594     hideSelColumns.addActionListener(new ActionListener()
1595     {
1596       @Override
1597       public void actionPerformed(ActionEvent e)
1598       {
1599         hideSelColumns_actionPerformed(e);
1600       }
1601     });
1602     JMenuItem hideAllSelection = new JMenuItem(
1603             MessageManager.getString("label.selected_region"));
1604     hideAllSelection.addActionListener(new ActionListener()
1605     {
1606       @Override
1607       public void actionPerformed(ActionEvent e)
1608       {
1609         hideAllSelection_actionPerformed(e);
1610       }
1611     });
1612     // TODO: should be hidden if no selection exists.
1613     JMenuItem hideAllButSelection = new JMenuItem(
1614             MessageManager.getString("label.all_but_selected_region"));
1615     hideAllButSelection.addActionListener(new ActionListener()
1616     {
1617       @Override
1618       public void actionPerformed(ActionEvent e)
1619       {
1620         hideAllButSelection_actionPerformed(e);
1621       }
1622     });
1623     JMenuItem showAllhidden = new JMenuItem(
1624             MessageManager.getString("label.all_sequences_columns"));
1625     showAllhidden.setToolTipText(MessageManager
1626             .getString("label.toggles_visibility_hidden_selected_regions"));
1627     showAllhidden.addActionListener(new ActionListener()
1628     {
1629       @Override
1630       public void actionPerformed(ActionEvent e)
1631       {
1632         showAllhidden_actionPerformed(e);
1633       }
1634     });
1635     hiddenMarkers.setText(
1636             MessageManager.getString("action.show_hidden_markers"));
1637     hiddenMarkers.addActionListener(new ActionListener()
1638     {
1639       @Override
1640       public void actionPerformed(ActionEvent e)
1641       {
1642         hiddenMarkers_actionPerformed(e);
1643       }
1644     });
1645
1646     JMenuItem invertColSel = new JMenuItem(
1647             MessageManager.getString("action.invert_column_selection"));
1648     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1649             Platform.SHORTCUT_KEY_MASK
1650                     | InputEvent.ALT_DOWN_MASK,
1651             false);
1652     al = new ActionListener()
1653     {
1654       @Override
1655       public void actionPerformed(ActionEvent e)
1656       {
1657         invertColSel_actionPerformed(e);
1658       }
1659     };
1660     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1661
1662     showComplementMenuItem.setVisible(false);
1663     showComplementMenuItem.addActionListener(new ActionListener()
1664     {
1665       @Override
1666       public void actionPerformed(ActionEvent e)
1667       {
1668         showComplement_actionPerformed(showComplementMenuItem.getState());
1669       }
1670     });
1671
1672     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1673     {
1674       @Override
1675       public void stateChanged(ChangeEvent evt)
1676       {
1677         JTabbedPane pane = (JTabbedPane) evt.getSource();
1678         int sel = pane.getSelectedIndex();
1679         tabSelectionChanged(sel);
1680       }
1681     });
1682     tabbedPane.addMouseListener(new MouseAdapter()
1683     {
1684       @Override
1685       public void mousePressed(MouseEvent e)
1686       {
1687         if (e.isPopupTrigger()) // Mac
1688         {
1689           tabbedPane_mousePressed(e);
1690         }
1691       }
1692
1693       @Override
1694       public void mouseReleased(MouseEvent e)
1695       {
1696         if (e.isPopupTrigger()) // Windows
1697         {
1698           tabbedPane_mousePressed(e);
1699         }
1700       }
1701     });
1702     tabbedPane.addFocusListener(new FocusAdapter()
1703     {
1704       @Override
1705       public void focusGained(FocusEvent e)
1706       {
1707         tabbedPane_focusGained(e);
1708       }
1709     });
1710
1711     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1712     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1713             Platform.SHORTCUT_KEY_MASK, false);
1714     al = new ActionListener()
1715     {
1716       @Override
1717       public void actionPerformed(ActionEvent e)
1718       {
1719         save_actionPerformed(e);
1720       }
1721     };
1722     addMenuActionAndAccelerator(keyStroke, save, al);
1723
1724     reload.setEnabled(false);
1725     reload.setText(MessageManager.getString("action.reload"));
1726     reload.addActionListener(new ActionListener()
1727     {
1728       @Override
1729       public void actionPerformed(ActionEvent e)
1730       {
1731         reload_actionPerformed(e);
1732       }
1733     });
1734
1735     JMenuItem newView = new JMenuItem(
1736             MessageManager.getString("action.new_view"));
1737     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1738             Platform.SHORTCUT_KEY_MASK, false);
1739     al = new ActionListener()
1740     {
1741       @Override
1742       public void actionPerformed(ActionEvent e)
1743       {
1744         newView_actionPerformed(e);
1745       }
1746     };
1747     addMenuActionAndAccelerator(keyStroke, newView, al);
1748
1749     tabbedPane.setToolTipText("<html><i>"
1750             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1751             + "</i></html>");
1752
1753     formatMenu.setText(MessageManager.getString("action.format"));
1754     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1755
1756     idRightAlign.setText(
1757             MessageManager.getString("label.right_align_sequence_id"));
1758     idRightAlign.addActionListener(new ActionListener()
1759     {
1760       @Override
1761       public void actionPerformed(ActionEvent e)
1762       {
1763         idRightAlign_actionPerformed(e);
1764       }
1765     });
1766
1767     gatherViews.setEnabled(false);
1768     gatherViews.setText(MessageManager.getString("action.gather_views"));
1769     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1770     al = new ActionListener()
1771     {
1772       @Override
1773       public void actionPerformed(ActionEvent e)
1774       {
1775         gatherViews_actionPerformed(e);
1776       }
1777     };
1778     addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1779
1780     expandViews.setEnabled(false);
1781     expandViews.setText(MessageManager.getString("action.expand_views"));
1782     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1783     al = new ActionListener()
1784     {
1785       @Override
1786       public void actionPerformed(ActionEvent e)
1787       {
1788         expandViews_actionPerformed(e);
1789       }
1790     };
1791     addMenuActionAndAccelerator(keyStroke, expandViews, al);
1792
1793     JMenuItem pageSetup = new JMenuItem(
1794             MessageManager.getString("action.page_setup"));
1795     pageSetup.addActionListener(new ActionListener()
1796     {
1797       @Override
1798       public void actionPerformed(ActionEvent e)
1799       {
1800         pageSetup_actionPerformed(e);
1801       }
1802     });
1803     JMenuItem alignmentProperties = new JMenuItem(
1804             MessageManager.getString("label.alignment_props"));
1805     alignmentProperties.addActionListener(new ActionListener()
1806     {
1807       @Override
1808       public void actionPerformed(ActionEvent actionEvent)
1809       {
1810         alignmentProperties();
1811       }
1812     });
1813     JMenuItem selectHighlighted = new JMenuItem(
1814             MessageManager.getString("action.select_highlighted_columns"));
1815     selectHighlighted.setToolTipText(JvSwingUtils.wrapTooltip(true,
1816             MessageManager.getString("tooltip.select_highlighted_columns")));
1817     al = new ActionListener()
1818     {
1819       @Override
1820       public void actionPerformed(ActionEvent actionEvent)
1821       {
1822         selectHighlightedColumns_actionPerformed(actionEvent);
1823       }
1824     };
1825     JMenuItem Filter = new JMenuItem(
1826             MessageManager.getString("action.select_highlighted_columns"));
1827     selectHighlighted.setToolTipText(
1828             MessageManager.getString("tooltip.select_highlighted_columns"));
1829     al = new ActionListener()
1830     {
1831       @Override
1832       public void actionPerformed(ActionEvent actionEvent)
1833       {
1834         selectHighlightedColumns_actionPerformed(actionEvent);
1835       }
1836     };
1837     selectHighlighted.addActionListener(al);
1838     JMenu tooltipSettingsMenu = new JMenu(
1839             MessageManager.getString("label.sequence_id_tooltip"));
1840     JMenu autoAnnMenu = new JMenu(
1841             MessageManager.getString("label.autocalculated_annotation"));
1842
1843     JMenu exportImageMenu = new JMenu(
1844             MessageManager.getString("label.export_image"));
1845     JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1846     alignFrameMenuBar.add(fileMenu);
1847     alignFrameMenuBar.add(editMenu);
1848     alignFrameMenuBar.add(selectMenu);
1849     alignFrameMenuBar.add(viewMenu);
1850     alignFrameMenuBar.add(annotationsMenu);
1851     alignFrameMenuBar.add(formatMenu);
1852     alignFrameMenuBar.add(colourMenu);
1853     alignFrameMenuBar.add(calculateMenu);
1854     alignFrameMenuBar.add(webService);
1855     if (!Platform.isJS())
1856     {
1857       alignFrameMenuBar.add(hmmerMenu);
1858     }
1859
1860     fileMenu.add(fetchSequence);
1861     fileMenu.add(addSequenceMenu);
1862     fileMenu.add(reload);
1863     fileMenu.addSeparator();
1864     fileMenu.add(vamsasStore);
1865     fileMenu.add(save);
1866     fileMenu.add(saveAs);
1867     fileMenu.add(outputTextboxMenu);
1868     fileMenu.add(pageSetup);
1869     fileMenu.add(printMenuItem);
1870     fileMenu.addSeparator();
1871     fileMenu.add(exportImageMenu);
1872     fileMenu.add(exportFeatures);
1873     fileMenu.add(exportAnnotations);
1874     fileMenu.add(loadTreeMenuItem);
1875     fileMenu.add(associatedData);
1876     if (!Platform.isJS())
1877     {
1878       fileMenu.add(loadVcf);
1879     }
1880     fileMenu.addSeparator();
1881     fileMenu.add(closeMenuItem);
1882
1883     pasteMenu.add(pasteNew);
1884     pasteMenu.add(pasteThis);
1885     editMenu.add(undoMenuItem);
1886     editMenu.add(redoMenuItem);
1887     editMenu.add(cut);
1888     editMenu.add(copy);
1889     editMenu.add(pasteMenu);
1890     editMenu.add(delete);
1891     editMenu.addSeparator();
1892     editMenu.add(remove2LeftMenuItem);
1893     editMenu.add(remove2RightMenuItem);
1894     editMenu.add(removeGappedColumnMenuItem);
1895     editMenu.add(removeAllGapsMenuItem);
1896     editMenu.add(removeRedundancyMenuItem);
1897     editMenu.addSeparator();
1898     // dont add these yet in the CVS build - they cannot be undone!
1899     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1900     // editMenu.add(justifyLeftMenuItem);
1901     // editMenu.add(justifyRightMenuItem);
1902     // editMenu.addSeparator();
1903     editMenu.add(padGapsMenuitem);
1904     editMenu.addSeparator();
1905     editMenu.add(filterByEValue);
1906     editMenu.add(filterByScore);
1907
1908     showMenu.add(showAllColumns);
1909     showMenu.add(showAllSeqs);
1910     showMenu.add(showAllhidden);
1911     hideMenu.add(hideSelColumns);
1912     hideMenu.add(hideSelSequences);
1913     hideMenu.add(hideAllSelection);
1914     hideMenu.add(hideAllButSelection);
1915     viewMenu.add(newView);
1916     viewMenu.add(expandViews);
1917     viewMenu.add(gatherViews);
1918     viewMenu.addSeparator();
1919     viewMenu.add(showMenu);
1920     viewMenu.add(hideMenu);
1921     viewMenu.add(showComplementMenuItem);
1922     viewMenu.addSeparator();
1923     viewMenu.add(followHighlightMenuItem);
1924     viewMenu.addSeparator();
1925     viewMenu.add(showSeqFeatures);
1926     // viewMenu.add(showSeqFeaturesHeight);
1927     viewMenu.add(openFeatureSettings);
1928     tooltipSettingsMenu.add(showDbRefsMenuitem);
1929     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1930     viewMenu.add(tooltipSettingsMenu);
1931     viewMenu.addSeparator();
1932     viewMenu.add(alignmentProperties);
1933     viewMenu.addSeparator();
1934     viewMenu.add(overviewMenuItem);
1935
1936     annotationsMenu.add(annotationPanelMenuItem);
1937     annotationsMenu.addSeparator();
1938     annotationsMenu.add(showAllAlAnnotations);
1939     annotationsMenu.add(hideAllAlAnnotations);
1940     annotationsMenu.addSeparator();
1941     annotationsMenu.add(showAllSeqAnnotations);
1942     annotationsMenu.add(hideAllSeqAnnotations);
1943     annotationsMenu.add(sortAnnBySequence);
1944     annotationsMenu.add(sortAnnByLabel);
1945     annotationsMenu.addSeparator();
1946     autoAnnMenu.add(showAutoFirst);
1947     autoAnnMenu.add(showAutoLast);
1948     autoAnnMenu.addSeparator();
1949     autoAnnMenu.add(applyAutoAnnotationSettings);
1950     autoAnnMenu.add(showConsensusHistogram);
1951     autoAnnMenu.add(showSequenceLogo);
1952     autoAnnMenu.add(normaliseSequenceLogo);
1953     autoAnnMenu.addSeparator();
1954     autoAnnMenu.add(showGroupConservation);
1955     autoAnnMenu.add(showGroupConsensus);
1956     annotationsMenu.add(autoAnnMenu);
1957
1958     sort.add(sortIDMenuItem);
1959     sort.add(sortLengthMenuItem);
1960     sort.add(sortGroupMenuItem);
1961     sort.add(sortPairwiseMenuItem);
1962     sort.add(sortEValueMenuItem);
1963     sort.add(sortBitScoreMenuItem);
1964     sort.add(sortByTreeMenu);
1965     calculateMenu.add(sort);
1966     calculateMenu.add(calculateTree);
1967     calculateMenu.addSeparator();
1968     calculateMenu.add(pairwiseAlignmentMenuItem);
1969     calculateMenu.addSeparator();
1970     calculateMenu.add(showTranslation);
1971     calculateMenu.add(showReverse);
1972     calculateMenu.add(showReverseComplement);
1973     calculateMenu.add(showProducts);
1974     calculateMenu.add(autoCalculate);
1975     calculateMenu.add(sortByTree);
1976     calculateMenu.addSeparator();
1977     calculateMenu.add(expandAlignment);
1978     calculateMenu.add(extractScores);
1979     if (!Platform.isJS())
1980     {
1981       calculateMenu.addSeparator();
1982       calculateMenu.add(runGroovy);
1983     }
1984     webServiceNoServices = new JMenuItem(
1985             MessageManager.getString("label.no_services"));
1986     webService.add(webServiceNoServices);
1987     if (!Platform.isJS())
1988     {
1989       exportImageMenu.add(htmlMenuItem);
1990     }
1991     exportImageMenu.add(epsFile);
1992     exportImageMenu.add(createPNG);
1993     if (!Platform.isJS())
1994     {
1995       exportImageMenu.add(createBioJS);
1996       exportImageMenu.add(createSVG);
1997     }
1998     addSequenceMenu.add(addFromFile);
1999     addSequenceMenu.add(addFromText);
2000     addSequenceMenu.add(addFromURL);
2001     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2002     statusPanel.add(statusBar, null);
2003     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2004
2005     formatMenu.add(font);
2006     formatMenu.addSeparator();
2007     formatMenu.add(wrapMenuItem);
2008     formatMenu.add(scaleAbove);
2009     formatMenu.add(scaleLeft);
2010     formatMenu.add(scaleRight);
2011     formatMenu.add(seqLimits);
2012     formatMenu.add(idRightAlign);
2013     formatMenu.add(hiddenMarkers);
2014     formatMenu.add(viewBoxesMenuItem);
2015     formatMenu.add(viewTextMenuItem);
2016     formatMenu.add(colourTextMenuItem);
2017     formatMenu.add(renderGapsMenuItem);
2018     formatMenu.add(centreColumnLabelsMenuItem);
2019     formatMenu.add(showNonconservedMenuItem);
2020     selectMenu.add(findMenuItem);
2021     selectMenu.addSeparator();
2022     selectMenu.add(selectAllSequenceMenuItem);
2023     selectMenu.add(deselectAllSequenceMenuItem);
2024     selectMenu.add(invertSequenceMenuItem);
2025     selectMenu.add(invertColSel);
2026     selectMenu.add(createGroup);
2027     selectMenu.add(unGroup);
2028     selectMenu.add(grpsFromSelection);
2029     selectMenu.add(deleteGroups);
2030     selectMenu.add(annotationColumn);
2031     selectMenu.add(selectHighlighted);
2032     // TODO - determine if the listenToViewSelections button is needed : see bug
2033     // JAL-574
2034     // selectMenu.addSeparator();
2035     // selectMenu.add(listenToViewSelections);
2036   }
2037
2038   /**
2039    * Constructs the entries on the HMMER menu
2040    */
2041   protected void initHMMERMenu()
2042   {
2043     /*
2044      * hmmbuild
2045      */
2046     JMenu hmmBuild = new JMenu(MessageManager.getString("label.hmmbuild"));
2047     JMenuItem hmmBuildSettings = new JMenuItem(
2048             MessageManager.getString("label.edit_settings_and_run"));
2049     hmmBuildSettings.addActionListener(new ActionListener()
2050     {
2051       @Override
2052       public void actionPerformed(ActionEvent e)
2053       {
2054         hmmBuild_actionPerformed(false);
2055       }
2056     });
2057     JMenuItem hmmBuildRun = new JMenuItem(MessageManager.formatMessage(
2058             "label.action_with_default_settings", "hmmbuild"));
2059     hmmBuildRun.addActionListener(new ActionListener()
2060     {
2061       @Override
2062       public void actionPerformed(ActionEvent e)
2063       {
2064         hmmBuild_actionPerformed(true);
2065       }
2066     });
2067     hmmBuild.add(hmmBuildRun);
2068     hmmBuild.add(hmmBuildSettings);
2069
2070     /*
2071      * hmmalign
2072      */
2073     JMenu hmmAlign = new JMenu(MessageManager.getString("label.hmmalign"));
2074     JMenuItem hmmAlignRun = new JMenuItem(MessageManager.formatMessage(
2075             "label.action_with_default_settings", "hmmalign"));
2076     hmmAlignRun.addActionListener(new ActionListener()
2077     {
2078       @Override
2079       public void actionPerformed(ActionEvent e)
2080       {
2081         hmmAlign_actionPerformed(true);
2082       }
2083     });
2084     JMenuItem hmmAlignSettings = new JMenuItem(
2085             MessageManager.getString("label.edit_settings_and_run"));
2086     hmmAlignSettings.addActionListener(new ActionListener()
2087     {
2088       @Override
2089       public void actionPerformed(ActionEvent e)
2090       {
2091         hmmAlign_actionPerformed(false);
2092       }
2093     });
2094     hmmAlign.add(hmmAlignRun);
2095     hmmAlign.add(hmmAlignSettings);
2096
2097     /*
2098      * hmmsearch
2099      */
2100     JMenu hmmSearch = new JMenu(
2101             MessageManager.getString("label.hmmsearch"));
2102     JMenuItem hmmSearchSettings = new JMenuItem(
2103             MessageManager.getString("label.edit_settings_and_run"));
2104     hmmSearchSettings.addActionListener(new ActionListener()
2105     {
2106       @Override
2107       public void actionPerformed(ActionEvent e)
2108       {
2109         hmmSearch_actionPerformed(false);
2110       }
2111     });
2112     JMenuItem hmmSearchRun = new JMenuItem(MessageManager.formatMessage(
2113             "label.action_with_default_settings", "hmmsearch"));
2114     hmmSearchRun.addActionListener(new ActionListener()
2115     {
2116       @Override
2117       public void actionPerformed(ActionEvent e)
2118       {
2119         hmmSearch_actionPerformed(true);
2120       }
2121     });
2122     JMenuItem addDatabase = new JMenuItem(
2123             MessageManager.getString("label.add_database"));
2124     addDatabase.addActionListener(new ActionListener()
2125     {
2126       @Override
2127       public void actionPerformed(ActionEvent e)
2128       {
2129         try
2130         {
2131           addDatabase_actionPerformed();
2132         } catch (IOException e1)
2133         {
2134           e1.printStackTrace();
2135         }
2136       }
2137     });
2138     hmmSearch.add(hmmSearchRun);
2139     hmmSearch.add(hmmSearchSettings);
2140     // hmmSearch.add(addDatabase);
2141
2142     /*
2143      * jackhmmer
2144      */
2145     JMenu jackhmmer = new JMenu(
2146             MessageManager.getString("label.jackhmmer"));
2147     JMenuItem jackhmmerSettings = new JMenuItem(
2148             MessageManager.getString("label.edit_settings_and_run"));
2149     jackhmmerSettings.addActionListener(new ActionListener()
2150     {
2151       @Override
2152       public void actionPerformed(ActionEvent e)
2153       {
2154         jackhmmer_actionPerformed(false);
2155       }
2156     });
2157     JMenuItem jackhmmerRun = new JMenuItem(MessageManager.formatMessage(
2158             "label.action_with_default_settings", "jackhmmer"));
2159     jackhmmerRun.addActionListener(new ActionListener()
2160     {
2161       @Override
2162       public void actionPerformed(ActionEvent e)
2163       {
2164         jackhmmer_actionPerformed(true);
2165       }
2166
2167     });
2168     /*
2169     JMenuItem addDatabase = new JMenuItem(
2170             MessageManager.getString("label.add_database"));
2171     addDatabase.addActionListener(new ActionListener()
2172     {
2173       @Override
2174       public void actionPerformed(ActionEvent e)
2175       {
2176         try
2177         {
2178           addDatabase_actionPerformed();
2179         } catch (IOException e1)
2180         {
2181           e1.printStackTrace();
2182         }
2183       }
2184     });
2185     */
2186     jackhmmer.add(jackhmmerRun);
2187     jackhmmer.add(jackhmmerSettings);
2188     // hmmSearch.add(addDatabase);
2189
2190     /*
2191      * top level menu
2192      */
2193     hmmerMenu.setText(MessageManager.getString("action.hmmer"));
2194     hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
2195     hmmerMenu.add(hmmBuild);
2196     hmmerMenu.add(hmmAlign);
2197     hmmerMenu.add(hmmSearch);
2198     hmmerMenu.add(jackhmmer);
2199
2200   }
2201
2202   protected void enableSortMenuOptions()
2203   {
2204   }
2205
2206   protected void loadVcf_actionPerformed()
2207   {
2208   }
2209
2210   /**
2211    * Constructs the entries on the Colour menu (but does not add them to the
2212    * menu).
2213    */
2214   protected void initColourMenu()
2215   {
2216     applyToAllGroups = new JCheckBoxMenuItem(
2217             MessageManager.getString("label.apply_colour_to_all_groups"));
2218     applyToAllGroups.addActionListener(new ActionListener()
2219     {
2220       @Override
2221       public void actionPerformed(ActionEvent e)
2222       {
2223         applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
2224       }
2225     });
2226
2227     textColour = new JMenuItem(
2228             MessageManager.getString("label.text_colour"));
2229     textColour.addActionListener(new ActionListener()
2230     {
2231       @Override
2232       public void actionPerformed(ActionEvent e)
2233       {
2234         textColour_actionPerformed();
2235       }
2236     });
2237
2238     conservationMenuItem = new JCheckBoxMenuItem(
2239             MessageManager.getString("action.by_conservation"));
2240     conservationMenuItem.addActionListener(new ActionListener()
2241     {
2242       @Override
2243       public void actionPerformed(ActionEvent e)
2244       {
2245         conservationMenuItem_actionPerformed(
2246                 conservationMenuItem.isSelected());
2247       }
2248     });
2249
2250     abovePIDThreshold = new JCheckBoxMenuItem(
2251             MessageManager.getString("label.above_identity_threshold"));
2252     abovePIDThreshold.addActionListener(new ActionListener()
2253     {
2254       @Override
2255       public void actionPerformed(ActionEvent e)
2256       {
2257         abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
2258       }
2259     });
2260     modifyPID = new JMenuItem(
2261             MessageManager.getString("label.modify_identity_threshold"));
2262     modifyPID.addActionListener(new ActionListener()
2263     {
2264       @Override
2265       public void actionPerformed(ActionEvent e)
2266       {
2267         modifyPID_actionPerformed();
2268       }
2269     });
2270     modifyConservation = new JMenuItem(MessageManager
2271             .getString("label.modify_conservation_threshold"));
2272     modifyConservation.addActionListener(new ActionListener()
2273     {
2274       @Override
2275       public void actionPerformed(ActionEvent e)
2276       {
2277         modifyConservation_actionPerformed();
2278       }
2279     });
2280
2281     annotationColour = new JRadioButtonMenuItem(
2282             MessageManager.getString("action.by_annotation"));
2283     annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
2284     annotationColour.addActionListener(new ActionListener()
2285     {
2286       @Override
2287       public void actionPerformed(ActionEvent e)
2288       {
2289         annotationColour_actionPerformed();
2290       }
2291     });
2292   }
2293
2294   protected void selectHighlightedColumns_actionPerformed(
2295           ActionEvent actionEvent)
2296   {
2297     // TODO Auto-generated method stub
2298
2299   }
2300
2301   /**
2302    * Generate the reverse sequence (or reverse complement if the flag is true)
2303    * and add it to the alignment
2304    *
2305    * @param complement
2306    */
2307   protected void showReverse_actionPerformed(boolean complement)
2308   {
2309   }
2310
2311   /**
2312    * Try to run script in a Groovy console, having first ensured that this
2313    * alignframe is set as currentAlignFrame in Desktop
2314    */
2315   protected void runGroovy_actionPerformed()
2316   {
2317
2318   }
2319
2320   /**
2321    * Adds the given action listener and key accelerator to the given menu item.
2322    * Also saves in a lookup table to support lookup of action by key stroke.
2323    *
2324    * @param keyStroke
2325    * @param menuItem
2326    * @param actionListener
2327    */
2328   protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2329           JMenuItem menuItem, ActionListener actionListener)
2330   {
2331     menuItem.setAccelerator(keyStroke);
2332     accelerators.put(keyStroke, menuItem);
2333     menuItem.addActionListener(actionListener);
2334   }
2335
2336   /**
2337    * Action on clicking sort annotations by type.
2338    *
2339    * @param sortOrder
2340    */
2341   protected void sortAnnotations_actionPerformed()
2342   {
2343   }
2344
2345   /**
2346    * Action on clicking Show all annotations.
2347    *
2348    * @param forSequences
2349    *          update sequence-related annotations
2350    * @param forAlignment
2351    *          update non-sequence-related annotations
2352    */
2353   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2354           boolean forAlignment)
2355   {
2356     setAnnotationsVisibility(true, forSequences, forAlignment);
2357   }
2358
2359   /**
2360    * Action on clicking Hide all annotations.
2361    *
2362    * @param forSequences
2363    *          update sequence-related annotations
2364    * @param forAlignment
2365    *          update non-sequence-related annotations
2366    */
2367   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2368           boolean forAlignment)
2369   {
2370     setAnnotationsVisibility(false, forSequences, forAlignment);
2371   }
2372
2373   /**
2374    * Set the visibility of annotations to true or false. Can act on
2375    * sequence-related annotations, or alignment-related, or both.
2376    *
2377    * @param visible
2378    * @param forSequences
2379    *          update sequence-related annotations
2380    * @param forAlignment
2381    *          update non-sequence-related annotations
2382    */
2383   protected void setAnnotationsVisibility(boolean visible,
2384           boolean forSequences, boolean forAlignment)
2385   {
2386
2387   }
2388
2389   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2390   {
2391     // TODO Auto-generated method stub
2392
2393   }
2394
2395   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2396   {
2397     // TODO Auto-generated method stub
2398
2399   }
2400
2401   protected void showAllhidden_actionPerformed(ActionEvent e)
2402   {
2403     // TODO Auto-generated method stub
2404
2405   }
2406
2407   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2408   {
2409     // TODO Auto-generated method stub
2410
2411   }
2412
2413   protected void hideAllSelection_actionPerformed(ActionEvent e)
2414   {
2415     // TODO Auto-generated method stub
2416
2417   }
2418
2419   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2420   {
2421     // TODO Auto-generated method stub
2422
2423   }
2424
2425   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2426   {
2427     // TODO Auto-generated method stub
2428
2429   }
2430
2431   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2432   {
2433     // TODO Auto-generated method stub
2434
2435   }
2436
2437   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2438   {
2439     // TODO Auto-generated method stub
2440
2441   }
2442
2443   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2444   {
2445     // TODO Auto-generated method stub
2446
2447   }
2448
2449   protected void showGroupConservation_actionPerformed(ActionEvent e)
2450   {
2451     // TODO Auto-generated method stub
2452
2453   }
2454
2455   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2456   {
2457     // TODO Auto-generated method stub
2458
2459   }
2460
2461   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2462   {
2463     // TODO Auto-generated method stub
2464
2465   }
2466
2467   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2468   {
2469     // TODO Auto-generated method stub
2470
2471   }
2472
2473   protected void followHighlight_actionPerformed()
2474   {
2475     // TODO Auto-generated method stub
2476
2477   }
2478
2479   protected void showNpFeats_actionPerformed(ActionEvent e)
2480   {
2481     // TODO Auto-generated method stub
2482
2483   }
2484
2485   protected void showDbRefs_actionPerformed(ActionEvent e)
2486   {
2487     // TODO Auto-generated method stub
2488
2489   }
2490
2491   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2492   {
2493   }
2494
2495   protected void buildSortByAnnotationScoresMenu()
2496   {
2497   }
2498
2499   protected void extractScores_actionPerformed(ActionEvent e)
2500   {
2501   }
2502
2503   protected void outputText_actionPerformed(String formatName)
2504   {
2505   }
2506
2507   public void addFromFile_actionPerformed(ActionEvent e)
2508   {
2509
2510   }
2511
2512   public void addFromText_actionPerformed(ActionEvent e)
2513   {
2514
2515   }
2516
2517   public void addFromURL_actionPerformed(ActionEvent e)
2518   {
2519
2520   }
2521
2522   public void exportFeatures_actionPerformed(ActionEvent e)
2523   {
2524
2525   }
2526
2527   public void exportAnnotations_actionPerformed(ActionEvent e)
2528   {
2529
2530   }
2531
2532   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2533   {
2534   }
2535
2536   protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2537   {
2538
2539   }
2540
2541   protected void closeMenuItem_actionPerformed(boolean b)
2542   {
2543   }
2544
2545   protected void redoMenuItem_actionPerformed(ActionEvent e)
2546   {
2547   }
2548
2549   protected void undoMenuItem_actionPerformed(ActionEvent e)
2550   {
2551   }
2552
2553   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2554   {
2555   }
2556
2557   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2558   {
2559   }
2560
2561   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2562   {
2563   }
2564
2565   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2566   {
2567   }
2568
2569   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2570   {
2571   }
2572
2573   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2574   {
2575   }
2576
2577   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2578   {
2579   }
2580
2581   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2582   {
2583   }
2584
2585   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2586   {
2587   }
2588
2589   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2590   {
2591   }
2592
2593   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2594   {
2595   }
2596
2597   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2598   {
2599   }
2600
2601   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2602   {
2603   }
2604
2605   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2606   {
2607   }
2608
2609   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2610   {
2611   }
2612
2613   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2614   {
2615   }
2616
2617   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2618   {
2619   }
2620
2621   protected void sortEValueMenuItem_actionPerformed(ActionEvent e)
2622   {
2623   }
2624
2625   protected void sortBitScoreMenuItem_actionPerformed(ActionEvent e)
2626   {
2627   }
2628
2629   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2630   {
2631   }
2632
2633   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2634   {
2635   }
2636
2637   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2638   {
2639   }
2640
2641   protected void conservationMenuItem_actionPerformed(boolean selected)
2642   {
2643   }
2644
2645   protected void printMenuItem_actionPerformed(ActionEvent e)
2646   {
2647   }
2648
2649   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2650   {
2651   }
2652
2653   protected void findMenuItem_actionPerformed(ActionEvent e)
2654   {
2655   }
2656
2657   protected void abovePIDThreshold_actionPerformed(boolean selected)
2658   {
2659   }
2660
2661   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2662   {
2663   }
2664
2665   protected void deleteGroups_actionPerformed(ActionEvent e)
2666   {
2667   }
2668
2669   protected void createGroup_actionPerformed(ActionEvent e)
2670   {
2671   }
2672
2673   protected void unGroup_actionPerformed(ActionEvent e)
2674   {
2675   }
2676
2677   protected void copy_actionPerformed()
2678   {
2679   }
2680
2681   protected void cut_actionPerformed()
2682   {
2683   }
2684
2685   protected void delete_actionPerformed()
2686   {
2687   }
2688
2689   protected void pasteNew_actionPerformed(ActionEvent e)
2690           throws IOException, InterruptedException
2691   {
2692   }
2693
2694   protected void pasteThis_actionPerformed(ActionEvent e)
2695           throws IOException, InterruptedException
2696   {
2697   }
2698
2699   protected void applyToAllGroups_actionPerformed(boolean selected)
2700   {
2701   }
2702
2703   protected void hmmBuild_actionPerformed(boolean withDefaults)
2704   {
2705   }
2706
2707   protected void hmmSearch_actionPerformed(boolean withDefaults)
2708   {
2709   }
2710
2711   protected void jackhmmer_actionPerformed(boolean b)
2712   {
2713   }
2714
2715   protected void addDatabase_actionPerformed()
2716           throws FileFormatException, IOException
2717   {
2718   }
2719
2720   protected void hmmAlign_actionPerformed(boolean withDefaults)
2721   {
2722   }
2723
2724   public void createPNG(java.io.File f)
2725   {
2726   }
2727
2728   protected void font_actionPerformed(ActionEvent e)
2729   {
2730   }
2731
2732   protected void seqLimit_actionPerformed(ActionEvent e)
2733   {
2734   }
2735
2736   public void seqDBRef_actionPerformed(ActionEvent e)
2737   {
2738
2739   }
2740
2741   public void createEPS(java.io.File f)
2742   {
2743   }
2744
2745   public void createSVG(java.io.File f)
2746   {
2747
2748   }
2749
2750   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2751   {
2752
2753   }
2754
2755   /**
2756    * Template method to handle the 'load T-Coffee scores' menu event.
2757    * <p>
2758    * Subclasses override this method to provide a custom action.
2759    *
2760    * @param event
2761    *          The raised event
2762    */
2763   protected void loadScores_actionPerformed(ActionEvent event)
2764   {
2765
2766   }
2767
2768   protected void jpred_actionPerformed(ActionEvent e)
2769   {
2770   }
2771
2772   protected void scaleAbove_actionPerformed(ActionEvent e)
2773   {
2774   }
2775
2776   protected void scaleLeft_actionPerformed(ActionEvent e)
2777   {
2778   }
2779
2780   protected void filterByEValue_actionPerformed()
2781   {
2782   }
2783
2784   protected void filterByScore_actionPerformed()
2785   {
2786   }
2787
2788   protected void scaleRight_actionPerformed(ActionEvent e)
2789   {
2790   }
2791
2792   protected void modifyPID_actionPerformed()
2793   {
2794   }
2795
2796   protected void modifyConservation_actionPerformed()
2797   {
2798   }
2799
2800   protected void saveAs_actionPerformed()
2801   {
2802   }
2803
2804   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2805   {
2806   }
2807
2808   public void vamsasStore_actionPerformed(ActionEvent e)
2809   {
2810
2811   }
2812
2813   public void vamsasLoad_actionPerformed(ActionEvent e)
2814   {
2815
2816   }
2817
2818   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
2819   {
2820
2821   }
2822
2823   public void featureSettings_actionPerformed(ActionEvent e)
2824   {
2825
2826   }
2827
2828   public void fetchSequence_actionPerformed()
2829   {
2830
2831   }
2832
2833   public void smoothFont_actionPerformed(ActionEvent e)
2834   {
2835
2836   }
2837
2838   public void annotationColour_actionPerformed()
2839   {
2840   }
2841
2842   public void annotationColumn_actionPerformed(ActionEvent e)
2843   {
2844   }
2845
2846   public void associatedData_actionPerformed(ActionEvent e)
2847           throws IOException, InterruptedException
2848   {
2849
2850   }
2851
2852   public void autoCalculate_actionPerformed(ActionEvent e)
2853   {
2854
2855   }
2856
2857   public void sortByTreeOption_actionPerformed(ActionEvent e)
2858   {
2859
2860   }
2861
2862   public void showAllSeqs_actionPerformed(ActionEvent e)
2863   {
2864
2865   }
2866
2867   public void showAllColumns_actionPerformed(ActionEvent e)
2868   {
2869
2870   }
2871
2872   public void hideSelSequences_actionPerformed(ActionEvent e)
2873   {
2874
2875   }
2876
2877   public void hideSelColumns_actionPerformed(ActionEvent e)
2878   {
2879
2880   }
2881
2882   public void hiddenMarkers_actionPerformed(ActionEvent e)
2883   {
2884
2885   }
2886
2887   public void findPdbId_actionPerformed(ActionEvent e)
2888   {
2889
2890   }
2891
2892   public void enterPdbId_actionPerformed(ActionEvent e)
2893   {
2894
2895   }
2896
2897   public void pdbFile_actionPerformed(ActionEvent e)
2898   {
2899
2900   }
2901
2902   public void invertColSel_actionPerformed(ActionEvent e)
2903   {
2904
2905   }
2906
2907   public void tabSelectionChanged(int sel)
2908   {
2909
2910   }
2911
2912   public void tabbedPane_mousePressed(MouseEvent e)
2913   {
2914
2915   }
2916
2917   public void tabbedPane_focusGained(FocusEvent e)
2918   {
2919     requestFocus();
2920   }
2921
2922   public void save_actionPerformed(ActionEvent e)
2923   {
2924
2925   }
2926
2927   public void reload_actionPerformed(ActionEvent e)
2928   {
2929
2930   }
2931
2932   public void newView_actionPerformed(ActionEvent e)
2933   {
2934
2935   }
2936
2937   public void textColour_actionPerformed()
2938   {
2939
2940   }
2941
2942   public void idRightAlign_actionPerformed(ActionEvent e)
2943   {
2944
2945   }
2946
2947   public void expandViews_actionPerformed(ActionEvent e)
2948   {
2949
2950   }
2951
2952   public void gatherViews_actionPerformed(ActionEvent e)
2953   {
2954
2955   }
2956
2957   public void buildTreeSortMenu()
2958   {
2959
2960   }
2961
2962   public void pageSetup_actionPerformed(ActionEvent e)
2963   {
2964
2965   }
2966
2967   public void alignmentProperties()
2968   {
2969
2970   }
2971
2972   protected void expand_newalign(ActionEvent e)
2973   {
2974     // TODO Auto-generated method stub
2975
2976   }
2977
2978   protected boolean isShowAutoCalculatedAbove()
2979   {
2980     return showAutoCalculatedAbove;
2981   }
2982
2983   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2984   {
2985     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2986   }
2987
2988   protected SequenceAnnotationOrder getAnnotationSortOrder()
2989   {
2990     return annotationSortOrder;
2991   }
2992
2993   protected void setAnnotationSortOrder(
2994           SequenceAnnotationOrder annotationSortOrder)
2995   {
2996     this.annotationSortOrder = annotationSortOrder;
2997   }
2998
2999   public Map<KeyStroke, JMenuItem> getAccelerators()
3000   {
3001     return this.accelerators;
3002   }
3003
3004   /**
3005    * Returns the selected index of the tabbed pane, or -1 if none selected
3006    * (including the case where the tabbed pane has not been made visible).
3007    *
3008    * @return
3009    */
3010   public int getTabIndex()
3011   {
3012     return tabbedPane.getSelectedIndex();
3013   }
3014
3015   public JPanel getStatusPanel()
3016   {
3017     return statusPanel;
3018   }
3019
3020   /**
3021    * Sets a reference to the containing split frame. Also makes the 'toggle
3022    * split view' menu item visible and checked.
3023    *
3024    * @param sf
3025    */
3026   public void setSplitFrame(SplitContainerI sf)
3027   {
3028     this.splitFrame = sf;
3029     if (sf != null)
3030     {
3031       this.showComplementMenuItem.setVisible(true);
3032       this.showComplementMenuItem.setState(true);
3033     }
3034   }
3035
3036   public SplitContainerI getSplitViewContainer()
3037   {
3038     return this.splitFrame;
3039   }
3040
3041   protected void showComplement_actionPerformed(boolean complement)
3042   {
3043   }
3044
3045
3046 }