src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.jbgui;
  22
  23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  24 import jalview.api.SplitContainerI;
  25 import jalview.bin.Cache;
  26 import jalview.gui.JvSwingUtils;
  27 import jalview.gui.Preferences;
  28 import jalview.io.FileFormats;
  29 import jalview.util.MessageManager;
  30 import jalview.util.Platform;
  31
  32 import java.awt.BorderLayout;
  33 import java.awt.Color;
  34 import java.awt.GridLayout;
  35 import java.awt.Toolkit;
  36 import java.awt.event.ActionEvent;
  37 import java.awt.event.ActionListener;
  38 import java.awt.event.FocusAdapter;
  39 import java.awt.event.FocusEvent;
  40 import java.awt.event.KeyEvent;
  41 import java.awt.event.MouseAdapter;
  42 import java.awt.event.MouseEvent;
  43 import java.io.IOException;
  44 import java.util.HashMap;
  45 import java.util.Map;
  46
  47 import javax.swing.BorderFactory;
  48 import javax.swing.ButtonGroup;
  49 import javax.swing.JCheckBoxMenuItem;
  50 import javax.swing.JInternalFrame;
  51 import javax.swing.JLabel;
  52 import javax.swing.JMenu;
  53 import javax.swing.JMenuBar;
  54 import javax.swing.JMenuItem;
  55 import javax.swing.JPanel;
  56 import javax.swing.JRadioButtonMenuItem;
  57 import javax.swing.JTabbedPane;
  58 import javax.swing.KeyStroke;
  59 import javax.swing.event.ChangeEvent;
  60 import javax.swing.event.MenuEvent;
  61 import javax.swing.event.MenuListener;
  62
  63 public class GAlignFrame extends JInternalFrame
  64 {
  65   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  66
  67   protected JMenuItem closeMenuItem = new JMenuItem();
  68
  69   protected JMenu webService = new JMenu();
  70
  71   protected JMenu hmmerMenu = new JMenu();
  72
  73   protected JMenuItem hmmAlign = new JMenuItem();
  74
  75   protected JMenuItem hmmSearch = new JMenuItem();
  76
  77   protected JMenuItem hmmBuild = new JCheckBoxMenuItem();
  78
  79   protected JMenuItem webServiceNoServices;
  80
  81   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  82
  83   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  84
  85   protected JMenu sortByAnnotScore = new JMenu();
  86
  87   public JLabel statusBar = new JLabel();
  88
  89   protected JMenu outputTextboxMenu = new JMenu();
  90
  91   protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
  92
  93   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
  94
  95   protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
  96
  97   protected JMenuItem undoMenuItem = new JMenuItem();
  98
  99   protected JMenuItem redoMenuItem = new JMenuItem();
 100
 101   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 102
 103   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 104
 105   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 106
 107   JMenuItem copy = new JMenuItem();
 108
 109   JMenuItem cut = new JMenuItem();
 110
 111   JMenu pasteMenu = new JMenu();
 112
 113   protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 114
 115   protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 116
 117   protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 118
 119   protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 120
 121   protected JCheckBoxMenuItem applyToAllGroups;
 122
 123   protected JMenu colourMenu = new JMenu();
 124
 125   protected JMenuItem textColour;
 126
 127   protected JCheckBoxMenuItem conservationMenuItem;
 128
 129   protected JMenuItem modifyConservation;
 130
 131   protected JCheckBoxMenuItem abovePIDThreshold;
 132
 133   protected JMenuItem modifyPID;
 134
 135   protected JMenuItem annotationColour;
 136
 137   protected JMenu sortByTreeMenu = new JMenu();
 138
 139   protected JMenu sort = new JMenu();
 140
 141   protected JMenuItem calculateTree = new JMenuItem();
 142
 143   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 144
 145   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 146
 147   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 148
 149   protected JMenuItem showTranslation = new JMenuItem();
 150
 151   protected JMenuItem showReverse = new JMenuItem();
 152
 153   protected JMenuItem showReverseComplement = new JMenuItem();
 154
 155   protected JMenu showProducts = new JMenu();
 156
 157   protected JMenuItem runGroovy = new JMenuItem();
 158
 159   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 160
 161   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 162
 163   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 164
 165   protected JPanel statusPanel = new JPanel();
 166
 167   protected JMenuItem showAllSeqAnnotations = new JMenuItem();
 168
 169   protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
 170
 171   protected JMenuItem showAllAlAnnotations = new JMenuItem();
 172
 173   protected JMenuItem hideAllAlAnnotations = new JMenuItem();
 174
 175   protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
 176
 177   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 178
 179   protected JTabbedPane tabbedPane = new JTabbedPane();
 180
 181   protected JMenuItem reload = new JMenuItem();
 182
 183   protected JMenu formatMenu = new JMenu();
 184
 185   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 186
 187   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 188
 189   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 190
 191   protected JMenuItem gatherViews = new JMenuItem();
 192
 193   protected JMenuItem expandViews = new JMenuItem();
 194
 195   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 196
 197   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 198
 199   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 200
 201   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 202
 203   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 204
 205   protected JCheckBoxMenuItem showInformationHistogram = new JCheckBoxMenuItem();
 206
 207   protected JCheckBoxMenuItem showHMMSequenceLogo = new JCheckBoxMenuItem();
 208
 209   protected JCheckBoxMenuItem normaliseHMMSequenceLogo = new JCheckBoxMenuItem();
 210
 211   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 212
 213   private SequenceAnnotationOrder annotationSortOrder;
 214
 215   private boolean showAutoCalculatedAbove = false;
 216
 217   private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
 218
 219   private SplitContainerI splitFrame;
 220
 221   public GAlignFrame()
 222   {
 223     try
 224     {
 225       jbInit();
 226       setJMenuBar(alignFrameMenuBar);
 227
 228       // dynamically fill save as menu with available formats
 229       for (String ff : FileFormats.getInstance().getWritableFormats(true))
 230       {
 231         JMenuItem item = new JMenuItem(ff);
 232
 233         item.addActionListener(new ActionListener()
 234         {
 235           @Override
 236           public void actionPerformed(ActionEvent e)
 237           {
 238             outputText_actionPerformed(e);
 239           }
 240         });
 241
 242         outputTextboxMenu.add(item);
 243       }
 244     } catch (Exception e)
 245     {
 246       System.err.println(e.toString());
 247     }
 248
 249     if (!Platform.isAMac())
 250     {
 251       closeMenuItem.setMnemonic('C');
 252       outputTextboxMenu.setMnemonic('T');
 253       undoMenuItem.setMnemonic('Z');
 254       redoMenuItem.setMnemonic('0');
 255       copy.setMnemonic('C');
 256       cut.setMnemonic('U');
 257       pasteMenu.setMnemonic('P');
 258       reload.setMnemonic('R');
 259     }
 260   }
 261
 262   private void jbInit() throws Exception
 263   {
 264     initColourMenu();
 265     initHMMERMenu();
 266
 267     JMenuItem saveAs = new JMenuItem(
 268             MessageManager.getString("action.save_as"));
 269     ActionListener al = new ActionListener()
 270     {
 271       @Override
 272       public void actionPerformed(ActionEvent e)
 273       {
 274         saveAs_actionPerformed(e);
 275       }
 276     };
 277
 278     // FIXME getDefaultToolkit throws an exception in Headless mode
 279     KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
 280             .getDefaultToolkit().getMenuShortcutKeyMask()
 281             | KeyEvent.SHIFT_MASK, false);
 282     addMenuActionAndAccelerator(keyStroke, saveAs, al);
 283
 284     closeMenuItem.setText(MessageManager.getString("action.close"));
 285     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
 286             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 287     al = new ActionListener()
 288     {
 289       @Override
 290       public void actionPerformed(ActionEvent e)
 291       {
 292         closeMenuItem_actionPerformed(false);
 293       }
 294     };
 295     addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
 296
 297     JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
 298     JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
 299     JMenu annotationsMenu = new JMenu(
 300             MessageManager.getString("action.annotations"));
 301     JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
 302     colourMenu.setText(MessageManager.getString("action.colour"));
 303     JMenu calculateMenu = new JMenu(
 304             MessageManager.getString("action.calculate"));
 305     webService.setText(MessageManager.getString("action.web_service"));
 306     hmmerMenu.setText(MessageManager.getString("action.hmmer"));
 307     String status = Cache.getProperty("HMMER_FUNCTIONING");
 308     if ("false".equals(status) || status == null)
 309     {
 310       hmmerMenu.setEnabled(false);
 311     }
 312     else
 313     {
 314       hmmerMenu.setEnabled(true);
 315     }
 316     hmmerMenu.addActionListener(new ActionListener()
 317     {
 318       @Override
 319       public void actionPerformed(ActionEvent e)
 320       {
 321         hmmerMenu_actionPerformed(e);
 322       }
 323     });
 324     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
 325             MessageManager.getString("action.select_all"));
 326     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
 327             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 328     al = new ActionListener()
 329     {
 330       @Override
 331       public void actionPerformed(ActionEvent e)
 332       {
 333         selectAllSequenceMenuItem_actionPerformed(e);
 334       }
 335     };
 336     addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
 337
 338     JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
 339             MessageManager.getString("action.deselect_all"));
 340     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
 341     al = new ActionListener()
 342     {
 343       @Override
 344       public void actionPerformed(ActionEvent e)
 345       {
 346         deselectAllSequenceMenuItem_actionPerformed(e);
 347       }
 348     };
 349     addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
 350
 351     JMenuItem invertSequenceMenuItem = new JMenuItem(
 352             MessageManager.getString("action.invert_sequence_selection"));
 353     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
 354             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 355     al = new ActionListener()
 356     {
 357       @Override
 358       public void actionPerformed(ActionEvent e)
 359       {
 360         invertSequenceMenuItem_actionPerformed(e);
 361       }
 362     };
 363     addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
 364
 365     JMenuItem grpsFromSelection = new JMenuItem(
 366             MessageManager.getString("action.make_groups_selection"));
 367     grpsFromSelection.addActionListener(new ActionListener()
 368     {
 369       @Override
 370       public void actionPerformed(ActionEvent e)
 371       {
 372         makeGrpsFromSelection_actionPerformed(e);
 373       }
 374     });
 375     JMenuItem expandAlignment = new JMenuItem(
 376             MessageManager.getString("action.view_flanking_regions"));
 377     expandAlignment.setToolTipText(MessageManager
 378             .getString("label.view_flanking_regions"));
 379     expandAlignment.addActionListener(new ActionListener()
 380     {
 381       @Override
 382       public void actionPerformed(ActionEvent e)
 383       {
 384         expand_newalign(e);
 385       }
 386     });
 387     JMenuItem remove2LeftMenuItem = new JMenuItem(
 388             MessageManager.getString("action.remove_left"));
 389     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
 390             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 391     al = new ActionListener()
 392     {
 393       @Override
 394       public void actionPerformed(ActionEvent e)
 395       {
 396         remove2LeftMenuItem_actionPerformed(e);
 397       }
 398     };
 399     addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
 400
 401     JMenuItem remove2RightMenuItem = new JMenuItem(
 402             MessageManager.getString("action.remove_right"));
 403     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
 404             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 405     al = new ActionListener()
 406     {
 407       @Override
 408       public void actionPerformed(ActionEvent e)
 409       {
 410         remove2RightMenuItem_actionPerformed(e);
 411       }
 412     };
 413     addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
 414
 415     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
 416             MessageManager.getString("action.remove_empty_columns"));
 417     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
 418             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 419     al = new ActionListener()
 420     {
 421       @Override
 422       public void actionPerformed(ActionEvent e)
 423       {
 424         removeGappedColumnMenuItem_actionPerformed(e);
 425       }
 426     };
 427     addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
 428
 429     JMenuItem removeAllGapsMenuItem = new JMenuItem(
 430             MessageManager.getString("action.remove_all_gaps"));
 431     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
 432             .getDefaultToolkit().getMenuShortcutKeyMask()
 433             | KeyEvent.SHIFT_MASK, false);
 434     al = new ActionListener()
 435     {
 436       @Override
 437       public void actionPerformed(ActionEvent e)
 438       {
 439         removeAllGapsMenuItem_actionPerformed(e);
 440       }
 441     };
 442     addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
 443
 444     JMenuItem justifyLeftMenuItem = new JMenuItem(
 445             MessageManager.getString("action.left_justify_alignment"));
 446     justifyLeftMenuItem.addActionListener(new ActionListener()
 447     {
 448       @Override
 449       public void actionPerformed(ActionEvent e)
 450       {
 451         justifyLeftMenuItem_actionPerformed(e);
 452       }
 453     });
 454     JMenuItem justifyRightMenuItem = new JMenuItem(
 455             MessageManager.getString("action.right_justify_alignment"));
 456     justifyRightMenuItem.addActionListener(new ActionListener()
 457     {
 458       @Override
 459       public void actionPerformed(ActionEvent e)
 460       {
 461         justifyRightMenuItem_actionPerformed(e);
 462       }
 463     });
 464     viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
 465     viewBoxesMenuItem.setState(true);
 466     viewBoxesMenuItem.addActionListener(new ActionListener()
 467     {
 468       @Override
 469       public void actionPerformed(ActionEvent e)
 470       {
 471         viewBoxesMenuItem_actionPerformed(e);
 472       }
 473     });
 474     viewTextMenuItem.setText(MessageManager.getString("action.text"));
 475     viewTextMenuItem.setState(true);
 476     viewTextMenuItem.addActionListener(new ActionListener()
 477     {
 478       @Override
 479       public void actionPerformed(ActionEvent e)
 480       {
 481         viewTextMenuItem_actionPerformed(e);
 482       }
 483     });
 484     showNonconservedMenuItem.setText(MessageManager
 485             .getString("label.show_non_conserved"));
 486     showNonconservedMenuItem.setState(false);
 487     showNonconservedMenuItem.addActionListener(new ActionListener()
 488     {
 489       @Override
 490       public void actionPerformed(ActionEvent e)
 491       {
 492         showUnconservedMenuItem_actionPerformed(e);
 493       }
 494     });
 495     JMenuItem sortPairwiseMenuItem = new JMenuItem(
 496             MessageManager.getString("action.by_pairwise_id"));
 497     sortPairwiseMenuItem.addActionListener(new ActionListener()
 498     {
 499       @Override
 500       public void actionPerformed(ActionEvent e)
 501       {
 502         sortPairwiseMenuItem_actionPerformed(e);
 503       }
 504     });
 505     JMenuItem sortIDMenuItem = new JMenuItem(
 506             MessageManager.getString("action.by_id"));
 507     sortIDMenuItem.addActionListener(new ActionListener()
 508     {
 509       @Override
 510       public void actionPerformed(ActionEvent e)
 511       {
 512         sortIDMenuItem_actionPerformed(e);
 513       }
 514     });
 515     JMenuItem sortLengthMenuItem = new JMenuItem(
 516             MessageManager.getString("action.by_length"));
 517     sortLengthMenuItem.addActionListener(new ActionListener()
 518     {
 519       @Override
 520       public void actionPerformed(ActionEvent e)
 521       {
 522         sortLengthMenuItem_actionPerformed(e);
 523       }
 524     });
 525     JMenuItem sortGroupMenuItem = new JMenuItem(
 526             MessageManager.getString("action.by_group"));
 527     sortGroupMenuItem.addActionListener(new ActionListener()
 528     {
 529       @Override
 530       public void actionPerformed(ActionEvent e)
 531       {
 532         sortGroupMenuItem_actionPerformed(e);
 533       }
 534     });
 535
 536     JMenuItem removeRedundancyMenuItem = new JMenuItem(
 537             MessageManager.getString("action.remove_redundancy"));
 538     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
 539             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 540     al = new ActionListener()
 541     {
 542       @Override
 543       public void actionPerformed(ActionEvent e)
 544       {
 545         removeRedundancyMenuItem_actionPerformed(e);
 546       }
 547     };
 548     addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
 549
 550     JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
 551             MessageManager.getString("action.pairwise_alignment"));
 552     pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
 553     {
 554       @Override
 555       public void actionPerformed(ActionEvent e)
 556       {
 557         pairwiseAlignmentMenuItem_actionPerformed(e);
 558       }
 559     });
 560
 561     this.getContentPane().setLayout(new BorderLayout());
 562     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 563     statusBar.setBackground(Color.white);
 564     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 565     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 566     statusBar.setText(MessageManager.getString("label.status_bar"));
 567     outputTextboxMenu.setText(MessageManager
 568             .getString("label.out_to_textbox"));
 569
 570     annotationPanelMenuItem.setActionCommand("");
 571     annotationPanelMenuItem.setText(MessageManager
 572             .getString("label.show_annotations"));
 573     annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
 574             true));
 575     annotationPanelMenuItem.addActionListener(new ActionListener()
 576     {
 577       @Override
 578       public void actionPerformed(ActionEvent e)
 579       {
 580         annotationPanelMenuItem_actionPerformed(e);
 581       }
 582     });
 583     showAllAlAnnotations.setText(MessageManager
 584             .getString("label.show_all_al_annotations"));
 585     final boolean isAnnotationPanelShown = annotationPanelMenuItem
 586             .getState();
 587     showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 588     showAllAlAnnotations.addActionListener(new ActionListener()
 589     {
 590       @Override
 591       public void actionPerformed(ActionEvent e)
 592       {
 593         showAllAnnotations_actionPerformed(false, true);
 594       }
 595     });
 596     hideAllAlAnnotations.setText(MessageManager
 597             .getString("label.hide_all_al_annotations"));
 598     hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 599     hideAllAlAnnotations.addActionListener(new ActionListener()
 600     {
 601       @Override
 602       public void actionPerformed(ActionEvent e)
 603       {
 604         hideAllAnnotations_actionPerformed(false, true);
 605       }
 606     });
 607     showAllSeqAnnotations.setText(MessageManager
 608             .getString("label.show_all_seq_annotations"));
 609     showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 610     showAllSeqAnnotations.addActionListener(new ActionListener()
 611     {
 612       @Override
 613       public void actionPerformed(ActionEvent e)
 614       {
 615         showAllAnnotations_actionPerformed(true, false);
 616       }
 617     });
 618     hideAllSeqAnnotations.setText(MessageManager
 619             .getString("label.hide_all_seq_annotations"));
 620     hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 621     hideAllSeqAnnotations.addActionListener(new ActionListener()
 622     {
 623       @Override
 624       public void actionPerformed(ActionEvent e)
 625       {
 626         hideAllAnnotations_actionPerformed(true, false);
 627       }
 628     });
 629     SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
 630             .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
 631                     SequenceAnnotationOrder.NONE.name()));
 632     final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
 633             MessageManager.getString("label.sort_annotations_by_sequence"));
 634     final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
 635             MessageManager.getString("label.sort_annotations_by_label"));
 636
 637     sortAnnBySequence
 638             .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
 639     sortAnnBySequence.addActionListener(new ActionListener()
 640     {
 641       @Override
 642       public void actionPerformed(ActionEvent e)
 643       {
 644         boolean newState = sortAnnBySequence.getState();
 645         sortAnnByLabel.setSelected(false);
 646         setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 647                 : SequenceAnnotationOrder.NONE);
 648         sortAnnotations_actionPerformed();
 649       }
 650     });
 651     sortAnnByLabel
 652             .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
 653     sortAnnByLabel.addActionListener(new ActionListener()
 654     {
 655       @Override
 656       public void actionPerformed(ActionEvent e)
 657       {
 658         boolean newState = sortAnnByLabel.getState();
 659         sortAnnBySequence.setSelected(false);
 660         setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 661                 : SequenceAnnotationOrder.NONE);
 662         sortAnnotations_actionPerformed();
 663       }
 664     });
 665     colourTextMenuItem = new JCheckBoxMenuItem(
 666             MessageManager
 667             .getString("label.colour_text"));
 668     colourTextMenuItem.addActionListener(new ActionListener()
 669     {
 670       @Override
 671       public void actionPerformed(ActionEvent e)
 672       {
 673         colourTextMenuItem_actionPerformed(e);
 674       }
 675     });
 676
 677     JMenuItem htmlMenuItem = new JMenuItem(
 678             MessageManager.getString("label.html"));
 679     htmlMenuItem.addActionListener(new ActionListener()
 680     {
 681       @Override
 682       public void actionPerformed(ActionEvent e)
 683       {
 684         htmlMenuItem_actionPerformed(e);
 685       }
 686     });
 687
 688     JMenuItem createBioJS = new JMenuItem(
 689             MessageManager.getString("label.biojs_html_export"));
 690     createBioJS.addActionListener(new java.awt.event.ActionListener()
 691     {
 692       @Override
 693       public void actionPerformed(ActionEvent e)
 694       {
 695         bioJSMenuItem_actionPerformed(e);
 696       }
 697     });
 698
 699     JMenuItem overviewMenuItem = new JMenuItem(
 700             MessageManager.getString("label.overview_window"));
 701     overviewMenuItem.addActionListener(new ActionListener()
 702     {
 703       @Override
 704       public void actionPerformed(ActionEvent e)
 705       {
 706         overviewMenuItem_actionPerformed(e);
 707       }
 708     });
 709
 710     undoMenuItem.setEnabled(false);
 711     undoMenuItem.setText(MessageManager.getString("action.undo"));
 712     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
 713             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 714     al = new ActionListener()
 715     {
 716       @Override
 717       public void actionPerformed(ActionEvent e)
 718       {
 719         undoMenuItem_actionPerformed(e);
 720       }
 721     };
 722     addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
 723
 724     redoMenuItem.setEnabled(false);
 725     redoMenuItem.setText(MessageManager.getString("action.redo"));
 726     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
 727             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 728     al = new ActionListener()
 729     {
 730       @Override
 731       public void actionPerformed(ActionEvent e)
 732       {
 733         redoMenuItem_actionPerformed(e);
 734       }
 735     };
 736     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
 737
 738     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
 739     wrapMenuItem.addActionListener(new ActionListener()
 740     {
 741       @Override
 742       public void actionPerformed(ActionEvent e)
 743       {
 744         wrapMenuItem_actionPerformed(e);
 745       }
 746     });
 747
 748     JMenuItem printMenuItem = new JMenuItem(
 749             MessageManager.getString("action.print"));
 750     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
 751             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 752     al = new ActionListener()
 753     {
 754       @Override
 755       public void actionPerformed(ActionEvent e)
 756       {
 757         printMenuItem_actionPerformed(e);
 758       }
 759     };
 760     addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
 761
 762     renderGapsMenuItem
 763             .setText(MessageManager.getString("action.show_gaps"));
 764     renderGapsMenuItem.setState(true);
 765     renderGapsMenuItem.addActionListener(new ActionListener()
 766     {
 767       @Override
 768       public void actionPerformed(ActionEvent e)
 769       {
 770         renderGapsMenuItem_actionPerformed(e);
 771       }
 772     });
 773
 774     JMenuItem findMenuItem = new JMenuItem(
 775             MessageManager.getString("action.find"));
 776     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
 777             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 778     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
 779             MessageManager.getString("label.find_tip")));
 780     al = new ActionListener()
 781     {
 782       @Override
 783       public void actionPerformed(ActionEvent e)
 784       {
 785         findMenuItem_actionPerformed(e);
 786       }
 787     };
 788     addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
 789
 790     showSeqFeatures.setText(MessageManager
 791             .getString("label.show_sequence_features"));
 792     showSeqFeatures.addActionListener(new ActionListener()
 793     {
 794       @Override
 795       public void actionPerformed(ActionEvent actionEvent)
 796       {
 797         showSeqFeatures_actionPerformed(actionEvent);
 798       }
 799     });
 800     /*
 801      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
 802      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
 803      * void actionPerformed(ActionEvent actionEvent) {
 804      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
 805      */
 806     showDbRefsMenuitem.setText(MessageManager
 807             .getString("label.show_database_refs"));
 808     showDbRefsMenuitem.addActionListener(new ActionListener()
 809     {
 810
 811       @Override
 812       public void actionPerformed(ActionEvent e)
 813       {
 814         showDbRefs_actionPerformed(e);
 815       }
 816
 817     });
 818     showNpFeatsMenuitem.setText(MessageManager
 819             .getString("label.show_non_positional_features"));
 820     showNpFeatsMenuitem.addActionListener(new ActionListener()
 821     {
 822
 823       @Override
 824       public void actionPerformed(ActionEvent e)
 825       {
 826         showNpFeats_actionPerformed(e);
 827       }
 828
 829     });
 830     showGroupConservation.setText(MessageManager
 831             .getString("label.group_conservation"));
 832     showGroupConservation.addActionListener(new ActionListener()
 833     {
 834
 835       @Override
 836       public void actionPerformed(ActionEvent e)
 837       {
 838         showGroupConservation_actionPerformed(e);
 839       }
 840
 841     });
 842
 843     showGroupConsensus.setText(MessageManager
 844             .getString("label.group_consensus"));
 845     showGroupConsensus.addActionListener(new ActionListener()
 846     {
 847
 848       @Override
 849       public void actionPerformed(ActionEvent e)
 850       {
 851         showGroupConsensus_actionPerformed(e);
 852       }
 853
 854     });
 855     showConsensusHistogram.setText(MessageManager
 856             .getString("label.show_consensus_histogram"));
 857     showConsensusHistogram.addActionListener(new ActionListener()
 858     {
 859
 860       @Override
 861       public void actionPerformed(ActionEvent e)
 862       {
 863         showConsensusHistogram_actionPerformed(e);
 864       }
 865
 866     });
 867     showSequenceLogo.setText(MessageManager
 868             .getString("label.show_consensus_logo"));
 869     showSequenceLogo.addActionListener(new ActionListener()
 870     {
 871
 872       @Override
 873       public void actionPerformed(ActionEvent e)
 874       {
 875         showSequenceLogo_actionPerformed(e);
 876       }
 877
 878     });
 879     normaliseSequenceLogo.setText(MessageManager
 880             .getString("label.norm_consensus_logo"));
 881     normaliseSequenceLogo.addActionListener(new ActionListener()
 882     {
 883
 884       @Override
 885       public void actionPerformed(ActionEvent e)
 886       {
 887         normaliseSequenceLogo_actionPerformed(e);
 888       }
 889
 890     });
 891     applyAutoAnnotationSettings.setText(MessageManager
 892             .getString("label.apply_all_groups"));
 893     applyAutoAnnotationSettings.setState(false);
 894     applyAutoAnnotationSettings.setVisible(true);
 895     applyAutoAnnotationSettings.addActionListener(new ActionListener()
 896     {
 897       @Override
 898       public void actionPerformed(ActionEvent e)
 899       {
 900         applyAutoAnnotationSettings_actionPerformed(e);
 901       }
 902     });
 903
 904     ButtonGroup buttonGroup = new ButtonGroup();
 905     final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
 906             MessageManager.getString("label.show_first"));
 907     final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
 908             MessageManager.getString("label.show_last"));
 909     buttonGroup.add(showAutoFirst);
 910     buttonGroup.add(showAutoLast);
 911     final boolean autoFirst = Cache.getDefault(
 912             Preferences.SHOW_AUTOCALC_ABOVE, false);
 913     showAutoFirst.setSelected(autoFirst);
 914     setShowAutoCalculatedAbove(autoFirst);
 915     showAutoFirst.addActionListener(new ActionListener()
 916     {
 917       @Override
 918       public void actionPerformed(ActionEvent e)
 919       {
 920         setShowAutoCalculatedAbove(showAutoFirst.isSelected());
 921         sortAnnotations_actionPerformed();
 922       }
 923     });
 924     showAutoLast.setSelected(!showAutoFirst.isSelected());
 925     showAutoLast.addActionListener(new ActionListener()
 926     {
 927       @Override
 928       public void actionPerformed(ActionEvent e)
 929       {
 930         setShowAutoCalculatedAbove(!showAutoLast.isSelected());
 931         sortAnnotations_actionPerformed();
 932       }
 933     });
 934
 935     JMenuItem deleteGroups = new JMenuItem(
 936             MessageManager.getString("action.undefine_groups"));
 937     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
 938             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 939     al = new ActionListener()
 940     {
 941       @Override
 942       public void actionPerformed(ActionEvent e)
 943       {
 944         deleteGroups_actionPerformed(e);
 945       }
 946     };
 947     addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
 948
 949     JMenuItem annotationColumn = new JMenuItem(
 950             MessageManager.getString("action.select_by_annotation"));
 951     annotationColumn.addActionListener(new ActionListener()
 952     {
 953       @Override
 954       public void actionPerformed(ActionEvent e)
 955       {
 956         annotationColumn_actionPerformed(e);
 957       }
 958     });
 959
 960     JMenuItem createGroup = new JMenuItem(
 961             MessageManager.getString("action.create_group"));
 962     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
 963             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 964     al = new ActionListener()
 965     {
 966       @Override
 967       public void actionPerformed(ActionEvent e)
 968       {
 969         createGroup_actionPerformed(e);
 970       }
 971     };
 972     addMenuActionAndAccelerator(keyStroke, createGroup, al);
 973
 974     JMenuItem unGroup = new JMenuItem(
 975             MessageManager.getString("action.remove_group"));
 976     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
 977             .getDefaultToolkit().getMenuShortcutKeyMask()
 978             | KeyEvent.SHIFT_MASK, false);
 979     al = new ActionListener()
 980     {
 981       @Override
 982       public void actionPerformed(ActionEvent e)
 983       {
 984         unGroup_actionPerformed(e);
 985       }
 986     };
 987     addMenuActionAndAccelerator(keyStroke, unGroup, al);
 988
 989     copy.setText(MessageManager.getString("action.copy"));
 990     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
 991             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 992
 993     al = new ActionListener()
 994     {
 995       @Override
 996       public void actionPerformed(ActionEvent e)
 997       {
 998         copy_actionPerformed(e);
 999       }
1000     };
1001     addMenuActionAndAccelerator(keyStroke, copy, al);
1002
1003     cut.setText(MessageManager.getString("action.cut"));
1004     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
1005             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1006     al = new ActionListener()
1007     {
1008       @Override
1009       public void actionPerformed(ActionEvent e)
1010       {
1011         cut_actionPerformed(e);
1012       }
1013     };
1014     addMenuActionAndAccelerator(keyStroke, cut, al);
1015
1016     JMenuItem delete = new JMenuItem(
1017             MessageManager.getString("action.delete"));
1018     delete.addActionListener(new ActionListener()
1019     {
1020       @Override
1021       public void actionPerformed(ActionEvent e)
1022       {
1023         delete_actionPerformed(e);
1024       }
1025     });
1026
1027     pasteMenu.setText(MessageManager.getString("action.paste"));
1028     JMenuItem pasteNew = new JMenuItem(
1029             MessageManager.getString("label.to_new_alignment"));
1030     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1031             .getDefaultToolkit().getMenuShortcutKeyMask()
1032             | KeyEvent.SHIFT_MASK, false);
1033     al = new ActionListener()
1034     {
1035       @Override
1036       public void actionPerformed(ActionEvent e)
1037       {
1038         try
1039         {
1040           pasteNew_actionPerformed(e);
1041         } catch (IOException | InterruptedException e1)
1042         {
1043           // TODO Auto-generated catch block
1044           e1.printStackTrace();
1045         }
1046       }
1047     };
1048     addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1049
1050     JMenuItem pasteThis = new JMenuItem(
1051             MessageManager.getString("label.to_this_alignment"));
1052     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1053             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1054     al = new ActionListener()
1055     {
1056       @Override
1057       public void actionPerformed(ActionEvent e)
1058       {
1059         try
1060         {
1061           pasteThis_actionPerformed(e);
1062         } catch (IOException | InterruptedException e1)
1063         {
1064           // TODO Auto-generated catch block
1065           e1.printStackTrace();
1066         }
1067       }
1068     };
1069     addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1070
1071     JMenuItem createPNG = new JMenuItem("PNG");
1072     createPNG.addActionListener(new ActionListener()
1073     {
1074       @Override
1075       public void actionPerformed(ActionEvent e)
1076       {
1077         createPNG(null);
1078       }
1079     });
1080     createPNG.setActionCommand(MessageManager
1081             .getString("label.save_png_image"));
1082
1083     JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1084     font.addActionListener(new ActionListener()
1085     {
1086       @Override
1087       public void actionPerformed(ActionEvent e)
1088       {
1089         font_actionPerformed(e);
1090       }
1091     });
1092     seqLimits.setText(MessageManager
1093             .getString("label.show_sequence_limits"));
1094     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1095     seqLimits.addActionListener(new ActionListener()
1096     {
1097       @Override
1098       public void actionPerformed(ActionEvent e)
1099       {
1100         seqLimit_actionPerformed(e);
1101       }
1102     });
1103     JMenuItem epsFile = new JMenuItem("EPS");
1104     epsFile.addActionListener(new ActionListener()
1105     {
1106       @Override
1107       public void actionPerformed(ActionEvent e)
1108       {
1109         createEPS(null);
1110       }
1111     });
1112
1113     JMenuItem createSVG = new JMenuItem("SVG");
1114     createSVG.addActionListener(new ActionListener()
1115     {
1116       @Override
1117       public void actionPerformed(ActionEvent e)
1118       {
1119         createSVG(null);
1120       }
1121     });
1122
1123     JMenuItem loadTreeMenuItem = new JMenuItem(
1124             MessageManager.getString("label.load_associated_tree"));
1125     loadTreeMenuItem.setActionCommand(MessageManager
1126             .getString("label.load_tree_for_sequence_set"));
1127     loadTreeMenuItem.addActionListener(new ActionListener()
1128     {
1129       @Override
1130       public void actionPerformed(ActionEvent e)
1131       {
1132         loadTreeMenuItem_actionPerformed(e);
1133       }
1134     });
1135
1136     scaleAbove.setVisible(false);
1137     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1138     scaleAbove.addActionListener(new ActionListener()
1139     {
1140       @Override
1141       public void actionPerformed(ActionEvent e)
1142       {
1143         scaleAbove_actionPerformed(e);
1144       }
1145     });
1146     scaleLeft.setVisible(false);
1147     scaleLeft.setSelected(true);
1148     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1149     scaleLeft.addActionListener(new ActionListener()
1150     {
1151       @Override
1152       public void actionPerformed(ActionEvent e)
1153       {
1154         scaleLeft_actionPerformed(e);
1155       }
1156     });
1157     scaleRight.setVisible(false);
1158     scaleRight.setSelected(true);
1159     scaleRight.setText(MessageManager.getString("action.scale_right"));
1160     scaleRight.addActionListener(new ActionListener()
1161     {
1162       @Override
1163       public void actionPerformed(ActionEvent e)
1164       {
1165         scaleRight_actionPerformed(e);
1166       }
1167     });
1168     centreColumnLabelsMenuItem.setVisible(true);
1169     centreColumnLabelsMenuItem.setState(false);
1170     centreColumnLabelsMenuItem.setText(MessageManager
1171             .getString("label.centre_column_labels"));
1172     centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1173     {
1174       @Override
1175       public void actionPerformed(ActionEvent e)
1176       {
1177         centreColumnLabels_actionPerformed(e);
1178       }
1179     });
1180     followHighlightMenuItem.setVisible(true);
1181     followHighlightMenuItem.setState(true);
1182     followHighlightMenuItem.setText(MessageManager
1183             .getString("label.automatic_scrolling"));
1184     followHighlightMenuItem.addActionListener(new ActionListener()
1185     {
1186
1187       @Override
1188       public void actionPerformed(ActionEvent e)
1189       {
1190         followHighlight_actionPerformed();
1191       }
1192
1193     });
1194
1195     sortByTreeMenu
1196             .setText(MessageManager.getString("action.by_tree_order"));
1197     sort.setText(MessageManager.getString("action.sort"));
1198     sort.addMenuListener(new MenuListener()
1199     {
1200       @Override
1201       public void menuSelected(MenuEvent e)
1202       {
1203         buildTreeSortMenu();
1204       }
1205
1206       @Override
1207       public void menuDeselected(MenuEvent e)
1208       {
1209       }
1210
1211       @Override
1212       public void menuCanceled(MenuEvent e)
1213       {
1214       }
1215     });
1216     sortByAnnotScore.setText(MessageManager
1217             .getString("label.sort_by_score"));
1218     sort.add(sortByAnnotScore);
1219     sort.addMenuListener(new javax.swing.event.MenuListener()
1220     {
1221
1222       @Override
1223       public void menuCanceled(MenuEvent e)
1224       {
1225       }
1226
1227       @Override
1228       public void menuDeselected(MenuEvent e)
1229       {
1230       }
1231
1232       @Override
1233       public void menuSelected(MenuEvent e)
1234       {
1235         buildSortByAnnotationScoresMenu();
1236       }
1237     });
1238     sortByAnnotScore.setVisible(false);
1239
1240     calculateTree.setText(MessageManager
1241             .getString("action.calculate_tree_pca"));
1242
1243     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1244     padGapsMenuitem.setState(jalview.bin.Cache
1245             .getDefault("PAD_GAPS", false));
1246     padGapsMenuitem.addActionListener(new ActionListener()
1247     {
1248       @Override
1249       public void actionPerformed(ActionEvent e)
1250       {
1251         padGapsMenuitem_actionPerformed(e);
1252       }
1253     });
1254     JMenuItem vamsasStore = new JMenuItem(
1255             MessageManager.getString("label.vamsas_store"));
1256     vamsasStore.setVisible(false);
1257     vamsasStore.addActionListener(new ActionListener()
1258     {
1259       @Override
1260       public void actionPerformed(ActionEvent e)
1261       {
1262         vamsasStore_actionPerformed(e);
1263       }
1264     });
1265     showTranslation.setText(MessageManager
1266             .getString("label.translate_cDNA"));
1267     showTranslation.addActionListener(new ActionListener()
1268     {
1269       @Override
1270       public void actionPerformed(ActionEvent e)
1271       {
1272         showTranslation_actionPerformed(e);
1273       }
1274     });
1275     showReverse.setText(MessageManager.getString("label.reverse"));
1276     showReverse.addActionListener(new ActionListener()
1277     {
1278       @Override
1279       public void actionPerformed(ActionEvent e)
1280       {
1281         showReverse_actionPerformed(false);
1282       }
1283     });
1284     showReverseComplement.setText(MessageManager
1285             .getString("label.reverse_complement"));
1286     showReverseComplement.addActionListener(new ActionListener()
1287     {
1288       @Override
1289       public void actionPerformed(ActionEvent e)
1290       {
1291         showReverse_actionPerformed(true);
1292       }
1293     });
1294
1295     JMenuItem extractScores = new JMenuItem(
1296             MessageManager.getString("label.extract_scores"));
1297     extractScores.addActionListener(new ActionListener()
1298     {
1299       @Override
1300       public void actionPerformed(ActionEvent e)
1301       {
1302         extractScores_actionPerformed(e);
1303       }
1304     });
1305     extractScores.setVisible(true);
1306     // JBPNote: TODO: make gui for regex based score extraction
1307
1308     // for show products actions see AlignFrame.canShowProducts
1309     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1310
1311     runGroovy.setText(MessageManager.getString("label.run_groovy"));
1312     runGroovy.setToolTipText(MessageManager
1313             .getString("label.run_groovy_tip"));
1314     runGroovy.addActionListener(new ActionListener()
1315     {
1316       @Override
1317       public void actionPerformed(ActionEvent e)
1318       {
1319         runGroovy_actionPerformed();
1320       }
1321     });
1322
1323     JMenuItem openFeatureSettings = new JMenuItem(
1324             MessageManager.getString("action.feature_settings"));
1325     openFeatureSettings.addActionListener(new ActionListener()
1326     {
1327       @Override
1328       public void actionPerformed(ActionEvent e)
1329       {
1330         featureSettings_actionPerformed(e);
1331       }
1332     });
1333     JMenuItem fetchSequence = new JMenuItem(
1334             MessageManager.getString("label.fetch_sequences"));
1335     fetchSequence.addActionListener(new ActionListener()
1336     {
1337       @Override
1338       public void actionPerformed(ActionEvent e)
1339       {
1340         fetchSequence_actionPerformed(e);
1341       }
1342     });
1343
1344     JMenuItem associatedData = new JMenuItem(
1345             MessageManager.getString("label.load_features_annotations"));
1346     associatedData.addActionListener(new ActionListener()
1347     {
1348       @Override
1349       public void actionPerformed(ActionEvent e)
1350       {
1351         try
1352         {
1353           associatedData_actionPerformed(e);
1354         } catch (IOException | InterruptedException e1)
1355         {
1356           // TODO Auto-generated catch block
1357           e1.printStackTrace();
1358         }
1359       }
1360     });
1361     autoCalculate.setText(MessageManager
1362             .getString("label.autocalculate_consensus"));
1363     autoCalculate.setState(jalview.bin.Cache.getDefault(
1364             "AUTO_CALC_CONSENSUS", true));
1365     autoCalculate.addActionListener(new ActionListener()
1366     {
1367       @Override
1368       public void actionPerformed(ActionEvent e)
1369       {
1370         autoCalculate_actionPerformed(e);
1371       }
1372     });
1373     sortByTree.setText(MessageManager
1374             .getString("label.sort_alignment_new_tree"));
1375     sortByTree
1376             .setToolTipText("<html>"
1377                     + MessageManager
1378                             .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1379     sortByTree
1380             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1381     sortByTree.addActionListener(new ActionListener()
1382     {
1383       @Override
1384       public void actionPerformed(ActionEvent e)
1385       {
1386         sortByTreeOption_actionPerformed(e);
1387       }
1388     });
1389
1390     listenToViewSelections.setText(MessageManager
1391             .getString("label.listen_for_selections"));
1392     listenToViewSelections
1393             .setToolTipText("<html>"
1394                     + MessageManager
1395                             .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1396     listenToViewSelections.setState(false);
1397     listenToViewSelections.addActionListener(new ActionListener()
1398     {
1399       @Override
1400       public void actionPerformed(ActionEvent e)
1401       {
1402         listenToViewSelections_actionPerformed(e);
1403       }
1404     });
1405
1406     JMenu addSequenceMenu = new JMenu(
1407             MessageManager.getString("label.add_sequences"));
1408     JMenuItem addFromFile = new JMenuItem(
1409             MessageManager.getString("label.from_file"));
1410     addFromFile.addActionListener(new ActionListener()
1411     {
1412       @Override
1413       public void actionPerformed(ActionEvent e)
1414       {
1415         addFromFile_actionPerformed(e);
1416       }
1417     });
1418     JMenuItem addFromText = new JMenuItem(
1419             MessageManager.getString("label.from_textbox"));
1420     addFromText.addActionListener(new ActionListener()
1421     {
1422       @Override
1423       public void actionPerformed(ActionEvent e)
1424       {
1425         addFromText_actionPerformed(e);
1426       }
1427     });
1428     JMenuItem addFromURL = new JMenuItem(
1429             MessageManager.getString("label.from_url"));
1430     addFromURL.addActionListener(new ActionListener()
1431     {
1432       @Override
1433       public void actionPerformed(ActionEvent e)
1434       {
1435         addFromURL_actionPerformed(e);
1436       }
1437     });
1438     JMenuItem exportFeatures = new JMenuItem(
1439             MessageManager.getString("label.export_features"));
1440     exportFeatures.addActionListener(new ActionListener()
1441     {
1442       @Override
1443       public void actionPerformed(ActionEvent e)
1444       {
1445         exportFeatures_actionPerformed(e);
1446       }
1447     });
1448     JMenuItem exportAnnotations = new JMenuItem(
1449             MessageManager.getString("label.export_annotations"));
1450     exportAnnotations.addActionListener(new ActionListener()
1451     {
1452       @Override
1453       public void actionPerformed(ActionEvent e)
1454       {
1455         exportAnnotations_actionPerformed(e);
1456       }
1457     });
1458     statusPanel.setLayout(new GridLayout());
1459     JMenuItem showAllSeqs = new JMenuItem(
1460             MessageManager.getString("label.all_sequences"));
1461     showAllSeqs.setToolTipText(MessageManager
1462             .getString("label.toggle_sequence_visibility"));
1463     showAllSeqs.addActionListener(new ActionListener()
1464     {
1465       @Override
1466       public void actionPerformed(ActionEvent e)
1467       {
1468         showAllSeqs_actionPerformed(e);
1469       }
1470     });
1471     JMenuItem showAllColumns = new JMenuItem(
1472             MessageManager.getString("label.all_columns"));
1473     showAllColumns.setToolTipText(MessageManager
1474             .getString("label.toggle_columns_visibility"));
1475     showAllColumns.addActionListener(new ActionListener()
1476     {
1477       @Override
1478       public void actionPerformed(ActionEvent e)
1479       {
1480         showAllColumns_actionPerformed(e);
1481       }
1482     });
1483     JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1484     JMenuItem hideSelSequences = new JMenuItem(
1485             MessageManager.getString("label.selected_sequences"));
1486     hideSelSequences.setToolTipText(MessageManager
1487             .getString("label.toggle_sequence_visibility"));
1488     hideSelSequences.addActionListener(new ActionListener()
1489     {
1490       @Override
1491       public void actionPerformed(ActionEvent e)
1492       {
1493         hideSelSequences_actionPerformed(e);
1494       }
1495     });
1496     JMenuItem hideSelColumns = new JMenuItem(
1497             MessageManager.getString("label.selected_columns"));
1498     hideSelColumns.setToolTipText(MessageManager
1499             .getString("label.toggle_columns_visibility"));
1500     hideSelColumns.addActionListener(new ActionListener()
1501     {
1502       @Override
1503       public void actionPerformed(ActionEvent e)
1504       {
1505         hideSelColumns_actionPerformed(e);
1506       }
1507     });
1508     JMenuItem hideAllSelection = new JMenuItem(
1509             MessageManager.getString("label.selected_region"));
1510     hideAllSelection.addActionListener(new ActionListener()
1511     {
1512       @Override
1513       public void actionPerformed(ActionEvent e)
1514       {
1515         hideAllSelection_actionPerformed(e);
1516       }
1517     });
1518     // TODO: should be hidden if no selection exists.
1519     JMenuItem hideAllButSelection = new JMenuItem(
1520             MessageManager.getString("label.all_but_selected_region"));
1521     hideAllButSelection.addActionListener(new ActionListener()
1522     {
1523       @Override
1524       public void actionPerformed(ActionEvent e)
1525       {
1526         hideAllButSelection_actionPerformed(e);
1527       }
1528     });
1529     JMenuItem showAllhidden = new JMenuItem(
1530             MessageManager.getString("label.all_sequences_columns"));
1531     showAllhidden.setToolTipText(MessageManager
1532             .getString("label.toggles_visibility_hidden_selected_regions"));
1533     showAllhidden.addActionListener(new ActionListener()
1534     {
1535       @Override
1536       public void actionPerformed(ActionEvent e)
1537       {
1538         showAllhidden_actionPerformed(e);
1539       }
1540     });
1541     hiddenMarkers.setText(MessageManager
1542             .getString("action.show_hidden_markers"));
1543     hiddenMarkers.addActionListener(new ActionListener()
1544     {
1545       @Override
1546       public void actionPerformed(ActionEvent e)
1547       {
1548         hiddenMarkers_actionPerformed(e);
1549       }
1550     });
1551
1552     JMenuItem invertColSel = new JMenuItem(
1553             MessageManager.getString("action.invert_column_selection"));
1554     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
1555             .getDefaultToolkit().getMenuShortcutKeyMask()
1556             | KeyEvent.ALT_MASK, false);
1557     al = new ActionListener()
1558     {
1559       @Override
1560       public void actionPerformed(ActionEvent e)
1561       {
1562         invertColSel_actionPerformed(e);
1563       }
1564     };
1565     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1566
1567     showComplementMenuItem.setVisible(false);
1568     showComplementMenuItem.addActionListener(new ActionListener()
1569     {
1570       @Override
1571       public void actionPerformed(ActionEvent e)
1572       {
1573         showComplement_actionPerformed(showComplementMenuItem.getState());
1574       }
1575     });
1576
1577     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1578     {
1579       @Override
1580       public void stateChanged(ChangeEvent evt)
1581       {
1582         JTabbedPane pane = (JTabbedPane) evt.getSource();
1583         int sel = pane.getSelectedIndex();
1584         tabSelectionChanged(sel);
1585       }
1586     });
1587     tabbedPane.addMouseListener(new MouseAdapter()
1588     {
1589       @Override
1590       public void mousePressed(MouseEvent e)
1591       {
1592         if (e.isPopupTrigger()) // Mac
1593         {
1594           tabbedPane_mousePressed(e);
1595         }
1596       }
1597
1598       @Override
1599       public void mouseReleased(MouseEvent e)
1600       {
1601         if (e.isPopupTrigger()) // Windows
1602         {
1603           tabbedPane_mousePressed(e);
1604         }
1605       }
1606     });
1607     tabbedPane.addFocusListener(new FocusAdapter()
1608     {
1609       @Override
1610       public void focusGained(FocusEvent e)
1611       {
1612         tabbedPane_focusGained(e);
1613       }
1614     });
1615
1616     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1617     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
1618             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1619     al = new ActionListener()
1620     {
1621       @Override
1622       public void actionPerformed(ActionEvent e)
1623       {
1624         save_actionPerformed(e);
1625       }
1626     };
1627     addMenuActionAndAccelerator(keyStroke, save, al);
1628
1629     reload.setEnabled(false);
1630     reload.setText(MessageManager.getString("action.reload"));
1631     reload.addActionListener(new ActionListener()
1632     {
1633       @Override
1634       public void actionPerformed(ActionEvent e)
1635       {
1636         reload_actionPerformed(e);
1637       }
1638     });
1639
1640     JMenuItem newView = new JMenuItem(
1641             MessageManager.getString("action.new_view"));
1642     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
1643             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1644     al = new ActionListener()
1645     {
1646       @Override
1647       public void actionPerformed(ActionEvent e)
1648       {
1649         newView_actionPerformed(e);
1650       }
1651     };
1652     addMenuActionAndAccelerator(keyStroke, newView, al);
1653
1654     tabbedPane.setToolTipText("<html><i>"
1655             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1656             + "</i></html>");
1657
1658     formatMenu.setText(MessageManager.getString("action.format"));
1659     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1660
1661     idRightAlign.setText(MessageManager
1662             .getString("label.right_align_sequence_id"));
1663     idRightAlign.addActionListener(new ActionListener()
1664     {
1665       @Override
1666       public void actionPerformed(ActionEvent e)
1667       {
1668         idRightAlign_actionPerformed(e);
1669       }
1670     });
1671
1672     gatherViews.setEnabled(false);
1673     gatherViews.setText(MessageManager.getString("action.gather_views"));
1674     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1675     al = new ActionListener()
1676     {
1677       @Override
1678       public void actionPerformed(ActionEvent e)
1679       {
1680         gatherViews_actionPerformed(e);
1681       }
1682     };
1683     addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1684
1685     expandViews.setEnabled(false);
1686     expandViews.setText(MessageManager.getString("action.expand_views"));
1687     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1688     al = new ActionListener()
1689     {
1690       @Override
1691       public void actionPerformed(ActionEvent e)
1692       {
1693         expandViews_actionPerformed(e);
1694       }
1695     };
1696     addMenuActionAndAccelerator(keyStroke, expandViews, al);
1697
1698     JMenuItem pageSetup = new JMenuItem(
1699             MessageManager.getString("action.page_setup"));
1700     pageSetup.addActionListener(new ActionListener()
1701     {
1702       @Override
1703       public void actionPerformed(ActionEvent e)
1704       {
1705         pageSetup_actionPerformed(e);
1706       }
1707     });
1708     JMenuItem alignmentProperties = new JMenuItem(
1709             MessageManager.getString("label.alignment_props"));
1710     alignmentProperties.addActionListener(new ActionListener()
1711     {
1712       @Override
1713       public void actionPerformed(ActionEvent actionEvent)
1714       {
1715         alignmentProperties();
1716       }
1717     });
1718     JMenuItem selectHighlighted = new JMenuItem(
1719             MessageManager.getString("action.select_highlighted_columns"));
1720     selectHighlighted.setToolTipText(MessageManager
1721             .getString("tooltip.select_highlighted_columns"));
1722     al = new ActionListener()
1723     {
1724       @Override
1725       public void actionPerformed(ActionEvent actionEvent)
1726       {
1727         selectHighlightedColumns_actionPerformed(actionEvent);
1728       }
1729     };
1730     hmmBuild.setText(MessageManager.getString("label.hmmbuild"));
1731     hmmBuild.addActionListener(new ActionListener()
1732     {
1733
1734       @Override
1735       public void actionPerformed(ActionEvent e)
1736       {
1737         try
1738         {
1739           hmmBuild_actionPerformed(e);
1740         } catch (IOException e1)
1741         {
1742           // TODO Auto-generated catch block
1743           e1.printStackTrace();
1744         } catch (InterruptedException e1)
1745         {
1746           // TODO Auto-generated catch block
1747           e1.printStackTrace();
1748         }
1749       }
1750
1751     });
1752     hmmAlign.setText(MessageManager.getString("label.hmmalign"));
1753     hmmAlign.addActionListener(new ActionListener()
1754     {
1755
1756       @Override
1757       public void actionPerformed(ActionEvent e)
1758       {
1759         try
1760         {
1761           hmmAlign_actionPerformed(e);
1762         } catch (IOException e1)
1763         {
1764           // TODO Auto-generated catch block
1765           e1.printStackTrace();
1766         } catch (InterruptedException e1)
1767         {
1768           // TODO Auto-generated catch block
1769           e1.printStackTrace();
1770         }
1771       }
1772
1773     });
1774     selectHighlighted.addActionListener(al);
1775     JMenu tooltipSettingsMenu = new JMenu(
1776             MessageManager.getString("label.sequence_id_tooltip"));
1777     JMenu autoAnnMenu = new JMenu(
1778             MessageManager.getString("label.autocalculated_annotation"));
1779
1780     JMenu exportImageMenu = new JMenu(
1781             MessageManager.getString("label.export_image"));
1782     JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1783     alignFrameMenuBar.add(fileMenu);
1784     alignFrameMenuBar.add(editMenu);
1785     alignFrameMenuBar.add(selectMenu);
1786     alignFrameMenuBar.add(viewMenu);
1787     alignFrameMenuBar.add(annotationsMenu);
1788     alignFrameMenuBar.add(formatMenu);
1789     alignFrameMenuBar.add(colourMenu);
1790     alignFrameMenuBar.add(calculateMenu);
1791     alignFrameMenuBar.add(webService);
1792     alignFrameMenuBar.add(hmmerMenu);
1793
1794     fileMenu.add(fetchSequence);
1795     fileMenu.add(addSequenceMenu);
1796     fileMenu.add(reload);
1797     fileMenu.addSeparator();
1798     fileMenu.add(vamsasStore);
1799     fileMenu.add(save);
1800     fileMenu.add(saveAs);
1801     fileMenu.add(outputTextboxMenu);
1802     fileMenu.add(pageSetup);
1803     fileMenu.add(printMenuItem);
1804     fileMenu.addSeparator();
1805     fileMenu.add(exportImageMenu);
1806     fileMenu.add(exportFeatures);
1807     fileMenu.add(exportAnnotations);
1808     fileMenu.add(loadTreeMenuItem);
1809     fileMenu.add(associatedData);
1810     fileMenu.addSeparator();
1811     fileMenu.add(closeMenuItem);
1812
1813     pasteMenu.add(pasteNew);
1814     pasteMenu.add(pasteThis);
1815     editMenu.add(undoMenuItem);
1816     editMenu.add(redoMenuItem);
1817     editMenu.add(cut);
1818     editMenu.add(copy);
1819     editMenu.add(pasteMenu);
1820     editMenu.add(delete);
1821     editMenu.addSeparator();
1822     editMenu.add(remove2LeftMenuItem);
1823     editMenu.add(remove2RightMenuItem);
1824     editMenu.add(removeGappedColumnMenuItem);
1825     editMenu.add(removeAllGapsMenuItem);
1826     editMenu.add(removeRedundancyMenuItem);
1827     editMenu.addSeparator();
1828     // dont add these yet in the CVS build - they cannot be undone!
1829     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1830     // editMenu.add(justifyLeftMenuItem);
1831     // editMenu.add(justifyRightMenuItem);
1832     // editMenu.addSeparator();
1833     editMenu.add(padGapsMenuitem);
1834
1835     showMenu.add(showAllColumns);
1836     showMenu.add(showAllSeqs);
1837     showMenu.add(showAllhidden);
1838     hideMenu.add(hideSelColumns);
1839     hideMenu.add(hideSelSequences);
1840     hideMenu.add(hideAllSelection);
1841     hideMenu.add(hideAllButSelection);
1842     viewMenu.add(newView);
1843     viewMenu.add(expandViews);
1844     viewMenu.add(gatherViews);
1845     viewMenu.addSeparator();
1846     viewMenu.add(showMenu);
1847     viewMenu.add(hideMenu);
1848     viewMenu.add(showComplementMenuItem);
1849     viewMenu.addSeparator();
1850     viewMenu.add(followHighlightMenuItem);
1851     viewMenu.addSeparator();
1852     viewMenu.add(showSeqFeatures);
1853     // viewMenu.add(showSeqFeaturesHeight);
1854     viewMenu.add(openFeatureSettings);
1855     tooltipSettingsMenu.add(showDbRefsMenuitem);
1856     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1857     viewMenu.add(tooltipSettingsMenu);
1858     viewMenu.addSeparator();
1859     viewMenu.add(alignmentProperties);
1860     viewMenu.addSeparator();
1861     viewMenu.add(overviewMenuItem);
1862
1863     annotationsMenu.add(annotationPanelMenuItem);
1864     annotationsMenu.addSeparator();
1865     annotationsMenu.add(showAllAlAnnotations);
1866     annotationsMenu.add(hideAllAlAnnotations);
1867     annotationsMenu.addSeparator();
1868     annotationsMenu.add(showAllSeqAnnotations);
1869     annotationsMenu.add(hideAllSeqAnnotations);
1870     annotationsMenu.add(sortAnnBySequence);
1871     annotationsMenu.add(sortAnnByLabel);
1872     annotationsMenu.addSeparator();
1873     autoAnnMenu.add(showAutoFirst);
1874     autoAnnMenu.add(showAutoLast);
1875     autoAnnMenu.addSeparator();
1876     autoAnnMenu.add(applyAutoAnnotationSettings);
1877     autoAnnMenu.add(showConsensusHistogram);
1878     autoAnnMenu.add(showSequenceLogo);
1879     autoAnnMenu.add(normaliseSequenceLogo);
1880     autoAnnMenu.addSeparator();
1881     autoAnnMenu.add(showGroupConservation);
1882     autoAnnMenu.add(showGroupConsensus);
1883     annotationsMenu.add(autoAnnMenu);
1884
1885
1886     sort.add(sortIDMenuItem);
1887     sort.add(sortLengthMenuItem);
1888     sort.add(sortGroupMenuItem);
1889     sort.add(sortPairwiseMenuItem);
1890     sort.add(sortByTreeMenu);
1891     calculateMenu.add(sort);
1892     calculateMenu.add(calculateTree);
1893     calculateMenu.addSeparator();
1894     calculateMenu.add(pairwiseAlignmentMenuItem);
1895     calculateMenu.addSeparator();
1896     calculateMenu.add(showTranslation);
1897     calculateMenu.add(showReverse);
1898     calculateMenu.add(showReverseComplement);
1899     calculateMenu.add(showProducts);
1900     calculateMenu.add(autoCalculate);
1901     calculateMenu.add(sortByTree);
1902     calculateMenu.addSeparator();
1903     calculateMenu.add(expandAlignment);
1904     calculateMenu.add(extractScores);
1905     calculateMenu.addSeparator();
1906     calculateMenu.add(runGroovy);
1907
1908     webServiceNoServices = new JMenuItem(
1909             MessageManager.getString("label.no_services"));
1910     webService.add(webServiceNoServices);
1911     exportImageMenu.add(htmlMenuItem);
1912     exportImageMenu.add(epsFile);
1913     exportImageMenu.add(createPNG);
1914     exportImageMenu.add(createBioJS);
1915     exportImageMenu.add(createSVG);
1916     addSequenceMenu.add(addFromFile);
1917     addSequenceMenu.add(addFromText);
1918     addSequenceMenu.add(addFromURL);
1919     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1920     statusPanel.add(statusBar, null);
1921     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1922
1923     formatMenu.add(font);
1924     formatMenu.addSeparator();
1925     formatMenu.add(wrapMenuItem);
1926     formatMenu.add(scaleAbove);
1927     formatMenu.add(scaleLeft);
1928     formatMenu.add(scaleRight);
1929     formatMenu.add(seqLimits);
1930     formatMenu.add(idRightAlign);
1931     formatMenu.add(hiddenMarkers);
1932     formatMenu.add(viewBoxesMenuItem);
1933     formatMenu.add(viewTextMenuItem);
1934     formatMenu.add(colourTextMenuItem);
1935     formatMenu.add(renderGapsMenuItem);
1936     formatMenu.add(centreColumnLabelsMenuItem);
1937     formatMenu.add(showNonconservedMenuItem);
1938     selectMenu.add(findMenuItem);
1939     selectMenu.addSeparator();
1940     selectMenu.add(selectAllSequenceMenuItem);
1941     selectMenu.add(deselectAllSequenceMenuItem);
1942     selectMenu.add(invertSequenceMenuItem);
1943     selectMenu.add(invertColSel);
1944     selectMenu.add(createGroup);
1945     selectMenu.add(unGroup);
1946     selectMenu.add(grpsFromSelection);
1947     selectMenu.add(deleteGroups);
1948     selectMenu.add(annotationColumn);
1949     selectMenu.add(selectHighlighted);
1950     // TODO - determine if the listenToViewSelections button is needed : see bug
1951     // JAL-574
1952     // selectMenu.addSeparator();
1953     // selectMenu.add(listenToViewSelections);
1954   }
1955
1956   public void hmmerMenu_actionPerformed(ActionEvent e)
1957   {
1958
1959   }
1960
1961   /**
1962    * Constructs the entries on the Colour menu (but does not add them to the
1963    * menu).
1964    */
1965   protected void initHMMERMenu()
1966   {
1967     hmmAlign = new JMenuItem(MessageManager.getString("label.hmmalign"));
1968     hmmBuild = new JMenuItem(MessageManager.getString("label.hmmbuild"));
1969     hmmSearch = new JMenuItem(MessageManager.getString("label.hmmsearch"));
1970   }
1971   protected void initColourMenu()
1972   {
1973     applyToAllGroups = new JCheckBoxMenuItem(
1974             MessageManager.getString("label.apply_colour_to_all_groups"));
1975     applyToAllGroups.addActionListener(new ActionListener()
1976     {
1977       @Override
1978       public void actionPerformed(ActionEvent e)
1979       {
1980         applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1981       }
1982     });
1983
1984     textColour = new JMenuItem(
1985             MessageManager.getString("label.text_colour"));
1986     textColour.addActionListener(new ActionListener()
1987     {
1988       @Override
1989       public void actionPerformed(ActionEvent e)
1990       {
1991         textColour_actionPerformed();
1992       }
1993     });
1994
1995     conservationMenuItem = new JCheckBoxMenuItem(
1996             MessageManager.getString("action.by_conservation"));
1997     conservationMenuItem.addActionListener(new ActionListener()
1998     {
1999       @Override
2000       public void actionPerformed(ActionEvent e)
2001       {
2002         conservationMenuItem_actionPerformed(conservationMenuItem
2003                 .isSelected());
2004       }
2005     });
2006
2007     abovePIDThreshold = new JCheckBoxMenuItem(
2008             MessageManager.getString("label.above_identity_threshold"));
2009     abovePIDThreshold.addActionListener(new ActionListener()
2010     {
2011       @Override
2012       public void actionPerformed(ActionEvent e)
2013       {
2014         abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
2015       }
2016     });
2017     modifyPID = new JMenuItem(
2018             MessageManager.getString("label.modify_identity_threshold"));
2019     modifyPID.addActionListener(new ActionListener()
2020     {
2021       @Override
2022       public void actionPerformed(ActionEvent e)
2023       {
2024         modifyPID_actionPerformed();
2025       }
2026     });
2027     modifyConservation = new JMenuItem(
2028             MessageManager
2029             .getString("label.modify_conservation_threshold"));
2030     modifyConservation.addActionListener(new ActionListener()
2031     {
2032       @Override
2033       public void actionPerformed(ActionEvent e)
2034       {
2035         modifyConservation_actionPerformed();
2036       }
2037     });
2038
2039     annotationColour = new JMenuItem(
2040             MessageManager.getString("action.by_annotation"));
2041     annotationColour.addActionListener(new ActionListener()
2042     {
2043       @Override
2044       public void actionPerformed(ActionEvent e)
2045       {
2046         annotationColour_actionPerformed();
2047       }
2048     });
2049   }
2050
2051   protected void selectHighlightedColumns_actionPerformed(
2052           ActionEvent actionEvent)
2053   {
2054     // TODO Auto-generated method stub
2055
2056   }
2057
2058   /**
2059    * Generate the reverse sequence (or reverse complement if the flag is true)
2060    * and add it to the alignment
2061    *
2062    * @param complement
2063    */
2064   protected void showReverse_actionPerformed(boolean complement)
2065   {
2066   }
2067
2068   /**
2069    * Try to run script in a Groovy console, having first ensured that this
2070    * alignframe is set as currentAlignFrame in Desktop
2071    */
2072   protected void runGroovy_actionPerformed()
2073   {
2074
2075   }
2076
2077   /**
2078    * Adds the given action listener and key accelerator to the given menu item.
2079    * Also saves in a lookup table to support lookup of action by key stroke.
2080    *
2081    * @param keyStroke
2082    * @param menuItem
2083    * @param actionListener
2084    */
2085   protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2086           JMenuItem menuItem, ActionListener actionListener)
2087   {
2088     menuItem.setAccelerator(keyStroke);
2089     accelerators.put(keyStroke, menuItem);
2090     menuItem.addActionListener(actionListener);
2091   }
2092
2093   /**
2094    * Action on clicking sort annotations by type.
2095    *
2096    * @param sortOrder
2097    */
2098   protected void sortAnnotations_actionPerformed()
2099   {
2100   }
2101
2102   /**
2103    * Action on clicking Show all annotations.
2104    *
2105    * @param forSequences
2106    *          update sequence-related annotations
2107    * @param forAlignment
2108    *          update non-sequence-related annotations
2109    */
2110   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2111           boolean forAlignment)
2112   {
2113     setAnnotationsVisibility(true, forSequences, forAlignment);
2114   }
2115
2116   /**
2117    * Action on clicking Hide all annotations.
2118    *
2119    * @param forSequences
2120    *          update sequence-related annotations
2121    * @param forAlignment
2122    *          update non-sequence-related annotations
2123    */
2124   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2125           boolean forAlignment)
2126   {
2127     setAnnotationsVisibility(false, forSequences, forAlignment);
2128   }
2129
2130   /**
2131    * Set the visibility of annotations to true or false. Can act on
2132    * sequence-related annotations, or alignment-related, or both.
2133    *
2134    * @param visible
2135    * @param forSequences
2136    *          update sequence-related annotations
2137    * @param forAlignment
2138    *          update non-sequence-related annotations
2139    */
2140   protected void setAnnotationsVisibility(boolean visible,
2141           boolean forSequences, boolean forAlignment)
2142   {
2143
2144   }
2145
2146   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2147   {
2148     // TODO Auto-generated method stub
2149
2150   }
2151
2152   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2153   {
2154     // TODO Auto-generated method stub
2155
2156   }
2157
2158   protected void showAllhidden_actionPerformed(ActionEvent e)
2159   {
2160     // TODO Auto-generated method stub
2161
2162   }
2163
2164   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2165   {
2166     // TODO Auto-generated method stub
2167
2168   }
2169
2170   protected void hideAllSelection_actionPerformed(ActionEvent e)
2171   {
2172     // TODO Auto-generated method stub
2173
2174   }
2175
2176   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2177   {
2178     // TODO Auto-generated method stub
2179
2180   }
2181
2182   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2183   {
2184     // TODO Auto-generated method stub
2185
2186   }
2187
2188   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2189   {
2190     // TODO Auto-generated method stub
2191
2192   }
2193
2194   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2195   {
2196     // TODO Auto-generated method stub
2197
2198   }
2199
2200   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2201   {
2202     // TODO Auto-generated method stub
2203
2204   }
2205
2206   protected void showGroupConservation_actionPerformed(ActionEvent e)
2207   {
2208     // TODO Auto-generated method stub
2209
2210   }
2211
2212   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2213   {
2214     // TODO Auto-generated method stub
2215
2216   }
2217
2218   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2219   {
2220     // TODO Auto-generated method stub
2221
2222   }
2223
2224   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2225   {
2226     // TODO Auto-generated method stub
2227
2228   }
2229
2230   protected void followHighlight_actionPerformed()
2231   {
2232     // TODO Auto-generated method stub
2233
2234   }
2235
2236   protected void showNpFeats_actionPerformed(ActionEvent e)
2237   {
2238     // TODO Auto-generated method stub
2239
2240   }
2241
2242   protected void showDbRefs_actionPerformed(ActionEvent e)
2243   {
2244     // TODO Auto-generated method stub
2245
2246   }
2247
2248   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2249   {
2250   }
2251
2252   protected void buildSortByAnnotationScoresMenu()
2253   {
2254   }
2255
2256   protected void extractScores_actionPerformed(ActionEvent e)
2257   {
2258   }
2259
2260   protected void outputText_actionPerformed(ActionEvent e)
2261   {
2262   }
2263
2264   public void addFromFile_actionPerformed(ActionEvent e)
2265   {
2266
2267   }
2268
2269   public void addFromText_actionPerformed(ActionEvent e)
2270   {
2271
2272   }
2273
2274   public void addFromURL_actionPerformed(ActionEvent e)
2275   {
2276
2277   }
2278
2279   public void exportFeatures_actionPerformed(ActionEvent e)
2280   {
2281
2282   }
2283
2284   public void exportAnnotations_actionPerformed(ActionEvent e)
2285   {
2286
2287   }
2288
2289   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2290   {
2291   }
2292
2293   protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2294   {
2295
2296   }
2297
2298   protected void closeMenuItem_actionPerformed(boolean b)
2299   {
2300   }
2301
2302   protected void redoMenuItem_actionPerformed(ActionEvent e)
2303   {
2304   }
2305
2306   protected void undoMenuItem_actionPerformed(ActionEvent e)
2307   {
2308   }
2309
2310   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2311   {
2312   }
2313
2314   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2315   {
2316   }
2317
2318   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2319   {
2320   }
2321
2322   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2323   {
2324   }
2325
2326   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2327   {
2328   }
2329
2330   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2331   {
2332   }
2333
2334   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2335   {
2336   }
2337
2338   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2339   {
2340   }
2341
2342   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2343   {
2344   }
2345
2346   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2347   {
2348   }
2349
2350   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2351   {
2352   }
2353
2354   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2355   {
2356   }
2357
2358   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2359   {
2360   }
2361
2362   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2363   {
2364   }
2365
2366   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2367   {
2368   }
2369
2370   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2371   {
2372   }
2373
2374   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2375   {
2376   }
2377
2378   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2379   {
2380   }
2381
2382   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2383   {
2384   }
2385
2386   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2387   {
2388   }
2389
2390   protected void conservationMenuItem_actionPerformed(boolean selected)
2391   {
2392   }
2393
2394   protected void printMenuItem_actionPerformed(ActionEvent e)
2395   {
2396   }
2397
2398   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2399   {
2400   }
2401
2402   protected void findMenuItem_actionPerformed(ActionEvent e)
2403   {
2404   }
2405
2406   protected void abovePIDThreshold_actionPerformed(boolean selected)
2407   {
2408   }
2409
2410   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2411   {
2412   }
2413
2414   protected void deleteGroups_actionPerformed(ActionEvent e)
2415   {
2416   }
2417
2418   protected void createGroup_actionPerformed(ActionEvent e)
2419   {
2420   }
2421
2422   protected void unGroup_actionPerformed(ActionEvent e)
2423   {
2424   }
2425
2426   protected void copy_actionPerformed(ActionEvent e)
2427   {
2428   }
2429
2430   protected void cut_actionPerformed(ActionEvent e)
2431   {
2432   }
2433
2434   protected void delete_actionPerformed(ActionEvent e)
2435   {
2436   }
2437
2438   protected void pasteNew_actionPerformed(ActionEvent e)
2439           throws IOException, InterruptedException
2440   {
2441   }
2442
2443   protected void pasteThis_actionPerformed(ActionEvent e)
2444           throws IOException, InterruptedException
2445   {
2446   }
2447
2448   protected void applyToAllGroups_actionPerformed(boolean selected)
2449   {
2450   }
2451
2452   protected void autoAlignSeqs_actionPerformed(boolean selected)
2453   {
2454   }
2455
2456   protected void hmmAlign_actionPerformed(ActionEvent e)
2457           throws IOException, InterruptedException
2458   {
2459   }
2460
2461   protected void changeHMMERLocation_actionPerformed(ActionEvent e)
2462   {
2463   }
2464
2465   protected void hmmBuild_actionPerformed(ActionEvent e)
2466           throws IOException, InterruptedException
2467   {
2468   }
2469
2470   protected void hmmSearch_actionPerformed(ActionEvent e)
2471   {
2472   }
2473
2474   public void createPNG(java.io.File f)
2475   {
2476   }
2477
2478   protected void font_actionPerformed(ActionEvent e)
2479   {
2480   }
2481
2482   protected void seqLimit_actionPerformed(ActionEvent e)
2483   {
2484   }
2485
2486   public void seqDBRef_actionPerformed(ActionEvent e)
2487   {
2488
2489   }
2490
2491   public void createEPS(java.io.File f)
2492   {
2493   }
2494
2495   public void createSVG(java.io.File f)
2496   {
2497
2498   }
2499
2500   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2501   {
2502
2503   }
2504
2505   /**
2506    * Template method to handle the 'load T-Coffee scores' menu event.
2507    * <p>
2508    * Subclasses override this method to provide a custom action.
2509    *
2510    * @param event
2511    *          The raised event
2512    */
2513   protected void loadScores_actionPerformed(ActionEvent event)
2514   {
2515
2516   }
2517
2518   protected void jpred_actionPerformed(ActionEvent e)
2519   {
2520   }
2521
2522   protected void scaleAbove_actionPerformed(ActionEvent e)
2523   {
2524   }
2525
2526   protected void scaleLeft_actionPerformed(ActionEvent e)
2527   {
2528   }
2529
2530   protected void scaleRight_actionPerformed(ActionEvent e)
2531   {
2532   }
2533
2534   protected void modifyPID_actionPerformed()
2535   {
2536   }
2537
2538   protected void modifyConservation_actionPerformed()
2539   {
2540   }
2541
2542   protected void saveAs_actionPerformed(ActionEvent e)
2543   {
2544   }
2545
2546   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2547   {
2548   }
2549
2550   public void vamsasStore_actionPerformed(ActionEvent e)
2551   {
2552
2553   }
2554
2555   public void vamsasLoad_actionPerformed(ActionEvent e)
2556   {
2557
2558   }
2559
2560   public void showTranslation_actionPerformed(ActionEvent e)
2561   {
2562
2563   }
2564
2565   public void featureSettings_actionPerformed(ActionEvent e)
2566   {
2567
2568   }
2569
2570   public void fetchSequence_actionPerformed(ActionEvent e)
2571   {
2572
2573   }
2574
2575   public void smoothFont_actionPerformed(ActionEvent e)
2576   {
2577
2578   }
2579
2580   public void annotationColour_actionPerformed()
2581   {
2582   }
2583
2584   public void annotationColumn_actionPerformed(ActionEvent e)
2585   {
2586   }
2587
2588   public void associatedData_actionPerformed(ActionEvent e)
2589           throws IOException, InterruptedException
2590   {
2591
2592   }
2593
2594   public void autoCalculate_actionPerformed(ActionEvent e)
2595   {
2596
2597   }
2598
2599   public void sortByTreeOption_actionPerformed(ActionEvent e)
2600   {
2601
2602   }
2603
2604   public void showAllSeqs_actionPerformed(ActionEvent e)
2605   {
2606
2607   }
2608
2609   public void showAllColumns_actionPerformed(ActionEvent e)
2610   {
2611
2612   }
2613
2614   public void hideSelSequences_actionPerformed(ActionEvent e)
2615   {
2616
2617   }
2618
2619   public void hideSelColumns_actionPerformed(ActionEvent e)
2620   {
2621
2622   }
2623
2624   public void hiddenMarkers_actionPerformed(ActionEvent e)
2625   {
2626
2627   }
2628
2629   public void findPdbId_actionPerformed(ActionEvent e)
2630   {
2631
2632   }
2633
2634   public void enterPdbId_actionPerformed(ActionEvent e)
2635   {
2636
2637   }
2638
2639   public void pdbFile_actionPerformed(ActionEvent e)
2640   {
2641
2642   }
2643
2644   public void invertColSel_actionPerformed(ActionEvent e)
2645   {
2646
2647   }
2648
2649   public void tabSelectionChanged(int sel)
2650   {
2651
2652   }
2653
2654   public void tabbedPane_mousePressed(MouseEvent e)
2655   {
2656
2657   }
2658
2659   public void tabbedPane_focusGained(FocusEvent e)
2660   {
2661     requestFocus();
2662   }
2663
2664   public void save_actionPerformed(ActionEvent e)
2665   {
2666
2667   }
2668
2669   public void reload_actionPerformed(ActionEvent e)
2670   {
2671
2672   }
2673
2674   public void newView_actionPerformed(ActionEvent e)
2675   {
2676
2677   }
2678
2679   public void textColour_actionPerformed()
2680   {
2681
2682   }
2683
2684   public void idRightAlign_actionPerformed(ActionEvent e)
2685   {
2686
2687   }
2688
2689   public void expandViews_actionPerformed(ActionEvent e)
2690   {
2691
2692   }
2693
2694   public void gatherViews_actionPerformed(ActionEvent e)
2695   {
2696
2697   }
2698
2699   public void buildTreeSortMenu()
2700   {
2701
2702   }
2703
2704   public void pageSetup_actionPerformed(ActionEvent e)
2705   {
2706
2707   }
2708
2709   public void alignmentProperties()
2710   {
2711
2712   }
2713
2714   protected void expand_newalign(ActionEvent e)
2715   {
2716     // TODO Auto-generated method stub
2717
2718   }
2719
2720   protected boolean isShowAutoCalculatedAbove()
2721   {
2722     return showAutoCalculatedAbove;
2723   }
2724
2725   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2726   {
2727     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2728   }
2729
2730   protected SequenceAnnotationOrder getAnnotationSortOrder()
2731   {
2732     return annotationSortOrder;
2733   }
2734
2735   protected void setAnnotationSortOrder(
2736           SequenceAnnotationOrder annotationSortOrder)
2737   {
2738     this.annotationSortOrder = annotationSortOrder;
2739   }
2740
2741   public Map<KeyStroke, JMenuItem> getAccelerators()
2742   {
2743     return this.accelerators;
2744   }
2745
2746   /**
2747    * Returns the selected index of the tabbed pane, or -1 if none selected
2748    * (including the case where the tabbed pane has not been made visible).
2749    *
2750    * @return
2751    */
2752   public int getTabIndex()
2753   {
2754     return tabbedPane.getSelectedIndex();
2755   }
2756
2757   public JPanel getStatusPanel()
2758   {
2759     return statusPanel;
2760   }
2761
2762   /**
2763    * Sets a reference to the containing split frame. Also makes the 'toggle
2764    * split view' menu item visible and checked.
2765    *
2766    * @param sf
2767    */
2768   public void setSplitFrame(SplitContainerI sf)
2769   {
2770     this.splitFrame = sf;
2771     if (sf != null)
2772     {
2773       this.showComplementMenuItem.setVisible(true);
2774       this.showComplementMenuItem.setState(true);
2775     }
2776   }
2777
2778   public SplitContainerI getSplitViewContainer()
2779   {
2780     return this.splitFrame;
2781   }
2782
2783   protected void showComplement_actionPerformed(boolean complement)
2784   {
2785   }
2786
2787   protected void showInformationHistogram_actionPerformed(ActionEvent e)
2788   {
2789     // TODO Auto-generated method stub
2790
2791   }
2792
2793   protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
2794   {
2795     // TODO Auto-generated method stub
2796
2797   }
2798
2799   protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
2800   {
2801     // TODO Auto-generated method stub
2802
2803   }
2804 }