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