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