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