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 JRadioButtonMenuItem 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 JMenu qualityScoreModel = new JMenu();
 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<KeyStroke, JMenuItem>();
 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, Toolkit
 266             .getDefaultToolkit().getMenuShortcutKeyMask()
 267             | KeyEvent.SHIFT_MASK, false);
 268     addMenuActionAndAccelerator(keyStroke, saveAs, al);
 269
 270     closeMenuItem.setText(MessageManager.getString("action.close"));
 271     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
 272             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 273     al = new ActionListener()
 274     {
 275       @Override
 276       public void actionPerformed(ActionEvent e)
 277       {
 278         closeMenuItem_actionPerformed(false);
 279       }
 280     };
 281     addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
 282
 283     JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
 284     JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
 285     JMenu annotationsMenu = new JMenu(
 286             MessageManager.getString("action.annotations"));
 287     JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
 288     colourMenu.setText(MessageManager.getString("action.colour"));
 289     JMenu calculateMenu = new JMenu(
 290             MessageManager.getString("action.calculate"));
 291     webService.setText(MessageManager.getString("action.web_service"));
 292     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
 293             MessageManager.getString("action.select_all"));
 294     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
 295             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 296     al = new ActionListener()
 297     {
 298       @Override
 299       public void actionPerformed(ActionEvent e)
 300       {
 301         selectAllSequenceMenuItem_actionPerformed(e);
 302       }
 303     };
 304     addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
 305
 306     JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
 307             MessageManager.getString("action.deselect_all"));
 308     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
 309     al = new ActionListener()
 310     {
 311       @Override
 312       public void actionPerformed(ActionEvent e)
 313       {
 314         deselectAllSequenceMenuItem_actionPerformed(e);
 315       }
 316     };
 317     addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
 318
 319     JMenuItem invertSequenceMenuItem = new JMenuItem(
 320             MessageManager.getString("action.invert_sequence_selection"));
 321     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
 322             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 323     al = new ActionListener()
 324     {
 325       @Override
 326       public void actionPerformed(ActionEvent e)
 327       {
 328         invertSequenceMenuItem_actionPerformed(e);
 329       }
 330     };
 331     addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
 332
 333     JMenuItem grpsFromSelection = new JMenuItem(
 334             MessageManager.getString("action.make_groups_selection"));
 335     grpsFromSelection.addActionListener(new ActionListener()
 336     {
 337       @Override
 338       public void actionPerformed(ActionEvent e)
 339       {
 340         makeGrpsFromSelection_actionPerformed(e);
 341       }
 342     });
 343     JMenuItem expandAlignment = new JMenuItem(
 344             MessageManager.getString("action.view_flanking_regions"));
 345     expandAlignment.setToolTipText(MessageManager
 346             .getString("label.view_flanking_regions"));
 347     expandAlignment.addActionListener(new ActionListener()
 348     {
 349       @Override
 350       public void actionPerformed(ActionEvent e)
 351       {
 352         expand_newalign(e);
 353       }
 354     });
 355     JMenuItem remove2LeftMenuItem = new JMenuItem(
 356             MessageManager.getString("action.remove_left"));
 357     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
 358             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 359     al = new ActionListener()
 360     {
 361       @Override
 362       public void actionPerformed(ActionEvent e)
 363       {
 364         remove2LeftMenuItem_actionPerformed(e);
 365       }
 366     };
 367     addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
 368
 369     JMenuItem remove2RightMenuItem = new JMenuItem(
 370             MessageManager.getString("action.remove_right"));
 371     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
 372             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 373     al = new ActionListener()
 374     {
 375       @Override
 376       public void actionPerformed(ActionEvent e)
 377       {
 378         remove2RightMenuItem_actionPerformed(e);
 379       }
 380     };
 381     addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
 382
 383     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
 384             MessageManager.getString("action.remove_empty_columns"));
 385     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
 386             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 387     al = new ActionListener()
 388     {
 389       @Override
 390       public void actionPerformed(ActionEvent e)
 391       {
 392         removeGappedColumnMenuItem_actionPerformed(e);
 393       }
 394     };
 395     addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
 396
 397     JMenuItem removeAllGapsMenuItem = new JMenuItem(
 398             MessageManager.getString("action.remove_all_gaps"));
 399     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
 400             .getDefaultToolkit().getMenuShortcutKeyMask()
 401             | KeyEvent.SHIFT_MASK, 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.setText(MessageManager
 453             .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, Toolkit
 507             .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     JMenuItem PCAMenuItem = new JMenuItem(
 529             MessageManager.getString("label.principal_component_analysis"));
 530     PCAMenuItem.addActionListener(new ActionListener()
 531     {
 532       @Override
 533       public void actionPerformed(ActionEvent e)
 534       {
 535         PCAMenuItem_actionPerformed(e);
 536       }
 537     });
 538
 539     this.getContentPane().setLayout(new BorderLayout());
 540     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 541     statusBar.setBackground(Color.white);
 542     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 543     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 544     statusBar.setText(MessageManager.getString("label.status_bar"));
 545     outputTextboxMenu.setText(MessageManager
 546             .getString("label.out_to_textbox"));
 547
 548     annotationPanelMenuItem.setActionCommand("");
 549     annotationPanelMenuItem.setText(MessageManager
 550             .getString("label.show_annotations"));
 551     annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
 552             true));
 553     annotationPanelMenuItem.addActionListener(new ActionListener()
 554     {
 555       @Override
 556       public void actionPerformed(ActionEvent e)
 557       {
 558         annotationPanelMenuItem_actionPerformed(e);
 559       }
 560     });
 561     showAllAlAnnotations.setText(MessageManager
 562             .getString("label.show_all_al_annotations"));
 563     final boolean isAnnotationPanelShown = annotationPanelMenuItem
 564             .getState();
 565     showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 566     showAllAlAnnotations.addActionListener(new ActionListener()
 567     {
 568       @Override
 569       public void actionPerformed(ActionEvent e)
 570       {
 571         showAllAnnotations_actionPerformed(false, true);
 572       }
 573     });
 574     hideAllAlAnnotations.setText(MessageManager
 575             .getString("label.hide_all_al_annotations"));
 576     hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 577     hideAllAlAnnotations.addActionListener(new ActionListener()
 578     {
 579       @Override
 580       public void actionPerformed(ActionEvent e)
 581       {
 582         hideAllAnnotations_actionPerformed(false, true);
 583       }
 584     });
 585     showAllSeqAnnotations.setText(MessageManager
 586             .getString("label.show_all_seq_annotations"));
 587     showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 588     showAllSeqAnnotations.addActionListener(new ActionListener()
 589     {
 590       @Override
 591       public void actionPerformed(ActionEvent e)
 592       {
 593         showAllAnnotations_actionPerformed(true, false);
 594       }
 595     });
 596     hideAllSeqAnnotations.setText(MessageManager
 597             .getString("label.hide_all_seq_annotations"));
 598     hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 599     hideAllSeqAnnotations.addActionListener(new ActionListener()
 600     {
 601       @Override
 602       public void actionPerformed(ActionEvent e)
 603       {
 604         hideAllAnnotations_actionPerformed(true, false);
 605       }
 606     });
 607     SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
 608             .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
 609                     SequenceAnnotationOrder.NONE.name()));
 610     final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
 611             MessageManager.getString("label.sort_annotations_by_sequence"));
 612     final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
 613             MessageManager.getString("label.sort_annotations_by_label"));
 614
 615     sortAnnBySequence
 616             .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
 617     sortAnnBySequence.addActionListener(new ActionListener()
 618     {
 619       @Override
 620       public void actionPerformed(ActionEvent e)
 621       {
 622         boolean newState = sortAnnBySequence.getState();
 623         sortAnnByLabel.setSelected(false);
 624         setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 625                 : SequenceAnnotationOrder.NONE);
 626         sortAnnotations_actionPerformed();
 627       }
 628     });
 629     sortAnnByLabel
 630             .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
 631     sortAnnByLabel.addActionListener(new ActionListener()
 632     {
 633       @Override
 634       public void actionPerformed(ActionEvent e)
 635       {
 636         boolean newState = sortAnnByLabel.getState();
 637         sortAnnBySequence.setSelected(false);
 638         setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 639                 : SequenceAnnotationOrder.NONE);
 640         sortAnnotations_actionPerformed();
 641       }
 642     });
 643     colourTextMenuItem = new JCheckBoxMenuItem(
 644             MessageManager
 645             .getString("label.colour_text"));
 646     colourTextMenuItem.addActionListener(new ActionListener()
 647     {
 648       @Override
 649       public void actionPerformed(ActionEvent e)
 650       {
 651         colourTextMenuItem_actionPerformed(e);
 652       }
 653     });
 654
 655     JMenuItem htmlMenuItem = new JMenuItem(
 656             MessageManager.getString("label.html"));
 657     htmlMenuItem.addActionListener(new ActionListener()
 658     {
 659       @Override
 660       public void actionPerformed(ActionEvent e)
 661       {
 662         htmlMenuItem_actionPerformed(e);
 663       }
 664     });
 665
 666     JMenuItem createBioJS = new JMenuItem(
 667             MessageManager.getString("label.biojs_html_export"));
 668     createBioJS.addActionListener(new java.awt.event.ActionListener()
 669     {
 670       @Override
 671       public void actionPerformed(ActionEvent e)
 672       {
 673         bioJSMenuItem_actionPerformed(e);
 674       }
 675     });
 676
 677     JMenuItem overviewMenuItem = new JMenuItem(
 678             MessageManager.getString("label.overview_window"));
 679     overviewMenuItem.addActionListener(new ActionListener()
 680     {
 681       @Override
 682       public void actionPerformed(ActionEvent e)
 683       {
 684         overviewMenuItem_actionPerformed(e);
 685       }
 686     });
 687
 688     undoMenuItem.setEnabled(false);
 689     undoMenuItem.setText(MessageManager.getString("action.undo"));
 690     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
 691             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 692     al = new ActionListener()
 693     {
 694       @Override
 695       public void actionPerformed(ActionEvent e)
 696       {
 697         undoMenuItem_actionPerformed(e);
 698       }
 699     };
 700     addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
 701
 702     redoMenuItem.setEnabled(false);
 703     redoMenuItem.setText(MessageManager.getString("action.redo"));
 704     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
 705             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 706     al = new ActionListener()
 707     {
 708       @Override
 709       public void actionPerformed(ActionEvent e)
 710       {
 711         redoMenuItem_actionPerformed(e);
 712       }
 713     };
 714     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
 715
 716     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
 717     wrapMenuItem.addActionListener(new ActionListener()
 718     {
 719       @Override
 720       public void actionPerformed(ActionEvent e)
 721       {
 722         wrapMenuItem_actionPerformed(e);
 723       }
 724     });
 725
 726     JMenuItem printMenuItem = new JMenuItem(
 727             MessageManager.getString("action.print"));
 728     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
 729             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 730     al = new ActionListener()
 731     {
 732       @Override
 733       public void actionPerformed(ActionEvent e)
 734       {
 735         printMenuItem_actionPerformed(e);
 736       }
 737     };
 738     addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
 739
 740     renderGapsMenuItem
 741             .setText(MessageManager.getString("action.show_gaps"));
 742     renderGapsMenuItem.setState(true);
 743     renderGapsMenuItem.addActionListener(new ActionListener()
 744     {
 745       @Override
 746       public void actionPerformed(ActionEvent e)
 747       {
 748         renderGapsMenuItem_actionPerformed(e);
 749       }
 750     });
 751
 752     JMenuItem findMenuItem = new JMenuItem(
 753             MessageManager.getString("action.find"));
 754     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
 755             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 756     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
 757             MessageManager.getString("label.find_tip")));
 758     al = new ActionListener()
 759     {
 760       @Override
 761       public void actionPerformed(ActionEvent e)
 762       {
 763         findMenuItem_actionPerformed(e);
 764       }
 765     };
 766     addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
 767
 768     showSeqFeatures.setText(MessageManager
 769             .getString("label.show_sequence_features"));
 770     showSeqFeatures.addActionListener(new ActionListener()
 771     {
 772       @Override
 773       public void actionPerformed(ActionEvent actionEvent)
 774       {
 775         showSeqFeatures_actionPerformed(actionEvent);
 776       }
 777     });
 778     /*
 779      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
 780      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
 781      * void actionPerformed(ActionEvent actionEvent) {
 782      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
 783      */
 784     showDbRefsMenuitem.setText(MessageManager
 785             .getString("label.show_database_refs"));
 786     showDbRefsMenuitem.addActionListener(new ActionListener()
 787     {
 788
 789       @Override
 790       public void actionPerformed(ActionEvent e)
 791       {
 792         showDbRefs_actionPerformed(e);
 793       }
 794
 795     });
 796     showNpFeatsMenuitem.setText(MessageManager
 797             .getString("label.show_non_positional_features"));
 798     showNpFeatsMenuitem.addActionListener(new ActionListener()
 799     {
 800
 801       @Override
 802       public void actionPerformed(ActionEvent e)
 803       {
 804         showNpFeats_actionPerformed(e);
 805       }
 806
 807     });
 808     showGroupConservation.setText(MessageManager
 809             .getString("label.group_conservation"));
 810     showGroupConservation.addActionListener(new ActionListener()
 811     {
 812
 813       @Override
 814       public void actionPerformed(ActionEvent e)
 815       {
 816         showGroupConservation_actionPerformed(e);
 817       }
 818
 819     });
 820
 821     showGroupConsensus.setText(MessageManager
 822             .getString("label.group_consensus"));
 823     showGroupConsensus.addActionListener(new ActionListener()
 824     {
 825
 826       @Override
 827       public void actionPerformed(ActionEvent e)
 828       {
 829         showGroupConsensus_actionPerformed(e);
 830       }
 831
 832     });
 833
 834     qualityScoreModel.setText("Quality Score Model"); // todo i18n
 835     qualityScoreModel.addMenuListener(new MenuListener()
 836     {
 837       @Override
 838       public void menuSelected(MenuEvent e)
 839       {
 840         scoreModel_menuSelected();
 841       }
 842
 843       @Override
 844       public void menuDeselected(MenuEvent e)
 845       {
 846       }
 847
 848       @Override
 849       public void menuCanceled(MenuEvent e)
 850       {
 851       }
 852     });
 853
 854     showConsensusHistogram.setText(MessageManager
 855             .getString("label.show_consensus_histogram"));
 856     showConsensusHistogram.addActionListener(new ActionListener()
 857     {
 858
 859       @Override
 860       public void actionPerformed(ActionEvent e)
 861       {
 862         showConsensusHistogram_actionPerformed(e);
 863       }
 864
 865     });
 866     showSequenceLogo.setText(MessageManager
 867             .getString("label.show_consensus_logo"));
 868     showSequenceLogo.addActionListener(new ActionListener()
 869     {
 870
 871       @Override
 872       public void actionPerformed(ActionEvent e)
 873       {
 874         showSequenceLogo_actionPerformed(e);
 875       }
 876
 877     });
 878     normaliseSequenceLogo.setText(MessageManager
 879             .getString("label.norm_consensus_logo"));
 880     normaliseSequenceLogo.addActionListener(new ActionListener()
 881     {
 882
 883       @Override
 884       public void actionPerformed(ActionEvent e)
 885       {
 886         normaliseSequenceLogo_actionPerformed(e);
 887       }
 888
 889     });
 890     applyAutoAnnotationSettings.setText(MessageManager
 891             .getString("label.apply_all_groups"));
 892     applyAutoAnnotationSettings.setState(false);
 893     applyAutoAnnotationSettings.setVisible(true);
 894     applyAutoAnnotationSettings.addActionListener(new ActionListener()
 895     {
 896       @Override
 897       public void actionPerformed(ActionEvent e)
 898       {
 899         applyAutoAnnotationSettings_actionPerformed(e);
 900       }
 901     });
 902
 903     ButtonGroup buttonGroup = new ButtonGroup();
 904     final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
 905             MessageManager.getString("label.show_first"));
 906     final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
 907             MessageManager.getString("label.show_last"));
 908     buttonGroup.add(showAutoFirst);
 909     buttonGroup.add(showAutoLast);
 910     final boolean autoFirst = Cache.getDefault(
 911             Preferences.SHOW_AUTOCALC_ABOVE, false);
 912     showAutoFirst.setSelected(autoFirst);
 913     setShowAutoCalculatedAbove(autoFirst);
 914     showAutoFirst.addActionListener(new ActionListener()
 915     {
 916       @Override
 917       public void actionPerformed(ActionEvent e)
 918       {
 919         setShowAutoCalculatedAbove(showAutoFirst.isSelected());
 920         sortAnnotations_actionPerformed();
 921       }
 922     });
 923     showAutoLast.setSelected(!showAutoFirst.isSelected());
 924     showAutoLast.addActionListener(new ActionListener()
 925     {
 926       @Override
 927       public void actionPerformed(ActionEvent e)
 928       {
 929         setShowAutoCalculatedAbove(!showAutoLast.isSelected());
 930         sortAnnotations_actionPerformed();
 931       }
 932     });
 933
 934     JMenuItem deleteGroups = new JMenuItem(
 935             MessageManager.getString("action.undefine_groups"));
 936     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
 937             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 938     al = new ActionListener()
 939     {
 940       @Override
 941       public void actionPerformed(ActionEvent e)
 942       {
 943         deleteGroups_actionPerformed(e);
 944       }
 945     };
 946     addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
 947
 948     JMenuItem annotationColumn = new JMenuItem(
 949             MessageManager.getString("action.select_by_annotation"));
 950     annotationColumn.addActionListener(new ActionListener()
 951     {
 952       @Override
 953       public void actionPerformed(ActionEvent e)
 954       {
 955         annotationColumn_actionPerformed(e);
 956       }
 957     });
 958
 959     JMenuItem createGroup = new JMenuItem(
 960             MessageManager.getString("action.create_groups"));
 961     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
 962             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 963     al = new ActionListener()
 964     {
 965       @Override
 966       public void actionPerformed(ActionEvent e)
 967       {
 968         createGroup_actionPerformed(e);
 969       }
 970     };
 971     addMenuActionAndAccelerator(keyStroke, createGroup, al);
 972
 973     JMenuItem unGroup = new JMenuItem(
 974             MessageManager.getString("action.remove_group"));
 975     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
 976             .getDefaultToolkit().getMenuShortcutKeyMask()
 977             | KeyEvent.SHIFT_MASK, false);
 978     al = new ActionListener()
 979     {
 980       @Override
 981       public void actionPerformed(ActionEvent e)
 982       {
 983         unGroup_actionPerformed(e);
 984       }
 985     };
 986     addMenuActionAndAccelerator(keyStroke, unGroup, al);
 987
 988     copy.setText(MessageManager.getString("action.copy"));
 989     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
 990             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 991
 992     al = new ActionListener()
 993     {
 994       @Override
 995       public void actionPerformed(ActionEvent e)
 996       {
 997         copy_actionPerformed(e);
 998       }
 999     };
1000     addMenuActionAndAccelerator(keyStroke, copy, al);
1001
1002     cut.setText(MessageManager.getString("action.cut"));
1003     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
1004             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1005     al = new ActionListener()
1006     {
1007       @Override
1008       public void actionPerformed(ActionEvent e)
1009       {
1010         cut_actionPerformed(e);
1011       }
1012     };
1013     addMenuActionAndAccelerator(keyStroke, cut, al);
1014
1015     JMenuItem delete = new JMenuItem(
1016             MessageManager.getString("action.delete"));
1017     delete.addActionListener(new ActionListener()
1018     {
1019       @Override
1020       public void actionPerformed(ActionEvent e)
1021       {
1022         delete_actionPerformed(e);
1023       }
1024     });
1025
1026     pasteMenu.setText(MessageManager.getString("action.paste"));
1027     JMenuItem pasteNew = new JMenuItem(
1028             MessageManager.getString("label.to_new_alignment"));
1029     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1030             .getDefaultToolkit().getMenuShortcutKeyMask()
1031             | KeyEvent.SHIFT_MASK, false);
1032     al = new ActionListener()
1033     {
1034       @Override
1035       public void actionPerformed(ActionEvent e)
1036       {
1037         pasteNew_actionPerformed(e);
1038       }
1039     };
1040     addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1041
1042     JMenuItem pasteThis = new JMenuItem(
1043             MessageManager.getString("label.to_this_alignment"));
1044     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1045             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1046     al = new ActionListener()
1047     {
1048       @Override
1049       public void actionPerformed(ActionEvent e)
1050       {
1051         pasteThis_actionPerformed(e);
1052       }
1053     };
1054     addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1055
1056     JMenuItem createPNG = new JMenuItem("PNG");
1057     createPNG.addActionListener(new ActionListener()
1058     {
1059       @Override
1060       public void actionPerformed(ActionEvent e)
1061       {
1062         createPNG(null);
1063       }
1064     });
1065     createPNG.setActionCommand(MessageManager
1066             .getString("label.save_png_image"));
1067
1068     JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1069     font.addActionListener(new ActionListener()
1070     {
1071       @Override
1072       public void actionPerformed(ActionEvent e)
1073       {
1074         font_actionPerformed(e);
1075       }
1076     });
1077     seqLimits.setText(MessageManager
1078             .getString("label.show_sequence_limits"));
1079     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1080     seqLimits.addActionListener(new ActionListener()
1081     {
1082       @Override
1083       public void actionPerformed(ActionEvent e)
1084       {
1085         seqLimit_actionPerformed(e);
1086       }
1087     });
1088     JMenuItem epsFile = new JMenuItem("EPS");
1089     epsFile.addActionListener(new ActionListener()
1090     {
1091       @Override
1092       public void actionPerformed(ActionEvent e)
1093       {
1094         createEPS(null);
1095       }
1096     });
1097
1098     JMenuItem createSVG = new JMenuItem("SVG");
1099     createSVG.addActionListener(new ActionListener()
1100     {
1101       @Override
1102       public void actionPerformed(ActionEvent e)
1103       {
1104         createSVG(null);
1105       }
1106     });
1107
1108     JMenuItem loadTreeMenuItem = new JMenuItem(
1109             MessageManager.getString("label.load_associated_tree"));
1110     loadTreeMenuItem.setActionCommand(MessageManager
1111             .getString("label.load_tree_for_sequence_set"));
1112     loadTreeMenuItem.addActionListener(new ActionListener()
1113     {
1114       @Override
1115       public void actionPerformed(ActionEvent e)
1116       {
1117         loadTreeMenuItem_actionPerformed(e);
1118       }
1119     });
1120
1121     scaleAbove.setVisible(false);
1122     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1123     scaleAbove.addActionListener(new ActionListener()
1124     {
1125       @Override
1126       public void actionPerformed(ActionEvent e)
1127       {
1128         scaleAbove_actionPerformed(e);
1129       }
1130     });
1131     scaleLeft.setVisible(false);
1132     scaleLeft.setSelected(true);
1133     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1134     scaleLeft.addActionListener(new ActionListener()
1135     {
1136       @Override
1137       public void actionPerformed(ActionEvent e)
1138       {
1139         scaleLeft_actionPerformed(e);
1140       }
1141     });
1142     scaleRight.setVisible(false);
1143     scaleRight.setSelected(true);
1144     scaleRight.setText(MessageManager.getString("action.scale_right"));
1145     scaleRight.addActionListener(new ActionListener()
1146     {
1147       @Override
1148       public void actionPerformed(ActionEvent e)
1149       {
1150         scaleRight_actionPerformed(e);
1151       }
1152     });
1153     centreColumnLabelsMenuItem.setVisible(true);
1154     centreColumnLabelsMenuItem.setState(false);
1155     centreColumnLabelsMenuItem.setText(MessageManager
1156             .getString("label.centre_column_labels"));
1157     centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1158     {
1159       @Override
1160       public void actionPerformed(ActionEvent e)
1161       {
1162         centreColumnLabels_actionPerformed(e);
1163       }
1164     });
1165     followHighlightMenuItem.setVisible(true);
1166     followHighlightMenuItem.setState(true);
1167     followHighlightMenuItem.setText(MessageManager
1168             .getString("label.automatic_scrolling"));
1169     followHighlightMenuItem.addActionListener(new ActionListener()
1170     {
1171
1172       @Override
1173       public void actionPerformed(ActionEvent e)
1174       {
1175         followHighlight_actionPerformed();
1176       }
1177
1178     });
1179
1180     sortByTreeMenu
1181             .setText(MessageManager.getString("action.by_tree_order"));
1182     sort.setText(MessageManager.getString("action.sort"));
1183     sort.addMenuListener(new MenuListener()
1184     {
1185       @Override
1186       public void menuSelected(MenuEvent e)
1187       {
1188         buildTreeSortMenu();
1189       }
1190
1191       @Override
1192       public void menuDeselected(MenuEvent e)
1193       {
1194       }
1195
1196       @Override
1197       public void menuCanceled(MenuEvent e)
1198       {
1199       }
1200     });
1201     sortByAnnotScore.setText(MessageManager
1202             .getString("label.sort_by_score"));
1203     sort.add(sortByAnnotScore);
1204     sort.addMenuListener(new javax.swing.event.MenuListener()
1205     {
1206
1207       @Override
1208       public void menuCanceled(MenuEvent e)
1209       {
1210       }
1211
1212       @Override
1213       public void menuDeselected(MenuEvent e)
1214       {
1215       }
1216
1217       @Override
1218       public void menuSelected(MenuEvent e)
1219       {
1220         buildSortByAnnotationScoresMenu();
1221       }
1222     });
1223     sortByAnnotScore.setVisible(false);
1224
1225     calculateTree.setText(MessageManager
1226             .getString("action.calculate_tree_pca"));
1227
1228     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1229     padGapsMenuitem.setState(jalview.bin.Cache
1230             .getDefault("PAD_GAPS", false));
1231     padGapsMenuitem.addActionListener(new ActionListener()
1232     {
1233       @Override
1234       public void actionPerformed(ActionEvent e)
1235       {
1236         padGapsMenuitem_actionPerformed(e);
1237       }
1238     });
1239     JMenuItem vamsasStore = new JMenuItem(
1240             MessageManager.getString("label.vamsas_store"));
1241     vamsasStore.setVisible(false);
1242     vamsasStore.addActionListener(new ActionListener()
1243     {
1244       @Override
1245       public void actionPerformed(ActionEvent e)
1246       {
1247         vamsasStore_actionPerformed(e);
1248       }
1249     });
1250     showTranslation.setText(MessageManager
1251             .getString("label.translate_cDNA"));
1252     showTranslation.addActionListener(new ActionListener()
1253     {
1254       @Override
1255       public void actionPerformed(ActionEvent e)
1256       {
1257         showTranslation_actionPerformed(e);
1258       }
1259     });
1260     showReverse.setText(MessageManager.getString("label.reverse"));
1261     showReverse.addActionListener(new ActionListener()
1262     {
1263       @Override
1264       public void actionPerformed(ActionEvent e)
1265       {
1266         showReverse_actionPerformed(false);
1267       }
1268     });
1269     showReverseComplement.setText(MessageManager
1270             .getString("label.reverse_complement"));
1271     showReverseComplement.addActionListener(new ActionListener()
1272     {
1273       @Override
1274       public void actionPerformed(ActionEvent e)
1275       {
1276         showReverse_actionPerformed(true);
1277       }
1278     });
1279
1280     JMenuItem extractScores = new JMenuItem(
1281             MessageManager.getString("label.extract_scores"));
1282     extractScores.addActionListener(new ActionListener()
1283     {
1284       @Override
1285       public void actionPerformed(ActionEvent e)
1286       {
1287         extractScores_actionPerformed(e);
1288       }
1289     });
1290     extractScores.setVisible(true);
1291     // JBPNote: TODO: make gui for regex based score extraction
1292
1293     // for show products actions see AlignFrame.canShowProducts
1294     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1295
1296     runGroovy.setText(MessageManager.getString("label.run_groovy"));
1297     runGroovy.setToolTipText(MessageManager
1298             .getString("label.run_groovy_tip"));
1299     runGroovy.addActionListener(new ActionListener()
1300     {
1301       @Override
1302       public void actionPerformed(ActionEvent e)
1303       {
1304         runGroovy_actionPerformed();
1305       }
1306     });
1307
1308     JMenuItem openFeatureSettings = new JMenuItem(
1309             MessageManager.getString("action.feature_settings"));
1310     openFeatureSettings.addActionListener(new ActionListener()
1311     {
1312       @Override
1313       public void actionPerformed(ActionEvent e)
1314       {
1315         featureSettings_actionPerformed(e);
1316       }
1317     });
1318     JMenuItem fetchSequence = new JMenuItem(
1319             MessageManager.getString("label.fetch_sequences"));
1320     fetchSequence.addActionListener(new ActionListener()
1321     {
1322       @Override
1323       public void actionPerformed(ActionEvent e)
1324       {
1325         fetchSequence_actionPerformed(e);
1326       }
1327     });
1328
1329     JMenuItem associatedData = new JMenuItem(
1330             MessageManager.getString("label.load_features_annotations"));
1331     associatedData.addActionListener(new ActionListener()
1332     {
1333       @Override
1334       public void actionPerformed(ActionEvent e)
1335       {
1336         associatedData_actionPerformed(e);
1337       }
1338     });
1339     autoCalculate.setText(MessageManager
1340             .getString("label.autocalculate_consensus"));
1341     autoCalculate.setState(jalview.bin.Cache.getDefault(
1342             "AUTO_CALC_CONSENSUS", true));
1343     autoCalculate.addActionListener(new ActionListener()
1344     {
1345       @Override
1346       public void actionPerformed(ActionEvent e)
1347       {
1348         autoCalculate_actionPerformed(e);
1349       }
1350     });
1351     sortByTree.setText(MessageManager
1352             .getString("label.sort_alignment_new_tree"));
1353     sortByTree
1354             .setToolTipText("<html>"
1355                     + MessageManager
1356                             .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1357     sortByTree
1358             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1359     sortByTree.addActionListener(new ActionListener()
1360     {
1361       @Override
1362       public void actionPerformed(ActionEvent e)
1363       {
1364         sortByTreeOption_actionPerformed(e);
1365       }
1366     });
1367
1368     listenToViewSelections.setText(MessageManager
1369             .getString("label.listen_for_selections"));
1370     listenToViewSelections
1371             .setToolTipText("<html>"
1372                     + MessageManager
1373                             .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1374     listenToViewSelections.setState(false);
1375     listenToViewSelections.addActionListener(new ActionListener()
1376     {
1377       @Override
1378       public void actionPerformed(ActionEvent e)
1379       {
1380         listenToViewSelections_actionPerformed(e);
1381       }
1382     });
1383
1384     JMenu addSequenceMenu = new JMenu(
1385             MessageManager.getString("label.add_sequences"));
1386     JMenuItem addFromFile = new JMenuItem(
1387             MessageManager.getString("label.from_file"));
1388     addFromFile.addActionListener(new ActionListener()
1389     {
1390       @Override
1391       public void actionPerformed(ActionEvent e)
1392       {
1393         addFromFile_actionPerformed(e);
1394       }
1395     });
1396     JMenuItem addFromText = new JMenuItem(
1397             MessageManager.getString("label.from_textbox"));
1398     addFromText.addActionListener(new ActionListener()
1399     {
1400       @Override
1401       public void actionPerformed(ActionEvent e)
1402       {
1403         addFromText_actionPerformed(e);
1404       }
1405     });
1406     JMenuItem addFromURL = new JMenuItem(
1407             MessageManager.getString("label.from_url"));
1408     addFromURL.addActionListener(new ActionListener()
1409     {
1410       @Override
1411       public void actionPerformed(ActionEvent e)
1412       {
1413         addFromURL_actionPerformed(e);
1414       }
1415     });
1416     JMenuItem exportFeatures = new JMenuItem(
1417             MessageManager.getString("label.export_features"));
1418     exportFeatures.addActionListener(new ActionListener()
1419     {
1420       @Override
1421       public void actionPerformed(ActionEvent e)
1422       {
1423         exportFeatures_actionPerformed(e);
1424       }
1425     });
1426     JMenuItem exportAnnotations = new JMenuItem(
1427             MessageManager.getString("label.export_annotations"));
1428     exportAnnotations.addActionListener(new ActionListener()
1429     {
1430       @Override
1431       public void actionPerformed(ActionEvent e)
1432       {
1433         exportAnnotations_actionPerformed(e);
1434       }
1435     });
1436     statusPanel.setLayout(new GridLayout());
1437     JMenuItem showAllSeqs = new JMenuItem(
1438             MessageManager.getString("label.all_sequences"));
1439     showAllSeqs.setToolTipText(MessageManager
1440             .getString("label.toggle_sequence_visibility"));
1441     showAllSeqs.addActionListener(new ActionListener()
1442     {
1443       @Override
1444       public void actionPerformed(ActionEvent e)
1445       {
1446         showAllSeqs_actionPerformed(e);
1447       }
1448     });
1449     JMenuItem showAllColumns = new JMenuItem(
1450             MessageManager.getString("label.all_columns"));
1451     showAllColumns.setToolTipText(MessageManager
1452             .getString("label.toggle_columns_visibility"));
1453     showAllColumns.addActionListener(new ActionListener()
1454     {
1455       @Override
1456       public void actionPerformed(ActionEvent e)
1457       {
1458         showAllColumns_actionPerformed(e);
1459       }
1460     });
1461     JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1462     JMenuItem hideSelSequences = new JMenuItem(
1463             MessageManager.getString("label.selected_sequences"));
1464     hideSelSequences.setToolTipText(MessageManager
1465             .getString("label.toggle_sequence_visibility"));
1466     hideSelSequences.addActionListener(new ActionListener()
1467     {
1468       @Override
1469       public void actionPerformed(ActionEvent e)
1470       {
1471         hideSelSequences_actionPerformed(e);
1472       }
1473     });
1474     JMenuItem hideSelColumns = new JMenuItem(
1475             MessageManager.getString("label.selected_columns"));
1476     hideSelColumns.setToolTipText(MessageManager
1477             .getString("label.toggle_columns_visibility"));
1478     hideSelColumns.addActionListener(new ActionListener()
1479     {
1480       @Override
1481       public void actionPerformed(ActionEvent e)
1482       {
1483         hideSelColumns_actionPerformed(e);
1484       }
1485     });
1486     JMenuItem hideAllSelection = new JMenuItem(
1487             MessageManager.getString("label.selected_region"));
1488     hideAllSelection.addActionListener(new ActionListener()
1489     {
1490       @Override
1491       public void actionPerformed(ActionEvent e)
1492       {
1493         hideAllSelection_actionPerformed(e);
1494       }
1495     });
1496     // TODO: should be hidden if no selection exists.
1497     JMenuItem hideAllButSelection = new JMenuItem(
1498             MessageManager.getString("label.all_but_selected_region"));
1499     hideAllButSelection.addActionListener(new ActionListener()
1500     {
1501       @Override
1502       public void actionPerformed(ActionEvent e)
1503       {
1504         hideAllButSelection_actionPerformed(e);
1505       }
1506     });
1507     JMenuItem showAllhidden = new JMenuItem(
1508             MessageManager.getString("label.all_sequences_columns"));
1509     showAllhidden.setToolTipText(MessageManager
1510             .getString("label.toggles_visibility_hidden_selected_regions"));
1511     showAllhidden.addActionListener(new ActionListener()
1512     {
1513       @Override
1514       public void actionPerformed(ActionEvent e)
1515       {
1516         showAllhidden_actionPerformed(e);
1517       }
1518     });
1519     hiddenMarkers.setText(MessageManager
1520             .getString("action.show_hidden_markers"));
1521     hiddenMarkers.addActionListener(new ActionListener()
1522     {
1523       @Override
1524       public void actionPerformed(ActionEvent e)
1525       {
1526         hiddenMarkers_actionPerformed(e);
1527       }
1528     });
1529
1530     JMenuItem invertColSel = new JMenuItem(
1531             MessageManager.getString("action.invert_column_selection"));
1532     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
1533             .getDefaultToolkit().getMenuShortcutKeyMask()
1534             | KeyEvent.ALT_MASK, false);
1535     al = new ActionListener()
1536     {
1537       @Override
1538       public void actionPerformed(ActionEvent e)
1539       {
1540         invertColSel_actionPerformed(e);
1541       }
1542     };
1543     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1544
1545     showComplementMenuItem.setVisible(false);
1546     showComplementMenuItem.addActionListener(new ActionListener()
1547     {
1548       @Override
1549       public void actionPerformed(ActionEvent e)
1550       {
1551         showComplement_actionPerformed(showComplementMenuItem.getState());
1552       }
1553     });
1554
1555     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1556     {
1557       @Override
1558       public void stateChanged(ChangeEvent evt)
1559       {
1560         JTabbedPane pane = (JTabbedPane) evt.getSource();
1561         int sel = pane.getSelectedIndex();
1562         tabSelectionChanged(sel);
1563       }
1564     });
1565     tabbedPane.addMouseListener(new MouseAdapter()
1566     {
1567       @Override
1568       public void mousePressed(MouseEvent e)
1569       {
1570         if (e.isPopupTrigger()) // Mac
1571         {
1572           tabbedPane_mousePressed(e);
1573         }
1574       }
1575
1576       @Override
1577       public void mouseReleased(MouseEvent e)
1578       {
1579         if (e.isPopupTrigger()) // Windows
1580         {
1581           tabbedPane_mousePressed(e);
1582         }
1583       }
1584     });
1585     tabbedPane.addFocusListener(new FocusAdapter()
1586     {
1587       @Override
1588       public void focusGained(FocusEvent e)
1589       {
1590         tabbedPane_focusGained(e);
1591       }
1592     });
1593
1594     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1595     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
1596             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1597     al = new ActionListener()
1598     {
1599       @Override
1600       public void actionPerformed(ActionEvent e)
1601       {
1602         save_actionPerformed(e);
1603       }
1604     };
1605     addMenuActionAndAccelerator(keyStroke, save, al);
1606
1607     reload.setEnabled(false);
1608     reload.setText(MessageManager.getString("action.reload"));
1609     reload.addActionListener(new ActionListener()
1610     {
1611       @Override
1612       public void actionPerformed(ActionEvent e)
1613       {
1614         reload_actionPerformed(e);
1615       }
1616     });
1617
1618     JMenuItem newView = new JMenuItem(
1619             MessageManager.getString("action.new_view"));
1620     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
1621             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1622     al = new ActionListener()
1623     {
1624       @Override
1625       public void actionPerformed(ActionEvent e)
1626       {
1627         newView_actionPerformed(e);
1628       }
1629     };
1630     addMenuActionAndAccelerator(keyStroke, newView, al);
1631
1632     tabbedPane.setToolTipText("<html><i>"
1633             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1634             + "</i></html>");
1635
1636     formatMenu.setText(MessageManager.getString("action.format"));
1637     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1638     idRightAlign.setText(MessageManager
1639             .getString("label.right_align_sequence_id"));
1640     idRightAlign.addActionListener(new ActionListener()
1641     {
1642       @Override
1643       public void actionPerformed(ActionEvent e)
1644       {
1645         idRightAlign_actionPerformed(e);
1646       }
1647     });
1648
1649     gatherViews.setEnabled(false);
1650     gatherViews.setText(MessageManager.getString("action.gather_views"));
1651     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1652     al = new ActionListener()
1653     {
1654       @Override
1655       public void actionPerformed(ActionEvent e)
1656       {
1657         gatherViews_actionPerformed(e);
1658       }
1659     };
1660     addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1661
1662     expandViews.setEnabled(false);
1663     expandViews.setText(MessageManager.getString("action.expand_views"));
1664     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1665     al = new ActionListener()
1666     {
1667       @Override
1668       public void actionPerformed(ActionEvent e)
1669       {
1670         expandViews_actionPerformed(e);
1671       }
1672     };
1673     addMenuActionAndAccelerator(keyStroke, expandViews, al);
1674
1675     JMenuItem pageSetup = new JMenuItem(
1676             MessageManager.getString("action.page_setup"));
1677     pageSetup.addActionListener(new ActionListener()
1678     {
1679       @Override
1680       public void actionPerformed(ActionEvent e)
1681       {
1682         pageSetup_actionPerformed(e);
1683       }
1684     });
1685     JMenuItem alignmentProperties = new JMenuItem(
1686             MessageManager.getString("label.alignment_props"));
1687     alignmentProperties.addActionListener(new ActionListener()
1688     {
1689       @Override
1690       public void actionPerformed(ActionEvent actionEvent)
1691       {
1692         alignmentProperties();
1693       }
1694     });
1695     JMenuItem selectHighlighted = new JMenuItem(
1696             MessageManager.getString("action.select_highlighted_columns"));
1697     selectHighlighted.setToolTipText(MessageManager
1698             .getString("tooltip.select_highlighted_columns"));
1699     al = new ActionListener()
1700     {
1701       @Override
1702       public void actionPerformed(ActionEvent actionEvent)
1703       {
1704         selectHighlightedColumns_actionPerformed(actionEvent);
1705       }
1706     };
1707     selectHighlighted.addActionListener(al);
1708     JMenu tooltipSettingsMenu = new JMenu(
1709             MessageManager.getString("label.sequence_id_tooltip"));
1710     JMenu autoAnnMenu = new JMenu(
1711             MessageManager.getString("label.autocalculated_annotation"));
1712
1713     JMenu exportImageMenu = new JMenu(
1714             MessageManager.getString("label.export_image"));
1715     JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1716     alignFrameMenuBar.add(fileMenu);
1717     alignFrameMenuBar.add(editMenu);
1718     alignFrameMenuBar.add(selectMenu);
1719     alignFrameMenuBar.add(viewMenu);
1720     alignFrameMenuBar.add(annotationsMenu);
1721     alignFrameMenuBar.add(formatMenu);
1722     alignFrameMenuBar.add(colourMenu);
1723     alignFrameMenuBar.add(calculateMenu);
1724     alignFrameMenuBar.add(webService);
1725
1726     fileMenu.add(fetchSequence);
1727     fileMenu.add(addSequenceMenu);
1728     fileMenu.add(reload);
1729     fileMenu.addSeparator();
1730     fileMenu.add(vamsasStore);
1731     fileMenu.add(save);
1732     fileMenu.add(saveAs);
1733     fileMenu.add(outputTextboxMenu);
1734     fileMenu.add(pageSetup);
1735     fileMenu.add(printMenuItem);
1736     fileMenu.addSeparator();
1737     fileMenu.add(exportImageMenu);
1738     fileMenu.add(exportFeatures);
1739     fileMenu.add(exportAnnotations);
1740     fileMenu.add(loadTreeMenuItem);
1741     fileMenu.add(associatedData);
1742     fileMenu.addSeparator();
1743     fileMenu.add(closeMenuItem);
1744
1745     pasteMenu.add(pasteNew);
1746     pasteMenu.add(pasteThis);
1747     editMenu.add(undoMenuItem);
1748     editMenu.add(redoMenuItem);
1749     editMenu.add(cut);
1750     editMenu.add(copy);
1751     editMenu.add(pasteMenu);
1752     editMenu.add(delete);
1753     editMenu.addSeparator();
1754     editMenu.add(remove2LeftMenuItem);
1755     editMenu.add(remove2RightMenuItem);
1756     editMenu.add(removeGappedColumnMenuItem);
1757     editMenu.add(removeAllGapsMenuItem);
1758     editMenu.add(removeRedundancyMenuItem);
1759     editMenu.addSeparator();
1760     // dont add these yet in the CVS build - they cannot be undone!
1761     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1762     // editMenu.add(justifyLeftMenuItem);
1763     // editMenu.add(justifyRightMenuItem);
1764     // editMenu.addSeparator();
1765     editMenu.add(padGapsMenuitem);
1766
1767     showMenu.add(showAllColumns);
1768     showMenu.add(showAllSeqs);
1769     showMenu.add(showAllhidden);
1770     hideMenu.add(hideSelColumns);
1771     hideMenu.add(hideSelSequences);
1772     hideMenu.add(hideAllSelection);
1773     hideMenu.add(hideAllButSelection);
1774     viewMenu.add(newView);
1775     viewMenu.add(expandViews);
1776     viewMenu.add(gatherViews);
1777     viewMenu.addSeparator();
1778     viewMenu.add(showMenu);
1779     viewMenu.add(hideMenu);
1780     viewMenu.add(showComplementMenuItem);
1781     viewMenu.addSeparator();
1782     viewMenu.add(followHighlightMenuItem);
1783     viewMenu.addSeparator();
1784     viewMenu.add(showSeqFeatures);
1785     // viewMenu.add(showSeqFeaturesHeight);
1786     viewMenu.add(openFeatureSettings);
1787     tooltipSettingsMenu.add(showDbRefsMenuitem);
1788     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1789     viewMenu.add(tooltipSettingsMenu);
1790     viewMenu.addSeparator();
1791     viewMenu.add(alignmentProperties);
1792     viewMenu.addSeparator();
1793     viewMenu.add(overviewMenuItem);
1794
1795     annotationsMenu.add(annotationPanelMenuItem);
1796     annotationsMenu.addSeparator();
1797     annotationsMenu.add(showAllAlAnnotations);
1798     annotationsMenu.add(hideAllAlAnnotations);
1799     annotationsMenu.addSeparator();
1800     annotationsMenu.add(showAllSeqAnnotations);
1801     annotationsMenu.add(hideAllSeqAnnotations);
1802     annotationsMenu.add(sortAnnBySequence);
1803     annotationsMenu.add(sortAnnByLabel);
1804     annotationsMenu.addSeparator();
1805     autoAnnMenu.add(showAutoFirst);
1806     autoAnnMenu.add(showAutoLast);
1807     autoAnnMenu.addSeparator();
1808     autoAnnMenu.add(applyAutoAnnotationSettings);
1809     autoAnnMenu.add(showConsensusHistogram);
1810     autoAnnMenu.add(showSequenceLogo);
1811     autoAnnMenu.add(normaliseSequenceLogo);
1812     autoAnnMenu.addSeparator();
1813     autoAnnMenu.add(showGroupConservation);
1814     autoAnnMenu.add(showGroupConsensus);
1815     autoAnnMenu.addSeparator();
1816     autoAnnMenu.add(qualityScoreModel);
1817     annotationsMenu.add(autoAnnMenu);
1818
1819
1820     sort.add(sortIDMenuItem);
1821     sort.add(sortLengthMenuItem);
1822     sort.add(sortGroupMenuItem);
1823     sort.add(sortPairwiseMenuItem);
1824     sort.add(sortByTreeMenu);
1825     calculateMenu.add(sort);
1826     calculateMenu.add(calculateTree);
1827     calculateMenu.addSeparator();
1828     calculateMenu.add(pairwiseAlignmentMenuItem);
1829     // calculateMenu.add(PCAMenuItem);
1830     calculateMenu.addSeparator();
1831     calculateMenu.add(showTranslation);
1832     calculateMenu.add(showReverse);
1833     calculateMenu.add(showReverseComplement);
1834     calculateMenu.add(showProducts);
1835     calculateMenu.add(autoCalculate);
1836     calculateMenu.add(sortByTree);
1837     calculateMenu.addSeparator();
1838     calculateMenu.add(expandAlignment);
1839     calculateMenu.add(extractScores);
1840     calculateMenu.addSeparator();
1841     calculateMenu.add(runGroovy);
1842
1843     webServiceNoServices = new JMenuItem(
1844             MessageManager.getString("label.no_services"));
1845     webService.add(webServiceNoServices);
1846     exportImageMenu.add(htmlMenuItem);
1847     exportImageMenu.add(epsFile);
1848     exportImageMenu.add(createPNG);
1849     exportImageMenu.add(createBioJS);
1850     exportImageMenu.add(createSVG);
1851     addSequenceMenu.add(addFromFile);
1852     addSequenceMenu.add(addFromText);
1853     addSequenceMenu.add(addFromURL);
1854     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1855     statusPanel.add(statusBar, null);
1856     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1857
1858     formatMenu.add(font);
1859     formatMenu.addSeparator();
1860     formatMenu.add(wrapMenuItem);
1861     formatMenu.add(scaleAbove);
1862     formatMenu.add(scaleLeft);
1863     formatMenu.add(scaleRight);
1864     formatMenu.add(seqLimits);
1865     formatMenu.add(idRightAlign);
1866     formatMenu.add(hiddenMarkers);
1867     formatMenu.add(viewBoxesMenuItem);
1868     formatMenu.add(viewTextMenuItem);
1869     formatMenu.add(colourTextMenuItem);
1870     formatMenu.add(renderGapsMenuItem);
1871     formatMenu.add(centreColumnLabelsMenuItem);
1872     formatMenu.add(showNonconservedMenuItem);
1873     selectMenu.add(findMenuItem);
1874     selectMenu.addSeparator();
1875     selectMenu.add(selectAllSequenceMenuItem);
1876     selectMenu.add(deselectAllSequenceMenuItem);
1877     selectMenu.add(invertSequenceMenuItem);
1878     selectMenu.add(invertColSel);
1879     selectMenu.add(createGroup);
1880     selectMenu.add(unGroup);
1881     selectMenu.add(grpsFromSelection);
1882     selectMenu.add(deleteGroups);
1883     selectMenu.add(annotationColumn);
1884     selectMenu.add(selectHighlighted);
1885     // TODO - determine if the listenToViewSelections button is needed : see bug
1886     // JAL-574
1887     // selectMenu.addSeparator();
1888     // selectMenu.add(listenToViewSelections);
1889   }
1890
1891   protected void scoreModel_menuSelected()
1892   {
1893   }
1894
1895   /**
1896    * Constructs the entries on the Colour menu (but does not add them to the
1897    * menu).
1898    */
1899   protected void initColourMenu()
1900   {
1901     applyToAllGroups = new JCheckBoxMenuItem(
1902             MessageManager.getString("label.apply_colour_to_all_groups"));
1903     applyToAllGroups.addActionListener(new ActionListener()
1904     {
1905       @Override
1906       public void actionPerformed(ActionEvent e)
1907       {
1908         applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1909       }
1910     });
1911
1912     textColour = new JRadioButtonMenuItem(
1913             MessageManager.getString("action.set_text_colour"));
1914     textColour.addActionListener(new ActionListener()
1915     {
1916       @Override
1917       public void actionPerformed(ActionEvent e)
1918       {
1919         textColour_actionPerformed();
1920       }
1921     });
1922
1923     conservationMenuItem = new JCheckBoxMenuItem(
1924             MessageManager.getString("action.by_conservation"));
1925     conservationMenuItem.addActionListener(new ActionListener()
1926     {
1927       @Override
1928       public void actionPerformed(ActionEvent e)
1929       {
1930         conservationMenuItem_actionPerformed(conservationMenuItem
1931                 .isSelected());
1932       }
1933     });
1934
1935     abovePIDThreshold = new JCheckBoxMenuItem(
1936             MessageManager.getString("label.above_identity_threshold"));
1937     abovePIDThreshold.addActionListener(new ActionListener()
1938     {
1939       @Override
1940       public void actionPerformed(ActionEvent e)
1941       {
1942         abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
1943       }
1944     });
1945     modifyPID = new JMenuItem(
1946             MessageManager.getString("label.modify_identity_threshold"));
1947     modifyPID.addActionListener(new ActionListener()
1948     {
1949       @Override
1950       public void actionPerformed(ActionEvent e)
1951       {
1952         modifyPID_actionPerformed();
1953       }
1954     });
1955     modifyConservation = new JMenuItem(
1956             MessageManager
1957             .getString("label.modify_conservation_threshold"));
1958     modifyConservation.addActionListener(new ActionListener()
1959     {
1960       @Override
1961       public void actionPerformed(ActionEvent e)
1962       {
1963         modifyConservation_actionPerformed();
1964       }
1965     });
1966
1967     annotationColour = new JMenuItem(
1968             MessageManager.getString("action.by_annotation"));
1969     annotationColour.addActionListener(new ActionListener()
1970     {
1971       @Override
1972       public void actionPerformed(ActionEvent e)
1973       {
1974         annotationColour_actionPerformed();
1975       }
1976     });
1977   }
1978
1979   protected void selectHighlightedColumns_actionPerformed(
1980           ActionEvent actionEvent)
1981   {
1982     // TODO Auto-generated method stub
1983
1984   }
1985
1986   /**
1987    * Generate the reverse sequence (or reverse complement if the flag is true)
1988    * and add it to the alignment
1989    *
1990    * @param complement
1991    */
1992   protected void showReverse_actionPerformed(boolean complement)
1993   {
1994   }
1995
1996   /**
1997    * Try to run script in a Groovy console, having first ensured that this
1998    * alignframe is set as currentAlignFrame in Desktop
1999    */
2000   protected void runGroovy_actionPerformed()
2001   {
2002
2003   }
2004
2005   /**
2006    * Adds the given action listener and key accelerator to the given menu item.
2007    * Also saves in a lookup table to support lookup of action by key stroke.
2008    *
2009    * @param keyStroke
2010    * @param menuItem
2011    * @param actionListener
2012    */
2013   protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2014           JMenuItem menuItem, ActionListener actionListener)
2015   {
2016     menuItem.setAccelerator(keyStroke);
2017     accelerators.put(keyStroke, menuItem);
2018     menuItem.addActionListener(actionListener);
2019   }
2020
2021   /**
2022    * Action on clicking sort annotations by type.
2023    *
2024    * @param sortOrder
2025    */
2026   protected void sortAnnotations_actionPerformed()
2027   {
2028   }
2029
2030   /**
2031    * Action on clicking Show all annotations.
2032    *
2033    * @param forSequences
2034    *          update sequence-related annotations
2035    * @param forAlignment
2036    *          update non-sequence-related annotations
2037    */
2038   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2039           boolean forAlignment)
2040   {
2041     setAnnotationsVisibility(true, forSequences, forAlignment);
2042   }
2043
2044   /**
2045    * Action on clicking Hide all annotations.
2046    *
2047    * @param forSequences
2048    *          update sequence-related annotations
2049    * @param forAlignment
2050    *          update non-sequence-related annotations
2051    */
2052   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2053           boolean forAlignment)
2054   {
2055     setAnnotationsVisibility(false, forSequences, forAlignment);
2056   }
2057
2058   /**
2059    * Set the visibility of annotations to true or false. Can act on
2060    * sequence-related annotations, or alignment-related, or both.
2061    *
2062    * @param visible
2063    * @param forSequences
2064    *          update sequence-related annotations
2065    * @param forAlignment
2066    *          update non-sequence-related annotations
2067    */
2068   protected void setAnnotationsVisibility(boolean visible,
2069           boolean forSequences, boolean forAlignment)
2070   {
2071
2072   }
2073
2074   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2075   {
2076     // TODO Auto-generated method stub
2077
2078   }
2079
2080   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2081   {
2082     // TODO Auto-generated method stub
2083
2084   }
2085
2086   protected void showAllhidden_actionPerformed(ActionEvent e)
2087   {
2088     // TODO Auto-generated method stub
2089
2090   }
2091
2092   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2093   {
2094     // TODO Auto-generated method stub
2095
2096   }
2097
2098   protected void hideAllSelection_actionPerformed(ActionEvent e)
2099   {
2100     // TODO Auto-generated method stub
2101
2102   }
2103
2104   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2105   {
2106     // TODO Auto-generated method stub
2107
2108   }
2109
2110   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2111   {
2112     // TODO Auto-generated method stub
2113
2114   }
2115
2116   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2117   {
2118     // TODO Auto-generated method stub
2119
2120   }
2121
2122   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2123   {
2124     // TODO Auto-generated method stub
2125
2126   }
2127
2128   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2129   {
2130     // TODO Auto-generated method stub
2131
2132   }
2133
2134   protected void showGroupConservation_actionPerformed(ActionEvent e)
2135   {
2136     // TODO Auto-generated method stub
2137
2138   }
2139
2140   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2141   {
2142     // TODO Auto-generated method stub
2143
2144   }
2145
2146   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2147   {
2148     // TODO Auto-generated method stub
2149
2150   }
2151
2152   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2153   {
2154     // TODO Auto-generated method stub
2155
2156   }
2157
2158   protected void followHighlight_actionPerformed()
2159   {
2160     // TODO Auto-generated method stub
2161
2162   }
2163
2164   protected void showNpFeats_actionPerformed(ActionEvent e)
2165   {
2166     // TODO Auto-generated method stub
2167
2168   }
2169
2170   protected void showDbRefs_actionPerformed(ActionEvent e)
2171   {
2172     // TODO Auto-generated method stub
2173
2174   }
2175
2176   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2177   {
2178   }
2179
2180   protected void buildSortByAnnotationScoresMenu()
2181   {
2182   }
2183
2184   protected void extractScores_actionPerformed(ActionEvent e)
2185   {
2186   }
2187
2188   protected void outputText_actionPerformed(ActionEvent e)
2189   {
2190   }
2191
2192   public void addFromFile_actionPerformed(ActionEvent e)
2193   {
2194
2195   }
2196
2197   public void addFromText_actionPerformed(ActionEvent e)
2198   {
2199
2200   }
2201
2202   public void addFromURL_actionPerformed(ActionEvent e)
2203   {
2204
2205   }
2206
2207   public void exportFeatures_actionPerformed(ActionEvent e)
2208   {
2209
2210   }
2211
2212   public void exportAnnotations_actionPerformed(ActionEvent e)
2213   {
2214
2215   }
2216
2217   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2218   {
2219   }
2220
2221   protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2222   {
2223
2224   }
2225
2226   protected void closeMenuItem_actionPerformed(boolean b)
2227   {
2228   }
2229
2230   protected void redoMenuItem_actionPerformed(ActionEvent e)
2231   {
2232   }
2233
2234   protected void undoMenuItem_actionPerformed(ActionEvent e)
2235   {
2236   }
2237
2238   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2239   {
2240   }
2241
2242   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2243   {
2244   }
2245
2246   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2247   {
2248   }
2249
2250   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2251   {
2252   }
2253
2254   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2255   {
2256   }
2257
2258   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2259   {
2260   }
2261
2262   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2263   {
2264   }
2265
2266   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2267   {
2268   }
2269
2270   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2271   {
2272   }
2273
2274   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2275   {
2276   }
2277
2278   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2279   {
2280   }
2281
2282   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2283   {
2284   }
2285
2286   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2287   {
2288   }
2289
2290   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2291   {
2292   }
2293
2294   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2295   {
2296   }
2297
2298   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2299   {
2300   }
2301
2302   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2303   {
2304   }
2305
2306   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2307   {
2308   }
2309
2310   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2311   {
2312   }
2313
2314   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2315   {
2316   }
2317
2318   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2319   {
2320   }
2321
2322   protected void conservationMenuItem_actionPerformed(boolean selected)
2323   {
2324   }
2325
2326   protected void printMenuItem_actionPerformed(ActionEvent e)
2327   {
2328   }
2329
2330   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2331   {
2332   }
2333
2334   protected void findMenuItem_actionPerformed(ActionEvent e)
2335   {
2336   }
2337
2338   protected void abovePIDThreshold_actionPerformed(boolean selected)
2339   {
2340   }
2341
2342   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2343   {
2344   }
2345
2346   protected void deleteGroups_actionPerformed(ActionEvent e)
2347   {
2348   }
2349
2350   protected void createGroup_actionPerformed(ActionEvent e)
2351   {
2352   }
2353
2354   protected void unGroup_actionPerformed(ActionEvent e)
2355   {
2356   }
2357
2358   protected void copy_actionPerformed(ActionEvent e)
2359   {
2360   }
2361
2362   protected void cut_actionPerformed(ActionEvent e)
2363   {
2364   }
2365
2366   protected void delete_actionPerformed(ActionEvent e)
2367   {
2368   }
2369
2370   protected void pasteNew_actionPerformed(ActionEvent e)
2371   {
2372   }
2373
2374   protected void pasteThis_actionPerformed(ActionEvent e)
2375   {
2376   }
2377
2378   protected void applyToAllGroups_actionPerformed(boolean selected)
2379   {
2380   }
2381
2382   public void createPNG(java.io.File f)
2383   {
2384   }
2385
2386   protected void font_actionPerformed(ActionEvent e)
2387   {
2388   }
2389
2390   protected void seqLimit_actionPerformed(ActionEvent e)
2391   {
2392   }
2393
2394   public void seqDBRef_actionPerformed(ActionEvent e)
2395   {
2396
2397   }
2398
2399   public void createEPS(java.io.File f)
2400   {
2401   }
2402
2403   public void createSVG(java.io.File f)
2404   {
2405
2406   }
2407
2408   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2409   {
2410
2411   }
2412
2413   /**
2414    * Template method to handle the 'load T-Coffee scores' menu event.
2415    * <p>
2416    * Subclasses override this method to provide a custom action.
2417    *
2418    * @param event
2419    *          The raised event
2420    */
2421   protected void loadScores_actionPerformed(ActionEvent event)
2422   {
2423
2424   }
2425
2426   protected void jpred_actionPerformed(ActionEvent e)
2427   {
2428   }
2429
2430   protected void scaleAbove_actionPerformed(ActionEvent e)
2431   {
2432   }
2433
2434   protected void scaleLeft_actionPerformed(ActionEvent e)
2435   {
2436   }
2437
2438   protected void scaleRight_actionPerformed(ActionEvent e)
2439   {
2440   }
2441
2442   protected void modifyPID_actionPerformed()
2443   {
2444   }
2445
2446   protected void modifyConservation_actionPerformed()
2447   {
2448   }
2449
2450   protected void saveAs_actionPerformed(ActionEvent e)
2451   {
2452   }
2453
2454   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2455   {
2456   }
2457
2458   public void vamsasStore_actionPerformed(ActionEvent e)
2459   {
2460
2461   }
2462
2463   public void vamsasLoad_actionPerformed(ActionEvent e)
2464   {
2465
2466   }
2467
2468   public void showTranslation_actionPerformed(ActionEvent e)
2469   {
2470
2471   }
2472
2473   public void featureSettings_actionPerformed(ActionEvent e)
2474   {
2475
2476   }
2477
2478   public void fetchSequence_actionPerformed(ActionEvent e)
2479   {
2480
2481   }
2482
2483   public void smoothFont_actionPerformed(ActionEvent e)
2484   {
2485
2486   }
2487
2488   public void annotationColour_actionPerformed()
2489   {
2490   }
2491
2492   public void annotationColumn_actionPerformed(ActionEvent e)
2493   {
2494   }
2495
2496   public void associatedData_actionPerformed(ActionEvent e)
2497   {
2498
2499   }
2500
2501   public void autoCalculate_actionPerformed(ActionEvent e)
2502   {
2503
2504   }
2505
2506   public void sortByTreeOption_actionPerformed(ActionEvent e)
2507   {
2508
2509   }
2510
2511   public void showAllSeqs_actionPerformed(ActionEvent e)
2512   {
2513
2514   }
2515
2516   public void showAllColumns_actionPerformed(ActionEvent e)
2517   {
2518
2519   }
2520
2521   public void hideSelSequences_actionPerformed(ActionEvent e)
2522   {
2523
2524   }
2525
2526   public void hideSelColumns_actionPerformed(ActionEvent e)
2527   {
2528
2529   }
2530
2531   public void hiddenMarkers_actionPerformed(ActionEvent e)
2532   {
2533
2534   }
2535
2536   public void findPdbId_actionPerformed(ActionEvent e)
2537   {
2538
2539   }
2540
2541   public void enterPdbId_actionPerformed(ActionEvent e)
2542   {
2543
2544   }
2545
2546   public void pdbFile_actionPerformed(ActionEvent e)
2547   {
2548
2549   }
2550
2551   public void invertColSel_actionPerformed(ActionEvent e)
2552   {
2553
2554   }
2555
2556   public void tabSelectionChanged(int sel)
2557   {
2558
2559   }
2560
2561   public void tabbedPane_mousePressed(MouseEvent e)
2562   {
2563
2564   }
2565
2566   public void tabbedPane_focusGained(FocusEvent e)
2567   {
2568     requestFocus();
2569   }
2570
2571   public void save_actionPerformed(ActionEvent e)
2572   {
2573
2574   }
2575
2576   public void reload_actionPerformed(ActionEvent e)
2577   {
2578
2579   }
2580
2581   public void newView_actionPerformed(ActionEvent e)
2582   {
2583
2584   }
2585
2586   public void textColour_actionPerformed()
2587   {
2588
2589   }
2590
2591   public void idRightAlign_actionPerformed(ActionEvent e)
2592   {
2593
2594   }
2595
2596   public void expandViews_actionPerformed(ActionEvent e)
2597   {
2598
2599   }
2600
2601   public void gatherViews_actionPerformed(ActionEvent e)
2602   {
2603
2604   }
2605
2606   public void buildTreeSortMenu()
2607   {
2608
2609   }
2610
2611   public void pageSetup_actionPerformed(ActionEvent e)
2612   {
2613
2614   }
2615
2616   public void alignmentProperties()
2617   {
2618
2619   }
2620
2621   protected void expand_newalign(ActionEvent e)
2622   {
2623     // TODO Auto-generated method stub
2624
2625   }
2626
2627   protected boolean isShowAutoCalculatedAbove()
2628   {
2629     return showAutoCalculatedAbove;
2630   }
2631
2632   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2633   {
2634     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2635   }
2636
2637   protected SequenceAnnotationOrder getAnnotationSortOrder()
2638   {
2639     return annotationSortOrder;
2640   }
2641
2642   protected void setAnnotationSortOrder(
2643           SequenceAnnotationOrder annotationSortOrder)
2644   {
2645     this.annotationSortOrder = annotationSortOrder;
2646   }
2647
2648   public Map<KeyStroke, JMenuItem> getAccelerators()
2649   {
2650     return this.accelerators;
2651   }
2652
2653   /**
2654    * Returns the selected index of the tabbed pane, or -1 if none selected
2655    * (including the case where the tabbed pane has not been made visible).
2656    *
2657    * @return
2658    */
2659   public int getTabIndex()
2660   {
2661     return tabbedPane.getSelectedIndex();
2662   }
2663
2664   public JPanel getStatusPanel()
2665   {
2666     return statusPanel;
2667   }
2668
2669   /**
2670    * Sets a reference to the containing split frame. Also makes the 'toggle
2671    * split view' menu item visible and checked.
2672    *
2673    * @param sf
2674    */
2675   public void setSplitFrame(SplitContainerI sf)
2676   {
2677     this.splitFrame = sf;
2678     if (sf != null)
2679     {
2680       this.showComplementMenuItem.setVisible(true);
2681       this.showComplementMenuItem.setState(true);
2682     }
2683   }
2684
2685   public SplitContainerI getSplitViewContainer()
2686   {
2687     return this.splitFrame;
2688   }
2689
2690   protected void showComplement_actionPerformed(boolean complement)
2691   {
2692   }
2693 }