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