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 JMenuItem loadVcf;
 151
 152   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 153
 154   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 155
 156   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 157
 158   protected JPanel statusPanel = new JPanel();
 159
 160   protected JMenuItem showAllSeqAnnotations = new JMenuItem();
 161
 162   protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
 163
 164   protected JMenuItem showAllAlAnnotations = new JMenuItem();
 165
 166   protected JMenuItem hideAllAlAnnotations = new JMenuItem();
 167
 168   protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
 169
 170   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 171
 172   protected JTabbedPane tabbedPane = new JTabbedPane();
 173
 174   protected JMenuItem reload = new JMenuItem();
 175
 176   protected JMenu formatMenu = new JMenu();
 177
 178   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 179
 180   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 181
 182   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 183
 184   protected JMenuItem gatherViews = new JMenuItem();
 185
 186   protected JMenuItem expandViews = new JMenuItem();
 187
 188   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 189
 190   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 191
 192   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 193
 194   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 195
 196   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 197
 198   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 199
 200   private SequenceAnnotationOrder annotationSortOrder;
 201
 202   private boolean showAutoCalculatedAbove = false;
 203
 204   private Map<KeyStroke, JMenuItem> accelerators = new HashMap<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,
 266             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
 267                     | KeyEvent.SHIFT_MASK,
 268             false);
 269     addMenuActionAndAccelerator(keyStroke, saveAs, al);
 270
 271     closeMenuItem.setText(MessageManager.getString("action.close"));
 272     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
 273             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 274     al = new ActionListener()
 275     {
 276       @Override
 277       public void actionPerformed(ActionEvent e)
 278       {
 279         closeMenuItem_actionPerformed(false);
 280       }
 281     };
 282     addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
 283
 284     JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
 285     JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
 286     JMenu annotationsMenu = new JMenu(
 287             MessageManager.getString("action.annotations"));
 288     JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
 289     colourMenu.setText(MessageManager.getString("action.colour"));
 290     JMenu calculateMenu = new JMenu(
 291             MessageManager.getString("action.calculate"));
 292     webService.setText(MessageManager.getString("action.web_service"));
 293     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
 294             MessageManager.getString("action.select_all"));
 295     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
 296             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 297     al = new ActionListener()
 298     {
 299       @Override
 300       public void actionPerformed(ActionEvent e)
 301       {
 302         selectAllSequenceMenuItem_actionPerformed(e);
 303       }
 304     };
 305     addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
 306
 307     JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
 308             MessageManager.getString("action.deselect_all"));
 309     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
 310     al = new ActionListener()
 311     {
 312       @Override
 313       public void actionPerformed(ActionEvent e)
 314       {
 315         deselectAllSequenceMenuItem_actionPerformed(e);
 316       }
 317     };
 318     addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
 319
 320     JMenuItem invertSequenceMenuItem = new JMenuItem(
 321             MessageManager.getString("action.invert_sequence_selection"));
 322     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
 323             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 324     al = new ActionListener()
 325     {
 326       @Override
 327       public void actionPerformed(ActionEvent e)
 328       {
 329         invertSequenceMenuItem_actionPerformed(e);
 330       }
 331     };
 332     addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
 333
 334     JMenuItem grpsFromSelection = new JMenuItem(
 335             MessageManager.getString("action.make_groups_selection"));
 336     grpsFromSelection.addActionListener(new ActionListener()
 337     {
 338       @Override
 339       public void actionPerformed(ActionEvent e)
 340       {
 341         makeGrpsFromSelection_actionPerformed(e);
 342       }
 343     });
 344     JMenuItem expandAlignment = new JMenuItem(
 345             MessageManager.getString("action.view_flanking_regions"));
 346     expandAlignment.setToolTipText(
 347             MessageManager.getString("label.view_flanking_regions"));
 348     expandAlignment.addActionListener(new ActionListener()
 349     {
 350       @Override
 351       public void actionPerformed(ActionEvent e)
 352       {
 353         expand_newalign(e);
 354       }
 355     });
 356     JMenuItem remove2LeftMenuItem = new JMenuItem(
 357             MessageManager.getString("action.remove_left"));
 358     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
 359             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 360     al = new ActionListener()
 361     {
 362       @Override
 363       public void actionPerformed(ActionEvent e)
 364       {
 365         remove2LeftMenuItem_actionPerformed(e);
 366       }
 367     };
 368     addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
 369
 370     JMenuItem remove2RightMenuItem = new JMenuItem(
 371             MessageManager.getString("action.remove_right"));
 372     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
 373             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 374     al = new ActionListener()
 375     {
 376       @Override
 377       public void actionPerformed(ActionEvent e)
 378       {
 379         remove2RightMenuItem_actionPerformed(e);
 380       }
 381     };
 382     addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
 383
 384     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
 385             MessageManager.getString("action.remove_empty_columns"));
 386     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
 387             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 388     al = new ActionListener()
 389     {
 390       @Override
 391       public void actionPerformed(ActionEvent e)
 392       {
 393         removeGappedColumnMenuItem_actionPerformed(e);
 394       }
 395     };
 396     addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
 397
 398     JMenuItem removeAllGapsMenuItem = new JMenuItem(
 399             MessageManager.getString("action.remove_all_gaps"));
 400     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
 401             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
 402                     | KeyEvent.SHIFT_MASK,
 403             false);
 404     al = new ActionListener()
 405     {
 406       @Override
 407       public void actionPerformed(ActionEvent e)
 408       {
 409         removeAllGapsMenuItem_actionPerformed(e);
 410       }
 411     };
 412     addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
 413
 414     JMenuItem justifyLeftMenuItem = new JMenuItem(
 415             MessageManager.getString("action.left_justify_alignment"));
 416     justifyLeftMenuItem.addActionListener(new ActionListener()
 417     {
 418       @Override
 419       public void actionPerformed(ActionEvent e)
 420       {
 421         justifyLeftMenuItem_actionPerformed(e);
 422       }
 423     });
 424     JMenuItem justifyRightMenuItem = new JMenuItem(
 425             MessageManager.getString("action.right_justify_alignment"));
 426     justifyRightMenuItem.addActionListener(new ActionListener()
 427     {
 428       @Override
 429       public void actionPerformed(ActionEvent e)
 430       {
 431         justifyRightMenuItem_actionPerformed(e);
 432       }
 433     });
 434     viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
 435     viewBoxesMenuItem.setState(true);
 436     viewBoxesMenuItem.addActionListener(new ActionListener()
 437     {
 438       @Override
 439       public void actionPerformed(ActionEvent e)
 440       {
 441         viewBoxesMenuItem_actionPerformed(e);
 442       }
 443     });
 444     viewTextMenuItem.setText(MessageManager.getString("action.text"));
 445     viewTextMenuItem.setState(true);
 446     viewTextMenuItem.addActionListener(new ActionListener()
 447     {
 448       @Override
 449       public void actionPerformed(ActionEvent e)
 450       {
 451         viewTextMenuItem_actionPerformed(e);
 452       }
 453     });
 454     showNonconservedMenuItem
 455             .setText(MessageManager.getString("label.show_non_conserved"));
 456     showNonconservedMenuItem.setState(false);
 457     showNonconservedMenuItem.addActionListener(new ActionListener()
 458     {
 459       @Override
 460       public void actionPerformed(ActionEvent e)
 461       {
 462         showUnconservedMenuItem_actionPerformed(e);
 463       }
 464     });
 465     JMenuItem sortPairwiseMenuItem = new JMenuItem(
 466             MessageManager.getString("action.by_pairwise_id"));
 467     sortPairwiseMenuItem.addActionListener(new ActionListener()
 468     {
 469       @Override
 470       public void actionPerformed(ActionEvent e)
 471       {
 472         sortPairwiseMenuItem_actionPerformed(e);
 473       }
 474     });
 475     JMenuItem sortIDMenuItem = new JMenuItem(
 476             MessageManager.getString("action.by_id"));
 477     sortIDMenuItem.addActionListener(new ActionListener()
 478     {
 479       @Override
 480       public void actionPerformed(ActionEvent e)
 481       {
 482         sortIDMenuItem_actionPerformed(e);
 483       }
 484     });
 485     JMenuItem sortLengthMenuItem = new JMenuItem(
 486             MessageManager.getString("action.by_length"));
 487     sortLengthMenuItem.addActionListener(new ActionListener()
 488     {
 489       @Override
 490       public void actionPerformed(ActionEvent e)
 491       {
 492         sortLengthMenuItem_actionPerformed(e);
 493       }
 494     });
 495     JMenuItem sortGroupMenuItem = new JMenuItem(
 496             MessageManager.getString("action.by_group"));
 497     sortGroupMenuItem.addActionListener(new ActionListener()
 498     {
 499       @Override
 500       public void actionPerformed(ActionEvent e)
 501       {
 502         sortGroupMenuItem_actionPerformed(e);
 503       }
 504     });
 505
 506     JMenuItem removeRedundancyMenuItem = new JMenuItem(
 507             MessageManager.getString("action.remove_redundancy"));
 508     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
 509             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 510     al = new ActionListener()
 511     {
 512       @Override
 513       public void actionPerformed(ActionEvent e)
 514       {
 515         removeRedundancyMenuItem_actionPerformed(e);
 516       }
 517     };
 518     addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
 519
 520     JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
 521             MessageManager.getString("action.pairwise_alignment"));
 522     pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
 523     {
 524       @Override
 525       public void actionPerformed(ActionEvent e)
 526       {
 527         pairwiseAlignmentMenuItem_actionPerformed(e);
 528       }
 529     });
 530
 531     this.getContentPane().setLayout(new BorderLayout());
 532     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 533     statusBar.setBackground(Color.white);
 534     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 535     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 536     statusBar.setText(MessageManager.getString("label.status_bar"));
 537     outputTextboxMenu
 538             .setText(MessageManager.getString("label.out_to_textbox"));
 539
 540     annotationPanelMenuItem.setActionCommand("");
 541     annotationPanelMenuItem
 542             .setText(MessageManager.getString("label.show_annotations"));
 543     annotationPanelMenuItem
 544             .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
 545     annotationPanelMenuItem.addActionListener(new ActionListener()
 546     {
 547       @Override
 548       public void actionPerformed(ActionEvent e)
 549       {
 550         annotationPanelMenuItem_actionPerformed(e);
 551       }
 552     });
 553     showAllAlAnnotations.setText(
 554             MessageManager.getString("label.show_all_al_annotations"));
 555     final boolean isAnnotationPanelShown = annotationPanelMenuItem
 556             .getState();
 557     showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 558     showAllAlAnnotations.addActionListener(new ActionListener()
 559     {
 560       @Override
 561       public void actionPerformed(ActionEvent e)
 562       {
 563         showAllAnnotations_actionPerformed(false, true);
 564       }
 565     });
 566     hideAllAlAnnotations.setText(
 567             MessageManager.getString("label.hide_all_al_annotations"));
 568     hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 569     hideAllAlAnnotations.addActionListener(new ActionListener()
 570     {
 571       @Override
 572       public void actionPerformed(ActionEvent e)
 573       {
 574         hideAllAnnotations_actionPerformed(false, true);
 575       }
 576     });
 577     showAllSeqAnnotations.setText(
 578             MessageManager.getString("label.show_all_seq_annotations"));
 579     showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 580     showAllSeqAnnotations.addActionListener(new ActionListener()
 581     {
 582       @Override
 583       public void actionPerformed(ActionEvent e)
 584       {
 585         showAllAnnotations_actionPerformed(true, false);
 586       }
 587     });
 588     hideAllSeqAnnotations.setText(
 589             MessageManager.getString("label.hide_all_seq_annotations"));
 590     hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 591     hideAllSeqAnnotations.addActionListener(new ActionListener()
 592     {
 593       @Override
 594       public void actionPerformed(ActionEvent e)
 595       {
 596         hideAllAnnotations_actionPerformed(true, false);
 597       }
 598     });
 599     SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
 600             .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
 601                     SequenceAnnotationOrder.NONE.name()));
 602     final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
 603             MessageManager.getString("label.sort_annotations_by_sequence"));
 604     final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
 605             MessageManager.getString("label.sort_annotations_by_label"));
 606
 607     sortAnnBySequence.setSelected(
 608             sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
 609     sortAnnBySequence.addActionListener(new ActionListener()
 610     {
 611       @Override
 612       public void actionPerformed(ActionEvent e)
 613       {
 614         boolean newState = sortAnnBySequence.getState();
 615         sortAnnByLabel.setSelected(false);
 616         setAnnotationSortOrder(
 617                 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 618                         : SequenceAnnotationOrder.NONE);
 619         sortAnnotations_actionPerformed();
 620       }
 621     });
 622     sortAnnByLabel.setSelected(
 623             sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
 624     sortAnnByLabel.addActionListener(new ActionListener()
 625     {
 626       @Override
 627       public void actionPerformed(ActionEvent e)
 628       {
 629         boolean newState = sortAnnByLabel.getState();
 630         sortAnnBySequence.setSelected(false);
 631         setAnnotationSortOrder(
 632                 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 633                         : SequenceAnnotationOrder.NONE);
 634         sortAnnotations_actionPerformed();
 635       }
 636     });
 637     colourTextMenuItem = new JCheckBoxMenuItem(
 638             MessageManager.getString("label.colour_text"));
 639     colourTextMenuItem.addActionListener(new ActionListener()
 640     {
 641       @Override
 642       public void actionPerformed(ActionEvent e)
 643       {
 644         colourTextMenuItem_actionPerformed(e);
 645       }
 646     });
 647
 648     JMenuItem htmlMenuItem = new JMenuItem(
 649             MessageManager.getString("label.html"));
 650     htmlMenuItem.addActionListener(new ActionListener()
 651     {
 652       @Override
 653       public void actionPerformed(ActionEvent e)
 654       {
 655         htmlMenuItem_actionPerformed(e);
 656       }
 657     });
 658
 659     JMenuItem createBioJS = new JMenuItem(
 660             MessageManager.getString("label.biojs_html_export"));
 661     createBioJS.addActionListener(new java.awt.event.ActionListener()
 662     {
 663       @Override
 664       public void actionPerformed(ActionEvent e)
 665       {
 666         bioJSMenuItem_actionPerformed(e);
 667       }
 668     });
 669
 670     JMenuItem overviewMenuItem = new JMenuItem(
 671             MessageManager.getString("label.overview_window"));
 672     overviewMenuItem.addActionListener(new ActionListener()
 673     {
 674       @Override
 675       public void actionPerformed(ActionEvent e)
 676       {
 677         overviewMenuItem_actionPerformed(e);
 678       }
 679     });
 680
 681     undoMenuItem.setEnabled(false);
 682     undoMenuItem.setText(MessageManager.getString("action.undo"));
 683     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
 684             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 685     al = new ActionListener()
 686     {
 687       @Override
 688       public void actionPerformed(ActionEvent e)
 689       {
 690         undoMenuItem_actionPerformed(e);
 691       }
 692     };
 693     addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
 694
 695     redoMenuItem.setEnabled(false);
 696     redoMenuItem.setText(MessageManager.getString("action.redo"));
 697     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
 698             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 699     al = new ActionListener()
 700     {
 701       @Override
 702       public void actionPerformed(ActionEvent e)
 703       {
 704         redoMenuItem_actionPerformed(e);
 705       }
 706     };
 707     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
 708
 709     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
 710     wrapMenuItem.addActionListener(new ActionListener()
 711     {
 712       @Override
 713       public void actionPerformed(ActionEvent e)
 714       {
 715         wrapMenuItem_actionPerformed(e);
 716       }
 717     });
 718
 719     JMenuItem printMenuItem = new JMenuItem(
 720             MessageManager.getString("action.print"));
 721     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
 722             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 723     al = new ActionListener()
 724     {
 725       @Override
 726       public void actionPerformed(ActionEvent e)
 727       {
 728         printMenuItem_actionPerformed(e);
 729       }
 730     };
 731     addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
 732
 733     renderGapsMenuItem
 734             .setText(MessageManager.getString("action.show_gaps"));
 735     renderGapsMenuItem.setState(true);
 736     renderGapsMenuItem.addActionListener(new ActionListener()
 737     {
 738       @Override
 739       public void actionPerformed(ActionEvent e)
 740       {
 741         renderGapsMenuItem_actionPerformed(e);
 742       }
 743     });
 744
 745     JMenuItem findMenuItem = new JMenuItem(
 746             MessageManager.getString("action.find"));
 747     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
 748             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 749     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
 750             MessageManager.getString("label.find_tip")));
 751     al = new ActionListener()
 752     {
 753       @Override
 754       public void actionPerformed(ActionEvent e)
 755       {
 756         findMenuItem_actionPerformed(e);
 757       }
 758     };
 759     addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
 760
 761     showSeqFeatures.setText(
 762             MessageManager.getString("label.show_sequence_features"));
 763     showSeqFeatures.addActionListener(new ActionListener()
 764     {
 765       @Override
 766       public void actionPerformed(ActionEvent actionEvent)
 767       {
 768         showSeqFeatures_actionPerformed(actionEvent);
 769       }
 770     });
 771     /*
 772      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
 773      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
 774      * void actionPerformed(ActionEvent actionEvent) {
 775      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
 776      */
 777     showDbRefsMenuitem
 778             .setText(MessageManager.getString("label.show_database_refs"));
 779     showDbRefsMenuitem.addActionListener(new ActionListener()
 780     {
 781
 782       @Override
 783       public void actionPerformed(ActionEvent e)
 784       {
 785         showDbRefs_actionPerformed(e);
 786       }
 787
 788     });
 789     showNpFeatsMenuitem.setText(
 790             MessageManager.getString("label.show_non_positional_features"));
 791     showNpFeatsMenuitem.addActionListener(new ActionListener()
 792     {
 793
 794       @Override
 795       public void actionPerformed(ActionEvent e)
 796       {
 797         showNpFeats_actionPerformed(e);
 798       }
 799
 800     });
 801     showGroupConservation
 802             .setText(MessageManager.getString("label.group_conservation"));
 803     showGroupConservation.addActionListener(new ActionListener()
 804     {
 805
 806       @Override
 807       public void actionPerformed(ActionEvent e)
 808       {
 809         showGroupConservation_actionPerformed(e);
 810       }
 811
 812     });
 813
 814     showGroupConsensus
 815             .setText(MessageManager.getString("label.group_consensus"));
 816     showGroupConsensus.addActionListener(new ActionListener()
 817     {
 818
 819       @Override
 820       public void actionPerformed(ActionEvent e)
 821       {
 822         showGroupConsensus_actionPerformed(e);
 823       }
 824
 825     });
 826     showConsensusHistogram.setText(
 827             MessageManager.getString("label.show_consensus_histogram"));
 828     showConsensusHistogram.addActionListener(new ActionListener()
 829     {
 830
 831       @Override
 832       public void actionPerformed(ActionEvent e)
 833       {
 834         showConsensusHistogram_actionPerformed(e);
 835       }
 836
 837     });
 838     showSequenceLogo
 839             .setText(MessageManager.getString("label.show_consensus_logo"));
 840     showSequenceLogo.addActionListener(new ActionListener()
 841     {
 842
 843       @Override
 844       public void actionPerformed(ActionEvent e)
 845       {
 846         showSequenceLogo_actionPerformed(e);
 847       }
 848
 849     });
 850     normaliseSequenceLogo
 851             .setText(MessageManager.getString("label.norm_consensus_logo"));
 852     normaliseSequenceLogo.addActionListener(new ActionListener()
 853     {
 854
 855       @Override
 856       public void actionPerformed(ActionEvent e)
 857       {
 858         normaliseSequenceLogo_actionPerformed(e);
 859       }
 860
 861     });
 862     applyAutoAnnotationSettings
 863             .setText(MessageManager.getString("label.apply_all_groups"));
 864     applyAutoAnnotationSettings.setState(false);
 865     applyAutoAnnotationSettings.setVisible(true);
 866     applyAutoAnnotationSettings.addActionListener(new ActionListener()
 867     {
 868       @Override
 869       public void actionPerformed(ActionEvent e)
 870       {
 871         applyAutoAnnotationSettings_actionPerformed(e);
 872       }
 873     });
 874
 875     ButtonGroup buttonGroup = new ButtonGroup();
 876     final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
 877             MessageManager.getString("label.show_first"));
 878     final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
 879             MessageManager.getString("label.show_last"));
 880     buttonGroup.add(showAutoFirst);
 881     buttonGroup.add(showAutoLast);
 882     final boolean autoFirst = Cache
 883             .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
 884     showAutoFirst.setSelected(autoFirst);
 885     setShowAutoCalculatedAbove(autoFirst);
 886     showAutoFirst.addActionListener(new ActionListener()
 887     {
 888       @Override
 889       public void actionPerformed(ActionEvent e)
 890       {
 891         setShowAutoCalculatedAbove(showAutoFirst.isSelected());
 892         sortAnnotations_actionPerformed();
 893       }
 894     });
 895     showAutoLast.setSelected(!showAutoFirst.isSelected());
 896     showAutoLast.addActionListener(new ActionListener()
 897     {
 898       @Override
 899       public void actionPerformed(ActionEvent e)
 900       {
 901         setShowAutoCalculatedAbove(!showAutoLast.isSelected());
 902         sortAnnotations_actionPerformed();
 903       }
 904     });
 905
 906     JMenuItem deleteGroups = new JMenuItem(
 907             MessageManager.getString("action.undefine_groups"));
 908     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
 909             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 910     al = new ActionListener()
 911     {
 912       @Override
 913       public void actionPerformed(ActionEvent e)
 914       {
 915         deleteGroups_actionPerformed(e);
 916       }
 917     };
 918     addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
 919
 920     JMenuItem annotationColumn = new JMenuItem(
 921             MessageManager.getString("action.select_by_annotation"));
 922     annotationColumn.addActionListener(new ActionListener()
 923     {
 924       @Override
 925       public void actionPerformed(ActionEvent e)
 926       {
 927         annotationColumn_actionPerformed(e);
 928       }
 929     });
 930
 931     JMenuItem createGroup = new JMenuItem(
 932             MessageManager.getString("action.create_group"));
 933     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
 934             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 935     al = new ActionListener()
 936     {
 937       @Override
 938       public void actionPerformed(ActionEvent e)
 939       {
 940         createGroup_actionPerformed(e);
 941       }
 942     };
 943     addMenuActionAndAccelerator(keyStroke, createGroup, al);
 944
 945     JMenuItem unGroup = new JMenuItem(
 946             MessageManager.getString("action.remove_group"));
 947     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
 948             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
 949                     | KeyEvent.SHIFT_MASK,
 950             false);
 951     al = new ActionListener()
 952     {
 953       @Override
 954       public void actionPerformed(ActionEvent e)
 955       {
 956         unGroup_actionPerformed(e);
 957       }
 958     };
 959     addMenuActionAndAccelerator(keyStroke, unGroup, al);
 960
 961     copy.setText(MessageManager.getString("action.copy"));
 962     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
 963             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 964
 965     al = new ActionListener()
 966     {
 967       @Override
 968       public void actionPerformed(ActionEvent e)
 969       {
 970         copy_actionPerformed(e);
 971       }
 972     };
 973     addMenuActionAndAccelerator(keyStroke, copy, al);
 974
 975     cut.setText(MessageManager.getString("action.cut"));
 976     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
 977             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 978     al = new ActionListener()
 979     {
 980       @Override
 981       public void actionPerformed(ActionEvent e)
 982       {
 983         cut_actionPerformed(e);
 984       }
 985     };
 986     addMenuActionAndAccelerator(keyStroke, cut, al);
 987
 988     JMenuItem delete = new JMenuItem(
 989             MessageManager.getString("action.delete"));
 990     delete.addActionListener(new ActionListener()
 991     {
 992       @Override
 993       public void actionPerformed(ActionEvent e)
 994       {
 995         delete_actionPerformed(e);
 996       }
 997     });
 998
 999     pasteMenu.setText(MessageManager.getString("action.paste"));
1000     JMenuItem pasteNew = new JMenuItem(
1001             MessageManager.getString("label.to_new_alignment"));
1002     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1003             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1004                     | KeyEvent.SHIFT_MASK,
1005             false);
1006     al = new ActionListener()
1007     {
1008       @Override
1009       public void actionPerformed(ActionEvent e)
1010       {
1011         pasteNew_actionPerformed(e);
1012       }
1013     };
1014     addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1015
1016     JMenuItem pasteThis = new JMenuItem(
1017             MessageManager.getString("label.to_this_alignment"));
1018     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1019             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1020     al = new ActionListener()
1021     {
1022       @Override
1023       public void actionPerformed(ActionEvent e)
1024       {
1025         pasteThis_actionPerformed(e);
1026       }
1027     };
1028     addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1029
1030     JMenuItem createPNG = new JMenuItem("PNG");
1031     createPNG.addActionListener(new ActionListener()
1032     {
1033       @Override
1034       public void actionPerformed(ActionEvent e)
1035       {
1036         createPNG(null);
1037       }
1038     });
1039     createPNG.setActionCommand(
1040             MessageManager.getString("label.save_png_image"));
1041
1042     JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1043     font.addActionListener(new ActionListener()
1044     {
1045       @Override
1046       public void actionPerformed(ActionEvent e)
1047       {
1048         font_actionPerformed(e);
1049       }
1050     });
1051     seqLimits.setText(
1052             MessageManager.getString("label.show_sequence_limits"));
1053     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1054     seqLimits.addActionListener(new ActionListener()
1055     {
1056       @Override
1057       public void actionPerformed(ActionEvent e)
1058       {
1059         seqLimit_actionPerformed(e);
1060       }
1061     });
1062     JMenuItem epsFile = new JMenuItem("EPS");
1063     epsFile.addActionListener(new ActionListener()
1064     {
1065       @Override
1066       public void actionPerformed(ActionEvent e)
1067       {
1068         createEPS(null);
1069       }
1070     });
1071
1072     JMenuItem createSVG = new JMenuItem("SVG");
1073     createSVG.addActionListener(new ActionListener()
1074     {
1075       @Override
1076       public void actionPerformed(ActionEvent e)
1077       {
1078         createSVG(null);
1079       }
1080     });
1081
1082     JMenuItem loadTreeMenuItem = new JMenuItem(
1083             MessageManager.getString("label.load_associated_tree"));
1084     loadTreeMenuItem.setActionCommand(
1085             MessageManager.getString("label.load_tree_for_sequence_set"));
1086     loadTreeMenuItem.addActionListener(new ActionListener()
1087     {
1088       @Override
1089       public void actionPerformed(ActionEvent e)
1090       {
1091         loadTreeMenuItem_actionPerformed(e);
1092       }
1093     });
1094
1095     scaleAbove.setVisible(false);
1096     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1097     scaleAbove.addActionListener(new ActionListener()
1098     {
1099       @Override
1100       public void actionPerformed(ActionEvent e)
1101       {
1102         scaleAbove_actionPerformed(e);
1103       }
1104     });
1105     scaleLeft.setVisible(false);
1106     scaleLeft.setSelected(true);
1107     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1108     scaleLeft.addActionListener(new ActionListener()
1109     {
1110       @Override
1111       public void actionPerformed(ActionEvent e)
1112       {
1113         scaleLeft_actionPerformed(e);
1114       }
1115     });
1116     scaleRight.setVisible(false);
1117     scaleRight.setSelected(true);
1118     scaleRight.setText(MessageManager.getString("action.scale_right"));
1119     scaleRight.addActionListener(new ActionListener()
1120     {
1121       @Override
1122       public void actionPerformed(ActionEvent e)
1123       {
1124         scaleRight_actionPerformed(e);
1125       }
1126     });
1127     centreColumnLabelsMenuItem.setVisible(true);
1128     centreColumnLabelsMenuItem.setState(false);
1129     centreColumnLabelsMenuItem.setText(
1130             MessageManager.getString("label.centre_column_labels"));
1131     centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1132     {
1133       @Override
1134       public void actionPerformed(ActionEvent e)
1135       {
1136         centreColumnLabels_actionPerformed(e);
1137       }
1138     });
1139     followHighlightMenuItem.setVisible(true);
1140     followHighlightMenuItem.setState(true);
1141     followHighlightMenuItem
1142             .setText(MessageManager.getString("label.automatic_scrolling"));
1143     followHighlightMenuItem.addActionListener(new ActionListener()
1144     {
1145
1146       @Override
1147       public void actionPerformed(ActionEvent e)
1148       {
1149         followHighlight_actionPerformed();
1150       }
1151
1152     });
1153
1154     sortByTreeMenu
1155             .setText(MessageManager.getString("action.by_tree_order"));
1156     sort.setText(MessageManager.getString("action.sort"));
1157     sort.addMenuListener(new MenuListener()
1158     {
1159       @Override
1160       public void menuSelected(MenuEvent e)
1161       {
1162         buildTreeSortMenu();
1163       }
1164
1165       @Override
1166       public void menuDeselected(MenuEvent e)
1167       {
1168       }
1169
1170       @Override
1171       public void menuCanceled(MenuEvent e)
1172       {
1173       }
1174     });
1175     sortByAnnotScore
1176             .setText(MessageManager.getString("label.sort_by_score"));
1177     sort.add(sortByAnnotScore);
1178     sort.addMenuListener(new javax.swing.event.MenuListener()
1179     {
1180
1181       @Override
1182       public void menuCanceled(MenuEvent e)
1183       {
1184       }
1185
1186       @Override
1187       public void menuDeselected(MenuEvent e)
1188       {
1189       }
1190
1191       @Override
1192       public void menuSelected(MenuEvent e)
1193       {
1194         buildSortByAnnotationScoresMenu();
1195       }
1196     });
1197     sortByAnnotScore.setVisible(false);
1198
1199     calculateTree
1200             .setText(MessageManager.getString("action.calculate_tree_pca"));
1201
1202     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1203     padGapsMenuitem
1204             .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
1205     padGapsMenuitem.addActionListener(new ActionListener()
1206     {
1207       @Override
1208       public void actionPerformed(ActionEvent e)
1209       {
1210         padGapsMenuitem_actionPerformed(e);
1211       }
1212     });
1213     JMenuItem vamsasStore = new JMenuItem(
1214             MessageManager.getString("label.vamsas_store"));
1215     vamsasStore.setVisible(false);
1216     vamsasStore.addActionListener(new ActionListener()
1217     {
1218       @Override
1219       public void actionPerformed(ActionEvent e)
1220       {
1221         vamsasStore_actionPerformed(e);
1222       }
1223     });
1224     showTranslation
1225             .setText(MessageManager.getString("label.translate_cDNA"));
1226     showTranslation.addActionListener(new ActionListener()
1227     {
1228       @Override
1229       public void actionPerformed(ActionEvent e)
1230       {
1231         showTranslation_actionPerformed(e);
1232       }
1233     });
1234     showReverse.setText(MessageManager.getString("label.reverse"));
1235     showReverse.addActionListener(new ActionListener()
1236     {
1237       @Override
1238       public void actionPerformed(ActionEvent e)
1239       {
1240         showReverse_actionPerformed(false);
1241       }
1242     });
1243     showReverseComplement
1244             .setText(MessageManager.getString("label.reverse_complement"));
1245     showReverseComplement.addActionListener(new ActionListener()
1246     {
1247       @Override
1248       public void actionPerformed(ActionEvent e)
1249       {
1250         showReverse_actionPerformed(true);
1251       }
1252     });
1253
1254     JMenuItem extractScores = new JMenuItem(
1255             MessageManager.getString("label.extract_scores"));
1256     extractScores.addActionListener(new ActionListener()
1257     {
1258       @Override
1259       public void actionPerformed(ActionEvent e)
1260       {
1261         extractScores_actionPerformed(e);
1262       }
1263     });
1264     extractScores.setVisible(true);
1265     // JBPNote: TODO: make gui for regex based score extraction
1266
1267     // for show products actions see AlignFrame.canShowProducts
1268     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1269
1270     runGroovy.setText(MessageManager.getString("label.run_groovy"));
1271     runGroovy.setToolTipText(
1272             MessageManager.getString("label.run_groovy_tip"));
1273     runGroovy.addActionListener(new ActionListener()
1274     {
1275       @Override
1276       public void actionPerformed(ActionEvent e)
1277       {
1278         runGroovy_actionPerformed();
1279       }
1280     });
1281
1282     JMenuItem openFeatureSettings = new JMenuItem(
1283             MessageManager.getString("action.feature_settings"));
1284     openFeatureSettings.addActionListener(new ActionListener()
1285     {
1286       @Override
1287       public void actionPerformed(ActionEvent e)
1288       {
1289         featureSettings_actionPerformed(e);
1290       }
1291     });
1292     JMenuItem fetchSequence = new JMenuItem(
1293             MessageManager.getString("label.fetch_sequences"));
1294     fetchSequence.addActionListener(new ActionListener()
1295     {
1296       @Override
1297       public void actionPerformed(ActionEvent e)
1298       {
1299         fetchSequence_actionPerformed(e);
1300       }
1301     });
1302
1303     JMenuItem associatedData = new JMenuItem(
1304             MessageManager.getString("label.load_features_annotations"));
1305     associatedData.addActionListener(new ActionListener()
1306     {
1307       @Override
1308       public void actionPerformed(ActionEvent e)
1309       {
1310         associatedData_actionPerformed(e);
1311       }
1312     });
1313     loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
1314     loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
1315     loadVcf.addActionListener(new ActionListener()
1316     {
1317       @Override
1318       public void actionPerformed(ActionEvent e)
1319       {
1320         loadVcf_actionPerformed();
1321       }
1322     });
1323     autoCalculate.setText(
1324             MessageManager.getString("label.autocalculate_consensus"));
1325     autoCalculate.setState(
1326             jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1327     autoCalculate.addActionListener(new ActionListener()
1328     {
1329       @Override
1330       public void actionPerformed(ActionEvent e)
1331       {
1332         autoCalculate_actionPerformed(e);
1333       }
1334     });
1335     sortByTree.setText(
1336             MessageManager.getString("label.sort_alignment_new_tree"));
1337     sortByTree.setToolTipText("<html>" + MessageManager.getString(
1338             "label.enable_automatically_sort_alignment_when_open_new_tree"));
1339     sortByTree
1340             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1341     sortByTree.addActionListener(new ActionListener()
1342     {
1343       @Override
1344       public void actionPerformed(ActionEvent e)
1345       {
1346         sortByTreeOption_actionPerformed(e);
1347       }
1348     });
1349
1350     listenToViewSelections.setText(
1351             MessageManager.getString("label.listen_for_selections"));
1352     listenToViewSelections
1353             .setToolTipText("<html>" + MessageManager.getString(
1354                     "label.selections_mirror_selections_made_same_sequences_other_views"));
1355     listenToViewSelections.setState(false);
1356     listenToViewSelections.addActionListener(new ActionListener()
1357     {
1358       @Override
1359       public void actionPerformed(ActionEvent e)
1360       {
1361         listenToViewSelections_actionPerformed(e);
1362       }
1363     });
1364
1365     JMenu addSequenceMenu = new JMenu(
1366             MessageManager.getString("label.add_sequences"));
1367     JMenuItem addFromFile = new JMenuItem(
1368             MessageManager.getString("label.from_file"));
1369     addFromFile.addActionListener(new ActionListener()
1370     {
1371       @Override
1372       public void actionPerformed(ActionEvent e)
1373       {
1374         addFromFile_actionPerformed(e);
1375       }
1376     });
1377     JMenuItem addFromText = new JMenuItem(
1378             MessageManager.getString("label.from_textbox"));
1379     addFromText.addActionListener(new ActionListener()
1380     {
1381       @Override
1382       public void actionPerformed(ActionEvent e)
1383       {
1384         addFromText_actionPerformed(e);
1385       }
1386     });
1387     JMenuItem addFromURL = new JMenuItem(
1388             MessageManager.getString("label.from_url"));
1389     addFromURL.addActionListener(new ActionListener()
1390     {
1391       @Override
1392       public void actionPerformed(ActionEvent e)
1393       {
1394         addFromURL_actionPerformed(e);
1395       }
1396     });
1397     JMenuItem exportFeatures = new JMenuItem(
1398             MessageManager.getString("label.export_features"));
1399     exportFeatures.addActionListener(new ActionListener()
1400     {
1401       @Override
1402       public void actionPerformed(ActionEvent e)
1403       {
1404         exportFeatures_actionPerformed(e);
1405       }
1406     });
1407     JMenuItem exportAnnotations = new JMenuItem(
1408             MessageManager.getString("label.export_annotations"));
1409     exportAnnotations.addActionListener(new ActionListener()
1410     {
1411       @Override
1412       public void actionPerformed(ActionEvent e)
1413       {
1414         exportAnnotations_actionPerformed(e);
1415       }
1416     });
1417     statusPanel.setLayout(new GridLayout());
1418     JMenuItem showAllSeqs = new JMenuItem(
1419             MessageManager.getString("label.all_sequences"));
1420     showAllSeqs.setToolTipText(
1421             MessageManager.getString("label.toggle_sequence_visibility"));
1422     showAllSeqs.addActionListener(new ActionListener()
1423     {
1424       @Override
1425       public void actionPerformed(ActionEvent e)
1426       {
1427         showAllSeqs_actionPerformed(e);
1428       }
1429     });
1430     JMenuItem showAllColumns = new JMenuItem(
1431             MessageManager.getString("label.all_columns"));
1432     showAllColumns.setToolTipText(
1433             MessageManager.getString("label.toggle_columns_visibility"));
1434     showAllColumns.addActionListener(new ActionListener()
1435     {
1436       @Override
1437       public void actionPerformed(ActionEvent e)
1438       {
1439         showAllColumns_actionPerformed(e);
1440       }
1441     });
1442     JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1443     JMenuItem hideSelSequences = new JMenuItem(
1444             MessageManager.getString("label.selected_sequences"));
1445     hideSelSequences.setToolTipText(
1446             MessageManager.getString("label.toggle_sequence_visibility"));
1447     hideSelSequences.addActionListener(new ActionListener()
1448     {
1449       @Override
1450       public void actionPerformed(ActionEvent e)
1451       {
1452         hideSelSequences_actionPerformed(e);
1453       }
1454     });
1455     JMenuItem hideSelColumns = new JMenuItem(
1456             MessageManager.getString("label.selected_columns"));
1457     hideSelColumns.setToolTipText(
1458             MessageManager.getString("label.toggle_columns_visibility"));
1459     hideSelColumns.addActionListener(new ActionListener()
1460     {
1461       @Override
1462       public void actionPerformed(ActionEvent e)
1463       {
1464         hideSelColumns_actionPerformed(e);
1465       }
1466     });
1467     JMenuItem hideAllSelection = new JMenuItem(
1468             MessageManager.getString("label.selected_region"));
1469     hideAllSelection.addActionListener(new ActionListener()
1470     {
1471       @Override
1472       public void actionPerformed(ActionEvent e)
1473       {
1474         hideAllSelection_actionPerformed(e);
1475       }
1476     });
1477     // TODO: should be hidden if no selection exists.
1478     JMenuItem hideAllButSelection = new JMenuItem(
1479             MessageManager.getString("label.all_but_selected_region"));
1480     hideAllButSelection.addActionListener(new ActionListener()
1481     {
1482       @Override
1483       public void actionPerformed(ActionEvent e)
1484       {
1485         hideAllButSelection_actionPerformed(e);
1486       }
1487     });
1488     JMenuItem showAllhidden = new JMenuItem(
1489             MessageManager.getString("label.all_sequences_columns"));
1490     showAllhidden.setToolTipText(MessageManager
1491             .getString("label.toggles_visibility_hidden_selected_regions"));
1492     showAllhidden.addActionListener(new ActionListener()
1493     {
1494       @Override
1495       public void actionPerformed(ActionEvent e)
1496       {
1497         showAllhidden_actionPerformed(e);
1498       }
1499     });
1500     hiddenMarkers.setText(
1501             MessageManager.getString("action.show_hidden_markers"));
1502     hiddenMarkers.addActionListener(new ActionListener()
1503     {
1504       @Override
1505       public void actionPerformed(ActionEvent e)
1506       {
1507         hiddenMarkers_actionPerformed(e);
1508       }
1509     });
1510
1511     JMenuItem invertColSel = new JMenuItem(
1512             MessageManager.getString("action.invert_column_selection"));
1513     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1514             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1515                     | KeyEvent.ALT_MASK,
1516             false);
1517     al = new ActionListener()
1518     {
1519       @Override
1520       public void actionPerformed(ActionEvent e)
1521       {
1522         invertColSel_actionPerformed(e);
1523       }
1524     };
1525     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1526
1527     showComplementMenuItem.setVisible(false);
1528     showComplementMenuItem.addActionListener(new ActionListener()
1529     {
1530       @Override
1531       public void actionPerformed(ActionEvent e)
1532       {
1533         showComplement_actionPerformed(showComplementMenuItem.getState());
1534       }
1535     });
1536
1537     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1538     {
1539       @Override
1540       public void stateChanged(ChangeEvent evt)
1541       {
1542         JTabbedPane pane = (JTabbedPane) evt.getSource();
1543         int sel = pane.getSelectedIndex();
1544         tabSelectionChanged(sel);
1545       }
1546     });
1547     tabbedPane.addMouseListener(new MouseAdapter()
1548     {
1549       @Override
1550       public void mousePressed(MouseEvent e)
1551       {
1552         if (e.isPopupTrigger()) // Mac
1553         {
1554           tabbedPane_mousePressed(e);
1555         }
1556       }
1557
1558       @Override
1559       public void mouseReleased(MouseEvent e)
1560       {
1561         if (e.isPopupTrigger()) // Windows
1562         {
1563           tabbedPane_mousePressed(e);
1564         }
1565       }
1566     });
1567     tabbedPane.addFocusListener(new FocusAdapter()
1568     {
1569       @Override
1570       public void focusGained(FocusEvent e)
1571       {
1572         tabbedPane_focusGained(e);
1573       }
1574     });
1575
1576     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1577     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1578             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1579     al = new ActionListener()
1580     {
1581       @Override
1582       public void actionPerformed(ActionEvent e)
1583       {
1584         save_actionPerformed(e);
1585       }
1586     };
1587     addMenuActionAndAccelerator(keyStroke, save, al);
1588
1589     reload.setEnabled(false);
1590     reload.setText(MessageManager.getString("action.reload"));
1591     reload.addActionListener(new ActionListener()
1592     {
1593       @Override
1594       public void actionPerformed(ActionEvent e)
1595       {
1596         reload_actionPerformed(e);
1597       }
1598     });
1599
1600     JMenuItem newView = new JMenuItem(
1601             MessageManager.getString("action.new_view"));
1602     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1603             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1604     al = new ActionListener()
1605     {
1606       @Override
1607       public void actionPerformed(ActionEvent e)
1608       {
1609         newView_actionPerformed(e);
1610       }
1611     };
1612     addMenuActionAndAccelerator(keyStroke, newView, al);
1613
1614     tabbedPane.setToolTipText("<html><i>"
1615             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1616             + "</i></html>");
1617
1618     formatMenu.setText(MessageManager.getString("action.format"));
1619     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1620
1621     idRightAlign.setText(
1622             MessageManager.getString("label.right_align_sequence_id"));
1623     idRightAlign.addActionListener(new ActionListener()
1624     {
1625       @Override
1626       public void actionPerformed(ActionEvent e)
1627       {
1628         idRightAlign_actionPerformed(e);
1629       }
1630     });
1631
1632     gatherViews.setEnabled(false);
1633     gatherViews.setText(MessageManager.getString("action.gather_views"));
1634     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1635     al = new ActionListener()
1636     {
1637       @Override
1638       public void actionPerformed(ActionEvent e)
1639       {
1640         gatherViews_actionPerformed(e);
1641       }
1642     };
1643     addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1644
1645     expandViews.setEnabled(false);
1646     expandViews.setText(MessageManager.getString("action.expand_views"));
1647     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1648     al = new ActionListener()
1649     {
1650       @Override
1651       public void actionPerformed(ActionEvent e)
1652       {
1653         expandViews_actionPerformed(e);
1654       }
1655     };
1656     addMenuActionAndAccelerator(keyStroke, expandViews, al);
1657
1658     JMenuItem pageSetup = new JMenuItem(
1659             MessageManager.getString("action.page_setup"));
1660     pageSetup.addActionListener(new ActionListener()
1661     {
1662       @Override
1663       public void actionPerformed(ActionEvent e)
1664       {
1665         pageSetup_actionPerformed(e);
1666       }
1667     });
1668     JMenuItem alignmentProperties = new JMenuItem(
1669             MessageManager.getString("label.alignment_props"));
1670     alignmentProperties.addActionListener(new ActionListener()
1671     {
1672       @Override
1673       public void actionPerformed(ActionEvent actionEvent)
1674       {
1675         alignmentProperties();
1676       }
1677     });
1678     JMenuItem selectHighlighted = new JMenuItem(
1679             MessageManager.getString("action.select_highlighted_columns"));
1680     selectHighlighted.setToolTipText(
1681             MessageManager.getString("tooltip.select_highlighted_columns"));
1682     al = new ActionListener()
1683     {
1684       @Override
1685       public void actionPerformed(ActionEvent actionEvent)
1686       {
1687         selectHighlightedColumns_actionPerformed(actionEvent);
1688       }
1689     };
1690     selectHighlighted.addActionListener(al);
1691     JMenu tooltipSettingsMenu = new JMenu(
1692             MessageManager.getString("label.sequence_id_tooltip"));
1693     JMenu autoAnnMenu = new JMenu(
1694             MessageManager.getString("label.autocalculated_annotation"));
1695
1696     JMenu exportImageMenu = new JMenu(
1697             MessageManager.getString("label.export_image"));
1698     JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1699     alignFrameMenuBar.add(fileMenu);
1700     alignFrameMenuBar.add(editMenu);
1701     alignFrameMenuBar.add(selectMenu);
1702     alignFrameMenuBar.add(viewMenu);
1703     alignFrameMenuBar.add(annotationsMenu);
1704     alignFrameMenuBar.add(formatMenu);
1705     alignFrameMenuBar.add(colourMenu);
1706     alignFrameMenuBar.add(calculateMenu);
1707     alignFrameMenuBar.add(webService);
1708
1709     fileMenu.add(fetchSequence);
1710     fileMenu.add(addSequenceMenu);
1711     fileMenu.add(reload);
1712     fileMenu.addSeparator();
1713     fileMenu.add(vamsasStore);
1714     fileMenu.add(save);
1715     fileMenu.add(saveAs);
1716     fileMenu.add(outputTextboxMenu);
1717     fileMenu.add(pageSetup);
1718     fileMenu.add(printMenuItem);
1719     fileMenu.addSeparator();
1720     fileMenu.add(exportImageMenu);
1721     fileMenu.add(exportFeatures);
1722     fileMenu.add(exportAnnotations);
1723     fileMenu.add(loadTreeMenuItem);
1724     fileMenu.add(associatedData);
1725     /*
1726      * No VCF import in Jalview-JS
1727      * @j2sNative
1728      */
1729     {
1730       fileMenu.add(loadVcf);
1731     }
1732     fileMenu.addSeparator();
1733     fileMenu.add(closeMenuItem);
1734
1735     pasteMenu.add(pasteNew);
1736     pasteMenu.add(pasteThis);
1737     editMenu.add(undoMenuItem);
1738     editMenu.add(redoMenuItem);
1739     editMenu.add(cut);
1740     editMenu.add(copy);
1741     editMenu.add(pasteMenu);
1742     editMenu.add(delete);
1743     editMenu.addSeparator();
1744     editMenu.add(remove2LeftMenuItem);
1745     editMenu.add(remove2RightMenuItem);
1746     editMenu.add(removeGappedColumnMenuItem);
1747     editMenu.add(removeAllGapsMenuItem);
1748     editMenu.add(removeRedundancyMenuItem);
1749     editMenu.addSeparator();
1750     // dont add these yet in the CVS build - they cannot be undone!
1751     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1752     // editMenu.add(justifyLeftMenuItem);
1753     // editMenu.add(justifyRightMenuItem);
1754     // editMenu.addSeparator();
1755     editMenu.add(padGapsMenuitem);
1756
1757     showMenu.add(showAllColumns);
1758     showMenu.add(showAllSeqs);
1759     showMenu.add(showAllhidden);
1760     hideMenu.add(hideSelColumns);
1761     hideMenu.add(hideSelSequences);
1762     hideMenu.add(hideAllSelection);
1763     hideMenu.add(hideAllButSelection);
1764     viewMenu.add(newView);
1765     viewMenu.add(expandViews);
1766     viewMenu.add(gatherViews);
1767     viewMenu.addSeparator();
1768     viewMenu.add(showMenu);
1769     viewMenu.add(hideMenu);
1770     viewMenu.add(showComplementMenuItem);
1771     viewMenu.addSeparator();
1772     viewMenu.add(followHighlightMenuItem);
1773     viewMenu.addSeparator();
1774     viewMenu.add(showSeqFeatures);
1775     // viewMenu.add(showSeqFeaturesHeight);
1776     viewMenu.add(openFeatureSettings);
1777     tooltipSettingsMenu.add(showDbRefsMenuitem);
1778     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1779     viewMenu.add(tooltipSettingsMenu);
1780     viewMenu.addSeparator();
1781     viewMenu.add(alignmentProperties);
1782     viewMenu.addSeparator();
1783     viewMenu.add(overviewMenuItem);
1784
1785     annotationsMenu.add(annotationPanelMenuItem);
1786     annotationsMenu.addSeparator();
1787     annotationsMenu.add(showAllAlAnnotations);
1788     annotationsMenu.add(hideAllAlAnnotations);
1789     annotationsMenu.addSeparator();
1790     annotationsMenu.add(showAllSeqAnnotations);
1791     annotationsMenu.add(hideAllSeqAnnotations);
1792     annotationsMenu.add(sortAnnBySequence);
1793     annotationsMenu.add(sortAnnByLabel);
1794     annotationsMenu.addSeparator();
1795     autoAnnMenu.add(showAutoFirst);
1796     autoAnnMenu.add(showAutoLast);
1797     autoAnnMenu.addSeparator();
1798     autoAnnMenu.add(applyAutoAnnotationSettings);
1799     autoAnnMenu.add(showConsensusHistogram);
1800     autoAnnMenu.add(showSequenceLogo);
1801     autoAnnMenu.add(normaliseSequenceLogo);
1802     autoAnnMenu.addSeparator();
1803     autoAnnMenu.add(showGroupConservation);
1804     autoAnnMenu.add(showGroupConsensus);
1805     annotationsMenu.add(autoAnnMenu);
1806
1807     sort.add(sortIDMenuItem);
1808     sort.add(sortLengthMenuItem);
1809     sort.add(sortGroupMenuItem);
1810     sort.add(sortPairwiseMenuItem);
1811     sort.add(sortByTreeMenu);
1812     calculateMenu.add(sort);
1813     calculateMenu.add(calculateTree);
1814     calculateMenu.addSeparator();
1815     calculateMenu.add(pairwiseAlignmentMenuItem);
1816     calculateMenu.addSeparator();
1817     calculateMenu.add(showTranslation);
1818     calculateMenu.add(showReverse);
1819     calculateMenu.add(showReverseComplement);
1820     calculateMenu.add(showProducts);
1821     calculateMenu.add(autoCalculate);
1822     calculateMenu.add(sortByTree);
1823     calculateMenu.addSeparator();
1824     calculateMenu.add(expandAlignment);
1825     calculateMenu.add(extractScores);
1826     calculateMenu.addSeparator();
1827     calculateMenu.add(runGroovy);
1828
1829     webServiceNoServices = new JMenuItem(
1830             MessageManager.getString("label.no_services"));
1831     webService.add(webServiceNoServices);
1832     exportImageMenu.add(htmlMenuItem);
1833     exportImageMenu.add(epsFile);
1834     exportImageMenu.add(createPNG);
1835     exportImageMenu.add(createBioJS);
1836     exportImageMenu.add(createSVG);
1837     addSequenceMenu.add(addFromFile);
1838     addSequenceMenu.add(addFromText);
1839     addSequenceMenu.add(addFromURL);
1840     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1841     statusPanel.add(statusBar, null);
1842     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1843
1844     formatMenu.add(font);
1845     formatMenu.addSeparator();
1846     formatMenu.add(wrapMenuItem);
1847     formatMenu.add(scaleAbove);
1848     formatMenu.add(scaleLeft);
1849     formatMenu.add(scaleRight);
1850     formatMenu.add(seqLimits);
1851     formatMenu.add(idRightAlign);
1852     formatMenu.add(hiddenMarkers);
1853     formatMenu.add(viewBoxesMenuItem);
1854     formatMenu.add(viewTextMenuItem);
1855     formatMenu.add(colourTextMenuItem);
1856     formatMenu.add(renderGapsMenuItem);
1857     formatMenu.add(centreColumnLabelsMenuItem);
1858     formatMenu.add(showNonconservedMenuItem);
1859     selectMenu.add(findMenuItem);
1860     selectMenu.addSeparator();
1861     selectMenu.add(selectAllSequenceMenuItem);
1862     selectMenu.add(deselectAllSequenceMenuItem);
1863     selectMenu.add(invertSequenceMenuItem);
1864     selectMenu.add(invertColSel);
1865     selectMenu.add(createGroup);
1866     selectMenu.add(unGroup);
1867     selectMenu.add(grpsFromSelection);
1868     selectMenu.add(deleteGroups);
1869     selectMenu.add(annotationColumn);
1870     selectMenu.add(selectHighlighted);
1871     // TODO - determine if the listenToViewSelections button is needed : see bug
1872     // JAL-574
1873     // selectMenu.addSeparator();
1874     // selectMenu.add(listenToViewSelections);
1875   }
1876
1877   protected void loadVcf_actionPerformed()
1878   {
1879   }
1880
1881   /**
1882    * Constructs the entries on the Colour menu (but does not add them to the
1883    * menu).
1884    */
1885   protected void initColourMenu()
1886   {
1887     applyToAllGroups = new JCheckBoxMenuItem(
1888             MessageManager.getString("label.apply_colour_to_all_groups"));
1889     applyToAllGroups.addActionListener(new ActionListener()
1890     {
1891       @Override
1892       public void actionPerformed(ActionEvent e)
1893       {
1894         applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1895       }
1896     });
1897
1898     textColour = new JMenuItem(
1899             MessageManager.getString("label.text_colour"));
1900     textColour.addActionListener(new ActionListener()
1901     {
1902       @Override
1903       public void actionPerformed(ActionEvent e)
1904       {
1905         textColour_actionPerformed();
1906       }
1907     });
1908
1909     conservationMenuItem = new JCheckBoxMenuItem(
1910             MessageManager.getString("action.by_conservation"));
1911     conservationMenuItem.addActionListener(new ActionListener()
1912     {
1913       @Override
1914       public void actionPerformed(ActionEvent e)
1915       {
1916         conservationMenuItem_actionPerformed(
1917                 conservationMenuItem.isSelected());
1918       }
1919     });
1920
1921     abovePIDThreshold = new JCheckBoxMenuItem(
1922             MessageManager.getString("label.above_identity_threshold"));
1923     abovePIDThreshold.addActionListener(new ActionListener()
1924     {
1925       @Override
1926       public void actionPerformed(ActionEvent e)
1927       {
1928         abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
1929       }
1930     });
1931     modifyPID = new JMenuItem(
1932             MessageManager.getString("label.modify_identity_threshold"));
1933     modifyPID.addActionListener(new ActionListener()
1934     {
1935       @Override
1936       public void actionPerformed(ActionEvent e)
1937       {
1938         modifyPID_actionPerformed();
1939       }
1940     });
1941     modifyConservation = new JMenuItem(MessageManager
1942             .getString("label.modify_conservation_threshold"));
1943     modifyConservation.addActionListener(new ActionListener()
1944     {
1945       @Override
1946       public void actionPerformed(ActionEvent e)
1947       {
1948         modifyConservation_actionPerformed();
1949       }
1950     });
1951
1952     annotationColour = new JMenuItem(
1953             MessageManager.getString("action.by_annotation"));
1954     annotationColour.addActionListener(new ActionListener()
1955     {
1956       @Override
1957       public void actionPerformed(ActionEvent e)
1958       {
1959         annotationColour_actionPerformed();
1960       }
1961     });
1962   }
1963
1964   protected void selectHighlightedColumns_actionPerformed(
1965           ActionEvent actionEvent)
1966   {
1967     // TODO Auto-generated method stub
1968
1969   }
1970
1971   /**
1972    * Generate the reverse sequence (or reverse complement if the flag is true)
1973    * and add it to the alignment
1974    *
1975    * @param complement
1976    */
1977   protected void showReverse_actionPerformed(boolean complement)
1978   {
1979   }
1980
1981   /**
1982    * Try to run script in a Groovy console, having first ensured that this
1983    * alignframe is set as currentAlignFrame in Desktop
1984    */
1985   protected void runGroovy_actionPerformed()
1986   {
1987
1988   }
1989
1990   /**
1991    * Adds the given action listener and key accelerator to the given menu item.
1992    * Also saves in a lookup table to support lookup of action by key stroke.
1993    *
1994    * @param keyStroke
1995    * @param menuItem
1996    * @param actionListener
1997    */
1998   protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
1999           JMenuItem menuItem, ActionListener actionListener)
2000   {
2001     menuItem.setAccelerator(keyStroke);
2002     accelerators.put(keyStroke, menuItem);
2003     menuItem.addActionListener(actionListener);
2004   }
2005
2006   /**
2007    * Action on clicking sort annotations by type.
2008    *
2009    * @param sortOrder
2010    */
2011   protected void sortAnnotations_actionPerformed()
2012   {
2013   }
2014
2015   /**
2016    * Action on clicking Show all annotations.
2017    *
2018    * @param forSequences
2019    *          update sequence-related annotations
2020    * @param forAlignment
2021    *          update non-sequence-related annotations
2022    */
2023   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2024           boolean forAlignment)
2025   {
2026     setAnnotationsVisibility(true, forSequences, forAlignment);
2027   }
2028
2029   /**
2030    * Action on clicking Hide all annotations.
2031    *
2032    * @param forSequences
2033    *          update sequence-related annotations
2034    * @param forAlignment
2035    *          update non-sequence-related annotations
2036    */
2037   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2038           boolean forAlignment)
2039   {
2040     setAnnotationsVisibility(false, forSequences, forAlignment);
2041   }
2042
2043   /**
2044    * Set the visibility of annotations to true or false. Can act on
2045    * sequence-related annotations, or alignment-related, or both.
2046    *
2047    * @param visible
2048    * @param forSequences
2049    *          update sequence-related annotations
2050    * @param forAlignment
2051    *          update non-sequence-related annotations
2052    */
2053   protected void setAnnotationsVisibility(boolean visible,
2054           boolean forSequences, boolean forAlignment)
2055   {
2056
2057   }
2058
2059   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2060   {
2061     // TODO Auto-generated method stub
2062
2063   }
2064
2065   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2066   {
2067     // TODO Auto-generated method stub
2068
2069   }
2070
2071   protected void showAllhidden_actionPerformed(ActionEvent e)
2072   {
2073     // TODO Auto-generated method stub
2074
2075   }
2076
2077   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2078   {
2079     // TODO Auto-generated method stub
2080
2081   }
2082
2083   protected void hideAllSelection_actionPerformed(ActionEvent e)
2084   {
2085     // TODO Auto-generated method stub
2086
2087   }
2088
2089   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2090   {
2091     // TODO Auto-generated method stub
2092
2093   }
2094
2095   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2096   {
2097     // TODO Auto-generated method stub
2098
2099   }
2100
2101   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2102   {
2103     // TODO Auto-generated method stub
2104
2105   }
2106
2107   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2108   {
2109     // TODO Auto-generated method stub
2110
2111   }
2112
2113   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2114   {
2115     // TODO Auto-generated method stub
2116
2117   }
2118
2119   protected void showGroupConservation_actionPerformed(ActionEvent e)
2120   {
2121     // TODO Auto-generated method stub
2122
2123   }
2124
2125   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2126   {
2127     // TODO Auto-generated method stub
2128
2129   }
2130
2131   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2132   {
2133     // TODO Auto-generated method stub
2134
2135   }
2136
2137   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2138   {
2139     // TODO Auto-generated method stub
2140
2141   }
2142
2143   protected void followHighlight_actionPerformed()
2144   {
2145     // TODO Auto-generated method stub
2146
2147   }
2148
2149   protected void showNpFeats_actionPerformed(ActionEvent e)
2150   {
2151     // TODO Auto-generated method stub
2152
2153   }
2154
2155   protected void showDbRefs_actionPerformed(ActionEvent e)
2156   {
2157     // TODO Auto-generated method stub
2158
2159   }
2160
2161   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2162   {
2163   }
2164
2165   protected void buildSortByAnnotationScoresMenu()
2166   {
2167   }
2168
2169   protected void extractScores_actionPerformed(ActionEvent e)
2170   {
2171   }
2172
2173   protected void outputText_actionPerformed(ActionEvent e)
2174   {
2175   }
2176
2177   public void addFromFile_actionPerformed(ActionEvent e)
2178   {
2179
2180   }
2181
2182   public void addFromText_actionPerformed(ActionEvent e)
2183   {
2184
2185   }
2186
2187   public void addFromURL_actionPerformed(ActionEvent e)
2188   {
2189
2190   }
2191
2192   public void exportFeatures_actionPerformed(ActionEvent e)
2193   {
2194
2195   }
2196
2197   public void exportAnnotations_actionPerformed(ActionEvent e)
2198   {
2199
2200   }
2201
2202   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2203   {
2204   }
2205
2206   protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2207   {
2208
2209   }
2210
2211   protected void closeMenuItem_actionPerformed(boolean b)
2212   {
2213   }
2214
2215   protected void redoMenuItem_actionPerformed(ActionEvent e)
2216   {
2217   }
2218
2219   protected void undoMenuItem_actionPerformed(ActionEvent e)
2220   {
2221   }
2222
2223   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2224   {
2225   }
2226
2227   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2228   {
2229   }
2230
2231   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2232   {
2233   }
2234
2235   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2236   {
2237   }
2238
2239   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2240   {
2241   }
2242
2243   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2244   {
2245   }
2246
2247   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2248   {
2249   }
2250
2251   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2252   {
2253   }
2254
2255   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2256   {
2257   }
2258
2259   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2260   {
2261   }
2262
2263   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2264   {
2265   }
2266
2267   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2268   {
2269   }
2270
2271   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2272   {
2273   }
2274
2275   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2276   {
2277   }
2278
2279   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2280   {
2281   }
2282
2283   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2284   {
2285   }
2286
2287   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2288   {
2289   }
2290
2291   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2292   {
2293   }
2294
2295   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2296   {
2297   }
2298
2299   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2300   {
2301   }
2302
2303   protected void conservationMenuItem_actionPerformed(boolean selected)
2304   {
2305   }
2306
2307   protected void printMenuItem_actionPerformed(ActionEvent e)
2308   {
2309   }
2310
2311   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2312   {
2313   }
2314
2315   protected void findMenuItem_actionPerformed(ActionEvent e)
2316   {
2317   }
2318
2319   protected void abovePIDThreshold_actionPerformed(boolean selected)
2320   {
2321   }
2322
2323   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2324   {
2325   }
2326
2327   protected void deleteGroups_actionPerformed(ActionEvent e)
2328   {
2329   }
2330
2331   protected void createGroup_actionPerformed(ActionEvent e)
2332   {
2333   }
2334
2335   protected void unGroup_actionPerformed(ActionEvent e)
2336   {
2337   }
2338
2339   protected void copy_actionPerformed(ActionEvent e)
2340   {
2341   }
2342
2343   protected void cut_actionPerformed(ActionEvent e)
2344   {
2345   }
2346
2347   protected void delete_actionPerformed(ActionEvent e)
2348   {
2349   }
2350
2351   protected void pasteNew_actionPerformed(ActionEvent e)
2352   {
2353   }
2354
2355   protected void pasteThis_actionPerformed(ActionEvent e)
2356   {
2357   }
2358
2359   protected void applyToAllGroups_actionPerformed(boolean selected)
2360   {
2361   }
2362
2363   public void createPNG(java.io.File f)
2364   {
2365   }
2366
2367   protected void font_actionPerformed(ActionEvent e)
2368   {
2369   }
2370
2371   protected void seqLimit_actionPerformed(ActionEvent e)
2372   {
2373   }
2374
2375   public void seqDBRef_actionPerformed(ActionEvent e)
2376   {
2377
2378   }
2379
2380   public void createEPS(java.io.File f)
2381   {
2382   }
2383
2384   public void createSVG(java.io.File f)
2385   {
2386
2387   }
2388
2389   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2390   {
2391
2392   }
2393
2394   /**
2395    * Template method to handle the 'load T-Coffee scores' menu event.
2396    * <p>
2397    * Subclasses override this method to provide a custom action.
2398    *
2399    * @param event
2400    *          The raised event
2401    */
2402   protected void loadScores_actionPerformed(ActionEvent event)
2403   {
2404
2405   }
2406
2407   protected void jpred_actionPerformed(ActionEvent e)
2408   {
2409   }
2410
2411   protected void scaleAbove_actionPerformed(ActionEvent e)
2412   {
2413   }
2414
2415   protected void scaleLeft_actionPerformed(ActionEvent e)
2416   {
2417   }
2418
2419   protected void scaleRight_actionPerformed(ActionEvent e)
2420   {
2421   }
2422
2423   protected void modifyPID_actionPerformed()
2424   {
2425   }
2426
2427   protected void modifyConservation_actionPerformed()
2428   {
2429   }
2430
2431   protected void saveAs_actionPerformed(ActionEvent e)
2432   {
2433   }
2434
2435   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2436   {
2437   }
2438
2439   public void vamsasStore_actionPerformed(ActionEvent e)
2440   {
2441
2442   }
2443
2444   public void vamsasLoad_actionPerformed(ActionEvent e)
2445   {
2446
2447   }
2448
2449   public void showTranslation_actionPerformed(ActionEvent e)
2450   {
2451
2452   }
2453
2454   public void featureSettings_actionPerformed(ActionEvent e)
2455   {
2456
2457   }
2458
2459   public void fetchSequence_actionPerformed(ActionEvent e)
2460   {
2461
2462   }
2463
2464   public void smoothFont_actionPerformed(ActionEvent e)
2465   {
2466
2467   }
2468
2469   public void annotationColour_actionPerformed()
2470   {
2471   }
2472
2473   public void annotationColumn_actionPerformed(ActionEvent e)
2474   {
2475   }
2476
2477   public void associatedData_actionPerformed(ActionEvent e)
2478   {
2479
2480   }
2481
2482   public void autoCalculate_actionPerformed(ActionEvent e)
2483   {
2484
2485   }
2486
2487   public void sortByTreeOption_actionPerformed(ActionEvent e)
2488   {
2489
2490   }
2491
2492   public void showAllSeqs_actionPerformed(ActionEvent e)
2493   {
2494
2495   }
2496
2497   public void showAllColumns_actionPerformed(ActionEvent e)
2498   {
2499
2500   }
2501
2502   public void hideSelSequences_actionPerformed(ActionEvent e)
2503   {
2504
2505   }
2506
2507   public void hideSelColumns_actionPerformed(ActionEvent e)
2508   {
2509
2510   }
2511
2512   public void hiddenMarkers_actionPerformed(ActionEvent e)
2513   {
2514
2515   }
2516
2517   public void findPdbId_actionPerformed(ActionEvent e)
2518   {
2519
2520   }
2521
2522   public void enterPdbId_actionPerformed(ActionEvent e)
2523   {
2524
2525   }
2526
2527   public void pdbFile_actionPerformed(ActionEvent e)
2528   {
2529
2530   }
2531
2532   public void invertColSel_actionPerformed(ActionEvent e)
2533   {
2534
2535   }
2536
2537   public void tabSelectionChanged(int sel)
2538   {
2539
2540   }
2541
2542   public void tabbedPane_mousePressed(MouseEvent e)
2543   {
2544
2545   }
2546
2547   public void tabbedPane_focusGained(FocusEvent e)
2548   {
2549     requestFocus();
2550   }
2551
2552   public void save_actionPerformed(ActionEvent e)
2553   {
2554
2555   }
2556
2557   public void reload_actionPerformed(ActionEvent e)
2558   {
2559
2560   }
2561
2562   public void newView_actionPerformed(ActionEvent e)
2563   {
2564
2565   }
2566
2567   public void textColour_actionPerformed()
2568   {
2569
2570   }
2571
2572   public void idRightAlign_actionPerformed(ActionEvent e)
2573   {
2574
2575   }
2576
2577   public void expandViews_actionPerformed(ActionEvent e)
2578   {
2579
2580   }
2581
2582   public void gatherViews_actionPerformed(ActionEvent e)
2583   {
2584
2585   }
2586
2587   public void buildTreeSortMenu()
2588   {
2589
2590   }
2591
2592   public void pageSetup_actionPerformed(ActionEvent e)
2593   {
2594
2595   }
2596
2597   public void alignmentProperties()
2598   {
2599
2600   }
2601
2602   protected void expand_newalign(ActionEvent e)
2603   {
2604     // TODO Auto-generated method stub
2605
2606   }
2607
2608   protected boolean isShowAutoCalculatedAbove()
2609   {
2610     return showAutoCalculatedAbove;
2611   }
2612
2613   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2614   {
2615     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2616   }
2617
2618   protected SequenceAnnotationOrder getAnnotationSortOrder()
2619   {
2620     return annotationSortOrder;
2621   }
2622
2623   protected void setAnnotationSortOrder(
2624           SequenceAnnotationOrder annotationSortOrder)
2625   {
2626     this.annotationSortOrder = annotationSortOrder;
2627   }
2628
2629   public Map<KeyStroke, JMenuItem> getAccelerators()
2630   {
2631     return this.accelerators;
2632   }
2633
2634   /**
2635    * Returns the selected index of the tabbed pane, or -1 if none selected
2636    * (including the case where the tabbed pane has not been made visible).
2637    *
2638    * @return
2639    */
2640   public int getTabIndex()
2641   {
2642     return tabbedPane.getSelectedIndex();
2643   }
2644
2645   public JPanel getStatusPanel()
2646   {
2647     return statusPanel;
2648   }
2649
2650   /**
2651    * Sets a reference to the containing split frame. Also makes the 'toggle
2652    * split view' menu item visible and checked.
2653    *
2654    * @param sf
2655    */
2656   public void setSplitFrame(SplitContainerI sf)
2657   {
2658     this.splitFrame = sf;
2659     if (sf != null)
2660     {
2661       this.showComplementMenuItem.setVisible(true);
2662       this.showComplementMenuItem.setState(true);
2663     }
2664   }
2665
2666   public SplitContainerI getSplitViewContainer()
2667   {
2668     return this.splitFrame;
2669   }
2670
2671   protected void showComplement_actionPerformed(boolean complement)
2672   {
2673   }
2674 }