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<>();
 203
 204   private SplitContainerI splitFrame;
 205
 206   public GAlignFrame()
 207   {
 208     try
 209     {
 210       jbInit();
 211       setJMenuBar(alignFrameMenuBar);
 212
 213       // dynamically fill save as menu with available formats
 214       for (String ff : FileFormats.getInstance().getWritableFormats(true))
 215       {
 216         JMenuItem item = new JMenuItem(ff);
 217
 218         item.addActionListener(new ActionListener()
 219         {
 220           @Override
 221           public void actionPerformed(ActionEvent e)
 222           {
 223             outputText_actionPerformed(e);
 224           }
 225         });
 226
 227         outputTextboxMenu.add(item);
 228       }
 229     } catch (Exception e)
 230     {
 231       System.err.println(e.toString());
 232     }
 233
 234     if (!Platform.isAMac())
 235     {
 236       closeMenuItem.setMnemonic('C');
 237       outputTextboxMenu.setMnemonic('T');
 238       undoMenuItem.setMnemonic('Z');
 239       redoMenuItem.setMnemonic('0');
 240       copy.setMnemonic('C');
 241       cut.setMnemonic('U');
 242       pasteMenu.setMnemonic('P');
 243       reload.setMnemonic('R');
 244     }
 245   }
 246
 247   private void jbInit() throws Exception
 248   {
 249     initColourMenu();
 250
 251     JMenuItem saveAs = new JMenuItem(
 252             MessageManager.getString("action.save_as"));
 253     ActionListener al = new ActionListener()
 254     {
 255       @Override
 256       public void actionPerformed(ActionEvent e)
 257       {
 258         saveAs_actionPerformed(e);
 259       }
 260     };
 261
 262     // FIXME getDefaultToolkit throws an exception in Headless mode
 263     KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
 264             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
 265                     | KeyEvent.SHIFT_MASK,
 266             false);
 267     addMenuActionAndAccelerator(keyStroke, saveAs, al);
 268
 269     closeMenuItem.setText(MessageManager.getString("action.close"));
 270     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
 271             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 272     al = new ActionListener()
 273     {
 274       @Override
 275       public void actionPerformed(ActionEvent e)
 276       {
 277         closeMenuItem_actionPerformed(false);
 278       }
 279     };
 280     addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
 281
 282     JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
 283     JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
 284     JMenu annotationsMenu = new JMenu(
 285             MessageManager.getString("action.annotations"));
 286     JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
 287     colourMenu.setText(MessageManager.getString("action.colour"));
 288     JMenu calculateMenu = new JMenu(
 289             MessageManager.getString("action.calculate"));
 290     webService.setText(MessageManager.getString("action.web_service"));
 291     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
 292             MessageManager.getString("action.select_all"));
 293     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
 294             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 295     al = new ActionListener()
 296     {
 297       @Override
 298       public void actionPerformed(ActionEvent e)
 299       {
 300         selectAllSequenceMenuItem_actionPerformed(e);
 301       }
 302     };
 303     addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
 304
 305     JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
 306             MessageManager.getString("action.deselect_all"));
 307     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
 308     al = new ActionListener()
 309     {
 310       @Override
 311       public void actionPerformed(ActionEvent e)
 312       {
 313         deselectAllSequenceMenuItem_actionPerformed(e);
 314       }
 315     };
 316     addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
 317
 318     JMenuItem invertSequenceMenuItem = new JMenuItem(
 319             MessageManager.getString("action.invert_sequence_selection"));
 320     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
 321             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 322     al = new ActionListener()
 323     {
 324       @Override
 325       public void actionPerformed(ActionEvent e)
 326       {
 327         invertSequenceMenuItem_actionPerformed(e);
 328       }
 329     };
 330     addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
 331
 332     JMenuItem grpsFromSelection = new JMenuItem(
 333             MessageManager.getString("action.make_groups_selection"));
 334     grpsFromSelection.addActionListener(new ActionListener()
 335     {
 336       @Override
 337       public void actionPerformed(ActionEvent e)
 338       {
 339         makeGrpsFromSelection_actionPerformed(e);
 340       }
 341     });
 342     JMenuItem expandAlignment = new JMenuItem(
 343             MessageManager.getString("action.view_flanking_regions"));
 344     expandAlignment.setToolTipText(
 345             MessageManager.getString("label.view_flanking_regions"));
 346     expandAlignment.addActionListener(new ActionListener()
 347     {
 348       @Override
 349       public void actionPerformed(ActionEvent e)
 350       {
 351         expand_newalign(e);
 352       }
 353     });
 354     JMenuItem remove2LeftMenuItem = new JMenuItem(
 355             MessageManager.getString("action.remove_left"));
 356     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
 357             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 358     al = new ActionListener()
 359     {
 360       @Override
 361       public void actionPerformed(ActionEvent e)
 362       {
 363         remove2LeftMenuItem_actionPerformed(e);
 364       }
 365     };
 366     addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
 367
 368     JMenuItem remove2RightMenuItem = new JMenuItem(
 369             MessageManager.getString("action.remove_right"));
 370     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
 371             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 372     al = new ActionListener()
 373     {
 374       @Override
 375       public void actionPerformed(ActionEvent e)
 376       {
 377         remove2RightMenuItem_actionPerformed(e);
 378       }
 379     };
 380     addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
 381
 382     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
 383             MessageManager.getString("action.remove_empty_columns"));
 384     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
 385             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 386     al = new ActionListener()
 387     {
 388       @Override
 389       public void actionPerformed(ActionEvent e)
 390       {
 391         removeGappedColumnMenuItem_actionPerformed(e);
 392       }
 393     };
 394     addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
 395
 396     JMenuItem removeAllGapsMenuItem = new JMenuItem(
 397             MessageManager.getString("action.remove_all_gaps"));
 398     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
 399             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
 400                     | KeyEvent.SHIFT_MASK,
 401             false);
 402     al = new ActionListener()
 403     {
 404       @Override
 405       public void actionPerformed(ActionEvent e)
 406       {
 407         removeAllGapsMenuItem_actionPerformed(e);
 408       }
 409     };
 410     addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
 411
 412     JMenuItem justifyLeftMenuItem = new JMenuItem(
 413             MessageManager.getString("action.left_justify_alignment"));
 414     justifyLeftMenuItem.addActionListener(new ActionListener()
 415     {
 416       @Override
 417       public void actionPerformed(ActionEvent e)
 418       {
 419         justifyLeftMenuItem_actionPerformed(e);
 420       }
 421     });
 422     JMenuItem justifyRightMenuItem = new JMenuItem(
 423             MessageManager.getString("action.right_justify_alignment"));
 424     justifyRightMenuItem.addActionListener(new ActionListener()
 425     {
 426       @Override
 427       public void actionPerformed(ActionEvent e)
 428       {
 429         justifyRightMenuItem_actionPerformed(e);
 430       }
 431     });
 432     viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
 433     viewBoxesMenuItem.setState(true);
 434     viewBoxesMenuItem.addActionListener(new ActionListener()
 435     {
 436       @Override
 437       public void actionPerformed(ActionEvent e)
 438       {
 439         viewBoxesMenuItem_actionPerformed(e);
 440       }
 441     });
 442     viewTextMenuItem.setText(MessageManager.getString("action.text"));
 443     viewTextMenuItem.setState(true);
 444     viewTextMenuItem.addActionListener(new ActionListener()
 445     {
 446       @Override
 447       public void actionPerformed(ActionEvent e)
 448       {
 449         viewTextMenuItem_actionPerformed(e);
 450       }
 451     });
 452     showNonconservedMenuItem
 453             .setText(MessageManager.getString("label.show_non_conserved"));
 454     showNonconservedMenuItem.setState(false);
 455     showNonconservedMenuItem.addActionListener(new ActionListener()
 456     {
 457       @Override
 458       public void actionPerformed(ActionEvent e)
 459       {
 460         showUnconservedMenuItem_actionPerformed(e);
 461       }
 462     });
 463     JMenuItem sortPairwiseMenuItem = new JMenuItem(
 464             MessageManager.getString("action.by_pairwise_id"));
 465     sortPairwiseMenuItem.addActionListener(new ActionListener()
 466     {
 467       @Override
 468       public void actionPerformed(ActionEvent e)
 469       {
 470         sortPairwiseMenuItem_actionPerformed(e);
 471       }
 472     });
 473     JMenuItem sortIDMenuItem = new JMenuItem(
 474             MessageManager.getString("action.by_id"));
 475     sortIDMenuItem.addActionListener(new ActionListener()
 476     {
 477       @Override
 478       public void actionPerformed(ActionEvent e)
 479       {
 480         sortIDMenuItem_actionPerformed(e);
 481       }
 482     });
 483     JMenuItem sortLengthMenuItem = new JMenuItem(
 484             MessageManager.getString("action.by_length"));
 485     sortLengthMenuItem.addActionListener(new ActionListener()
 486     {
 487       @Override
 488       public void actionPerformed(ActionEvent e)
 489       {
 490         sortLengthMenuItem_actionPerformed(e);
 491       }
 492     });
 493     JMenuItem sortGroupMenuItem = new JMenuItem(
 494             MessageManager.getString("action.by_group"));
 495     sortGroupMenuItem.addActionListener(new ActionListener()
 496     {
 497       @Override
 498       public void actionPerformed(ActionEvent e)
 499       {
 500         sortGroupMenuItem_actionPerformed(e);
 501       }
 502     });
 503
 504     JMenuItem removeRedundancyMenuItem = new JMenuItem(
 505             MessageManager.getString("action.remove_redundancy"));
 506     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
 507             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 508     al = new ActionListener()
 509     {
 510       @Override
 511       public void actionPerformed(ActionEvent e)
 512       {
 513         removeRedundancyMenuItem_actionPerformed(e);
 514       }
 515     };
 516     addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
 517
 518     JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
 519             MessageManager.getString("action.pairwise_alignment"));
 520     pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
 521     {
 522       @Override
 523       public void actionPerformed(ActionEvent e)
 524       {
 525         pairwiseAlignmentMenuItem_actionPerformed(e);
 526       }
 527     });
 528
 529     this.getContentPane().setLayout(new BorderLayout());
 530     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 531     statusBar.setBackground(Color.white);
 532     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 533     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 534     statusBar.setText(MessageManager.getString("label.status_bar"));
 535     outputTextboxMenu
 536             .setText(MessageManager.getString("label.out_to_textbox"));
 537
 538     annotationPanelMenuItem.setActionCommand("");
 539     annotationPanelMenuItem
 540             .setText(MessageManager.getString("label.show_annotations"));
 541     annotationPanelMenuItem
 542             .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
 543     annotationPanelMenuItem.addActionListener(new ActionListener()
 544     {
 545       @Override
 546       public void actionPerformed(ActionEvent e)
 547       {
 548         annotationPanelMenuItem_actionPerformed(e);
 549       }
 550     });
 551     showAllAlAnnotations.setText(
 552             MessageManager.getString("label.show_all_al_annotations"));
 553     final boolean isAnnotationPanelShown = annotationPanelMenuItem
 554             .getState();
 555     showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 556     showAllAlAnnotations.addActionListener(new ActionListener()
 557     {
 558       @Override
 559       public void actionPerformed(ActionEvent e)
 560       {
 561         showAllAnnotations_actionPerformed(false, true);
 562       }
 563     });
 564     hideAllAlAnnotations.setText(
 565             MessageManager.getString("label.hide_all_al_annotations"));
 566     hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 567     hideAllAlAnnotations.addActionListener(new ActionListener()
 568     {
 569       @Override
 570       public void actionPerformed(ActionEvent e)
 571       {
 572         hideAllAnnotations_actionPerformed(false, true);
 573       }
 574     });
 575     showAllSeqAnnotations.setText(
 576             MessageManager.getString("label.show_all_seq_annotations"));
 577     showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 578     showAllSeqAnnotations.addActionListener(new ActionListener()
 579     {
 580       @Override
 581       public void actionPerformed(ActionEvent e)
 582       {
 583         showAllAnnotations_actionPerformed(true, false);
 584       }
 585     });
 586     hideAllSeqAnnotations.setText(
 587             MessageManager.getString("label.hide_all_seq_annotations"));
 588     hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 589     hideAllSeqAnnotations.addActionListener(new ActionListener()
 590     {
 591       @Override
 592       public void actionPerformed(ActionEvent e)
 593       {
 594         hideAllAnnotations_actionPerformed(true, false);
 595       }
 596     });
 597     SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
 598             .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
 599                     SequenceAnnotationOrder.NONE.name()));
 600     final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
 601             MessageManager.getString("label.sort_annotations_by_sequence"));
 602     final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
 603             MessageManager.getString("label.sort_annotations_by_label"));
 604
 605     sortAnnBySequence.setSelected(
 606             sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
 607     sortAnnBySequence.addActionListener(new ActionListener()
 608     {
 609       @Override
 610       public void actionPerformed(ActionEvent e)
 611       {
 612         boolean newState = sortAnnBySequence.getState();
 613         sortAnnByLabel.setSelected(false);
 614         setAnnotationSortOrder(
 615                 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 616                         : SequenceAnnotationOrder.NONE);
 617         sortAnnotations_actionPerformed();
 618       }
 619     });
 620     sortAnnByLabel.setSelected(
 621             sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
 622     sortAnnByLabel.addActionListener(new ActionListener()
 623     {
 624       @Override
 625       public void actionPerformed(ActionEvent e)
 626       {
 627         boolean newState = sortAnnByLabel.getState();
 628         sortAnnBySequence.setSelected(false);
 629         setAnnotationSortOrder(
 630                 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 631                         : SequenceAnnotationOrder.NONE);
 632         sortAnnotations_actionPerformed();
 633       }
 634     });
 635     colourTextMenuItem = new JCheckBoxMenuItem(
 636             MessageManager.getString("label.colour_text"));
 637     colourTextMenuItem.addActionListener(new ActionListener()
 638     {
 639       @Override
 640       public void actionPerformed(ActionEvent e)
 641       {
 642         colourTextMenuItem_actionPerformed(e);
 643       }
 644     });
 645
 646     JMenuItem htmlMenuItem = new JMenuItem(
 647             MessageManager.getString("label.html"));
 648     htmlMenuItem.addActionListener(new ActionListener()
 649     {
 650       @Override
 651       public void actionPerformed(ActionEvent e)
 652       {
 653         htmlMenuItem_actionPerformed(e);
 654       }
 655     });
 656
 657     JMenuItem createBioJS = new JMenuItem(
 658             MessageManager.getString("label.biojs_html_export"));
 659     createBioJS.addActionListener(new java.awt.event.ActionListener()
 660     {
 661       @Override
 662       public void actionPerformed(ActionEvent e)
 663       {
 664         bioJSMenuItem_actionPerformed(e);
 665       }
 666     });
 667
 668     JMenuItem overviewMenuItem = new JMenuItem(
 669             MessageManager.getString("label.overview_window"));
 670     overviewMenuItem.addActionListener(new ActionListener()
 671     {
 672       @Override
 673       public void actionPerformed(ActionEvent e)
 674       {
 675         overviewMenuItem_actionPerformed(e);
 676       }
 677     });
 678
 679     undoMenuItem.setEnabled(false);
 680     undoMenuItem.setText(MessageManager.getString("action.undo"));
 681     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
 682             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 683     al = new ActionListener()
 684     {
 685       @Override
 686       public void actionPerformed(ActionEvent e)
 687       {
 688         undoMenuItem_actionPerformed(e);
 689       }
 690     };
 691     addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
 692
 693     redoMenuItem.setEnabled(false);
 694     redoMenuItem.setText(MessageManager.getString("action.redo"));
 695     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
 696             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 697     al = new ActionListener()
 698     {
 699       @Override
 700       public void actionPerformed(ActionEvent e)
 701       {
 702         redoMenuItem_actionPerformed(e);
 703       }
 704     };
 705     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
 706
 707     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
 708     wrapMenuItem.addActionListener(new ActionListener()
 709     {
 710       @Override
 711       public void actionPerformed(ActionEvent e)
 712       {
 713         wrapMenuItem_actionPerformed(e);
 714       }
 715     });
 716
 717     JMenuItem printMenuItem = new JMenuItem(
 718             MessageManager.getString("action.print"));
 719     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
 720             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 721     al = new ActionListener()
 722     {
 723       @Override
 724       public void actionPerformed(ActionEvent e)
 725       {
 726         printMenuItem_actionPerformed(e);
 727       }
 728     };
 729     addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
 730
 731     renderGapsMenuItem
 732             .setText(MessageManager.getString("action.show_gaps"));
 733     renderGapsMenuItem.setState(true);
 734     renderGapsMenuItem.addActionListener(new ActionListener()
 735     {
 736       @Override
 737       public void actionPerformed(ActionEvent e)
 738       {
 739         renderGapsMenuItem_actionPerformed(e);
 740       }
 741     });
 742
 743     JMenuItem findMenuItem = new JMenuItem(
 744             MessageManager.getString("action.find"));
 745     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
 746             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 747     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
 748             MessageManager.getString("label.find_tip")));
 749     al = new ActionListener()
 750     {
 751       @Override
 752       public void actionPerformed(ActionEvent e)
 753       {
 754         findMenuItem_actionPerformed(e);
 755       }
 756     };
 757     addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
 758
 759     showSeqFeatures.setText(
 760             MessageManager.getString("label.show_sequence_features"));
 761     showSeqFeatures.addActionListener(new ActionListener()
 762     {
 763       @Override
 764       public void actionPerformed(ActionEvent actionEvent)
 765       {
 766         showSeqFeatures_actionPerformed(actionEvent);
 767       }
 768     });
 769     /*
 770      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
 771      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
 772      * void actionPerformed(ActionEvent actionEvent) {
 773      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
 774      */
 775     showDbRefsMenuitem
 776             .setText(MessageManager.getString("label.show_database_refs"));
 777     showDbRefsMenuitem.addActionListener(new ActionListener()
 778     {
 779
 780       @Override
 781       public void actionPerformed(ActionEvent e)
 782       {
 783         showDbRefs_actionPerformed(e);
 784       }
 785
 786     });
 787     showNpFeatsMenuitem.setText(
 788             MessageManager.getString("label.show_non_positional_features"));
 789     showNpFeatsMenuitem.addActionListener(new ActionListener()
 790     {
 791
 792       @Override
 793       public void actionPerformed(ActionEvent e)
 794       {
 795         showNpFeats_actionPerformed(e);
 796       }
 797
 798     });
 799     showGroupConservation
 800             .setText(MessageManager.getString("label.group_conservation"));
 801     showGroupConservation.addActionListener(new ActionListener()
 802     {
 803
 804       @Override
 805       public void actionPerformed(ActionEvent e)
 806       {
 807         showGroupConservation_actionPerformed(e);
 808       }
 809
 810     });
 811
 812     showGroupConsensus
 813             .setText(MessageManager.getString("label.group_consensus"));
 814     showGroupConsensus.addActionListener(new ActionListener()
 815     {
 816
 817       @Override
 818       public void actionPerformed(ActionEvent e)
 819       {
 820         showGroupConsensus_actionPerformed(e);
 821       }
 822
 823     });
 824     showConsensusHistogram.setText(
 825             MessageManager.getString("label.show_consensus_histogram"));
 826     showConsensusHistogram.addActionListener(new ActionListener()
 827     {
 828
 829       @Override
 830       public void actionPerformed(ActionEvent e)
 831       {
 832         showConsensusHistogram_actionPerformed(e);
 833       }
 834
 835     });
 836     showSequenceLogo
 837             .setText(MessageManager.getString("label.show_consensus_logo"));
 838     showSequenceLogo.addActionListener(new ActionListener()
 839     {
 840
 841       @Override
 842       public void actionPerformed(ActionEvent e)
 843       {
 844         showSequenceLogo_actionPerformed(e);
 845       }
 846
 847     });
 848     normaliseSequenceLogo
 849             .setText(MessageManager.getString("label.norm_consensus_logo"));
 850     normaliseSequenceLogo.addActionListener(new ActionListener()
 851     {
 852
 853       @Override
 854       public void actionPerformed(ActionEvent e)
 855       {
 856         normaliseSequenceLogo_actionPerformed(e);
 857       }
 858
 859     });
 860     applyAutoAnnotationSettings
 861             .setText(MessageManager.getString("label.apply_all_groups"));
 862     applyAutoAnnotationSettings.setState(false);
 863     applyAutoAnnotationSettings.setVisible(true);
 864     applyAutoAnnotationSettings.addActionListener(new ActionListener()
 865     {
 866       @Override
 867       public void actionPerformed(ActionEvent e)
 868       {
 869         applyAutoAnnotationSettings_actionPerformed(e);
 870       }
 871     });
 872
 873     ButtonGroup buttonGroup = new ButtonGroup();
 874     final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
 875             MessageManager.getString("label.show_first"));
 876     final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
 877             MessageManager.getString("label.show_last"));
 878     buttonGroup.add(showAutoFirst);
 879     buttonGroup.add(showAutoLast);
 880     final boolean autoFirst = Cache
 881             .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
 882     showAutoFirst.setSelected(autoFirst);
 883     setShowAutoCalculatedAbove(autoFirst);
 884     showAutoFirst.addActionListener(new ActionListener()
 885     {
 886       @Override
 887       public void actionPerformed(ActionEvent e)
 888       {
 889         setShowAutoCalculatedAbove(showAutoFirst.isSelected());
 890         sortAnnotations_actionPerformed();
 891       }
 892     });
 893     showAutoLast.setSelected(!showAutoFirst.isSelected());
 894     showAutoLast.addActionListener(new ActionListener()
 895     {
 896       @Override
 897       public void actionPerformed(ActionEvent e)
 898       {
 899         setShowAutoCalculatedAbove(!showAutoLast.isSelected());
 900         sortAnnotations_actionPerformed();
 901       }
 902     });
 903
 904     JMenuItem deleteGroups = new JMenuItem(
 905             MessageManager.getString("action.undefine_groups"));
 906     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
 907             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 908     al = new ActionListener()
 909     {
 910       @Override
 911       public void actionPerformed(ActionEvent e)
 912       {
 913         deleteGroups_actionPerformed(e);
 914       }
 915     };
 916     addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
 917
 918     JMenuItem annotationColumn = new JMenuItem(
 919             MessageManager.getString("action.select_by_annotation"));
 920     annotationColumn.addActionListener(new ActionListener()
 921     {
 922       @Override
 923       public void actionPerformed(ActionEvent e)
 924       {
 925         annotationColumn_actionPerformed(e);
 926       }
 927     });
 928
 929     JMenuItem createGroup = new JMenuItem(
 930             MessageManager.getString("action.create_group"));
 931     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
 932             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 933     al = new ActionListener()
 934     {
 935       @Override
 936       public void actionPerformed(ActionEvent e)
 937       {
 938         createGroup_actionPerformed(e);
 939       }
 940     };
 941     addMenuActionAndAccelerator(keyStroke, createGroup, al);
 942
 943     JMenuItem unGroup = new JMenuItem(
 944             MessageManager.getString("action.remove_group"));
 945     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
 946             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
 947                     | KeyEvent.SHIFT_MASK,
 948             false);
 949     al = new ActionListener()
 950     {
 951       @Override
 952       public void actionPerformed(ActionEvent e)
 953       {
 954         unGroup_actionPerformed(e);
 955       }
 956     };
 957     addMenuActionAndAccelerator(keyStroke, unGroup, al);
 958
 959     copy.setText(MessageManager.getString("action.copy"));
 960     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
 961             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 962
 963     al = new ActionListener()
 964     {
 965       @Override
 966       public void actionPerformed(ActionEvent e)
 967       {
 968         copy_actionPerformed(e);
 969       }
 970     };
 971     addMenuActionAndAccelerator(keyStroke, copy, al);
 972
 973     cut.setText(MessageManager.getString("action.cut"));
 974     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
 975             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 976     al = new ActionListener()
 977     {
 978       @Override
 979       public void actionPerformed(ActionEvent e)
 980       {
 981         cut_actionPerformed(e);
 982       }
 983     };
 984     addMenuActionAndAccelerator(keyStroke, cut, al);
 985
 986     JMenuItem delete = new JMenuItem(
 987             MessageManager.getString("action.delete"));
 988     delete.addActionListener(new ActionListener()
 989     {
 990       @Override
 991       public void actionPerformed(ActionEvent e)
 992       {
 993         delete_actionPerformed(e);
 994       }
 995     });
 996
 997     pasteMenu.setText(MessageManager.getString("action.paste"));
 998     JMenuItem pasteNew = new JMenuItem(
 999             MessageManager.getString("label.to_new_alignment"));
1000     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1001             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1002                     | KeyEvent.SHIFT_MASK,
1003             false);
1004     al = new ActionListener()
1005     {
1006       @Override
1007       public void actionPerformed(ActionEvent e)
1008       {
1009         pasteNew_actionPerformed(e);
1010       }
1011     };
1012     addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1013
1014     JMenuItem pasteThis = new JMenuItem(
1015             MessageManager.getString("label.to_this_alignment"));
1016     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1017             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1018     al = new ActionListener()
1019     {
1020       @Override
1021       public void actionPerformed(ActionEvent e)
1022       {
1023         pasteThis_actionPerformed(e);
1024       }
1025     };
1026     addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1027
1028     JMenuItem createPNG = new JMenuItem("PNG");
1029     createPNG.addActionListener(new ActionListener()
1030     {
1031       @Override
1032       public void actionPerformed(ActionEvent e)
1033       {
1034         createPNG(null);
1035       }
1036     });
1037     createPNG.setActionCommand(
1038             MessageManager.getString("label.save_png_image"));
1039
1040     JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1041     font.addActionListener(new ActionListener()
1042     {
1043       @Override
1044       public void actionPerformed(ActionEvent e)
1045       {
1046         font_actionPerformed(e);
1047       }
1048     });
1049     seqLimits.setText(
1050             MessageManager.getString("label.show_sequence_limits"));
1051     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1052     seqLimits.addActionListener(new ActionListener()
1053     {
1054       @Override
1055       public void actionPerformed(ActionEvent e)
1056       {
1057         seqLimit_actionPerformed(e);
1058       }
1059     });
1060     JMenuItem epsFile = new JMenuItem("EPS");
1061     epsFile.addActionListener(new ActionListener()
1062     {
1063       @Override
1064       public void actionPerformed(ActionEvent e)
1065       {
1066         createEPS(null);
1067       }
1068     });
1069
1070     JMenuItem createSVG = new JMenuItem("SVG");
1071     createSVG.addActionListener(new ActionListener()
1072     {
1073       @Override
1074       public void actionPerformed(ActionEvent e)
1075       {
1076         createSVG(null);
1077       }
1078     });
1079
1080     JMenuItem loadTreeFile = new JMenuItem(
1081             MessageManager.getString("label.from_file"));
1082     // loadTreeMenuItem.setActionCommand(
1083     // MessageManager.getString());
1084     loadTreeFile.addActionListener(new ActionListener()
1085     {
1086       @Override
1087       public void actionPerformed(ActionEvent e)
1088       {
1089         loadTreeMenuItem_actionPerformed(e);
1090       }
1091     });
1092
1093     JMenuItem loadTreeUrl = new JMenuItem(
1094             MessageManager.getString("label.from_url"));
1095     loadTreeUrl.addActionListener(new ActionListener()
1096     {
1097       @Override
1098       public void actionPerformed(ActionEvent e)
1099       {
1100         loadTreeUrlItem_actionPerformed(e);
1101       }
1102     });
1103
1104     JMenuItem loadTreeDb = new JMenuItem(
1105             MessageManager.getString("FIX ME"));
1106     loadTreeDb.addActionListener(new ActionListener()
1107     {
1108       @Override
1109       public void actionPerformed(ActionEvent e)
1110       {
1111         loadTreeDbItem_actionPerformed(e);
1112       }
1113     });
1114
1115     scaleAbove.setVisible(false);
1116     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1117     scaleAbove.addActionListener(new ActionListener()
1118     {
1119       @Override
1120       public void actionPerformed(ActionEvent e)
1121       {
1122         scaleAbove_actionPerformed(e);
1123       }
1124     });
1125     scaleLeft.setVisible(false);
1126     scaleLeft.setSelected(true);
1127     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1128     scaleLeft.addActionListener(new ActionListener()
1129     {
1130       @Override
1131       public void actionPerformed(ActionEvent e)
1132       {
1133         scaleLeft_actionPerformed(e);
1134       }
1135     });
1136     scaleRight.setVisible(false);
1137     scaleRight.setSelected(true);
1138     scaleRight.setText(MessageManager.getString("action.scale_right"));
1139     scaleRight.addActionListener(new ActionListener()
1140     {
1141       @Override
1142       public void actionPerformed(ActionEvent e)
1143       {
1144         scaleRight_actionPerformed(e);
1145       }
1146     });
1147     centreColumnLabelsMenuItem.setVisible(true);
1148     centreColumnLabelsMenuItem.setState(false);
1149     centreColumnLabelsMenuItem.setText(
1150             MessageManager.getString("label.centre_column_labels"));
1151     centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1152     {
1153       @Override
1154       public void actionPerformed(ActionEvent e)
1155       {
1156         centreColumnLabels_actionPerformed(e);
1157       }
1158     });
1159     followHighlightMenuItem.setVisible(true);
1160     followHighlightMenuItem.setState(true);
1161     followHighlightMenuItem
1162             .setText(MessageManager.getString("label.automatic_scrolling"));
1163     followHighlightMenuItem.addActionListener(new ActionListener()
1164     {
1165
1166       @Override
1167       public void actionPerformed(ActionEvent e)
1168       {
1169         followHighlight_actionPerformed();
1170       }
1171
1172     });
1173
1174     sortByTreeMenu
1175             .setText(MessageManager.getString("action.by_tree_order"));
1176     sort.setText(MessageManager.getString("action.sort"));
1177     sort.addMenuListener(new MenuListener()
1178     {
1179       @Override
1180       public void menuSelected(MenuEvent e)
1181       {
1182         buildTreeSortMenu();
1183       }
1184
1185       @Override
1186       public void menuDeselected(MenuEvent e)
1187       {
1188       }
1189
1190       @Override
1191       public void menuCanceled(MenuEvent e)
1192       {
1193       }
1194     });
1195     sortByAnnotScore
1196             .setText(MessageManager.getString("label.sort_by_score"));
1197     sort.add(sortByAnnotScore);
1198     sort.addMenuListener(new javax.swing.event.MenuListener()
1199     {
1200
1201       @Override
1202       public void menuCanceled(MenuEvent e)
1203       {
1204       }
1205
1206       @Override
1207       public void menuDeselected(MenuEvent e)
1208       {
1209       }
1210
1211       @Override
1212       public void menuSelected(MenuEvent e)
1213       {
1214         buildSortByAnnotationScoresMenu();
1215       }
1216     });
1217     sortByAnnotScore.setVisible(false);
1218
1219     calculateTree
1220             .setText(MessageManager.getString("action.calculate_tree_pca"));
1221
1222     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1223     padGapsMenuitem
1224             .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
1225     padGapsMenuitem.addActionListener(new ActionListener()
1226     {
1227       @Override
1228       public void actionPerformed(ActionEvent e)
1229       {
1230         padGapsMenuitem_actionPerformed(e);
1231       }
1232     });
1233     JMenuItem vamsasStore = new JMenuItem(
1234             MessageManager.getString("label.vamsas_store"));
1235     vamsasStore.setVisible(false);
1236     vamsasStore.addActionListener(new ActionListener()
1237     {
1238       @Override
1239       public void actionPerformed(ActionEvent e)
1240       {
1241         vamsasStore_actionPerformed(e);
1242       }
1243     });
1244     showTranslation
1245             .setText(MessageManager.getString("label.translate_cDNA"));
1246     showTranslation.addActionListener(new ActionListener()
1247     {
1248       @Override
1249       public void actionPerformed(ActionEvent e)
1250       {
1251         showTranslation_actionPerformed(e);
1252       }
1253     });
1254     showReverse.setText(MessageManager.getString("label.reverse"));
1255     showReverse.addActionListener(new ActionListener()
1256     {
1257       @Override
1258       public void actionPerformed(ActionEvent e)
1259       {
1260         showReverse_actionPerformed(false);
1261       }
1262     });
1263     showReverseComplement
1264             .setText(MessageManager.getString("label.reverse_complement"));
1265     showReverseComplement.addActionListener(new ActionListener()
1266     {
1267       @Override
1268       public void actionPerformed(ActionEvent e)
1269       {
1270         showReverse_actionPerformed(true);
1271       }
1272     });
1273
1274     JMenuItem extractScores = new JMenuItem(
1275             MessageManager.getString("label.extract_scores"));
1276     extractScores.addActionListener(new ActionListener()
1277     {
1278       @Override
1279       public void actionPerformed(ActionEvent e)
1280       {
1281         extractScores_actionPerformed(e);
1282       }
1283     });
1284     extractScores.setVisible(true);
1285     // JBPNote: TODO: make gui for regex based score extraction
1286
1287     // for show products actions see AlignFrame.canShowProducts
1288     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1289
1290     runGroovy.setText(MessageManager.getString("label.run_groovy"));
1291     runGroovy.setToolTipText(
1292             MessageManager.getString("label.run_groovy_tip"));
1293     runGroovy.addActionListener(new ActionListener()
1294     {
1295       @Override
1296       public void actionPerformed(ActionEvent e)
1297       {
1298         runGroovy_actionPerformed();
1299       }
1300     });
1301
1302     JMenuItem openFeatureSettings = new JMenuItem(
1303             MessageManager.getString("action.feature_settings"));
1304     openFeatureSettings.addActionListener(new ActionListener()
1305     {
1306       @Override
1307       public void actionPerformed(ActionEvent e)
1308       {
1309         featureSettings_actionPerformed(e);
1310       }
1311     });
1312     JMenuItem fetchSequence = new JMenuItem(
1313             MessageManager.getString("label.fetch_sequences"));
1314     fetchSequence.addActionListener(new ActionListener()
1315     {
1316       @Override
1317       public void actionPerformed(ActionEvent e)
1318       {
1319         fetchSequence_actionPerformed(e);
1320       }
1321     });
1322
1323     JMenuItem associatedData = new JMenuItem(
1324             MessageManager.getString("label.load_features_annotations"));
1325     associatedData.addActionListener(new ActionListener()
1326     {
1327       @Override
1328       public void actionPerformed(ActionEvent e)
1329       {
1330         associatedData_actionPerformed(e);
1331       }
1332     });
1333     autoCalculate.setText(
1334             MessageManager.getString("label.autocalculate_consensus"));
1335     autoCalculate.setState(
1336             jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1337     autoCalculate.addActionListener(new ActionListener()
1338     {
1339       @Override
1340       public void actionPerformed(ActionEvent e)
1341       {
1342         autoCalculate_actionPerformed(e);
1343       }
1344     });
1345     sortByTree.setText(
1346             MessageManager.getString("label.sort_alignment_new_tree"));
1347     sortByTree.setToolTipText("<html>" + MessageManager.getString(
1348             "label.enable_automatically_sort_alignment_when_open_new_tree"));
1349     sortByTree
1350             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1351     sortByTree.addActionListener(new ActionListener()
1352     {
1353       @Override
1354       public void actionPerformed(ActionEvent e)
1355       {
1356         sortByTreeOption_actionPerformed(e);
1357       }
1358     });
1359
1360     listenToViewSelections.setText(
1361             MessageManager.getString("label.listen_for_selections"));
1362     listenToViewSelections
1363             .setToolTipText("<html>" + MessageManager.getString(
1364                     "label.selections_mirror_selections_made_same_sequences_other_views"));
1365     listenToViewSelections.setState(false);
1366     listenToViewSelections.addActionListener(new ActionListener()
1367     {
1368       @Override
1369       public void actionPerformed(ActionEvent e)
1370       {
1371         listenToViewSelections_actionPerformed(e);
1372       }
1373     });
1374
1375     JMenu addSequenceMenu = new JMenu(
1376             MessageManager.getString("label.add_sequences"));
1377     JMenuItem addFromFile = new JMenuItem(
1378             MessageManager.getString("label.from_file"));
1379     addFromFile.addActionListener(new ActionListener()
1380     {
1381       @Override
1382       public void actionPerformed(ActionEvent e)
1383       {
1384         addFromFile_actionPerformed(e);
1385       }
1386     });
1387     JMenuItem addFromText = new JMenuItem(
1388             MessageManager.getString("label.from_textbox"));
1389     addFromText.addActionListener(new ActionListener()
1390     {
1391       @Override
1392       public void actionPerformed(ActionEvent e)
1393       {
1394         addFromText_actionPerformed(e);
1395       }
1396     });
1397     JMenuItem addFromURL = new JMenuItem(
1398             MessageManager.getString("label.from_url"));
1399     addFromURL.addActionListener(new ActionListener()
1400     {
1401       @Override
1402       public void actionPerformed(ActionEvent e)
1403       {
1404         addFromURL_actionPerformed(e);
1405       }
1406     });
1407     JMenuItem exportFeatures = new JMenuItem(
1408             MessageManager.getString("label.export_features"));
1409     exportFeatures.addActionListener(new ActionListener()
1410     {
1411       @Override
1412       public void actionPerformed(ActionEvent e)
1413       {
1414         exportFeatures_actionPerformed(e);
1415       }
1416     });
1417     JMenuItem exportAnnotations = new JMenuItem(
1418             MessageManager.getString("label.export_annotations"));
1419     exportAnnotations.addActionListener(new ActionListener()
1420     {
1421       @Override
1422       public void actionPerformed(ActionEvent e)
1423       {
1424         exportAnnotations_actionPerformed(e);
1425       }
1426     });
1427     statusPanel.setLayout(new GridLayout());
1428     JMenuItem showAllSeqs = new JMenuItem(
1429             MessageManager.getString("label.all_sequences"));
1430     showAllSeqs.setToolTipText(
1431             MessageManager.getString("label.toggle_sequence_visibility"));
1432     showAllSeqs.addActionListener(new ActionListener()
1433     {
1434       @Override
1435       public void actionPerformed(ActionEvent e)
1436       {
1437         showAllSeqs_actionPerformed(e);
1438       }
1439     });
1440     JMenuItem showAllColumns = new JMenuItem(
1441             MessageManager.getString("label.all_columns"));
1442     showAllColumns.setToolTipText(
1443             MessageManager.getString("label.toggle_columns_visibility"));
1444     showAllColumns.addActionListener(new ActionListener()
1445     {
1446       @Override
1447       public void actionPerformed(ActionEvent e)
1448       {
1449         showAllColumns_actionPerformed(e);
1450       }
1451     });
1452     JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1453     JMenuItem hideSelSequences = new JMenuItem(
1454             MessageManager.getString("label.selected_sequences"));
1455     hideSelSequences.setToolTipText(
1456             MessageManager.getString("label.toggle_sequence_visibility"));
1457     hideSelSequences.addActionListener(new ActionListener()
1458     {
1459       @Override
1460       public void actionPerformed(ActionEvent e)
1461       {
1462         hideSelSequences_actionPerformed(e);
1463       }
1464     });
1465     JMenuItem hideSelColumns = new JMenuItem(
1466             MessageManager.getString("label.selected_columns"));
1467     hideSelColumns.setToolTipText(
1468             MessageManager.getString("label.toggle_columns_visibility"));
1469     hideSelColumns.addActionListener(new ActionListener()
1470     {
1471       @Override
1472       public void actionPerformed(ActionEvent e)
1473       {
1474         hideSelColumns_actionPerformed(e);
1475       }
1476     });
1477     JMenuItem hideAllSelection = new JMenuItem(
1478             MessageManager.getString("label.selected_region"));
1479     hideAllSelection.addActionListener(new ActionListener()
1480     {
1481       @Override
1482       public void actionPerformed(ActionEvent e)
1483       {
1484         hideAllSelection_actionPerformed(e);
1485       }
1486     });
1487     // TODO: should be hidden if no selection exists.
1488     JMenuItem hideAllButSelection = new JMenuItem(
1489             MessageManager.getString("label.all_but_selected_region"));
1490     hideAllButSelection.addActionListener(new ActionListener()
1491     {
1492       @Override
1493       public void actionPerformed(ActionEvent e)
1494       {
1495         hideAllButSelection_actionPerformed(e);
1496       }
1497     });
1498     JMenuItem showAllhidden = new JMenuItem(
1499             MessageManager.getString("label.all_sequences_columns"));
1500     showAllhidden.setToolTipText(MessageManager
1501             .getString("label.toggles_visibility_hidden_selected_regions"));
1502     showAllhidden.addActionListener(new ActionListener()
1503     {
1504       @Override
1505       public void actionPerformed(ActionEvent e)
1506       {
1507         showAllhidden_actionPerformed(e);
1508       }
1509     });
1510     hiddenMarkers.setText(
1511             MessageManager.getString("action.show_hidden_markers"));
1512     hiddenMarkers.addActionListener(new ActionListener()
1513     {
1514       @Override
1515       public void actionPerformed(ActionEvent e)
1516       {
1517         hiddenMarkers_actionPerformed(e);
1518       }
1519     });
1520
1521     JMenuItem invertColSel = new JMenuItem(
1522             MessageManager.getString("action.invert_column_selection"));
1523     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1524             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1525                     | KeyEvent.ALT_MASK,
1526             false);
1527     al = new ActionListener()
1528     {
1529       @Override
1530       public void actionPerformed(ActionEvent e)
1531       {
1532         invertColSel_actionPerformed(e);
1533       }
1534     };
1535     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1536
1537     showComplementMenuItem.setVisible(false);
1538     showComplementMenuItem.addActionListener(new ActionListener()
1539     {
1540       @Override
1541       public void actionPerformed(ActionEvent e)
1542       {
1543         showComplement_actionPerformed(showComplementMenuItem.getState());
1544       }
1545     });
1546
1547     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1548     {
1549       @Override
1550       public void stateChanged(ChangeEvent evt)
1551       {
1552         JTabbedPane pane = (JTabbedPane) evt.getSource();
1553         int sel = pane.getSelectedIndex();
1554         tabSelectionChanged(sel);
1555       }
1556     });
1557     tabbedPane.addMouseListener(new MouseAdapter()
1558     {
1559       @Override
1560       public void mousePressed(MouseEvent e)
1561       {
1562         if (e.isPopupTrigger()) // Mac
1563         {
1564           tabbedPane_mousePressed(e);
1565         }
1566       }
1567
1568       @Override
1569       public void mouseReleased(MouseEvent e)
1570       {
1571         if (e.isPopupTrigger()) // Windows
1572         {
1573           tabbedPane_mousePressed(e);
1574         }
1575       }
1576     });
1577     tabbedPane.addFocusListener(new FocusAdapter()
1578     {
1579       @Override
1580       public void focusGained(FocusEvent e)
1581       {
1582         tabbedPane_focusGained(e);
1583       }
1584     });
1585
1586     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1587     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1588             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1589     al = new ActionListener()
1590     {
1591       @Override
1592       public void actionPerformed(ActionEvent e)
1593       {
1594         save_actionPerformed(e);
1595       }
1596     };
1597     addMenuActionAndAccelerator(keyStroke, save, al);
1598
1599     reload.setEnabled(false);
1600     reload.setText(MessageManager.getString("action.reload"));
1601     reload.addActionListener(new ActionListener()
1602     {
1603       @Override
1604       public void actionPerformed(ActionEvent e)
1605       {
1606         reload_actionPerformed(e);
1607       }
1608     });
1609
1610     JMenuItem newView = new JMenuItem(
1611             MessageManager.getString("action.new_view"));
1612     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1613             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1614     al = new ActionListener()
1615     {
1616       @Override
1617       public void actionPerformed(ActionEvent e)
1618       {
1619         newView_actionPerformed(e);
1620       }
1621     };
1622     addMenuActionAndAccelerator(keyStroke, newView, al);
1623
1624     tabbedPane.setToolTipText("<html><i>"
1625             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1626             + "</i></html>");
1627
1628     formatMenu.setText(MessageManager.getString("action.format"));
1629     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1630
1631     idRightAlign.setText(
1632             MessageManager.getString("label.right_align_sequence_id"));
1633     idRightAlign.addActionListener(new ActionListener()
1634     {
1635       @Override
1636       public void actionPerformed(ActionEvent e)
1637       {
1638         idRightAlign_actionPerformed(e);
1639       }
1640     });
1641
1642     gatherViews.setEnabled(false);
1643     gatherViews.setText(MessageManager.getString("action.gather_views"));
1644     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1645     al = new ActionListener()
1646     {
1647       @Override
1648       public void actionPerformed(ActionEvent e)
1649       {
1650         gatherViews_actionPerformed(e);
1651       }
1652     };
1653     addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1654
1655     expandViews.setEnabled(false);
1656     expandViews.setText(MessageManager.getString("action.expand_views"));
1657     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1658     al = new ActionListener()
1659     {
1660       @Override
1661       public void actionPerformed(ActionEvent e)
1662       {
1663         expandViews_actionPerformed(e);
1664       }
1665     };
1666     addMenuActionAndAccelerator(keyStroke, expandViews, al);
1667
1668     JMenuItem pageSetup = new JMenuItem(
1669             MessageManager.getString("action.page_setup"));
1670     pageSetup.addActionListener(new ActionListener()
1671     {
1672       @Override
1673       public void actionPerformed(ActionEvent e)
1674       {
1675         pageSetup_actionPerformed(e);
1676       }
1677     });
1678     JMenuItem alignmentProperties = new JMenuItem(
1679             MessageManager.getString("label.alignment_props"));
1680     alignmentProperties.addActionListener(new ActionListener()
1681     {
1682       @Override
1683       public void actionPerformed(ActionEvent actionEvent)
1684       {
1685         alignmentProperties();
1686       }
1687     });
1688     JMenuItem selectHighlighted = new JMenuItem(
1689             MessageManager.getString("action.select_highlighted_columns"));
1690     selectHighlighted.setToolTipText(
1691             MessageManager.getString("tooltip.select_highlighted_columns"));
1692     al = new ActionListener()
1693     {
1694       @Override
1695       public void actionPerformed(ActionEvent actionEvent)
1696       {
1697         selectHighlightedColumns_actionPerformed(actionEvent);
1698       }
1699     };
1700     selectHighlighted.addActionListener(al);
1701     JMenu tooltipSettingsMenu = new JMenu(
1702             MessageManager.getString("label.sequence_id_tooltip"));
1703     JMenu autoAnnMenu = new JMenu(
1704             MessageManager.getString("label.autocalculated_annotation"));
1705
1706     JMenu exportImageMenu = new JMenu(
1707             MessageManager.getString("label.export_image"));
1708     JMenu loadTreeMenu = new JMenu(
1709             MessageManager.getString("label.load_associated_tree"));
1710     loadTreeMenu.setActionCommand("label.load_tree_for_sequence_set");
1711
1712     JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1713
1714     loadTreeMenu.add(loadTreeFile);
1715     loadTreeMenu.add(loadTreeUrl);
1716     loadTreeMenu.add(loadTreeDb);
1717
1718     alignFrameMenuBar.add(fileMenu);
1719     alignFrameMenuBar.add(editMenu);
1720     alignFrameMenuBar.add(selectMenu);
1721     alignFrameMenuBar.add(viewMenu);
1722     alignFrameMenuBar.add(annotationsMenu);
1723     alignFrameMenuBar.add(formatMenu);
1724     alignFrameMenuBar.add(colourMenu);
1725     alignFrameMenuBar.add(calculateMenu);
1726     alignFrameMenuBar.add(webService);
1727
1728     fileMenu.add(fetchSequence);
1729     fileMenu.add(addSequenceMenu);
1730     fileMenu.add(reload);
1731     fileMenu.addSeparator();
1732     fileMenu.add(vamsasStore);
1733     fileMenu.add(save);
1734     fileMenu.add(saveAs);
1735     fileMenu.add(outputTextboxMenu);
1736     fileMenu.add(pageSetup);
1737     fileMenu.add(printMenuItem);
1738     fileMenu.addSeparator();
1739     fileMenu.add(exportImageMenu);
1740     fileMenu.add(exportFeatures);
1741     fileMenu.add(exportAnnotations);
1742     fileMenu.add(loadTreeMenu);
1743     fileMenu.add(associatedData);
1744     fileMenu.addSeparator();
1745     fileMenu.add(closeMenuItem);
1746
1747     pasteMenu.add(pasteNew);
1748     pasteMenu.add(pasteThis);
1749     editMenu.add(undoMenuItem);
1750     editMenu.add(redoMenuItem);
1751     editMenu.add(cut);
1752     editMenu.add(copy);
1753     editMenu.add(pasteMenu);
1754     editMenu.add(delete);
1755     editMenu.addSeparator();
1756     editMenu.add(remove2LeftMenuItem);
1757     editMenu.add(remove2RightMenuItem);
1758     editMenu.add(removeGappedColumnMenuItem);
1759     editMenu.add(removeAllGapsMenuItem);
1760     editMenu.add(removeRedundancyMenuItem);
1761     editMenu.addSeparator();
1762     // dont add these yet in the CVS build - they cannot be undone!
1763     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1764     // editMenu.add(justifyLeftMenuItem);
1765     // editMenu.add(justifyRightMenuItem);
1766     // editMenu.addSeparator();
1767     editMenu.add(padGapsMenuitem);
1768
1769     showMenu.add(showAllColumns);
1770     showMenu.add(showAllSeqs);
1771     showMenu.add(showAllhidden);
1772     hideMenu.add(hideSelColumns);
1773     hideMenu.add(hideSelSequences);
1774     hideMenu.add(hideAllSelection);
1775     hideMenu.add(hideAllButSelection);
1776     viewMenu.add(newView);
1777     viewMenu.add(expandViews);
1778     viewMenu.add(gatherViews);
1779     viewMenu.addSeparator();
1780     viewMenu.add(showMenu);
1781     viewMenu.add(hideMenu);
1782     viewMenu.add(showComplementMenuItem);
1783     viewMenu.addSeparator();
1784     viewMenu.add(followHighlightMenuItem);
1785     viewMenu.addSeparator();
1786     viewMenu.add(showSeqFeatures);
1787     // viewMenu.add(showSeqFeaturesHeight);
1788     viewMenu.add(openFeatureSettings);
1789     tooltipSettingsMenu.add(showDbRefsMenuitem);
1790     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1791     viewMenu.add(tooltipSettingsMenu);
1792     viewMenu.addSeparator();
1793     viewMenu.add(alignmentProperties);
1794     viewMenu.addSeparator();
1795     viewMenu.add(overviewMenuItem);
1796
1797     annotationsMenu.add(annotationPanelMenuItem);
1798     annotationsMenu.addSeparator();
1799     annotationsMenu.add(showAllAlAnnotations);
1800     annotationsMenu.add(hideAllAlAnnotations);
1801     annotationsMenu.addSeparator();
1802     annotationsMenu.add(showAllSeqAnnotations);
1803     annotationsMenu.add(hideAllSeqAnnotations);
1804     annotationsMenu.add(sortAnnBySequence);
1805     annotationsMenu.add(sortAnnByLabel);
1806     annotationsMenu.addSeparator();
1807     autoAnnMenu.add(showAutoFirst);
1808     autoAnnMenu.add(showAutoLast);
1809     autoAnnMenu.addSeparator();
1810     autoAnnMenu.add(applyAutoAnnotationSettings);
1811     autoAnnMenu.add(showConsensusHistogram);
1812     autoAnnMenu.add(showSequenceLogo);
1813     autoAnnMenu.add(normaliseSequenceLogo);
1814     autoAnnMenu.addSeparator();
1815     autoAnnMenu.add(showGroupConservation);
1816     autoAnnMenu.add(showGroupConsensus);
1817     annotationsMenu.add(autoAnnMenu);
1818
1819     sort.add(sortIDMenuItem);
1820     sort.add(sortLengthMenuItem);
1821     sort.add(sortGroupMenuItem);
1822     sort.add(sortPairwiseMenuItem);
1823     sort.add(sortByTreeMenu);
1824     calculateMenu.add(sort);
1825     calculateMenu.add(calculateTree);
1826     calculateMenu.addSeparator();
1827     calculateMenu.add(pairwiseAlignmentMenuItem);
1828     calculateMenu.addSeparator();
1829     calculateMenu.add(showTranslation);
1830     calculateMenu.add(showReverse);
1831     calculateMenu.add(showReverseComplement);
1832     calculateMenu.add(showProducts);
1833     calculateMenu.add(autoCalculate);
1834     calculateMenu.add(sortByTree);
1835     calculateMenu.addSeparator();
1836     calculateMenu.add(expandAlignment);
1837     calculateMenu.add(extractScores);
1838     calculateMenu.addSeparator();
1839     calculateMenu.add(runGroovy);
1840
1841     webServiceNoServices = new JMenuItem(
1842             MessageManager.getString("label.no_services"));
1843     webService.add(webServiceNoServices);
1844     exportImageMenu.add(htmlMenuItem);
1845     exportImageMenu.add(epsFile);
1846     exportImageMenu.add(createPNG);
1847     exportImageMenu.add(createBioJS);
1848     exportImageMenu.add(createSVG);
1849     addSequenceMenu.add(addFromFile);
1850     addSequenceMenu.add(addFromText);
1851     addSequenceMenu.add(addFromURL);
1852     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1853     statusPanel.add(statusBar, null);
1854     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1855
1856     formatMenu.add(font);
1857     formatMenu.addSeparator();
1858     formatMenu.add(wrapMenuItem);
1859     formatMenu.add(scaleAbove);
1860     formatMenu.add(scaleLeft);
1861     formatMenu.add(scaleRight);
1862     formatMenu.add(seqLimits);
1863     formatMenu.add(idRightAlign);
1864     formatMenu.add(hiddenMarkers);
1865     formatMenu.add(viewBoxesMenuItem);
1866     formatMenu.add(viewTextMenuItem);
1867     formatMenu.add(colourTextMenuItem);
1868     formatMenu.add(renderGapsMenuItem);
1869     formatMenu.add(centreColumnLabelsMenuItem);
1870     formatMenu.add(showNonconservedMenuItem);
1871     selectMenu.add(findMenuItem);
1872     selectMenu.addSeparator();
1873     selectMenu.add(selectAllSequenceMenuItem);
1874     selectMenu.add(deselectAllSequenceMenuItem);
1875     selectMenu.add(invertSequenceMenuItem);
1876     selectMenu.add(invertColSel);
1877     selectMenu.add(createGroup);
1878     selectMenu.add(unGroup);
1879     selectMenu.add(grpsFromSelection);
1880     selectMenu.add(deleteGroups);
1881     selectMenu.add(annotationColumn);
1882     selectMenu.add(selectHighlighted);
1883     // TODO - determine if the listenToViewSelections button is needed : see bug
1884     // JAL-574
1885     // selectMenu.addSeparator();
1886     // selectMenu.add(listenToViewSelections);
1887   }
1888
1889   /**
1890    * Constructs the entries on the Colour menu (but does not add them to the
1891    * menu).
1892    */
1893   protected void initColourMenu()
1894   {
1895     applyToAllGroups = new JCheckBoxMenuItem(
1896             MessageManager.getString("label.apply_colour_to_all_groups"));
1897     applyToAllGroups.addActionListener(new ActionListener()
1898     {
1899       @Override
1900       public void actionPerformed(ActionEvent e)
1901       {
1902         applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1903       }
1904     });
1905
1906     textColour = new JMenuItem(
1907             MessageManager.getString("label.text_colour"));
1908     textColour.addActionListener(new ActionListener()
1909     {
1910       @Override
1911       public void actionPerformed(ActionEvent e)
1912       {
1913         textColour_actionPerformed();
1914       }
1915     });
1916
1917     conservationMenuItem = new JCheckBoxMenuItem(
1918             MessageManager.getString("action.by_conservation"));
1919     conservationMenuItem.addActionListener(new ActionListener()
1920     {
1921       @Override
1922       public void actionPerformed(ActionEvent e)
1923       {
1924         conservationMenuItem_actionPerformed(
1925                 conservationMenuItem.isSelected());
1926       }
1927     });
1928
1929     abovePIDThreshold = new JCheckBoxMenuItem(
1930             MessageManager.getString("label.above_identity_threshold"));
1931     abovePIDThreshold.addActionListener(new ActionListener()
1932     {
1933       @Override
1934       public void actionPerformed(ActionEvent e)
1935       {
1936         abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
1937       }
1938     });
1939     modifyPID = new JMenuItem(
1940             MessageManager.getString("label.modify_identity_threshold"));
1941     modifyPID.addActionListener(new ActionListener()
1942     {
1943       @Override
1944       public void actionPerformed(ActionEvent e)
1945       {
1946         modifyPID_actionPerformed();
1947       }
1948     });
1949     modifyConservation = new JMenuItem(MessageManager
1950             .getString("label.modify_conservation_threshold"));
1951     modifyConservation.addActionListener(new ActionListener()
1952     {
1953       @Override
1954       public void actionPerformed(ActionEvent e)
1955       {
1956         modifyConservation_actionPerformed();
1957       }
1958     });
1959
1960     annotationColour = new JMenuItem(
1961             MessageManager.getString("action.by_annotation"));
1962     annotationColour.addActionListener(new ActionListener()
1963     {
1964       @Override
1965       public void actionPerformed(ActionEvent e)
1966       {
1967         annotationColour_actionPerformed();
1968       }
1969     });
1970   }
1971
1972   protected void selectHighlightedColumns_actionPerformed(
1973           ActionEvent actionEvent)
1974   {
1975     // TODO Auto-generated method stub
1976
1977   }
1978
1979   /**
1980    * Generate the reverse sequence (or reverse complement if the flag is true)
1981    * and add it to the alignment
1982    *
1983    * @param complement
1984    */
1985   protected void showReverse_actionPerformed(boolean complement)
1986   {
1987   }
1988
1989   /**
1990    * Try to run script in a Groovy console, having first ensured that this
1991    * alignframe is set as currentAlignFrame in Desktop
1992    */
1993   protected void runGroovy_actionPerformed()
1994   {
1995
1996   }
1997
1998   /**
1999    * Adds the given action listener and key accelerator to the given menu item.
2000    * Also saves in a lookup table to support lookup of action by key stroke.
2001    *
2002    * @param keyStroke
2003    * @param menuItem
2004    * @param actionListener
2005    */
2006   protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2007           JMenuItem menuItem, ActionListener actionListener)
2008   {
2009     menuItem.setAccelerator(keyStroke);
2010     accelerators.put(keyStroke, menuItem);
2011     menuItem.addActionListener(actionListener);
2012   }
2013
2014   /**
2015    * Action on clicking sort annotations by type.
2016    *
2017    * @param sortOrder
2018    */
2019   protected void sortAnnotations_actionPerformed()
2020   {
2021   }
2022
2023   /**
2024    * Action on clicking Show all annotations.
2025    *
2026    * @param forSequences
2027    *          update sequence-related annotations
2028    * @param forAlignment
2029    *          update non-sequence-related annotations
2030    */
2031   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2032           boolean forAlignment)
2033   {
2034     setAnnotationsVisibility(true, forSequences, forAlignment);
2035   }
2036
2037   /**
2038    * Action on clicking Hide all annotations.
2039    *
2040    * @param forSequences
2041    *          update sequence-related annotations
2042    * @param forAlignment
2043    *          update non-sequence-related annotations
2044    */
2045   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2046           boolean forAlignment)
2047   {
2048     setAnnotationsVisibility(false, forSequences, forAlignment);
2049   }
2050
2051   /**
2052    * Set the visibility of annotations to true or false. Can act on
2053    * sequence-related annotations, or alignment-related, or both.
2054    *
2055    * @param visible
2056    * @param forSequences
2057    *          update sequence-related annotations
2058    * @param forAlignment
2059    *          update non-sequence-related annotations
2060    */
2061   protected void setAnnotationsVisibility(boolean visible,
2062           boolean forSequences, boolean forAlignment)
2063   {
2064
2065   }
2066
2067   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2068   {
2069     // TODO Auto-generated method stub
2070
2071   }
2072
2073   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2074   {
2075     // TODO Auto-generated method stub
2076
2077   }
2078
2079   protected void showAllhidden_actionPerformed(ActionEvent e)
2080   {
2081     // TODO Auto-generated method stub
2082
2083   }
2084
2085   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2086   {
2087     // TODO Auto-generated method stub
2088
2089   }
2090
2091   protected void hideAllSelection_actionPerformed(ActionEvent e)
2092   {
2093     // TODO Auto-generated method stub
2094
2095   }
2096
2097   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2098   {
2099     // TODO Auto-generated method stub
2100
2101   }
2102
2103   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2104   {
2105     // TODO Auto-generated method stub
2106
2107   }
2108
2109   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2110   {
2111     // TODO Auto-generated method stub
2112
2113   }
2114
2115   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2116   {
2117     // TODO Auto-generated method stub
2118
2119   }
2120
2121   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2122   {
2123     // TODO Auto-generated method stub
2124
2125   }
2126
2127   protected void showGroupConservation_actionPerformed(ActionEvent e)
2128   {
2129     // TODO Auto-generated method stub
2130
2131   }
2132
2133   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2134   {
2135     // TODO Auto-generated method stub
2136
2137   }
2138
2139   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2140   {
2141     // TODO Auto-generated method stub
2142
2143   }
2144
2145   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2146   {
2147     // TODO Auto-generated method stub
2148
2149   }
2150
2151   protected void followHighlight_actionPerformed()
2152   {
2153     // TODO Auto-generated method stub
2154
2155   }
2156
2157   protected void showNpFeats_actionPerformed(ActionEvent e)
2158   {
2159     // TODO Auto-generated method stub
2160
2161   }
2162
2163   protected void showDbRefs_actionPerformed(ActionEvent e)
2164   {
2165     // TODO Auto-generated method stub
2166
2167   }
2168
2169   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2170   {
2171   }
2172
2173   protected void buildSortByAnnotationScoresMenu()
2174   {
2175   }
2176
2177   protected void extractScores_actionPerformed(ActionEvent e)
2178   {
2179   }
2180
2181   protected void outputText_actionPerformed(ActionEvent e)
2182   {
2183   }
2184
2185   public void addFromFile_actionPerformed(ActionEvent e)
2186   {
2187
2188   }
2189
2190   public void addFromText_actionPerformed(ActionEvent e)
2191   {
2192
2193   }
2194
2195   public void addFromURL_actionPerformed(ActionEvent e)
2196   {
2197
2198   }
2199
2200   public void exportFeatures_actionPerformed(ActionEvent e)
2201   {
2202
2203   }
2204
2205   public void exportAnnotations_actionPerformed(ActionEvent e)
2206   {
2207
2208   }
2209
2210   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2211   {
2212   }
2213
2214   protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2215   {
2216
2217   }
2218
2219   protected void closeMenuItem_actionPerformed(boolean b)
2220   {
2221   }
2222
2223   protected void redoMenuItem_actionPerformed(ActionEvent e)
2224   {
2225   }
2226
2227   protected void undoMenuItem_actionPerformed(ActionEvent e)
2228   {
2229   }
2230
2231   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2232   {
2233   }
2234
2235   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2236   {
2237   }
2238
2239   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2240   {
2241   }
2242
2243   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2244   {
2245   }
2246
2247   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2248   {
2249   }
2250
2251   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2252   {
2253   }
2254
2255   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2256   {
2257   }
2258
2259   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2260   {
2261   }
2262
2263   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2264   {
2265   }
2266
2267   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2268   {
2269   }
2270
2271   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2272   {
2273   }
2274
2275   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2276   {
2277   }
2278
2279   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2280   {
2281   }
2282
2283   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2284   {
2285   }
2286
2287   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2288   {
2289   }
2290
2291   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2292   {
2293   }
2294
2295   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2296   {
2297   }
2298
2299   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2300   {
2301   }
2302
2303   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2304   {
2305   }
2306
2307   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2308   {
2309   }
2310
2311   protected void conservationMenuItem_actionPerformed(boolean selected)
2312   {
2313   }
2314
2315   protected void printMenuItem_actionPerformed(ActionEvent e)
2316   {
2317   }
2318
2319   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2320   {
2321   }
2322
2323   protected void findMenuItem_actionPerformed(ActionEvent e)
2324   {
2325   }
2326
2327   protected void abovePIDThreshold_actionPerformed(boolean selected)
2328   {
2329   }
2330
2331   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2332   {
2333   }
2334
2335   protected void deleteGroups_actionPerformed(ActionEvent e)
2336   {
2337   }
2338
2339   protected void createGroup_actionPerformed(ActionEvent e)
2340   {
2341   }
2342
2343   protected void unGroup_actionPerformed(ActionEvent e)
2344   {
2345   }
2346
2347   protected void copy_actionPerformed(ActionEvent e)
2348   {
2349   }
2350
2351   protected void cut_actionPerformed(ActionEvent e)
2352   {
2353   }
2354
2355   protected void delete_actionPerformed(ActionEvent e)
2356   {
2357   }
2358
2359   protected void pasteNew_actionPerformed(ActionEvent e)
2360   {
2361   }
2362
2363   protected void pasteThis_actionPerformed(ActionEvent e)
2364   {
2365   }
2366
2367   protected void applyToAllGroups_actionPerformed(boolean selected)
2368   {
2369   }
2370
2371   public void createPNG(java.io.File f)
2372   {
2373   }
2374
2375   protected void font_actionPerformed(ActionEvent e)
2376   {
2377   }
2378
2379   protected void seqLimit_actionPerformed(ActionEvent e)
2380   {
2381   }
2382
2383   public void seqDBRef_actionPerformed(ActionEvent e)
2384   {
2385
2386   }
2387
2388   public void createEPS(java.io.File f)
2389   {
2390   }
2391
2392   public void createSVG(java.io.File f)
2393   {
2394
2395   }
2396
2397   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2398   {
2399
2400   }
2401
2402   protected void loadTreeUrlItem_actionPerformed(ActionEvent e)
2403   {
2404
2405   }
2406
2407   protected void loadTreeDbItem_actionPerformed(ActionEvent e)
2408   {
2409
2410   }
2411
2412   /**
2413    * Template method to handle the 'load T-Coffee scores' menu event.
2414    * <p>
2415    * Subclasses override this method to provide a custom action.
2416    *
2417    * @param event
2418    *          The raised event
2419    */
2420   protected void loadScores_actionPerformed(ActionEvent event)
2421   {
2422
2423   }
2424
2425   protected void jpred_actionPerformed(ActionEvent e)
2426   {
2427   }
2428
2429   protected void scaleAbove_actionPerformed(ActionEvent e)
2430   {
2431   }
2432
2433   protected void scaleLeft_actionPerformed(ActionEvent e)
2434   {
2435   }
2436
2437   protected void scaleRight_actionPerformed(ActionEvent e)
2438   {
2439   }
2440
2441   protected void modifyPID_actionPerformed()
2442   {
2443   }
2444
2445   protected void modifyConservation_actionPerformed()
2446   {
2447   }
2448
2449   protected void saveAs_actionPerformed(ActionEvent e)
2450   {
2451   }
2452
2453   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2454   {
2455   }
2456
2457   public void vamsasStore_actionPerformed(ActionEvent e)
2458   {
2459
2460   }
2461
2462   public void vamsasLoad_actionPerformed(ActionEvent e)
2463   {
2464
2465   }
2466
2467   public void showTranslation_actionPerformed(ActionEvent e)
2468   {
2469
2470   }
2471
2472   public void featureSettings_actionPerformed(ActionEvent e)
2473   {
2474
2475   }
2476
2477   public void fetchSequence_actionPerformed(ActionEvent e)
2478   {
2479
2480   }
2481
2482   public void smoothFont_actionPerformed(ActionEvent e)
2483   {
2484
2485   }
2486
2487   public void annotationColour_actionPerformed()
2488   {
2489   }
2490
2491   public void annotationColumn_actionPerformed(ActionEvent e)
2492   {
2493   }
2494
2495   public void associatedData_actionPerformed(ActionEvent e)
2496   {
2497
2498   }
2499
2500   public void autoCalculate_actionPerformed(ActionEvent e)
2501   {
2502
2503   }
2504
2505   public void sortByTreeOption_actionPerformed(ActionEvent e)
2506   {
2507
2508   }
2509
2510   public void showAllSeqs_actionPerformed(ActionEvent e)
2511   {
2512
2513   }
2514
2515   public void showAllColumns_actionPerformed(ActionEvent e)
2516   {
2517
2518   }
2519
2520   public void hideSelSequences_actionPerformed(ActionEvent e)
2521   {
2522
2523   }
2524
2525   public void hideSelColumns_actionPerformed(ActionEvent e)
2526   {
2527
2528   }
2529
2530   public void hiddenMarkers_actionPerformed(ActionEvent e)
2531   {
2532
2533   }
2534
2535   public void findPdbId_actionPerformed(ActionEvent e)
2536   {
2537
2538   }
2539
2540   public void enterPdbId_actionPerformed(ActionEvent e)
2541   {
2542
2543   }
2544
2545   public void pdbFile_actionPerformed(ActionEvent e)
2546   {
2547
2548   }
2549
2550   public void invertColSel_actionPerformed(ActionEvent e)
2551   {
2552
2553   }
2554
2555   public void tabSelectionChanged(int sel)
2556   {
2557
2558   }
2559
2560   public void tabbedPane_mousePressed(MouseEvent e)
2561   {
2562
2563   }
2564
2565   public void tabbedPane_focusGained(FocusEvent e)
2566   {
2567     requestFocus();
2568   }
2569
2570   public void save_actionPerformed(ActionEvent e)
2571   {
2572
2573   }
2574
2575   public void reload_actionPerformed(ActionEvent e)
2576   {
2577
2578   }
2579
2580   public void newView_actionPerformed(ActionEvent e)
2581   {
2582
2583   }
2584
2585   public void textColour_actionPerformed()
2586   {
2587
2588   }
2589
2590   public void idRightAlign_actionPerformed(ActionEvent e)
2591   {
2592
2593   }
2594
2595   public void expandViews_actionPerformed(ActionEvent e)
2596   {
2597
2598   }
2599
2600   public void gatherViews_actionPerformed(ActionEvent e)
2601   {
2602
2603   }
2604
2605   public void buildTreeSortMenu()
2606   {
2607
2608   }
2609
2610   public void pageSetup_actionPerformed(ActionEvent e)
2611   {
2612
2613   }
2614
2615   public void alignmentProperties()
2616   {
2617
2618   }
2619
2620   protected void expand_newalign(ActionEvent e)
2621   {
2622     // TODO Auto-generated method stub
2623
2624   }
2625
2626   protected boolean isShowAutoCalculatedAbove()
2627   {
2628     return showAutoCalculatedAbove;
2629   }
2630
2631   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2632   {
2633     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2634   }
2635
2636   protected SequenceAnnotationOrder getAnnotationSortOrder()
2637   {
2638     return annotationSortOrder;
2639   }
2640
2641   protected void setAnnotationSortOrder(
2642           SequenceAnnotationOrder annotationSortOrder)
2643   {
2644     this.annotationSortOrder = annotationSortOrder;
2645   }
2646
2647   public Map<KeyStroke, JMenuItem> getAccelerators()
2648   {
2649     return this.accelerators;
2650   }
2651
2652   /**
2653    * Returns the selected index of the tabbed pane, or -1 if none selected
2654    * (including the case where the tabbed pane has not been made visible).
2655    *
2656    * @return
2657    */
2658   public int getTabIndex()
2659   {
2660     return tabbedPane.getSelectedIndex();
2661   }
2662
2663   public JPanel getStatusPanel()
2664   {
2665     return statusPanel;
2666   }
2667
2668   /**
2669    * Sets a reference to the containing split frame. Also makes the 'toggle
2670    * split view' menu item visible and checked.
2671    *
2672    * @param sf
2673    */
2674   public void setSplitFrame(SplitContainerI sf)
2675   {
2676     this.splitFrame = sf;
2677     if (sf != null)
2678     {
2679       this.showComplementMenuItem.setVisible(true);
2680       this.showComplementMenuItem.setState(true);
2681     }
2682   }
2683
2684   public SplitContainerI getSplitViewContainer()
2685   {
2686     return this.splitFrame;
2687   }
2688
2689   protected void showComplement_actionPerformed(boolean complement)
2690   {
2691   }
2692 }