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
1083     loadTreeFile.addActionListener(new ActionListener()
1084     {
1085       @Override
1086       public void actionPerformed(ActionEvent e)
1087       {
1088         loadTreeMenuItem_actionPerformed(e);
1089       }
1090     });
1091
1092     JMenuItem loadTreeUrl = new JMenuItem(
1093             MessageManager.getString("label.from_url"));
1094     loadTreeUrl.addActionListener(new ActionListener()
1095     {
1096       @Override
1097       public void actionPerformed(ActionEvent e)
1098       {
1099         loadTreeUrlItem_actionPerformed(e);
1100       }
1101     });
1102
1103     JMenuItem loadTreeDb = new JMenuItem(
1104             MessageManager.getString("label.from_database"));
1105     loadTreeDb.addActionListener(new ActionListener()
1106     {
1107       @Override
1108       public void actionPerformed(ActionEvent e)
1109       {
1110         loadTreeDbItem_actionPerformed(e);
1111       }
1112     });
1113
1114     scaleAbove.setVisible(false);
1115     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1116     scaleAbove.addActionListener(new ActionListener()
1117     {
1118       @Override
1119       public void actionPerformed(ActionEvent e)
1120       {
1121         scaleAbove_actionPerformed(e);
1122       }
1123     });
1124     scaleLeft.setVisible(false);
1125     scaleLeft.setSelected(true);
1126     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1127     scaleLeft.addActionListener(new ActionListener()
1128     {
1129       @Override
1130       public void actionPerformed(ActionEvent e)
1131       {
1132         scaleLeft_actionPerformed(e);
1133       }
1134     });
1135     scaleRight.setVisible(false);
1136     scaleRight.setSelected(true);
1137     scaleRight.setText(MessageManager.getString("action.scale_right"));
1138     scaleRight.addActionListener(new ActionListener()
1139     {
1140       @Override
1141       public void actionPerformed(ActionEvent e)
1142       {
1143         scaleRight_actionPerformed(e);
1144       }
1145     });
1146     centreColumnLabelsMenuItem.setVisible(true);
1147     centreColumnLabelsMenuItem.setState(false);
1148     centreColumnLabelsMenuItem.setText(
1149             MessageManager.getString("label.centre_column_labels"));
1150     centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1151     {
1152       @Override
1153       public void actionPerformed(ActionEvent e)
1154       {
1155         centreColumnLabels_actionPerformed(e);
1156       }
1157     });
1158     followHighlightMenuItem.setVisible(true);
1159     followHighlightMenuItem.setState(true);
1160     followHighlightMenuItem
1161             .setText(MessageManager.getString("label.automatic_scrolling"));
1162     followHighlightMenuItem.addActionListener(new ActionListener()
1163     {
1164
1165       @Override
1166       public void actionPerformed(ActionEvent e)
1167       {
1168         followHighlight_actionPerformed();
1169       }
1170
1171     });
1172
1173     sortByTreeMenu
1174             .setText(MessageManager.getString("action.by_tree_order"));
1175     sort.setText(MessageManager.getString("action.sort"));
1176     sort.addMenuListener(new MenuListener()
1177     {
1178       @Override
1179       public void menuSelected(MenuEvent e)
1180       {
1181         buildTreeSortMenu();
1182       }
1183
1184       @Override
1185       public void menuDeselected(MenuEvent e)
1186       {
1187       }
1188
1189       @Override
1190       public void menuCanceled(MenuEvent e)
1191       {
1192       }
1193     });
1194     sortByAnnotScore
1195             .setText(MessageManager.getString("label.sort_by_score"));
1196     sort.add(sortByAnnotScore);
1197     sort.addMenuListener(new javax.swing.event.MenuListener()
1198     {
1199
1200       @Override
1201       public void menuCanceled(MenuEvent e)
1202       {
1203       }
1204
1205       @Override
1206       public void menuDeselected(MenuEvent e)
1207       {
1208       }
1209
1210       @Override
1211       public void menuSelected(MenuEvent e)
1212       {
1213         buildSortByAnnotationScoresMenu();
1214       }
1215     });
1216     sortByAnnotScore.setVisible(false);
1217
1218     calculateTree
1219             .setText(MessageManager.getString("action.calculate_tree_pca"));
1220
1221     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1222     padGapsMenuitem
1223             .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
1224     padGapsMenuitem.addActionListener(new ActionListener()
1225     {
1226       @Override
1227       public void actionPerformed(ActionEvent e)
1228       {
1229         padGapsMenuitem_actionPerformed(e);
1230       }
1231     });
1232     JMenuItem vamsasStore = new JMenuItem(
1233             MessageManager.getString("label.vamsas_store"));
1234     vamsasStore.setVisible(false);
1235     vamsasStore.addActionListener(new ActionListener()
1236     {
1237       @Override
1238       public void actionPerformed(ActionEvent e)
1239       {
1240         vamsasStore_actionPerformed(e);
1241       }
1242     });
1243     showTranslation
1244             .setText(MessageManager.getString("label.translate_cDNA"));
1245     showTranslation.addActionListener(new ActionListener()
1246     {
1247       @Override
1248       public void actionPerformed(ActionEvent e)
1249       {
1250         showTranslation_actionPerformed(e);
1251       }
1252     });
1253     showReverse.setText(MessageManager.getString("label.reverse"));
1254     showReverse.addActionListener(new ActionListener()
1255     {
1256       @Override
1257       public void actionPerformed(ActionEvent e)
1258       {
1259         showReverse_actionPerformed(false);
1260       }
1261     });
1262     showReverseComplement
1263             .setText(MessageManager.getString("label.reverse_complement"));
1264     showReverseComplement.addActionListener(new ActionListener()
1265     {
1266       @Override
1267       public void actionPerformed(ActionEvent e)
1268       {
1269         showReverse_actionPerformed(true);
1270       }
1271     });
1272
1273     JMenuItem extractScores = new JMenuItem(
1274             MessageManager.getString("label.extract_scores"));
1275     extractScores.addActionListener(new ActionListener()
1276     {
1277       @Override
1278       public void actionPerformed(ActionEvent e)
1279       {
1280         extractScores_actionPerformed(e);
1281       }
1282     });
1283     extractScores.setVisible(true);
1284     // JBPNote: TODO: make gui for regex based score extraction
1285
1286     // for show products actions see AlignFrame.canShowProducts
1287     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1288
1289     runGroovy.setText(MessageManager.getString("label.run_groovy"));
1290     runGroovy.setToolTipText(
1291             MessageManager.getString("label.run_groovy_tip"));
1292     runGroovy.addActionListener(new ActionListener()
1293     {
1294       @Override
1295       public void actionPerformed(ActionEvent e)
1296       {
1297         runGroovy_actionPerformed();
1298       }
1299     });
1300
1301     JMenuItem openFeatureSettings = new JMenuItem(
1302             MessageManager.getString("action.feature_settings"));
1303     openFeatureSettings.addActionListener(new ActionListener()
1304     {
1305       @Override
1306       public void actionPerformed(ActionEvent e)
1307       {
1308         featureSettings_actionPerformed(e);
1309       }
1310     });
1311     JMenuItem fetchSequence = new JMenuItem(
1312             MessageManager.getString("label.fetch_sequences"));
1313     fetchSequence.addActionListener(new ActionListener()
1314     {
1315       @Override
1316       public void actionPerformed(ActionEvent e)
1317       {
1318         fetchSequence_actionPerformed(e);
1319       }
1320     });
1321
1322     JMenuItem associatedData = new JMenuItem(
1323             MessageManager.getString("label.load_features_annotations"));
1324     associatedData.addActionListener(new ActionListener()
1325     {
1326       @Override
1327       public void actionPerformed(ActionEvent e)
1328       {
1329         associatedData_actionPerformed(e);
1330       }
1331     });
1332     autoCalculate.setText(
1333             MessageManager.getString("label.autocalculate_consensus"));
1334     autoCalculate.setState(
1335             jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1336     autoCalculate.addActionListener(new ActionListener()
1337     {
1338       @Override
1339       public void actionPerformed(ActionEvent e)
1340       {
1341         autoCalculate_actionPerformed(e);
1342       }
1343     });
1344     sortByTree.setText(
1345             MessageManager.getString("label.sort_alignment_new_tree"));
1346     sortByTree.setToolTipText("<html>" + MessageManager.getString(
1347             "label.enable_automatically_sort_alignment_when_open_new_tree"));
1348     sortByTree
1349             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1350     sortByTree.addActionListener(new ActionListener()
1351     {
1352       @Override
1353       public void actionPerformed(ActionEvent e)
1354       {
1355         sortByTreeOption_actionPerformed(e);
1356       }
1357     });
1358
1359     listenToViewSelections.setText(
1360             MessageManager.getString("label.listen_for_selections"));
1361     listenToViewSelections
1362             .setToolTipText("<html>" + MessageManager.getString(
1363                     "label.selections_mirror_selections_made_same_sequences_other_views"));
1364     listenToViewSelections.setState(false);
1365     listenToViewSelections.addActionListener(new ActionListener()
1366     {
1367       @Override
1368       public void actionPerformed(ActionEvent e)
1369       {
1370         listenToViewSelections_actionPerformed(e);
1371       }
1372     });
1373
1374     JMenu addSequenceMenu = new JMenu(
1375             MessageManager.getString("label.add_sequences"));
1376     JMenuItem addFromFile = new JMenuItem(
1377             MessageManager.getString("label.from_file"));
1378     addFromFile.addActionListener(new ActionListener()
1379     {
1380       @Override
1381       public void actionPerformed(ActionEvent e)
1382       {
1383         addFromFile_actionPerformed(e);
1384       }
1385     });
1386     JMenuItem addFromText = new JMenuItem(
1387             MessageManager.getString("label.from_textbox"));
1388     addFromText.addActionListener(new ActionListener()
1389     {
1390       @Override
1391       public void actionPerformed(ActionEvent e)
1392       {
1393         addFromText_actionPerformed(e);
1394       }
1395     });
1396     JMenuItem addFromURL = new JMenuItem(
1397             MessageManager.getString("label.from_url"));
1398     addFromURL.addActionListener(new ActionListener()
1399     {
1400       @Override
1401       public void actionPerformed(ActionEvent e)
1402       {
1403         addFromURL_actionPerformed(e);
1404       }
1405     });
1406     JMenuItem exportFeatures = new JMenuItem(
1407             MessageManager.getString("label.export_features"));
1408     exportFeatures.addActionListener(new ActionListener()
1409     {
1410       @Override
1411       public void actionPerformed(ActionEvent e)
1412       {
1413         exportFeatures_actionPerformed(e);
1414       }
1415     });
1416     JMenuItem exportAnnotations = new JMenuItem(
1417             MessageManager.getString("label.export_annotations"));
1418     exportAnnotations.addActionListener(new ActionListener()
1419     {
1420       @Override
1421       public void actionPerformed(ActionEvent e)
1422       {
1423         exportAnnotations_actionPerformed(e);
1424       }
1425     });
1426     statusPanel.setLayout(new GridLayout());
1427     JMenuItem showAllSeqs = new JMenuItem(
1428             MessageManager.getString("label.all_sequences"));
1429     showAllSeqs.setToolTipText(
1430             MessageManager.getString("label.toggle_sequence_visibility"));
1431     showAllSeqs.addActionListener(new ActionListener()
1432     {
1433       @Override
1434       public void actionPerformed(ActionEvent e)
1435       {
1436         showAllSeqs_actionPerformed(e);
1437       }
1438     });
1439     JMenuItem showAllColumns = new JMenuItem(
1440             MessageManager.getString("label.all_columns"));
1441     showAllColumns.setToolTipText(
1442             MessageManager.getString("label.toggle_columns_visibility"));
1443     showAllColumns.addActionListener(new ActionListener()
1444     {
1445       @Override
1446       public void actionPerformed(ActionEvent e)
1447       {
1448         showAllColumns_actionPerformed(e);
1449       }
1450     });
1451     JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1452     JMenuItem hideSelSequences = new JMenuItem(
1453             MessageManager.getString("label.selected_sequences"));
1454     hideSelSequences.setToolTipText(
1455             MessageManager.getString("label.toggle_sequence_visibility"));
1456     hideSelSequences.addActionListener(new ActionListener()
1457     {
1458       @Override
1459       public void actionPerformed(ActionEvent e)
1460       {
1461         hideSelSequences_actionPerformed(e);
1462       }
1463     });
1464     JMenuItem hideSelColumns = new JMenuItem(
1465             MessageManager.getString("label.selected_columns"));
1466     hideSelColumns.setToolTipText(
1467             MessageManager.getString("label.toggle_columns_visibility"));
1468     hideSelColumns.addActionListener(new ActionListener()
1469     {
1470       @Override
1471       public void actionPerformed(ActionEvent e)
1472       {
1473         hideSelColumns_actionPerformed(e);
1474       }
1475     });
1476     JMenuItem hideAllSelection = new JMenuItem(
1477             MessageManager.getString("label.selected_region"));
1478     hideAllSelection.addActionListener(new ActionListener()
1479     {
1480       @Override
1481       public void actionPerformed(ActionEvent e)
1482       {
1483         hideAllSelection_actionPerformed(e);
1484       }
1485     });
1486     // TODO: should be hidden if no selection exists.
1487     JMenuItem hideAllButSelection = new JMenuItem(
1488             MessageManager.getString("label.all_but_selected_region"));
1489     hideAllButSelection.addActionListener(new ActionListener()
1490     {
1491       @Override
1492       public void actionPerformed(ActionEvent e)
1493       {
1494         hideAllButSelection_actionPerformed(e);
1495       }
1496     });
1497     JMenuItem showAllhidden = new JMenuItem(
1498             MessageManager.getString("label.all_sequences_columns"));
1499     showAllhidden.setToolTipText(MessageManager
1500             .getString("label.toggles_visibility_hidden_selected_regions"));
1501     showAllhidden.addActionListener(new ActionListener()
1502     {
1503       @Override
1504       public void actionPerformed(ActionEvent e)
1505       {
1506         showAllhidden_actionPerformed(e);
1507       }
1508     });
1509     hiddenMarkers.setText(
1510             MessageManager.getString("action.show_hidden_markers"));
1511     hiddenMarkers.addActionListener(new ActionListener()
1512     {
1513       @Override
1514       public void actionPerformed(ActionEvent e)
1515       {
1516         hiddenMarkers_actionPerformed(e);
1517       }
1518     });
1519
1520     JMenuItem invertColSel = new JMenuItem(
1521             MessageManager.getString("action.invert_column_selection"));
1522     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1523             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1524                     | KeyEvent.ALT_MASK,
1525             false);
1526     al = new ActionListener()
1527     {
1528       @Override
1529       public void actionPerformed(ActionEvent e)
1530       {
1531         invertColSel_actionPerformed(e);
1532       }
1533     };
1534     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1535
1536     showComplementMenuItem.setVisible(false);
1537     showComplementMenuItem.addActionListener(new ActionListener()
1538     {
1539       @Override
1540       public void actionPerformed(ActionEvent e)
1541       {
1542         showComplement_actionPerformed(showComplementMenuItem.getState());
1543       }
1544     });
1545
1546     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1547     {
1548       @Override
1549       public void stateChanged(ChangeEvent evt)
1550       {
1551         JTabbedPane pane = (JTabbedPane) evt.getSource();
1552         int sel = pane.getSelectedIndex();
1553         tabSelectionChanged(sel);
1554       }
1555     });
1556     tabbedPane.addMouseListener(new MouseAdapter()
1557     {
1558       @Override
1559       public void mousePressed(MouseEvent e)
1560       {
1561         if (e.isPopupTrigger()) // Mac
1562         {
1563           tabbedPane_mousePressed(e);
1564         }
1565       }
1566
1567       @Override
1568       public void mouseReleased(MouseEvent e)
1569       {
1570         if (e.isPopupTrigger()) // Windows
1571         {
1572           tabbedPane_mousePressed(e);
1573         }
1574       }
1575     });
1576     tabbedPane.addFocusListener(new FocusAdapter()
1577     {
1578       @Override
1579       public void focusGained(FocusEvent e)
1580       {
1581         tabbedPane_focusGained(e);
1582       }
1583     });
1584
1585     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1586     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1587             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1588     al = new ActionListener()
1589     {
1590       @Override
1591       public void actionPerformed(ActionEvent e)
1592       {
1593         save_actionPerformed(e);
1594       }
1595     };
1596     addMenuActionAndAccelerator(keyStroke, save, al);
1597
1598     reload.setEnabled(false);
1599     reload.setText(MessageManager.getString("action.reload"));
1600     reload.addActionListener(new ActionListener()
1601     {
1602       @Override
1603       public void actionPerformed(ActionEvent e)
1604       {
1605         reload_actionPerformed(e);
1606       }
1607     });
1608
1609     JMenuItem newView = new JMenuItem(
1610             MessageManager.getString("action.new_view"));
1611     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1612             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1613     al = new ActionListener()
1614     {
1615       @Override
1616       public void actionPerformed(ActionEvent e)
1617       {
1618         newView_actionPerformed(e);
1619       }
1620     };
1621     addMenuActionAndAccelerator(keyStroke, newView, al);
1622
1623     tabbedPane.setToolTipText("<html><i>"
1624             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1625             + "</i></html>");
1626
1627     formatMenu.setText(MessageManager.getString("action.format"));
1628     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1629
1630     idRightAlign.setText(
1631             MessageManager.getString("label.right_align_sequence_id"));
1632     idRightAlign.addActionListener(new ActionListener()
1633     {
1634       @Override
1635       public void actionPerformed(ActionEvent e)
1636       {
1637         idRightAlign_actionPerformed(e);
1638       }
1639     });
1640
1641     gatherViews.setEnabled(false);
1642     gatherViews.setText(MessageManager.getString("action.gather_views"));
1643     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1644     al = new ActionListener()
1645     {
1646       @Override
1647       public void actionPerformed(ActionEvent e)
1648       {
1649         gatherViews_actionPerformed(e);
1650       }
1651     };
1652     addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1653
1654     expandViews.setEnabled(false);
1655     expandViews.setText(MessageManager.getString("action.expand_views"));
1656     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1657     al = new ActionListener()
1658     {
1659       @Override
1660       public void actionPerformed(ActionEvent e)
1661       {
1662         expandViews_actionPerformed(e);
1663       }
1664     };
1665     addMenuActionAndAccelerator(keyStroke, expandViews, al);
1666
1667     JMenuItem pageSetup = new JMenuItem(
1668             MessageManager.getString("action.page_setup"));
1669     pageSetup.addActionListener(new ActionListener()
1670     {
1671       @Override
1672       public void actionPerformed(ActionEvent e)
1673       {
1674         pageSetup_actionPerformed(e);
1675       }
1676     });
1677     JMenuItem alignmentProperties = new JMenuItem(
1678             MessageManager.getString("label.alignment_props"));
1679     alignmentProperties.addActionListener(new ActionListener()
1680     {
1681       @Override
1682       public void actionPerformed(ActionEvent actionEvent)
1683       {
1684         alignmentProperties();
1685       }
1686     });
1687     JMenuItem selectHighlighted = new JMenuItem(
1688             MessageManager.getString("action.select_highlighted_columns"));
1689     selectHighlighted.setToolTipText(
1690             MessageManager.getString("tooltip.select_highlighted_columns"));
1691     al = new ActionListener()
1692     {
1693       @Override
1694       public void actionPerformed(ActionEvent actionEvent)
1695       {
1696         selectHighlightedColumns_actionPerformed(actionEvent);
1697       }
1698     };
1699     selectHighlighted.addActionListener(al);
1700     JMenu tooltipSettingsMenu = new JMenu(
1701             MessageManager.getString("label.sequence_id_tooltip"));
1702     JMenu autoAnnMenu = new JMenu(
1703             MessageManager.getString("label.autocalculated_annotation"));
1704
1705     JMenu exportImageMenu = new JMenu(
1706             MessageManager.getString("label.export_image"));
1707     JMenu loadTreeMenu = new JMenu(
1708             MessageManager.getString("label.load_associated_tree"));
1709     // loadTreeMenu.setToolTipText(
1710     // MessageManager.getString("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
1891   /**
1892    * Constructs the entries on the Colour menu (but does not add them to the
1893    * menu).
1894    */
1895   protected void initColourMenu()
1896   {
1897     applyToAllGroups = new JCheckBoxMenuItem(
1898             MessageManager.getString("label.apply_colour_to_all_groups"));
1899     applyToAllGroups.addActionListener(new ActionListener()
1900     {
1901       @Override
1902       public void actionPerformed(ActionEvent e)
1903       {
1904         applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1905       }
1906     });
1907
1908     textColour = new JMenuItem(
1909             MessageManager.getString("label.text_colour"));
1910     textColour.addActionListener(new ActionListener()
1911     {
1912       @Override
1913       public void actionPerformed(ActionEvent e)
1914       {
1915         textColour_actionPerformed();
1916       }
1917     });
1918
1919     conservationMenuItem = new JCheckBoxMenuItem(
1920             MessageManager.getString("action.by_conservation"));
1921     conservationMenuItem.addActionListener(new ActionListener()
1922     {
1923       @Override
1924       public void actionPerformed(ActionEvent e)
1925       {
1926         conservationMenuItem_actionPerformed(
1927                 conservationMenuItem.isSelected());
1928       }
1929     });
1930
1931     abovePIDThreshold = new JCheckBoxMenuItem(
1932             MessageManager.getString("label.above_identity_threshold"));
1933     abovePIDThreshold.addActionListener(new ActionListener()
1934     {
1935       @Override
1936       public void actionPerformed(ActionEvent e)
1937       {
1938         abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
1939       }
1940     });
1941     modifyPID = new JMenuItem(
1942             MessageManager.getString("label.modify_identity_threshold"));
1943     modifyPID.addActionListener(new ActionListener()
1944     {
1945       @Override
1946       public void actionPerformed(ActionEvent e)
1947       {
1948         modifyPID_actionPerformed();
1949       }
1950     });
1951     modifyConservation = new JMenuItem(MessageManager
1952             .getString("label.modify_conservation_threshold"));
1953     modifyConservation.addActionListener(new ActionListener()
1954     {
1955       @Override
1956       public void actionPerformed(ActionEvent e)
1957       {
1958         modifyConservation_actionPerformed();
1959       }
1960     });
1961
1962     annotationColour = new JMenuItem(
1963             MessageManager.getString("action.by_annotation"));
1964     annotationColour.addActionListener(new ActionListener()
1965     {
1966       @Override
1967       public void actionPerformed(ActionEvent e)
1968       {
1969         annotationColour_actionPerformed();
1970       }
1971     });
1972   }
1973
1974   protected void selectHighlightedColumns_actionPerformed(
1975           ActionEvent actionEvent)
1976   {
1977     // TODO Auto-generated method stub
1978
1979   }
1980
1981   /**
1982    * Generate the reverse sequence (or reverse complement if the flag is true)
1983    * and add it to the alignment
1984    *
1985    * @param complement
1986    */
1987   protected void showReverse_actionPerformed(boolean complement)
1988   {
1989   }
1990
1991   /**
1992    * Try to run script in a Groovy console, having first ensured that this
1993    * alignframe is set as currentAlignFrame in Desktop
1994    */
1995   protected void runGroovy_actionPerformed()
1996   {
1997
1998   }
1999
2000   /**
2001    * Adds the given action listener and key accelerator to the given menu item.
2002    * Also saves in a lookup table to support lookup of action by key stroke.
2003    *
2004    * @param keyStroke
2005    * @param menuItem
2006    * @param actionListener
2007    */
2008   protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2009           JMenuItem menuItem, ActionListener actionListener)
2010   {
2011     menuItem.setAccelerator(keyStroke);
2012     accelerators.put(keyStroke, menuItem);
2013     menuItem.addActionListener(actionListener);
2014   }
2015
2016   /**
2017    * Action on clicking sort annotations by type.
2018    *
2019    * @param sortOrder
2020    */
2021   protected void sortAnnotations_actionPerformed()
2022   {
2023   }
2024
2025   /**
2026    * Action on clicking Show all annotations.
2027    *
2028    * @param forSequences
2029    *          update sequence-related annotations
2030    * @param forAlignment
2031    *          update non-sequence-related annotations
2032    */
2033   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2034           boolean forAlignment)
2035   {
2036     setAnnotationsVisibility(true, forSequences, forAlignment);
2037   }
2038
2039   /**
2040    * Action on clicking Hide all annotations.
2041    *
2042    * @param forSequences
2043    *          update sequence-related annotations
2044    * @param forAlignment
2045    *          update non-sequence-related annotations
2046    */
2047   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2048           boolean forAlignment)
2049   {
2050     setAnnotationsVisibility(false, forSequences, forAlignment);
2051   }
2052
2053   /**
2054    * Set the visibility of annotations to true or false. Can act on
2055    * sequence-related annotations, or alignment-related, or both.
2056    *
2057    * @param visible
2058    * @param forSequences
2059    *          update sequence-related annotations
2060    * @param forAlignment
2061    *          update non-sequence-related annotations
2062    */
2063   protected void setAnnotationsVisibility(boolean visible,
2064           boolean forSequences, boolean forAlignment)
2065   {
2066
2067   }
2068
2069   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2070   {
2071     // TODO Auto-generated method stub
2072
2073   }
2074
2075   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2076   {
2077     // TODO Auto-generated method stub
2078
2079   }
2080
2081   protected void showAllhidden_actionPerformed(ActionEvent e)
2082   {
2083     // TODO Auto-generated method stub
2084
2085   }
2086
2087   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2088   {
2089     // TODO Auto-generated method stub
2090
2091   }
2092
2093   protected void hideAllSelection_actionPerformed(ActionEvent e)
2094   {
2095     // TODO Auto-generated method stub
2096
2097   }
2098
2099   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2100   {
2101     // TODO Auto-generated method stub
2102
2103   }
2104
2105   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2106   {
2107     // TODO Auto-generated method stub
2108
2109   }
2110
2111   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2112   {
2113     // TODO Auto-generated method stub
2114
2115   }
2116
2117   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2118   {
2119     // TODO Auto-generated method stub
2120
2121   }
2122
2123   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2124   {
2125     // TODO Auto-generated method stub
2126
2127   }
2128
2129   protected void showGroupConservation_actionPerformed(ActionEvent e)
2130   {
2131     // TODO Auto-generated method stub
2132
2133   }
2134
2135   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2136   {
2137     // TODO Auto-generated method stub
2138
2139   }
2140
2141   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2142   {
2143     // TODO Auto-generated method stub
2144
2145   }
2146
2147   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2148   {
2149     // TODO Auto-generated method stub
2150
2151   }
2152
2153   protected void followHighlight_actionPerformed()
2154   {
2155     // TODO Auto-generated method stub
2156
2157   }
2158
2159   protected void showNpFeats_actionPerformed(ActionEvent e)
2160   {
2161     // TODO Auto-generated method stub
2162
2163   }
2164
2165   protected void showDbRefs_actionPerformed(ActionEvent e)
2166   {
2167     // TODO Auto-generated method stub
2168
2169   }
2170
2171   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2172   {
2173   }
2174
2175   protected void buildSortByAnnotationScoresMenu()
2176   {
2177   }
2178
2179   protected void extractScores_actionPerformed(ActionEvent e)
2180   {
2181   }
2182
2183   protected void outputText_actionPerformed(ActionEvent e)
2184   {
2185   }
2186
2187   public void addFromFile_actionPerformed(ActionEvent e)
2188   {
2189
2190   }
2191
2192   public void addFromText_actionPerformed(ActionEvent e)
2193   {
2194
2195   }
2196
2197   public void addFromURL_actionPerformed(ActionEvent e)
2198   {
2199
2200   }
2201
2202   public void exportFeatures_actionPerformed(ActionEvent e)
2203   {
2204
2205   }
2206
2207   public void exportAnnotations_actionPerformed(ActionEvent e)
2208   {
2209
2210   }
2211
2212   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2213   {
2214   }
2215
2216   protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2217   {
2218
2219   }
2220
2221   protected void closeMenuItem_actionPerformed(boolean b)
2222   {
2223   }
2224
2225   protected void redoMenuItem_actionPerformed(ActionEvent e)
2226   {
2227   }
2228
2229   protected void undoMenuItem_actionPerformed(ActionEvent e)
2230   {
2231   }
2232
2233   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2234   {
2235   }
2236
2237   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2238   {
2239   }
2240
2241   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2242   {
2243   }
2244
2245   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2246   {
2247   }
2248
2249   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2250   {
2251   }
2252
2253   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2254   {
2255   }
2256
2257   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2258   {
2259   }
2260
2261   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2262   {
2263   }
2264
2265   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2266   {
2267   }
2268
2269   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2270   {
2271   }
2272
2273   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2274   {
2275   }
2276
2277   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2278   {
2279   }
2280
2281   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2282   {
2283   }
2284
2285   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2286   {
2287   }
2288
2289   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2290   {
2291   }
2292
2293   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2294   {
2295   }
2296
2297   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2298   {
2299   }
2300
2301   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2302   {
2303   }
2304
2305   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2306   {
2307   }
2308
2309   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2310   {
2311   }
2312
2313   protected void conservationMenuItem_actionPerformed(boolean selected)
2314   {
2315   }
2316
2317   protected void printMenuItem_actionPerformed(ActionEvent e)
2318   {
2319   }
2320
2321   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2322   {
2323   }
2324
2325   protected void findMenuItem_actionPerformed(ActionEvent e)
2326   {
2327   }
2328
2329   protected void abovePIDThreshold_actionPerformed(boolean selected)
2330   {
2331   }
2332
2333   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2334   {
2335   }
2336
2337   protected void deleteGroups_actionPerformed(ActionEvent e)
2338   {
2339   }
2340
2341   protected void createGroup_actionPerformed(ActionEvent e)
2342   {
2343   }
2344
2345   protected void unGroup_actionPerformed(ActionEvent e)
2346   {
2347   }
2348
2349   protected void copy_actionPerformed(ActionEvent e)
2350   {
2351   }
2352
2353   protected void cut_actionPerformed(ActionEvent e)
2354   {
2355   }
2356
2357   protected void delete_actionPerformed(ActionEvent e)
2358   {
2359   }
2360
2361   protected void pasteNew_actionPerformed(ActionEvent e)
2362   {
2363   }
2364
2365   protected void pasteThis_actionPerformed(ActionEvent e)
2366   {
2367   }
2368
2369   protected void applyToAllGroups_actionPerformed(boolean selected)
2370   {
2371   }
2372
2373   public void createPNG(java.io.File f)
2374   {
2375   }
2376
2377   protected void font_actionPerformed(ActionEvent e)
2378   {
2379   }
2380
2381   protected void seqLimit_actionPerformed(ActionEvent e)
2382   {
2383   }
2384
2385   public void seqDBRef_actionPerformed(ActionEvent e)
2386   {
2387
2388   }
2389
2390   public void createEPS(java.io.File f)
2391   {
2392   }
2393
2394   public void createSVG(java.io.File f)
2395   {
2396
2397   }
2398
2399   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2400   {
2401
2402   }
2403
2404   protected void loadTreeUrlItem_actionPerformed(ActionEvent e)
2405   {
2406
2407   }
2408
2409   protected void loadTreeDbItem_actionPerformed(ActionEvent e)
2410   {
2411
2412   }
2413
2414   /**
2415    * Template method to handle the 'load T-Coffee scores' menu event.
2416    * <p>
2417    * Subclasses override this method to provide a custom action.
2418    *
2419    * @param event
2420    *          The raised event
2421    */
2422   protected void loadScores_actionPerformed(ActionEvent event)
2423   {
2424
2425   }
2426
2427   protected void jpred_actionPerformed(ActionEvent e)
2428   {
2429   }
2430
2431   protected void scaleAbove_actionPerformed(ActionEvent e)
2432   {
2433   }
2434
2435   protected void scaleLeft_actionPerformed(ActionEvent e)
2436   {
2437   }
2438
2439   protected void scaleRight_actionPerformed(ActionEvent e)
2440   {
2441   }
2442
2443   protected void modifyPID_actionPerformed()
2444   {
2445   }
2446
2447   protected void modifyConservation_actionPerformed()
2448   {
2449   }
2450
2451   protected void saveAs_actionPerformed(ActionEvent e)
2452   {
2453   }
2454
2455   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2456   {
2457   }
2458
2459   public void vamsasStore_actionPerformed(ActionEvent e)
2460   {
2461
2462   }
2463
2464   public void vamsasLoad_actionPerformed(ActionEvent e)
2465   {
2466
2467   }
2468
2469   public void showTranslation_actionPerformed(ActionEvent e)
2470   {
2471
2472   }
2473
2474   public void featureSettings_actionPerformed(ActionEvent e)
2475   {
2476
2477   }
2478
2479   public void fetchSequence_actionPerformed(ActionEvent e)
2480   {
2481
2482   }
2483
2484   public void smoothFont_actionPerformed(ActionEvent e)
2485   {
2486
2487   }
2488
2489   public void annotationColour_actionPerformed()
2490   {
2491   }
2492
2493   public void annotationColumn_actionPerformed(ActionEvent e)
2494   {
2495   }
2496
2497   public void associatedData_actionPerformed(ActionEvent e)
2498   {
2499
2500   }
2501
2502   public void autoCalculate_actionPerformed(ActionEvent e)
2503   {
2504
2505   }
2506
2507   public void sortByTreeOption_actionPerformed(ActionEvent e)
2508   {
2509
2510   }
2511
2512   public void showAllSeqs_actionPerformed(ActionEvent e)
2513   {
2514
2515   }
2516
2517   public void showAllColumns_actionPerformed(ActionEvent e)
2518   {
2519
2520   }
2521
2522   public void hideSelSequences_actionPerformed(ActionEvent e)
2523   {
2524
2525   }
2526
2527   public void hideSelColumns_actionPerformed(ActionEvent e)
2528   {
2529
2530   }
2531
2532   public void hiddenMarkers_actionPerformed(ActionEvent e)
2533   {
2534
2535   }
2536
2537   public void findPdbId_actionPerformed(ActionEvent e)
2538   {
2539
2540   }
2541
2542   public void enterPdbId_actionPerformed(ActionEvent e)
2543   {
2544
2545   }
2546
2547   public void pdbFile_actionPerformed(ActionEvent e)
2548   {
2549
2550   }
2551
2552   public void invertColSel_actionPerformed(ActionEvent e)
2553   {
2554
2555   }
2556
2557   public void tabSelectionChanged(int sel)
2558   {
2559
2560   }
2561
2562   public void tabbedPane_mousePressed(MouseEvent e)
2563   {
2564
2565   }
2566
2567   public void tabbedPane_focusGained(FocusEvent e)
2568   {
2569     requestFocus();
2570   }
2571
2572   public void save_actionPerformed(ActionEvent e)
2573   {
2574
2575   }
2576
2577   public void reload_actionPerformed(ActionEvent e)
2578   {
2579
2580   }
2581
2582   public void newView_actionPerformed(ActionEvent e)
2583   {
2584
2585   }
2586
2587   public void textColour_actionPerformed()
2588   {
2589
2590   }
2591
2592   public void idRightAlign_actionPerformed(ActionEvent e)
2593   {
2594
2595   }
2596
2597   public void expandViews_actionPerformed(ActionEvent e)
2598   {
2599
2600   }
2601
2602   public void gatherViews_actionPerformed(ActionEvent e)
2603   {
2604
2605   }
2606
2607   public void buildTreeSortMenu()
2608   {
2609
2610   }
2611
2612   public void pageSetup_actionPerformed(ActionEvent e)
2613   {
2614
2615   }
2616
2617   public void alignmentProperties()
2618   {
2619
2620   }
2621
2622   protected void expand_newalign(ActionEvent e)
2623   {
2624     // TODO Auto-generated method stub
2625
2626   }
2627
2628   protected boolean isShowAutoCalculatedAbove()
2629   {
2630     return showAutoCalculatedAbove;
2631   }
2632
2633   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2634   {
2635     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2636   }
2637
2638   protected SequenceAnnotationOrder getAnnotationSortOrder()
2639   {
2640     return annotationSortOrder;
2641   }
2642
2643   protected void setAnnotationSortOrder(
2644           SequenceAnnotationOrder annotationSortOrder)
2645   {
2646     this.annotationSortOrder = annotationSortOrder;
2647   }
2648
2649   public Map<KeyStroke, JMenuItem> getAccelerators()
2650   {
2651     return this.accelerators;
2652   }
2653
2654   /**
2655    * Returns the selected index of the tabbed pane, or -1 if none selected
2656    * (including the case where the tabbed pane has not been made visible).
2657    *
2658    * @return
2659    */
2660   public int getTabIndex()
2661   {
2662     return tabbedPane.getSelectedIndex();
2663   }
2664
2665   public JPanel getStatusPanel()
2666   {
2667     return statusPanel;
2668   }
2669
2670   /**
2671    * Sets a reference to the containing split frame. Also makes the 'toggle
2672    * split view' menu item visible and checked.
2673    *
2674    * @param sf
2675    */
2676   public void setSplitFrame(SplitContainerI sf)
2677   {
2678     this.splitFrame = sf;
2679     if (sf != null)
2680     {
2681       this.showComplementMenuItem.setVisible(true);
2682       this.showComplementMenuItem.setState(true);
2683     }
2684   }
2685
2686   public SplitContainerI getSplitViewContainer()
2687   {
2688     return this.splitFrame;
2689   }
2690
2691   protected void showComplement_actionPerformed(boolean complement)
2692   {
2693   }
2694 }