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
1104
1105     JMenuItem loadTreeBaseStudy = new JMenuItem(
1106             MessageManager.getString("label.treebase_study"));
1107     loadTreeBaseStudy.addActionListener(new ActionListener()
1108     {
1109
1110       @Override
1111       public void actionPerformed(ActionEvent e)
1112       {
1113         loadTreeBaseStudy_actionPerformed(e);
1114
1115       }    });
1116
1117
1118
1119     JMenuItem loadTreeBase = new JMenuItem(
1120             MessageManager.getString("label.treebase"));
1121     loadTreeBase.addActionListener(new ActionListener()
1122     {
1123
1124       @Override
1125       public void actionPerformed(ActionEvent e)
1126       {
1127         loadTreeBase_actionPerformed(e);
1128
1129       }
1130
1131
1132     });
1133     JMenuItem loadTreePfam = new JMenuItem(
1134             MessageManager.getString("label.pfam"));
1135     loadTreePfam.addActionListener(new ActionListener()
1136     {
1137
1138       @Override
1139       public void actionPerformed(ActionEvent e)
1140       {
1141         loadTreePfam_actionPerformed(e);
1142
1143       }
1144
1145     });
1146     JMenuItem loadTreeFam = new JMenuItem(
1147             MessageManager.getString("label.treefam"));
1148     loadTreeFam.addActionListener(new ActionListener()
1149     {
1150
1151       @Override
1152       public void actionPerformed(ActionEvent e)
1153       {
1154         loadTreeFam_actionPerformed(e);
1155
1156       }
1157
1158     });
1159
1160     JMenuItem loadTreeOfLife = new JMenuItem(
1161             MessageManager.getString("label.tree_of_life"));
1162     loadTreeOfLife.addActionListener(new ActionListener()
1163     {
1164
1165       @Override
1166       public void actionPerformed(ActionEvent e)
1167       {
1168         loadTreeOfLife_actionPerformed(e);
1169
1170       }
1171
1172
1173     });
1174
1175     scaleAbove.setVisible(false);
1176     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1177     scaleAbove.addActionListener(new ActionListener()
1178     {
1179       @Override
1180       public void actionPerformed(ActionEvent e)
1181       {
1182         scaleAbove_actionPerformed(e);
1183       }
1184     });
1185     scaleLeft.setVisible(false);
1186     scaleLeft.setSelected(true);
1187     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1188     scaleLeft.addActionListener(new ActionListener()
1189     {
1190       @Override
1191       public void actionPerformed(ActionEvent e)
1192       {
1193         scaleLeft_actionPerformed(e);
1194       }
1195     });
1196     scaleRight.setVisible(false);
1197     scaleRight.setSelected(true);
1198     scaleRight.setText(MessageManager.getString("action.scale_right"));
1199     scaleRight.addActionListener(new ActionListener()
1200     {
1201       @Override
1202       public void actionPerformed(ActionEvent e)
1203       {
1204         scaleRight_actionPerformed(e);
1205       }
1206     });
1207     centreColumnLabelsMenuItem.setVisible(true);
1208     centreColumnLabelsMenuItem.setState(false);
1209     centreColumnLabelsMenuItem.setText(
1210             MessageManager.getString("label.centre_column_labels"));
1211     centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1212     {
1213       @Override
1214       public void actionPerformed(ActionEvent e)
1215       {
1216         centreColumnLabels_actionPerformed(e);
1217       }
1218     });
1219     followHighlightMenuItem.setVisible(true);
1220     followHighlightMenuItem.setState(true);
1221     followHighlightMenuItem
1222             .setText(MessageManager.getString("label.automatic_scrolling"));
1223     followHighlightMenuItem.addActionListener(new ActionListener()
1224     {
1225
1226       @Override
1227       public void actionPerformed(ActionEvent e)
1228       {
1229         followHighlight_actionPerformed();
1230       }
1231
1232     });
1233
1234     sortByTreeMenu
1235             .setText(MessageManager.getString("action.by_tree_order"));
1236     sort.setText(MessageManager.getString("action.sort"));
1237     sort.addMenuListener(new MenuListener()
1238     {
1239       @Override
1240       public void menuSelected(MenuEvent e)
1241       {
1242         buildTreeSortMenu();
1243       }
1244
1245       @Override
1246       public void menuDeselected(MenuEvent e)
1247       {
1248       }
1249
1250       @Override
1251       public void menuCanceled(MenuEvent e)
1252       {
1253       }
1254     });
1255     sortByAnnotScore
1256             .setText(MessageManager.getString("label.sort_by_score"));
1257     sort.add(sortByAnnotScore);
1258     sort.addMenuListener(new javax.swing.event.MenuListener()
1259     {
1260
1261       @Override
1262       public void menuCanceled(MenuEvent e)
1263       {
1264       }
1265
1266       @Override
1267       public void menuDeselected(MenuEvent e)
1268       {
1269       }
1270
1271       @Override
1272       public void menuSelected(MenuEvent e)
1273       {
1274         buildSortByAnnotationScoresMenu();
1275       }
1276     });
1277     sortByAnnotScore.setVisible(false);
1278
1279     calculateTree
1280             .setText(MessageManager.getString("action.calculate_tree_pca"));
1281
1282     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1283     padGapsMenuitem
1284             .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
1285     padGapsMenuitem.addActionListener(new ActionListener()
1286     {
1287       @Override
1288       public void actionPerformed(ActionEvent e)
1289       {
1290         padGapsMenuitem_actionPerformed(e);
1291       }
1292     });
1293     JMenuItem vamsasStore = new JMenuItem(
1294             MessageManager.getString("label.vamsas_store"));
1295     vamsasStore.setVisible(false);
1296     vamsasStore.addActionListener(new ActionListener()
1297     {
1298       @Override
1299       public void actionPerformed(ActionEvent e)
1300       {
1301         vamsasStore_actionPerformed(e);
1302       }
1303     });
1304     showTranslation
1305             .setText(MessageManager.getString("label.translate_cDNA"));
1306     showTranslation.addActionListener(new ActionListener()
1307     {
1308       @Override
1309       public void actionPerformed(ActionEvent e)
1310       {
1311         showTranslation_actionPerformed(e);
1312       }
1313     });
1314     showReverse.setText(MessageManager.getString("label.reverse"));
1315     showReverse.addActionListener(new ActionListener()
1316     {
1317       @Override
1318       public void actionPerformed(ActionEvent e)
1319       {
1320         showReverse_actionPerformed(false);
1321       }
1322     });
1323     showReverseComplement
1324             .setText(MessageManager.getString("label.reverse_complement"));
1325     showReverseComplement.addActionListener(new ActionListener()
1326     {
1327       @Override
1328       public void actionPerformed(ActionEvent e)
1329       {
1330         showReverse_actionPerformed(true);
1331       }
1332     });
1333
1334     JMenuItem extractScores = new JMenuItem(
1335             MessageManager.getString("label.extract_scores"));
1336     extractScores.addActionListener(new ActionListener()
1337     {
1338       @Override
1339       public void actionPerformed(ActionEvent e)
1340       {
1341         extractScores_actionPerformed(e);
1342       }
1343     });
1344     extractScores.setVisible(true);
1345     // JBPNote: TODO: make gui for regex based score extraction
1346
1347     // for show products actions see AlignFrame.canShowProducts
1348     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1349
1350     runGroovy.setText(MessageManager.getString("label.run_groovy"));
1351     runGroovy.setToolTipText(
1352             MessageManager.getString("label.run_groovy_tip"));
1353     runGroovy.addActionListener(new ActionListener()
1354     {
1355       @Override
1356       public void actionPerformed(ActionEvent e)
1357       {
1358         runGroovy_actionPerformed();
1359       }
1360     });
1361
1362     JMenuItem openFeatureSettings = new JMenuItem(
1363             MessageManager.getString("action.feature_settings"));
1364     openFeatureSettings.addActionListener(new ActionListener()
1365     {
1366       @Override
1367       public void actionPerformed(ActionEvent e)
1368       {
1369         featureSettings_actionPerformed(e);
1370       }
1371     });
1372     JMenuItem fetchSequence = new JMenuItem(
1373             MessageManager.getString("label.fetch_sequences"));
1374     fetchSequence.addActionListener(new ActionListener()
1375     {
1376       @Override
1377       public void actionPerformed(ActionEvent e)
1378       {
1379         fetchSequence_actionPerformed(e);
1380       }
1381     });
1382
1383     JMenuItem associatedData = new JMenuItem(
1384             MessageManager.getString("label.load_features_annotations"));
1385     associatedData.addActionListener(new ActionListener()
1386     {
1387       @Override
1388       public void actionPerformed(ActionEvent e)
1389       {
1390         associatedData_actionPerformed(e);
1391       }
1392     });
1393     autoCalculate.setText(
1394             MessageManager.getString("label.autocalculate_consensus"));
1395     autoCalculate.setState(
1396             jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1397     autoCalculate.addActionListener(new ActionListener()
1398     {
1399       @Override
1400       public void actionPerformed(ActionEvent e)
1401       {
1402         autoCalculate_actionPerformed(e);
1403       }
1404     });
1405     sortByTree.setText(
1406             MessageManager.getString("label.sort_alignment_new_tree"));
1407     sortByTree.setToolTipText("<html>" + MessageManager.getString(
1408             "label.enable_automatically_sort_alignment_when_open_new_tree"));
1409     sortByTree
1410             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1411     sortByTree.addActionListener(new ActionListener()
1412     {
1413       @Override
1414       public void actionPerformed(ActionEvent e)
1415       {
1416         sortByTreeOption_actionPerformed(e);
1417       }
1418     });
1419
1420     listenToViewSelections.setText(
1421             MessageManager.getString("label.listen_for_selections"));
1422     listenToViewSelections
1423             .setToolTipText("<html>" + MessageManager.getString(
1424                     "label.selections_mirror_selections_made_same_sequences_other_views"));
1425     listenToViewSelections.setState(false);
1426     listenToViewSelections.addActionListener(new ActionListener()
1427     {
1428       @Override
1429       public void actionPerformed(ActionEvent e)
1430       {
1431         listenToViewSelections_actionPerformed(e);
1432       }
1433     });
1434
1435     JMenu addSequenceMenu = new JMenu(
1436             MessageManager.getString("label.add_sequences"));
1437     JMenuItem addFromFile = new JMenuItem(
1438             MessageManager.getString("label.from_file"));
1439     addFromFile.addActionListener(new ActionListener()
1440     {
1441       @Override
1442       public void actionPerformed(ActionEvent e)
1443       {
1444         addFromFile_actionPerformed(e);
1445       }
1446     });
1447     JMenuItem addFromText = new JMenuItem(
1448             MessageManager.getString("label.from_textbox"));
1449     addFromText.addActionListener(new ActionListener()
1450     {
1451       @Override
1452       public void actionPerformed(ActionEvent e)
1453       {
1454         addFromText_actionPerformed(e);
1455       }
1456     });
1457     JMenuItem addFromURL = new JMenuItem(
1458             MessageManager.getString("label.from_url"));
1459     addFromURL.addActionListener(new ActionListener()
1460     {
1461       @Override
1462       public void actionPerformed(ActionEvent e)
1463       {
1464         addFromURL_actionPerformed(e);
1465       }
1466     });
1467     JMenuItem exportFeatures = new JMenuItem(
1468             MessageManager.getString("label.export_features"));
1469     exportFeatures.addActionListener(new ActionListener()
1470     {
1471       @Override
1472       public void actionPerformed(ActionEvent e)
1473       {
1474         exportFeatures_actionPerformed(e);
1475       }
1476     });
1477     JMenuItem exportAnnotations = new JMenuItem(
1478             MessageManager.getString("label.export_annotations"));
1479     exportAnnotations.addActionListener(new ActionListener()
1480     {
1481       @Override
1482       public void actionPerformed(ActionEvent e)
1483       {
1484         exportAnnotations_actionPerformed(e);
1485       }
1486     });
1487     statusPanel.setLayout(new GridLayout());
1488     JMenuItem showAllSeqs = new JMenuItem(
1489             MessageManager.getString("label.all_sequences"));
1490     showAllSeqs.setToolTipText(
1491             MessageManager.getString("label.toggle_sequence_visibility"));
1492     showAllSeqs.addActionListener(new ActionListener()
1493     {
1494       @Override
1495       public void actionPerformed(ActionEvent e)
1496       {
1497         showAllSeqs_actionPerformed(e);
1498       }
1499     });
1500     JMenuItem showAllColumns = new JMenuItem(
1501             MessageManager.getString("label.all_columns"));
1502     showAllColumns.setToolTipText(
1503             MessageManager.getString("label.toggle_columns_visibility"));
1504     showAllColumns.addActionListener(new ActionListener()
1505     {
1506       @Override
1507       public void actionPerformed(ActionEvent e)
1508       {
1509         showAllColumns_actionPerformed(e);
1510       }
1511     });
1512     JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1513     JMenuItem hideSelSequences = new JMenuItem(
1514             MessageManager.getString("label.selected_sequences"));
1515     hideSelSequences.setToolTipText(
1516             MessageManager.getString("label.toggle_sequence_visibility"));
1517     hideSelSequences.addActionListener(new ActionListener()
1518     {
1519       @Override
1520       public void actionPerformed(ActionEvent e)
1521       {
1522         hideSelSequences_actionPerformed(e);
1523       }
1524     });
1525     JMenuItem hideSelColumns = new JMenuItem(
1526             MessageManager.getString("label.selected_columns"));
1527     hideSelColumns.setToolTipText(
1528             MessageManager.getString("label.toggle_columns_visibility"));
1529     hideSelColumns.addActionListener(new ActionListener()
1530     {
1531       @Override
1532       public void actionPerformed(ActionEvent e)
1533       {
1534         hideSelColumns_actionPerformed(e);
1535       }
1536     });
1537     JMenuItem hideAllSelection = new JMenuItem(
1538             MessageManager.getString("label.selected_region"));
1539     hideAllSelection.addActionListener(new ActionListener()
1540     {
1541       @Override
1542       public void actionPerformed(ActionEvent e)
1543       {
1544         hideAllSelection_actionPerformed(e);
1545       }
1546     });
1547     // TODO: should be hidden if no selection exists.
1548     JMenuItem hideAllButSelection = new JMenuItem(
1549             MessageManager.getString("label.all_but_selected_region"));
1550     hideAllButSelection.addActionListener(new ActionListener()
1551     {
1552       @Override
1553       public void actionPerformed(ActionEvent e)
1554       {
1555         hideAllButSelection_actionPerformed(e);
1556       }
1557     });
1558     JMenuItem showAllhidden = new JMenuItem(
1559             MessageManager.getString("label.all_sequences_columns"));
1560     showAllhidden.setToolTipText(MessageManager
1561             .getString("label.toggles_visibility_hidden_selected_regions"));
1562     showAllhidden.addActionListener(new ActionListener()
1563     {
1564       @Override
1565       public void actionPerformed(ActionEvent e)
1566       {
1567         showAllhidden_actionPerformed(e);
1568       }
1569     });
1570     hiddenMarkers.setText(
1571             MessageManager.getString("action.show_hidden_markers"));
1572     hiddenMarkers.addActionListener(new ActionListener()
1573     {
1574       @Override
1575       public void actionPerformed(ActionEvent e)
1576       {
1577         hiddenMarkers_actionPerformed(e);
1578       }
1579     });
1580
1581     JMenuItem invertColSel = new JMenuItem(
1582             MessageManager.getString("action.invert_column_selection"));
1583     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1584             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1585                     | KeyEvent.ALT_MASK,
1586             false);
1587     al = new ActionListener()
1588     {
1589       @Override
1590       public void actionPerformed(ActionEvent e)
1591       {
1592         invertColSel_actionPerformed(e);
1593       }
1594     };
1595     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1596
1597     showComplementMenuItem.setVisible(false);
1598     showComplementMenuItem.addActionListener(new ActionListener()
1599     {
1600       @Override
1601       public void actionPerformed(ActionEvent e)
1602       {
1603         showComplement_actionPerformed(showComplementMenuItem.getState());
1604       }
1605     });
1606
1607     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1608     {
1609       @Override
1610       public void stateChanged(ChangeEvent evt)
1611       {
1612         JTabbedPane pane = (JTabbedPane) evt.getSource();
1613         int sel = pane.getSelectedIndex();
1614         tabSelectionChanged(sel);
1615       }
1616     });
1617     tabbedPane.addMouseListener(new MouseAdapter()
1618     {
1619       @Override
1620       public void mousePressed(MouseEvent e)
1621       {
1622         if (e.isPopupTrigger()) // Mac
1623         {
1624           tabbedPane_mousePressed(e);
1625         }
1626       }
1627
1628       @Override
1629       public void mouseReleased(MouseEvent e)
1630       {
1631         if (e.isPopupTrigger()) // Windows
1632         {
1633           tabbedPane_mousePressed(e);
1634         }
1635       }
1636     });
1637     tabbedPane.addFocusListener(new FocusAdapter()
1638     {
1639       @Override
1640       public void focusGained(FocusEvent e)
1641       {
1642         tabbedPane_focusGained(e);
1643       }
1644     });
1645
1646     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1647     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1648             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1649     al = new ActionListener()
1650     {
1651       @Override
1652       public void actionPerformed(ActionEvent e)
1653       {
1654         save_actionPerformed(e);
1655       }
1656     };
1657     addMenuActionAndAccelerator(keyStroke, save, al);
1658
1659     reload.setEnabled(false);
1660     reload.setText(MessageManager.getString("action.reload"));
1661     reload.addActionListener(new ActionListener()
1662     {
1663       @Override
1664       public void actionPerformed(ActionEvent e)
1665       {
1666         reload_actionPerformed(e);
1667       }
1668     });
1669
1670     JMenuItem newView = new JMenuItem(
1671             MessageManager.getString("action.new_view"));
1672     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1673             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1674     al = new ActionListener()
1675     {
1676       @Override
1677       public void actionPerformed(ActionEvent e)
1678       {
1679         newView_actionPerformed(e);
1680       }
1681     };
1682     addMenuActionAndAccelerator(keyStroke, newView, al);
1683
1684     tabbedPane.setToolTipText("<html><i>"
1685             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1686             + "</i></html>");
1687
1688     formatMenu.setText(MessageManager.getString("action.format"));
1689     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1690
1691     idRightAlign.setText(
1692             MessageManager.getString("label.right_align_sequence_id"));
1693     idRightAlign.addActionListener(new ActionListener()
1694     {
1695       @Override
1696       public void actionPerformed(ActionEvent e)
1697       {
1698         idRightAlign_actionPerformed(e);
1699       }
1700     });
1701
1702     gatherViews.setEnabled(false);
1703     gatherViews.setText(MessageManager.getString("action.gather_views"));
1704     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1705     al = new ActionListener()
1706     {
1707       @Override
1708       public void actionPerformed(ActionEvent e)
1709       {
1710         gatherViews_actionPerformed(e);
1711       }
1712     };
1713     addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1714
1715     expandViews.setEnabled(false);
1716     expandViews.setText(MessageManager.getString("action.expand_views"));
1717     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1718     al = new ActionListener()
1719     {
1720       @Override
1721       public void actionPerformed(ActionEvent e)
1722       {
1723         expandViews_actionPerformed(e);
1724       }
1725     };
1726     addMenuActionAndAccelerator(keyStroke, expandViews, al);
1727
1728     JMenuItem pageSetup = new JMenuItem(
1729             MessageManager.getString("action.page_setup"));
1730     pageSetup.addActionListener(new ActionListener()
1731     {
1732       @Override
1733       public void actionPerformed(ActionEvent e)
1734       {
1735         pageSetup_actionPerformed(e);
1736       }
1737     });
1738     JMenuItem alignmentProperties = new JMenuItem(
1739             MessageManager.getString("label.alignment_props"));
1740     alignmentProperties.addActionListener(new ActionListener()
1741     {
1742       @Override
1743       public void actionPerformed(ActionEvent actionEvent)
1744       {
1745         alignmentProperties();
1746       }
1747     });
1748     JMenuItem selectHighlighted = new JMenuItem(
1749             MessageManager.getString("action.select_highlighted_columns"));
1750     selectHighlighted.setToolTipText(
1751             MessageManager.getString("tooltip.select_highlighted_columns"));
1752     al = new ActionListener()
1753     {
1754       @Override
1755       public void actionPerformed(ActionEvent actionEvent)
1756       {
1757         selectHighlightedColumns_actionPerformed(actionEvent);
1758       }
1759     };
1760     selectHighlighted.addActionListener(al);
1761     JMenu tooltipSettingsMenu = new JMenu(
1762             MessageManager.getString("label.sequence_id_tooltip"));
1763     JMenu autoAnnMenu = new JMenu(
1764             MessageManager.getString("label.autocalculated_annotation"));
1765
1766     JMenu exportImageMenu = new JMenu(
1767             MessageManager.getString("label.export_image"));
1768
1769     JMenu loadTreeDb = new JMenu(
1770             MessageManager.getString("label.from_database"));
1771
1772     JMenu loadTreeMenu = new JMenu(
1773             MessageManager.getString("label.load_associated_tree"));
1774     // loadTreeMenu.setToolTipText(
1775     // MessageManager.getString("label.load_tree_for_sequence_set"));
1776
1777     JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1778
1779     loadTreeDb.add(loadTreeBaseStudy);
1780     loadTreeDb.add(loadTreeBase);
1781     loadTreeDb.add(loadTreePfam);
1782     loadTreeDb.add(loadTreeFam);
1783     loadTreeDb.add(loadTreeOfLife);
1784
1785     loadTreeMenu.add(loadTreeFile);
1786     loadTreeMenu.add(loadTreeUrl);
1787     loadTreeMenu.add(loadTreeDb);
1788
1789     alignFrameMenuBar.add(fileMenu);
1790     alignFrameMenuBar.add(editMenu);
1791     alignFrameMenuBar.add(selectMenu);
1792     alignFrameMenuBar.add(viewMenu);
1793     alignFrameMenuBar.add(annotationsMenu);
1794     alignFrameMenuBar.add(formatMenu);
1795     alignFrameMenuBar.add(colourMenu);
1796     alignFrameMenuBar.add(calculateMenu);
1797     alignFrameMenuBar.add(webService);
1798
1799     fileMenu.add(fetchSequence);
1800     fileMenu.add(addSequenceMenu);
1801     fileMenu.add(reload);
1802     fileMenu.addSeparator();
1803     fileMenu.add(vamsasStore);
1804     fileMenu.add(save);
1805     fileMenu.add(saveAs);
1806     fileMenu.add(outputTextboxMenu);
1807     fileMenu.add(pageSetup);
1808     fileMenu.add(printMenuItem);
1809     fileMenu.addSeparator();
1810     fileMenu.add(exportImageMenu);
1811     fileMenu.add(exportFeatures);
1812     fileMenu.add(exportAnnotations);
1813     fileMenu.add(loadTreeMenu);
1814     fileMenu.add(associatedData);
1815     fileMenu.addSeparator();
1816     fileMenu.add(closeMenuItem);
1817
1818     pasteMenu.add(pasteNew);
1819     pasteMenu.add(pasteThis);
1820     editMenu.add(undoMenuItem);
1821     editMenu.add(redoMenuItem);
1822     editMenu.add(cut);
1823     editMenu.add(copy);
1824     editMenu.add(pasteMenu);
1825     editMenu.add(delete);
1826     editMenu.addSeparator();
1827     editMenu.add(remove2LeftMenuItem);
1828     editMenu.add(remove2RightMenuItem);
1829     editMenu.add(removeGappedColumnMenuItem);
1830     editMenu.add(removeAllGapsMenuItem);
1831     editMenu.add(removeRedundancyMenuItem);
1832     editMenu.addSeparator();
1833     // dont add these yet in the CVS build - they cannot be undone!
1834     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1835     // editMenu.add(justifyLeftMenuItem);
1836     // editMenu.add(justifyRightMenuItem);
1837     // editMenu.addSeparator();
1838     editMenu.add(padGapsMenuitem);
1839
1840     showMenu.add(showAllColumns);
1841     showMenu.add(showAllSeqs);
1842     showMenu.add(showAllhidden);
1843     hideMenu.add(hideSelColumns);
1844     hideMenu.add(hideSelSequences);
1845     hideMenu.add(hideAllSelection);
1846     hideMenu.add(hideAllButSelection);
1847     viewMenu.add(newView);
1848     viewMenu.add(expandViews);
1849     viewMenu.add(gatherViews);
1850     viewMenu.addSeparator();
1851     viewMenu.add(showMenu);
1852     viewMenu.add(hideMenu);
1853     viewMenu.add(showComplementMenuItem);
1854     viewMenu.addSeparator();
1855     viewMenu.add(followHighlightMenuItem);
1856     viewMenu.addSeparator();
1857     viewMenu.add(showSeqFeatures);
1858     // viewMenu.add(showSeqFeaturesHeight);
1859     viewMenu.add(openFeatureSettings);
1860     tooltipSettingsMenu.add(showDbRefsMenuitem);
1861     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1862     viewMenu.add(tooltipSettingsMenu);
1863     viewMenu.addSeparator();
1864     viewMenu.add(alignmentProperties);
1865     viewMenu.addSeparator();
1866     viewMenu.add(overviewMenuItem);
1867
1868     annotationsMenu.add(annotationPanelMenuItem);
1869     annotationsMenu.addSeparator();
1870     annotationsMenu.add(showAllAlAnnotations);
1871     annotationsMenu.add(hideAllAlAnnotations);
1872     annotationsMenu.addSeparator();
1873     annotationsMenu.add(showAllSeqAnnotations);
1874     annotationsMenu.add(hideAllSeqAnnotations);
1875     annotationsMenu.add(sortAnnBySequence);
1876     annotationsMenu.add(sortAnnByLabel);
1877     annotationsMenu.addSeparator();
1878     autoAnnMenu.add(showAutoFirst);
1879     autoAnnMenu.add(showAutoLast);
1880     autoAnnMenu.addSeparator();
1881     autoAnnMenu.add(applyAutoAnnotationSettings);
1882     autoAnnMenu.add(showConsensusHistogram);
1883     autoAnnMenu.add(showSequenceLogo);
1884     autoAnnMenu.add(normaliseSequenceLogo);
1885     autoAnnMenu.addSeparator();
1886     autoAnnMenu.add(showGroupConservation);
1887     autoAnnMenu.add(showGroupConsensus);
1888     annotationsMenu.add(autoAnnMenu);
1889
1890     sort.add(sortIDMenuItem);
1891     sort.add(sortLengthMenuItem);
1892     sort.add(sortGroupMenuItem);
1893     sort.add(sortPairwiseMenuItem);
1894     sort.add(sortByTreeMenu);
1895     calculateMenu.add(sort);
1896     calculateMenu.add(calculateTree);
1897     calculateMenu.addSeparator();
1898     calculateMenu.add(pairwiseAlignmentMenuItem);
1899     calculateMenu.addSeparator();
1900     calculateMenu.add(showTranslation);
1901     calculateMenu.add(showReverse);
1902     calculateMenu.add(showReverseComplement);
1903     calculateMenu.add(showProducts);
1904     calculateMenu.add(autoCalculate);
1905     calculateMenu.add(sortByTree);
1906     calculateMenu.addSeparator();
1907     calculateMenu.add(expandAlignment);
1908     calculateMenu.add(extractScores);
1909     calculateMenu.addSeparator();
1910     calculateMenu.add(runGroovy);
1911
1912     webServiceNoServices = new JMenuItem(
1913             MessageManager.getString("label.no_services"));
1914     webService.add(webServiceNoServices);
1915     exportImageMenu.add(htmlMenuItem);
1916     exportImageMenu.add(epsFile);
1917     exportImageMenu.add(createPNG);
1918     exportImageMenu.add(createBioJS);
1919     exportImageMenu.add(createSVG);
1920     addSequenceMenu.add(addFromFile);
1921     addSequenceMenu.add(addFromText);
1922     addSequenceMenu.add(addFromURL);
1923     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1924     statusPanel.add(statusBar, null);
1925     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1926
1927     formatMenu.add(font);
1928     formatMenu.addSeparator();
1929     formatMenu.add(wrapMenuItem);
1930     formatMenu.add(scaleAbove);
1931     formatMenu.add(scaleLeft);
1932     formatMenu.add(scaleRight);
1933     formatMenu.add(seqLimits);
1934     formatMenu.add(idRightAlign);
1935     formatMenu.add(hiddenMarkers);
1936     formatMenu.add(viewBoxesMenuItem);
1937     formatMenu.add(viewTextMenuItem);
1938     formatMenu.add(colourTextMenuItem);
1939     formatMenu.add(renderGapsMenuItem);
1940     formatMenu.add(centreColumnLabelsMenuItem);
1941     formatMenu.add(showNonconservedMenuItem);
1942     selectMenu.add(findMenuItem);
1943     selectMenu.addSeparator();
1944     selectMenu.add(selectAllSequenceMenuItem);
1945     selectMenu.add(deselectAllSequenceMenuItem);
1946     selectMenu.add(invertSequenceMenuItem);
1947     selectMenu.add(invertColSel);
1948     selectMenu.add(createGroup);
1949     selectMenu.add(unGroup);
1950     selectMenu.add(grpsFromSelection);
1951     selectMenu.add(deleteGroups);
1952     selectMenu.add(annotationColumn);
1953     selectMenu.add(selectHighlighted);
1954     // TODO - determine if the listenToViewSelections button is needed : see bug
1955     // JAL-574
1956     // selectMenu.addSeparator();
1957     // selectMenu.add(listenToViewSelections);
1958
1959
1960   }
1961
1962   protected void loadTreeOfLife_actionPerformed(ActionEvent e)
1963   {
1964     // TODO Auto-generated method stub
1965
1966   }
1967
1968   protected void loadTreeFam_actionPerformed(ActionEvent e)
1969   {
1970     // TODO Auto-generated method stub
1971
1972   }
1973
1974   protected void loadTreePfam_actionPerformed(ActionEvent e)
1975   {
1976     // TODO Auto-generated method stub
1977
1978   }
1979
1980   protected void loadTreeBase_actionPerformed(ActionEvent e)
1981   {
1982     // TODO Auto-generated method stub
1983
1984   }
1985
1986   protected void loadTreeBaseStudy_actionPerformed(ActionEvent e)
1987   {
1988     // TODO Auto-generated method stub
1989
1990   }
1991
1992   /**
1993    * Constructs the entries on the Colour menu (but does not add them to the
1994    * menu).
1995    */
1996   protected void initColourMenu()
1997   {
1998     applyToAllGroups = new JCheckBoxMenuItem(
1999             MessageManager.getString("label.apply_colour_to_all_groups"));
2000     applyToAllGroups.addActionListener(new ActionListener()
2001     {
2002       @Override
2003       public void actionPerformed(ActionEvent e)
2004       {
2005         applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
2006       }
2007     });
2008
2009     textColour = new JMenuItem(
2010             MessageManager.getString("label.text_colour"));
2011     textColour.addActionListener(new ActionListener()
2012     {
2013       @Override
2014       public void actionPerformed(ActionEvent e)
2015       {
2016         textColour_actionPerformed();
2017       }
2018     });
2019
2020     conservationMenuItem = new JCheckBoxMenuItem(
2021             MessageManager.getString("action.by_conservation"));
2022     conservationMenuItem.addActionListener(new ActionListener()
2023     {
2024       @Override
2025       public void actionPerformed(ActionEvent e)
2026       {
2027         conservationMenuItem_actionPerformed(
2028                 conservationMenuItem.isSelected());
2029       }
2030     });
2031
2032     abovePIDThreshold = new JCheckBoxMenuItem(
2033             MessageManager.getString("label.above_identity_threshold"));
2034     abovePIDThreshold.addActionListener(new ActionListener()
2035     {
2036       @Override
2037       public void actionPerformed(ActionEvent e)
2038       {
2039         abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
2040       }
2041     });
2042     modifyPID = new JMenuItem(
2043             MessageManager.getString("label.modify_identity_threshold"));
2044     modifyPID.addActionListener(new ActionListener()
2045     {
2046       @Override
2047       public void actionPerformed(ActionEvent e)
2048       {
2049         modifyPID_actionPerformed();
2050       }
2051     });
2052     modifyConservation = new JMenuItem(MessageManager
2053             .getString("label.modify_conservation_threshold"));
2054     modifyConservation.addActionListener(new ActionListener()
2055     {
2056       @Override
2057       public void actionPerformed(ActionEvent e)
2058       {
2059         modifyConservation_actionPerformed();
2060       }
2061     });
2062
2063     annotationColour = new JMenuItem(
2064             MessageManager.getString("action.by_annotation"));
2065     annotationColour.addActionListener(new ActionListener()
2066     {
2067       @Override
2068       public void actionPerformed(ActionEvent e)
2069       {
2070         annotationColour_actionPerformed();
2071       }
2072     });
2073   }
2074
2075   protected void selectHighlightedColumns_actionPerformed(
2076           ActionEvent actionEvent)
2077   {
2078     // TODO Auto-generated method stub
2079
2080   }
2081
2082   /**
2083    * Generate the reverse sequence (or reverse complement if the flag is true)
2084    * and add it to the alignment
2085    *
2086    * @param complement
2087    */
2088   protected void showReverse_actionPerformed(boolean complement)
2089   {
2090   }
2091
2092   /**
2093    * Try to run script in a Groovy console, having first ensured that this
2094    * alignframe is set as currentAlignFrame in Desktop
2095    */
2096   protected void runGroovy_actionPerformed()
2097   {
2098
2099   }
2100
2101   /**
2102    * Adds the given action listener and key accelerator to the given menu item.
2103    * Also saves in a lookup table to support lookup of action by key stroke.
2104    *
2105    * @param keyStroke
2106    * @param menuItem
2107    * @param actionListener
2108    */
2109   protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2110           JMenuItem menuItem, ActionListener actionListener)
2111   {
2112     menuItem.setAccelerator(keyStroke);
2113     accelerators.put(keyStroke, menuItem);
2114     menuItem.addActionListener(actionListener);
2115   }
2116
2117   /**
2118    * Action on clicking sort annotations by type.
2119    *
2120    * @param sortOrder
2121    */
2122   protected void sortAnnotations_actionPerformed()
2123   {
2124   }
2125
2126   /**
2127    * Action on clicking Show all annotations.
2128    *
2129    * @param forSequences
2130    *          update sequence-related annotations
2131    * @param forAlignment
2132    *          update non-sequence-related annotations
2133    */
2134   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2135           boolean forAlignment)
2136   {
2137     setAnnotationsVisibility(true, forSequences, forAlignment);
2138   }
2139
2140   /**
2141    * Action on clicking Hide all annotations.
2142    *
2143    * @param forSequences
2144    *          update sequence-related annotations
2145    * @param forAlignment
2146    *          update non-sequence-related annotations
2147    */
2148   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2149           boolean forAlignment)
2150   {
2151     setAnnotationsVisibility(false, forSequences, forAlignment);
2152   }
2153
2154   /**
2155    * Set the visibility of annotations to true or false. Can act on
2156    * sequence-related annotations, or alignment-related, or both.
2157    *
2158    * @param visible
2159    * @param forSequences
2160    *          update sequence-related annotations
2161    * @param forAlignment
2162    *          update non-sequence-related annotations
2163    */
2164   protected void setAnnotationsVisibility(boolean visible,
2165           boolean forSequences, boolean forAlignment)
2166   {
2167
2168   }
2169
2170   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2171   {
2172     // TODO Auto-generated method stub
2173
2174   }
2175
2176   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2177   {
2178     // TODO Auto-generated method stub
2179
2180   }
2181
2182   protected void showAllhidden_actionPerformed(ActionEvent e)
2183   {
2184     // TODO Auto-generated method stub
2185
2186   }
2187
2188   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2189   {
2190     // TODO Auto-generated method stub
2191
2192   }
2193
2194   protected void hideAllSelection_actionPerformed(ActionEvent e)
2195   {
2196     // TODO Auto-generated method stub
2197
2198   }
2199
2200   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2201   {
2202     // TODO Auto-generated method stub
2203
2204   }
2205
2206   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2207   {
2208     // TODO Auto-generated method stub
2209
2210   }
2211
2212   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2213   {
2214     // TODO Auto-generated method stub
2215
2216   }
2217
2218   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2219   {
2220     // TODO Auto-generated method stub
2221
2222   }
2223
2224   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2225   {
2226     // TODO Auto-generated method stub
2227
2228   }
2229
2230   protected void showGroupConservation_actionPerformed(ActionEvent e)
2231   {
2232     // TODO Auto-generated method stub
2233
2234   }
2235
2236   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2237   {
2238     // TODO Auto-generated method stub
2239
2240   }
2241
2242   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2243   {
2244     // TODO Auto-generated method stub
2245
2246   }
2247
2248   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2249   {
2250     // TODO Auto-generated method stub
2251
2252   }
2253
2254   protected void followHighlight_actionPerformed()
2255   {
2256     // TODO Auto-generated method stub
2257
2258   }
2259
2260   protected void showNpFeats_actionPerformed(ActionEvent e)
2261   {
2262     // TODO Auto-generated method stub
2263
2264   }
2265
2266   protected void showDbRefs_actionPerformed(ActionEvent e)
2267   {
2268     // TODO Auto-generated method stub
2269
2270   }
2271
2272   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2273   {
2274   }
2275
2276   protected void buildSortByAnnotationScoresMenu()
2277   {
2278   }
2279
2280   protected void extractScores_actionPerformed(ActionEvent e)
2281   {
2282   }
2283
2284   protected void outputText_actionPerformed(ActionEvent e)
2285   {
2286   }
2287
2288   public void addFromFile_actionPerformed(ActionEvent e)
2289   {
2290
2291   }
2292
2293   public void addFromText_actionPerformed(ActionEvent e)
2294   {
2295
2296   }
2297
2298   public void addFromURL_actionPerformed(ActionEvent e)
2299   {
2300
2301   }
2302
2303   public void exportFeatures_actionPerformed(ActionEvent e)
2304   {
2305
2306   }
2307
2308   public void exportAnnotations_actionPerformed(ActionEvent e)
2309   {
2310
2311   }
2312
2313   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2314   {
2315   }
2316
2317   protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2318   {
2319
2320   }
2321
2322   protected void closeMenuItem_actionPerformed(boolean b)
2323   {
2324   }
2325
2326   protected void redoMenuItem_actionPerformed(ActionEvent e)
2327   {
2328   }
2329
2330   protected void undoMenuItem_actionPerformed(ActionEvent e)
2331   {
2332   }
2333
2334   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2335   {
2336   }
2337
2338   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2339   {
2340   }
2341
2342   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2343   {
2344   }
2345
2346   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2347   {
2348   }
2349
2350   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2351   {
2352   }
2353
2354   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2355   {
2356   }
2357
2358   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2359   {
2360   }
2361
2362   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2363   {
2364   }
2365
2366   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2367   {
2368   }
2369
2370   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2371   {
2372   }
2373
2374   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2375   {
2376   }
2377
2378   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2379   {
2380   }
2381
2382   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2383   {
2384   }
2385
2386   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2387   {
2388   }
2389
2390   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2391   {
2392   }
2393
2394   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2395   {
2396   }
2397
2398   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2399   {
2400   }
2401
2402   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2403   {
2404   }
2405
2406   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2407   {
2408   }
2409
2410   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2411   {
2412   }
2413
2414   protected void conservationMenuItem_actionPerformed(boolean selected)
2415   {
2416   }
2417
2418   protected void printMenuItem_actionPerformed(ActionEvent e)
2419   {
2420   }
2421
2422   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2423   {
2424   }
2425
2426   protected void findMenuItem_actionPerformed(ActionEvent e)
2427   {
2428   }
2429
2430   protected void abovePIDThreshold_actionPerformed(boolean selected)
2431   {
2432   }
2433
2434   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2435   {
2436   }
2437
2438   protected void deleteGroups_actionPerformed(ActionEvent e)
2439   {
2440   }
2441
2442   protected void createGroup_actionPerformed(ActionEvent e)
2443   {
2444   }
2445
2446   protected void unGroup_actionPerformed(ActionEvent e)
2447   {
2448   }
2449
2450   protected void copy_actionPerformed(ActionEvent e)
2451   {
2452   }
2453
2454   protected void cut_actionPerformed(ActionEvent e)
2455   {
2456   }
2457
2458   protected void delete_actionPerformed(ActionEvent e)
2459   {
2460   }
2461
2462   protected void pasteNew_actionPerformed(ActionEvent e)
2463   {
2464   }
2465
2466   protected void pasteThis_actionPerformed(ActionEvent e)
2467   {
2468   }
2469
2470   protected void applyToAllGroups_actionPerformed(boolean selected)
2471   {
2472   }
2473
2474   public void createPNG(java.io.File f)
2475   {
2476   }
2477
2478   protected void font_actionPerformed(ActionEvent e)
2479   {
2480   }
2481
2482   protected void seqLimit_actionPerformed(ActionEvent e)
2483   {
2484   }
2485
2486   public void seqDBRef_actionPerformed(ActionEvent e)
2487   {
2488
2489   }
2490
2491   public void createEPS(java.io.File f)
2492   {
2493   }
2494
2495   public void createSVG(java.io.File f)
2496   {
2497
2498   }
2499
2500   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2501   {
2502
2503   }
2504
2505   protected void loadTreeUrlItem_actionPerformed(ActionEvent e)
2506   {
2507
2508   }
2509
2510
2511
2512   /**
2513    * Template method to handle the 'load T-Coffee scores' menu event.
2514    * <p>
2515    * Subclasses override this method to provide a custom action.
2516    *
2517    * @param event
2518    *          The raised event
2519    */
2520   protected void loadScores_actionPerformed(ActionEvent event)
2521   {
2522
2523   }
2524
2525   protected void jpred_actionPerformed(ActionEvent e)
2526   {
2527   }
2528
2529   protected void scaleAbove_actionPerformed(ActionEvent e)
2530   {
2531   }
2532
2533   protected void scaleLeft_actionPerformed(ActionEvent e)
2534   {
2535   }
2536
2537   protected void scaleRight_actionPerformed(ActionEvent e)
2538   {
2539   }
2540
2541   protected void modifyPID_actionPerformed()
2542   {
2543   }
2544
2545   protected void modifyConservation_actionPerformed()
2546   {
2547   }
2548
2549   protected void saveAs_actionPerformed(ActionEvent e)
2550   {
2551   }
2552
2553   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2554   {
2555   }
2556
2557   public void vamsasStore_actionPerformed(ActionEvent e)
2558   {
2559
2560   }
2561
2562   public void vamsasLoad_actionPerformed(ActionEvent e)
2563   {
2564
2565   }
2566
2567   public void showTranslation_actionPerformed(ActionEvent e)
2568   {
2569
2570   }
2571
2572   public void featureSettings_actionPerformed(ActionEvent e)
2573   {
2574
2575   }
2576
2577   public void fetchSequence_actionPerformed(ActionEvent e)
2578   {
2579
2580   }
2581
2582   public void smoothFont_actionPerformed(ActionEvent e)
2583   {
2584
2585   }
2586
2587   public void annotationColour_actionPerformed()
2588   {
2589   }
2590
2591   public void annotationColumn_actionPerformed(ActionEvent e)
2592   {
2593   }
2594
2595   public void associatedData_actionPerformed(ActionEvent e)
2596   {
2597
2598   }
2599
2600   public void autoCalculate_actionPerformed(ActionEvent e)
2601   {
2602
2603   }
2604
2605   public void sortByTreeOption_actionPerformed(ActionEvent e)
2606   {
2607
2608   }
2609
2610   public void showAllSeqs_actionPerformed(ActionEvent e)
2611   {
2612
2613   }
2614
2615   public void showAllColumns_actionPerformed(ActionEvent e)
2616   {
2617
2618   }
2619
2620   public void hideSelSequences_actionPerformed(ActionEvent e)
2621   {
2622
2623   }
2624
2625   public void hideSelColumns_actionPerformed(ActionEvent e)
2626   {
2627
2628   }
2629
2630   public void hiddenMarkers_actionPerformed(ActionEvent e)
2631   {
2632
2633   }
2634
2635   public void findPdbId_actionPerformed(ActionEvent e)
2636   {
2637
2638   }
2639
2640   public void enterPdbId_actionPerformed(ActionEvent e)
2641   {
2642
2643   }
2644
2645   public void pdbFile_actionPerformed(ActionEvent e)
2646   {
2647
2648   }
2649
2650   public void invertColSel_actionPerformed(ActionEvent e)
2651   {
2652
2653   }
2654
2655   public void tabSelectionChanged(int sel)
2656   {
2657
2658   }
2659
2660   public void tabbedPane_mousePressed(MouseEvent e)
2661   {
2662
2663   }
2664
2665   public void tabbedPane_focusGained(FocusEvent e)
2666   {
2667     requestFocus();
2668   }
2669
2670   public void save_actionPerformed(ActionEvent e)
2671   {
2672
2673   }
2674
2675   public void reload_actionPerformed(ActionEvent e)
2676   {
2677
2678   }
2679
2680   public void newView_actionPerformed(ActionEvent e)
2681   {
2682
2683   }
2684
2685   public void textColour_actionPerformed()
2686   {
2687
2688   }
2689
2690   public void idRightAlign_actionPerformed(ActionEvent e)
2691   {
2692
2693   }
2694
2695   public void expandViews_actionPerformed(ActionEvent e)
2696   {
2697
2698   }
2699
2700   public void gatherViews_actionPerformed(ActionEvent e)
2701   {
2702
2703   }
2704
2705   public void buildTreeSortMenu()
2706   {
2707
2708   }
2709
2710   public void pageSetup_actionPerformed(ActionEvent e)
2711   {
2712
2713   }
2714
2715   public void alignmentProperties()
2716   {
2717
2718   }
2719
2720   protected void expand_newalign(ActionEvent e)
2721   {
2722     // TODO Auto-generated method stub
2723
2724   }
2725
2726   protected boolean isShowAutoCalculatedAbove()
2727   {
2728     return showAutoCalculatedAbove;
2729   }
2730
2731   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2732   {
2733     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2734   }
2735
2736   protected SequenceAnnotationOrder getAnnotationSortOrder()
2737   {
2738     return annotationSortOrder;
2739   }
2740
2741   protected void setAnnotationSortOrder(
2742           SequenceAnnotationOrder annotationSortOrder)
2743   {
2744     this.annotationSortOrder = annotationSortOrder;
2745   }
2746
2747   public Map<KeyStroke, JMenuItem> getAccelerators()
2748   {
2749     return this.accelerators;
2750   }
2751
2752   /**
2753    * Returns the selected index of the tabbed pane, or -1 if none selected
2754    * (including the case where the tabbed pane has not been made visible).
2755    *
2756    * @return
2757    */
2758   public int getTabIndex()
2759   {
2760     return tabbedPane.getSelectedIndex();
2761   }
2762
2763   public JPanel getStatusPanel()
2764   {
2765     return statusPanel;
2766   }
2767
2768   /**
2769    * Sets a reference to the containing split frame. Also makes the 'toggle
2770    * split view' menu item visible and checked.
2771    *
2772    * @param sf
2773    */
2774   public void setSplitFrame(SplitContainerI sf)
2775   {
2776     this.splitFrame = sf;
2777     if (sf != null)
2778     {
2779       this.showComplementMenuItem.setVisible(true);
2780       this.showComplementMenuItem.setState(true);
2781     }
2782   }
2783
2784   public SplitContainerI getSplitViewContainer()
2785   {
2786     return this.splitFrame;
2787   }
2788
2789   protected void showComplement_actionPerformed(boolean complement)
2790   {
2791   }
2792 }