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.analysis.GeneticCodeI;
  25 import jalview.analysis.GeneticCodes;
  26 import jalview.api.SplitContainerI;
  27 import jalview.bin.Cache;
  28 import jalview.gui.JvSwingUtils;
  29 import jalview.gui.Preferences;
  30 import jalview.io.FileFormats;
  31 import jalview.schemes.ResidueColourScheme;
  32 import jalview.util.MessageManager;
  33 import jalview.util.Platform;
  34
  35 import java.awt.BorderLayout;
  36 import java.awt.Color;
  37 import java.awt.GridLayout;
  38 import java.awt.event.ActionEvent;
  39 import java.awt.event.ActionListener;
  40 import java.awt.event.FocusAdapter;
  41 import java.awt.event.FocusEvent;
  42 import java.awt.event.KeyEvent;
  43 import java.awt.event.MouseAdapter;
  44 import java.awt.event.MouseEvent;
  45 import java.util.HashMap;
  46 import java.util.Map;
  47
  48 import javax.swing.BorderFactory;
  49 import javax.swing.ButtonGroup;
  50 import javax.swing.JCheckBoxMenuItem;
  51 import javax.swing.JInternalFrame;
  52 import javax.swing.JLabel;
  53 import javax.swing.JMenu;
  54 import javax.swing.JMenuBar;
  55 import javax.swing.JMenuItem;
  56 import javax.swing.JPanel;
  57 import javax.swing.JRadioButtonMenuItem;
  58 import javax.swing.JTabbedPane;
  59 import javax.swing.KeyStroke;
  60 import javax.swing.event.ChangeEvent;
  61 import javax.swing.event.MenuEvent;
  62 import javax.swing.event.MenuListener;
  63
  64 public class GAlignFrame extends JInternalFrame
  65 {
  66   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  67
  68   protected JMenuItem closeMenuItem = new JMenuItem();
  69
  70   protected JMenu webService = new JMenu();
  71
  72   protected JMenuItem webServiceNoServices;
  73
  74   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  75
  76   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  77
  78   protected JMenu sortByAnnotScore = new JMenu();
  79
  80   protected JLabel statusBar = new JLabel();
  81
  82   protected JMenu outputTextboxMenu = new JMenu();
  83
  84   protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
  85
  86   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
  87
  88   protected JCheckBoxMenuItem colourGapsMenuItem = new JCheckBoxMenuItem();
  89
  90   protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
  91
  92   protected JMenuItem undoMenuItem = new JMenuItem();
  93
  94   protected JMenuItem redoMenuItem = new JMenuItem();
  95
  96   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
  97
  98   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
  99
 100   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 101
 102   JMenuItem copy = new JMenuItem();
 103
 104   JMenuItem cut = new JMenuItem();
 105
 106   JMenu pasteMenu = new JMenu();
 107
 108   protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 109
 110   protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 111
 112   protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 113
 114   protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 115
 116   protected JCheckBoxMenuItem applyToAllGroups;
 117
 118   protected JMenu colourMenu = new JMenu();
 119
 120   protected JMenuItem textColour;
 121
 122   protected JCheckBoxMenuItem conservationMenuItem;
 123
 124   protected JMenuItem modifyConservation;
 125
 126   protected JCheckBoxMenuItem abovePIDThreshold;
 127
 128   protected JMenuItem modifyPID;
 129
 130   protected JRadioButtonMenuItem annotationColour;
 131
 132   protected JMenu sortByTreeMenu = new JMenu();
 133
 134   protected JMenu sort = new JMenu();
 135
 136   protected JMenuItem calculateTree = new JMenuItem();
 137
 138   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 139
 140   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 141
 142   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 143
 144   protected JMenu showTranslation = new JMenu();
 145
 146   protected JMenuItem showReverse = new JMenuItem();
 147
 148   protected JMenuItem showReverseComplement = new JMenuItem();
 149
 150   protected JMenu showProducts = new JMenu();
 151
 152   protected JMenuItem runGroovy = new JMenuItem();
 153
 154   protected JMenuItem loadVcf;
 155
 156   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 157
 158   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 159
 160   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 161
 162   protected JPanel statusPanel = new JPanel();
 163
 164   protected JMenuItem showAllSeqAnnotations = new JMenuItem();
 165
 166   protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
 167
 168   protected JMenuItem showAllAlAnnotations = new JMenuItem();
 169
 170   protected JMenuItem hideAllAlAnnotations = new JMenuItem();
 171
 172   protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
 173
 174   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 175
 176   protected JTabbedPane tabbedPane = new JTabbedPane();
 177
 178   protected JMenuItem reload = new JMenuItem();
 179
 180   protected JMenu formatMenu = new JMenu();
 181
 182   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 183
 184   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 185
 186   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 187
 188   protected JMenuItem gatherViews = new JMenuItem();
 189
 190   protected JMenuItem expandViews = new JMenuItem();
 191
 192   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 193
 194   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 195
 196   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 197
 198   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 199
 200   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 201
 202   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 203
 204   private SequenceAnnotationOrder annotationSortOrder;
 205
 206   private boolean showAutoCalculatedAbove = false;
 207
 208   private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
 209
 210   private SplitContainerI splitFrame;
 211
 212   public GAlignFrame()
 213   {
 214     try
 215     {
 216       jbInit();
 217       setJMenuBar(alignFrameMenuBar);
 218
 219       // dynamically fill save as menu with available formats
 220       for (String ff : FileFormats.getInstance().getWritableFormats(true))
 221       {
 222         JMenuItem item = new JMenuItem(ff);
 223
 224         item.addActionListener(new ActionListener()
 225         {
 226           @Override
 227           public void actionPerformed(ActionEvent e)
 228           {
 229             outputText_actionPerformed(e);
 230           }
 231         });
 232
 233         outputTextboxMenu.add(item);
 234       }
 235     } catch (Exception e)
 236     {
 237       System.err.println(e.toString());
 238     }
 239
 240     if (!Platform.isAMac())
 241     {
 242       closeMenuItem.setMnemonic('C');
 243       outputTextboxMenu.setMnemonic('T');
 244       undoMenuItem.setMnemonic('Z');
 245       redoMenuItem.setMnemonic('0');
 246       copy.setMnemonic('C');
 247       cut.setMnemonic('U');
 248       pasteMenu.setMnemonic('P');
 249       reload.setMnemonic('R');
 250     }
 251   }
 252
 253   private void jbInit() throws Exception
 254   {
 255     initColourMenu();
 256
 257     JMenuItem saveAs = new JMenuItem(
 258             MessageManager.getString("action.save_as"));
 259     ActionListener al = new ActionListener()
 260     {
 261       @Override
 262       public void actionPerformed(ActionEvent e)
 263       {
 264         saveAs_actionPerformed(e);
 265       }
 266     };
 267
 268     // FIXME getDefaultToolkit throws an exception in Headless mode
 269     KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
 270             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
 271                     | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
 272             false);
 273     addMenuActionAndAccelerator(keyStroke, saveAs, al);
 274
 275     closeMenuItem.setText(MessageManager.getString("action.close"));
 276     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
 277             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 278     al = new ActionListener()
 279     {
 280       @Override
 281       public void actionPerformed(ActionEvent e)
 282       {
 283         closeMenuItem_actionPerformed(false);
 284       }
 285     };
 286     addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
 287
 288     JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
 289     JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
 290     JMenu annotationsMenu = new JMenu(
 291             MessageManager.getString("action.annotations"));
 292     JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
 293     colourMenu.setText(MessageManager.getString("action.colour"));
 294     JMenu calculateMenu = new JMenu(
 295             MessageManager.getString("action.calculate"));
 296     webService.setText(MessageManager.getString("action.web_service"));
 297     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
 298             MessageManager.getString("action.select_all"));
 299     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
 300             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 301     al = new ActionListener()
 302     {
 303       @Override
 304       public void actionPerformed(ActionEvent e)
 305       {
 306         selectAllSequenceMenuItem_actionPerformed(e);
 307       }
 308     };
 309     addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
 310
 311     JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
 312             MessageManager.getString("action.deselect_all"));
 313     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
 314     al = new ActionListener()
 315     {
 316       @Override
 317       public void actionPerformed(ActionEvent e)
 318       {
 319         deselectAllSequenceMenuItem_actionPerformed(e);
 320       }
 321     };
 322     addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
 323
 324     JMenuItem invertSequenceMenuItem = new JMenuItem(
 325             MessageManager.getString("action.invert_sequence_selection"));
 326     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
 327             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 328     al = new ActionListener()
 329     {
 330       @Override
 331       public void actionPerformed(ActionEvent e)
 332       {
 333         invertSequenceMenuItem_actionPerformed(e);
 334       }
 335     };
 336     addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
 337
 338     JMenuItem grpsFromSelection = new JMenuItem(
 339             MessageManager.getString("action.make_groups_selection"));
 340     grpsFromSelection.addActionListener(new ActionListener()
 341     {
 342       @Override
 343       public void actionPerformed(ActionEvent e)
 344       {
 345         makeGrpsFromSelection_actionPerformed(e);
 346       }
 347     });
 348     JMenuItem expandAlignment = new JMenuItem(
 349             MessageManager.getString("action.view_flanking_regions"));
 350     expandAlignment.setToolTipText(
 351             MessageManager.getString("label.view_flanking_regions"));
 352     expandAlignment.addActionListener(new ActionListener()
 353     {
 354       @Override
 355       public void actionPerformed(ActionEvent e)
 356       {
 357         expand_newalign(e);
 358       }
 359     });
 360     JMenuItem remove2LeftMenuItem = new JMenuItem(
 361             MessageManager.getString("action.remove_left"));
 362     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
 363             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 364     al = new ActionListener()
 365     {
 366       @Override
 367       public void actionPerformed(ActionEvent e)
 368       {
 369         remove2LeftMenuItem_actionPerformed(e);
 370       }
 371     };
 372     addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
 373
 374     JMenuItem remove2RightMenuItem = new JMenuItem(
 375             MessageManager.getString("action.remove_right"));
 376     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
 377             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 378     al = new ActionListener()
 379     {
 380       @Override
 381       public void actionPerformed(ActionEvent e)
 382       {
 383         remove2RightMenuItem_actionPerformed(e);
 384       }
 385     };
 386     addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
 387
 388     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
 389             MessageManager.getString("action.remove_empty_columns"));
 390     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
 391             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 392     al = new ActionListener()
 393     {
 394       @Override
 395       public void actionPerformed(ActionEvent e)
 396       {
 397         removeGappedColumnMenuItem_actionPerformed(e);
 398       }
 399     };
 400     addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
 401
 402     JMenuItem removeAllGapsMenuItem = new JMenuItem(
 403             MessageManager.getString("action.remove_all_gaps"));
 404     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
 405             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
 406                     | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
 407             false);
 408     al = new ActionListener()
 409     {
 410       @Override
 411       public void actionPerformed(ActionEvent e)
 412       {
 413         removeAllGapsMenuItem_actionPerformed(e);
 414       }
 415     };
 416     addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
 417
 418     JMenuItem justifyLeftMenuItem = new JMenuItem(
 419             MessageManager.getString("action.left_justify_alignment"));
 420     justifyLeftMenuItem.addActionListener(new ActionListener()
 421     {
 422       @Override
 423       public void actionPerformed(ActionEvent e)
 424       {
 425         justifyLeftMenuItem_actionPerformed(e);
 426       }
 427     });
 428     JMenuItem justifyRightMenuItem = new JMenuItem(
 429             MessageManager.getString("action.right_justify_alignment"));
 430     justifyRightMenuItem.addActionListener(new ActionListener()
 431     {
 432       @Override
 433       public void actionPerformed(ActionEvent e)
 434       {
 435         justifyRightMenuItem_actionPerformed(e);
 436       }
 437     });
 438     viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
 439     viewBoxesMenuItem.setState(true);
 440     viewBoxesMenuItem.addActionListener(new ActionListener()
 441     {
 442       @Override
 443       public void actionPerformed(ActionEvent e)
 444       {
 445         viewBoxesMenuItem_actionPerformed(e);
 446       }
 447     });
 448     viewTextMenuItem.setText(MessageManager.getString("action.text"));
 449     viewTextMenuItem.setState(true);
 450     viewTextMenuItem.addActionListener(new ActionListener()
 451     {
 452       @Override
 453       public void actionPerformed(ActionEvent e)
 454       {
 455         viewTextMenuItem_actionPerformed(e);
 456       }
 457     });
 458     showNonconservedMenuItem
 459             .setText(MessageManager.getString("label.show_non_conserved"));
 460     showNonconservedMenuItem.setState(false);
 461     showNonconservedMenuItem.addActionListener(new ActionListener()
 462     {
 463       @Override
 464       public void actionPerformed(ActionEvent e)
 465       {
 466         showUnconservedMenuItem_actionPerformed(e);
 467       }
 468     });
 469     JMenuItem sortPairwiseMenuItem = new JMenuItem(
 470             MessageManager.getString("action.by_pairwise_id"));
 471     sortPairwiseMenuItem.addActionListener(new ActionListener()
 472     {
 473       @Override
 474       public void actionPerformed(ActionEvent e)
 475       {
 476         sortPairwiseMenuItem_actionPerformed(e);
 477       }
 478     });
 479     JMenuItem sortIDMenuItem = new JMenuItem(
 480             MessageManager.getString("action.by_id"));
 481     sortIDMenuItem.addActionListener(new ActionListener()
 482     {
 483       @Override
 484       public void actionPerformed(ActionEvent e)
 485       {
 486         sortIDMenuItem_actionPerformed(e);
 487       }
 488     });
 489     JMenuItem sortLengthMenuItem = new JMenuItem(
 490             MessageManager.getString("action.by_length"));
 491     sortLengthMenuItem.addActionListener(new ActionListener()
 492     {
 493       @Override
 494       public void actionPerformed(ActionEvent e)
 495       {
 496         sortLengthMenuItem_actionPerformed(e);
 497       }
 498     });
 499     JMenuItem sortGroupMenuItem = new JMenuItem(
 500             MessageManager.getString("action.by_group"));
 501     sortGroupMenuItem.addActionListener(new ActionListener()
 502     {
 503       @Override
 504       public void actionPerformed(ActionEvent e)
 505       {
 506         sortGroupMenuItem_actionPerformed(e);
 507       }
 508     });
 509
 510     JMenuItem removeRedundancyMenuItem = new JMenuItem(
 511             MessageManager.getString("action.remove_redundancy"));
 512     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
 513             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 514     al = new ActionListener()
 515     {
 516       @Override
 517       public void actionPerformed(ActionEvent e)
 518       {
 519         removeRedundancyMenuItem_actionPerformed(e);
 520       }
 521     };
 522     addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
 523
 524     JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
 525             MessageManager.getString("action.pairwise_alignment"));
 526     pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
 527     {
 528       @Override
 529       public void actionPerformed(ActionEvent e)
 530       {
 531         pairwiseAlignmentMenuItem_actionPerformed(e);
 532       }
 533     });
 534
 535     this.getContentPane().setLayout(new BorderLayout());
 536     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 537     statusBar.setBackground(Color.white);
 538     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 539     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 540     statusBar.setText(MessageManager.getString("label.status_bar"));
 541     outputTextboxMenu
 542             .setText(MessageManager.getString("label.out_to_textbox"));
 543
 544     annotationPanelMenuItem.setActionCommand("");
 545     annotationPanelMenuItem
 546             .setText(MessageManager.getString("label.show_annotations"));
 547     annotationPanelMenuItem
 548             .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
 549     annotationPanelMenuItem.addActionListener(new ActionListener()
 550     {
 551       @Override
 552       public void actionPerformed(ActionEvent e)
 553       {
 554         annotationPanelMenuItem_actionPerformed(e);
 555       }
 556     });
 557     showAllAlAnnotations.setText(
 558             MessageManager.getString("label.show_all_al_annotations"));
 559     final boolean isAnnotationPanelShown = annotationPanelMenuItem
 560             .getState();
 561     showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 562     showAllAlAnnotations.addActionListener(new ActionListener()
 563     {
 564       @Override
 565       public void actionPerformed(ActionEvent e)
 566       {
 567         showAllAnnotations_actionPerformed(false, true);
 568       }
 569     });
 570     hideAllAlAnnotations.setText(
 571             MessageManager.getString("label.hide_all_al_annotations"));
 572     hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 573     hideAllAlAnnotations.addActionListener(new ActionListener()
 574     {
 575       @Override
 576       public void actionPerformed(ActionEvent e)
 577       {
 578         hideAllAnnotations_actionPerformed(false, true);
 579       }
 580     });
 581     showAllSeqAnnotations.setText(
 582             MessageManager.getString("label.show_all_seq_annotations"));
 583     showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 584     showAllSeqAnnotations.addActionListener(new ActionListener()
 585     {
 586       @Override
 587       public void actionPerformed(ActionEvent e)
 588       {
 589         showAllAnnotations_actionPerformed(true, false);
 590       }
 591     });
 592     hideAllSeqAnnotations.setText(
 593             MessageManager.getString("label.hide_all_seq_annotations"));
 594     hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 595     hideAllSeqAnnotations.addActionListener(new ActionListener()
 596     {
 597       @Override
 598       public void actionPerformed(ActionEvent e)
 599       {
 600         hideAllAnnotations_actionPerformed(true, false);
 601       }
 602     });
 603     SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
 604             .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
 605                     SequenceAnnotationOrder.NONE.name()));
 606     final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
 607             MessageManager.getString("label.sort_annotations_by_sequence"));
 608     final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
 609             MessageManager.getString("label.sort_annotations_by_label"));
 610
 611     sortAnnBySequence.setSelected(
 612             sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
 613     sortAnnBySequence.addActionListener(new ActionListener()
 614     {
 615       @Override
 616       public void actionPerformed(ActionEvent e)
 617       {
 618         boolean newState = sortAnnBySequence.getState();
 619         sortAnnByLabel.setSelected(false);
 620         setAnnotationSortOrder(
 621                 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 622                         : SequenceAnnotationOrder.NONE);
 623         sortAnnotations_actionPerformed();
 624       }
 625     });
 626     sortAnnByLabel.setSelected(
 627             sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
 628     sortAnnByLabel.addActionListener(new ActionListener()
 629     {
 630       @Override
 631       public void actionPerformed(ActionEvent e)
 632       {
 633         boolean newState = sortAnnByLabel.getState();
 634         sortAnnBySequence.setSelected(false);
 635         setAnnotationSortOrder(
 636                 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 637                         : SequenceAnnotationOrder.NONE);
 638         sortAnnotations_actionPerformed();
 639       }
 640     });
 641     colourTextMenuItem = new JCheckBoxMenuItem(
 642             MessageManager.getString("label.colour_text"));
 643     colourTextMenuItem.addActionListener(new ActionListener()
 644     {
 645       @Override
 646       public void actionPerformed(ActionEvent e)
 647       {
 648         colourTextMenuItem_actionPerformed(e);
 649       }
 650     });
 651     colourGapsMenuItem = new JCheckBoxMenuItem(
 652             MessageManager.getString("label.colour_gaps"));
 653     colourGapsMenuItem.addActionListener(new ActionListener()
 654     {
 655       @Override
 656       public void actionPerformed(ActionEvent e)
 657       {
 658         colourGapsMenuItem_actionPerformed(e);
 659       }
 660     });
 661     JMenuItem htmlMenuItem = new JMenuItem(
 662             MessageManager.getString("label.html"));
 663     htmlMenuItem.addActionListener(new ActionListener()
 664     {
 665       @Override
 666       public void actionPerformed(ActionEvent e)
 667       {
 668         htmlMenuItem_actionPerformed(e);
 669       }
 670     });
 671
 672     JMenuItem createBioJS = new JMenuItem(
 673             MessageManager.getString("label.biojs_html_export"));
 674     createBioJS.addActionListener(new java.awt.event.ActionListener()
 675     {
 676       @Override
 677       public void actionPerformed(ActionEvent e)
 678       {
 679         bioJSMenuItem_actionPerformed(e);
 680       }
 681     });
 682
 683     JMenuItem overviewMenuItem = new JMenuItem(
 684             MessageManager.getString("label.overview_window"));
 685     overviewMenuItem.addActionListener(new ActionListener()
 686     {
 687       @Override
 688       public void actionPerformed(ActionEvent e)
 689       {
 690         overviewMenuItem_actionPerformed(e);
 691       }
 692     });
 693
 694     undoMenuItem.setEnabled(false);
 695     undoMenuItem.setText(MessageManager.getString("action.undo"));
 696     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
 697             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 698     al = new ActionListener()
 699     {
 700       @Override
 701       public void actionPerformed(ActionEvent e)
 702       {
 703         undoMenuItem_actionPerformed(e);
 704       }
 705     };
 706     addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
 707
 708     redoMenuItem.setEnabled(false);
 709     redoMenuItem.setText(MessageManager.getString("action.redo"));
 710     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
 711             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 712     al = new ActionListener()
 713     {
 714       @Override
 715       public void actionPerformed(ActionEvent e)
 716       {
 717         redoMenuItem_actionPerformed(e);
 718       }
 719     };
 720     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
 721
 722     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
 723     wrapMenuItem.addActionListener(new ActionListener()
 724     {
 725       @Override
 726       public void actionPerformed(ActionEvent e)
 727       {
 728         wrapMenuItem_actionPerformed(e);
 729       }
 730     });
 731
 732     JMenuItem printMenuItem = new JMenuItem(
 733             MessageManager.getString("action.print"));
 734     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
 735             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 736     al = new ActionListener()
 737     {
 738       @Override
 739       public void actionPerformed(ActionEvent e)
 740       {
 741         printMenuItem_actionPerformed(e);
 742       }
 743     };
 744     addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
 745
 746     renderGapsMenuItem
 747             .setText(MessageManager.getString("action.show_gaps"));
 748     renderGapsMenuItem.setState(true);
 749     renderGapsMenuItem.addActionListener(new ActionListener()
 750     {
 751       @Override
 752       public void actionPerformed(ActionEvent e)
 753       {
 754         renderGapsMenuItem_actionPerformed(e);
 755       }
 756     });
 757
 758     JMenuItem findMenuItem = new JMenuItem(
 759             MessageManager.getString("action.find"));
 760     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
 761             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 762     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
 763             MessageManager.getString("label.find_tip")));
 764     al = new ActionListener()
 765     {
 766       @Override
 767       public void actionPerformed(ActionEvent e)
 768       {
 769         findMenuItem_actionPerformed(e);
 770       }
 771     };
 772     addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
 773
 774     showSeqFeatures.setText(
 775             MessageManager.getString("label.show_sequence_features"));
 776     showSeqFeatures.addActionListener(new ActionListener()
 777     {
 778       @Override
 779       public void actionPerformed(ActionEvent actionEvent)
 780       {
 781         showSeqFeatures_actionPerformed(actionEvent);
 782       }
 783     });
 784     /*
 785      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
 786      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
 787      * void actionPerformed(ActionEvent actionEvent) {
 788      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
 789      */
 790     showDbRefsMenuitem
 791             .setText(MessageManager.getString("label.show_database_refs"));
 792     showDbRefsMenuitem.addActionListener(new ActionListener()
 793     {
 794
 795       @Override
 796       public void actionPerformed(ActionEvent e)
 797       {
 798         showDbRefs_actionPerformed(e);
 799       }
 800
 801     });
 802     showNpFeatsMenuitem.setText(
 803             MessageManager.getString("label.show_non_positional_features"));
 804     showNpFeatsMenuitem.addActionListener(new ActionListener()
 805     {
 806
 807       @Override
 808       public void actionPerformed(ActionEvent e)
 809       {
 810         showNpFeats_actionPerformed(e);
 811       }
 812
 813     });
 814     showGroupConservation
 815             .setText(MessageManager.getString("label.group_conservation"));
 816     showGroupConservation.addActionListener(new ActionListener()
 817     {
 818
 819       @Override
 820       public void actionPerformed(ActionEvent e)
 821       {
 822         showGroupConservation_actionPerformed(e);
 823       }
 824
 825     });
 826
 827     showGroupConsensus
 828             .setText(MessageManager.getString("label.group_consensus"));
 829     showGroupConsensus.addActionListener(new ActionListener()
 830     {
 831
 832       @Override
 833       public void actionPerformed(ActionEvent e)
 834       {
 835         showGroupConsensus_actionPerformed(e);
 836       }
 837
 838     });
 839     showConsensusHistogram.setText(
 840             MessageManager.getString("label.show_consensus_histogram"));
 841     showConsensusHistogram.addActionListener(new ActionListener()
 842     {
 843
 844       @Override
 845       public void actionPerformed(ActionEvent e)
 846       {
 847         showConsensusHistogram_actionPerformed(e);
 848       }
 849
 850     });
 851     showSequenceLogo
 852             .setText(MessageManager.getString("label.show_consensus_logo"));
 853     showSequenceLogo.addActionListener(new ActionListener()
 854     {
 855
 856       @Override
 857       public void actionPerformed(ActionEvent e)
 858       {
 859         showSequenceLogo_actionPerformed(e);
 860       }
 861
 862     });
 863     normaliseSequenceLogo
 864             .setText(MessageManager.getString("label.norm_consensus_logo"));
 865     normaliseSequenceLogo.addActionListener(new ActionListener()
 866     {
 867
 868       @Override
 869       public void actionPerformed(ActionEvent e)
 870       {
 871         normaliseSequenceLogo_actionPerformed(e);
 872       }
 873
 874     });
 875     applyAutoAnnotationSettings
 876             .setText(MessageManager.getString("label.apply_all_groups"));
 877     applyAutoAnnotationSettings.setState(false);
 878     applyAutoAnnotationSettings.setVisible(true);
 879     applyAutoAnnotationSettings.addActionListener(new ActionListener()
 880     {
 881       @Override
 882       public void actionPerformed(ActionEvent e)
 883       {
 884         applyAutoAnnotationSettings_actionPerformed(e);
 885       }
 886     });
 887
 888     ButtonGroup buttonGroup = new ButtonGroup();
 889     final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
 890             MessageManager.getString("label.show_first"));
 891     final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
 892             MessageManager.getString("label.show_last"));
 893     buttonGroup.add(showAutoFirst);
 894     buttonGroup.add(showAutoLast);
 895     final boolean autoFirst = Cache
 896             .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
 897     showAutoFirst.setSelected(autoFirst);
 898     setShowAutoCalculatedAbove(autoFirst);
 899     showAutoFirst.addActionListener(new ActionListener()
 900     {
 901       @Override
 902       public void actionPerformed(ActionEvent e)
 903       {
 904         setShowAutoCalculatedAbove(showAutoFirst.isSelected());
 905         sortAnnotations_actionPerformed();
 906       }
 907     });
 908     showAutoLast.setSelected(!showAutoFirst.isSelected());
 909     showAutoLast.addActionListener(new ActionListener()
 910     {
 911       @Override
 912       public void actionPerformed(ActionEvent e)
 913       {
 914         setShowAutoCalculatedAbove(!showAutoLast.isSelected());
 915         sortAnnotations_actionPerformed();
 916       }
 917     });
 918
 919     JMenuItem deleteGroups = new JMenuItem(
 920             MessageManager.getString("action.undefine_groups"));
 921     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
 922             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 923     al = new ActionListener()
 924     {
 925       @Override
 926       public void actionPerformed(ActionEvent e)
 927       {
 928         deleteGroups_actionPerformed(e);
 929       }
 930     };
 931     addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
 932
 933     JMenuItem annotationColumn = new JMenuItem(
 934             MessageManager.getString("action.select_by_annotation"));
 935     annotationColumn.addActionListener(new ActionListener()
 936     {
 937       @Override
 938       public void actionPerformed(ActionEvent e)
 939       {
 940         annotationColumn_actionPerformed(e);
 941       }
 942     });
 943
 944     JMenuItem createGroup = new JMenuItem(
 945             MessageManager.getString("action.create_group"));
 946     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
 947             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 948     al = new ActionListener()
 949     {
 950       @Override
 951       public void actionPerformed(ActionEvent e)
 952       {
 953         createGroup_actionPerformed(e);
 954       }
 955     };
 956     addMenuActionAndAccelerator(keyStroke, createGroup, al);
 957
 958     JMenuItem unGroup = new JMenuItem(
 959             MessageManager.getString("action.remove_group"));
 960     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
 961             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
 962                     | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
 963             false);
 964     al = new ActionListener()
 965     {
 966       @Override
 967       public void actionPerformed(ActionEvent e)
 968       {
 969         unGroup_actionPerformed(e);
 970       }
 971     };
 972     addMenuActionAndAccelerator(keyStroke, unGroup, al);
 973
 974     copy.setText(MessageManager.getString("action.copy"));
 975     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
 976             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 977
 978     al = new ActionListener()
 979     {
 980       @Override
 981       public void actionPerformed(ActionEvent e)
 982       {
 983         copy_actionPerformed(e);
 984       }
 985     };
 986     addMenuActionAndAccelerator(keyStroke, copy, al);
 987
 988     cut.setText(MessageManager.getString("action.cut"));
 989     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
 990             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 991     al = new ActionListener()
 992     {
 993       @Override
 994       public void actionPerformed(ActionEvent e)
 995       {
 996         cut_actionPerformed(e);
 997       }
 998     };
 999     addMenuActionAndAccelerator(keyStroke, cut, al);
1000
1001     JMenuItem delete = new JMenuItem(
1002             MessageManager.getString("action.delete"));
1003     delete.addActionListener(new ActionListener()
1004     {
1005       @Override
1006       public void actionPerformed(ActionEvent e)
1007       {
1008         delete_actionPerformed(e);
1009       }
1010     });
1011
1012     pasteMenu.setText(MessageManager.getString("action.paste"));
1013     JMenuItem pasteNew = new JMenuItem(
1014             MessageManager.getString("label.to_new_alignment"));
1015     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1016             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1017                     | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
1018             false);
1019     al = new ActionListener()
1020     {
1021       @Override
1022       public void actionPerformed(ActionEvent e)
1023       {
1024         pasteNew_actionPerformed(e);
1025       }
1026     };
1027     addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1028
1029     JMenuItem pasteThis = new JMenuItem(
1030             MessageManager.getString("label.to_this_alignment"));
1031     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1032             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
1033     al = new ActionListener()
1034     {
1035       @Override
1036       public void actionPerformed(ActionEvent e)
1037       {
1038         pasteThis_actionPerformed(e);
1039       }
1040     };
1041     addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1042
1043     JMenuItem createPNG = new JMenuItem("PNG");
1044     createPNG.addActionListener(new ActionListener()
1045     {
1046       @Override
1047       public void actionPerformed(ActionEvent e)
1048       {
1049         createPNG(null);
1050       }
1051     });
1052     createPNG.setActionCommand(
1053             MessageManager.getString("label.save_png_image"));
1054
1055     JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1056     font.addActionListener(new ActionListener()
1057     {
1058       @Override
1059       public void actionPerformed(ActionEvent e)
1060       {
1061         font_actionPerformed(e);
1062       }
1063     });
1064     seqLimits.setText(
1065             MessageManager.getString("label.show_sequence_limits"));
1066     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1067     seqLimits.addActionListener(new ActionListener()
1068     {
1069       @Override
1070       public void actionPerformed(ActionEvent e)
1071       {
1072         seqLimit_actionPerformed(e);
1073       }
1074     });
1075     JMenuItem epsFile = new JMenuItem("EPS");
1076     epsFile.addActionListener(new ActionListener()
1077     {
1078       @Override
1079       public void actionPerformed(ActionEvent e)
1080       {
1081         createEPS(null);
1082       }
1083     });
1084
1085     JMenuItem createSVG = new JMenuItem("SVG");
1086     createSVG.addActionListener(new ActionListener()
1087     {
1088       @Override
1089       public void actionPerformed(ActionEvent e)
1090       {
1091         createSVG(null);
1092       }
1093     });
1094
1095     JMenuItem loadTreeMenuItem = new JMenuItem(
1096             MessageManager.getString("label.load_associated_tree"));
1097     loadTreeMenuItem.setActionCommand(
1098             MessageManager.getString("label.load_tree_for_sequence_set"));
1099     loadTreeMenuItem.addActionListener(new ActionListener()
1100     {
1101       @Override
1102       public void actionPerformed(ActionEvent e)
1103       {
1104         loadTreeMenuItem_actionPerformed(e);
1105       }
1106     });
1107
1108     scaleAbove.setVisible(false);
1109     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1110     scaleAbove.addActionListener(new ActionListener()
1111     {
1112       @Override
1113       public void actionPerformed(ActionEvent e)
1114       {
1115         scaleAbove_actionPerformed(e);
1116       }
1117     });
1118     scaleLeft.setVisible(false);
1119     scaleLeft.setSelected(true);
1120     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1121     scaleLeft.addActionListener(new ActionListener()
1122     {
1123       @Override
1124       public void actionPerformed(ActionEvent e)
1125       {
1126         scaleLeft_actionPerformed(e);
1127       }
1128     });
1129     scaleRight.setVisible(false);
1130     scaleRight.setSelected(true);
1131     scaleRight.setText(MessageManager.getString("action.scale_right"));
1132     scaleRight.addActionListener(new ActionListener()
1133     {
1134       @Override
1135       public void actionPerformed(ActionEvent e)
1136       {
1137         scaleRight_actionPerformed(e);
1138       }
1139     });
1140     centreColumnLabelsMenuItem.setVisible(true);
1141     centreColumnLabelsMenuItem.setState(false);
1142     centreColumnLabelsMenuItem.setText(
1143             MessageManager.getString("label.centre_column_labels"));
1144     centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1145     {
1146       @Override
1147       public void actionPerformed(ActionEvent e)
1148       {
1149         centreColumnLabels_actionPerformed(e);
1150       }
1151     });
1152     followHighlightMenuItem.setVisible(true);
1153     followHighlightMenuItem.setState(true);
1154     followHighlightMenuItem
1155             .setText(MessageManager.getString("label.automatic_scrolling"));
1156     followHighlightMenuItem.addActionListener(new ActionListener()
1157     {
1158
1159       @Override
1160       public void actionPerformed(ActionEvent e)
1161       {
1162         followHighlight_actionPerformed();
1163       }
1164
1165     });
1166
1167     sortByTreeMenu
1168             .setText(MessageManager.getString("action.by_tree_order"));
1169     sort.setText(MessageManager.getString("action.sort"));
1170     sort.addMenuListener(new MenuListener()
1171     {
1172       @Override
1173       public void menuSelected(MenuEvent e)
1174       {
1175         buildTreeSortMenu();
1176       }
1177
1178       @Override
1179       public void menuDeselected(MenuEvent e)
1180       {
1181       }
1182
1183       @Override
1184       public void menuCanceled(MenuEvent e)
1185       {
1186       }
1187     });
1188     sortByAnnotScore
1189             .setText(MessageManager.getString("label.sort_by_score"));
1190     sort.add(sortByAnnotScore);
1191     sort.addMenuListener(new javax.swing.event.MenuListener()
1192     {
1193
1194       @Override
1195       public void menuCanceled(MenuEvent e)
1196       {
1197       }
1198
1199       @Override
1200       public void menuDeselected(MenuEvent e)
1201       {
1202       }
1203
1204       @Override
1205       public void menuSelected(MenuEvent e)
1206       {
1207         buildSortByAnnotationScoresMenu();
1208       }
1209     });
1210     sortByAnnotScore.setVisible(false);
1211
1212     calculateTree
1213             .setText(MessageManager.getString("action.calculate_tree_pca"));
1214
1215     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1216     padGapsMenuitem
1217             .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
1218     padGapsMenuitem.addActionListener(new ActionListener()
1219     {
1220       @Override
1221       public void actionPerformed(ActionEvent e)
1222       {
1223         padGapsMenuitem_actionPerformed(e);
1224       }
1225     });
1226     JMenuItem vamsasStore = new JMenuItem(
1227             MessageManager.getString("label.vamsas_store"));
1228     vamsasStore.setVisible(false);
1229     vamsasStore.addActionListener(new ActionListener()
1230     {
1231       @Override
1232       public void actionPerformed(ActionEvent e)
1233       {
1234         vamsasStore_actionPerformed(e);
1235       }
1236     });
1237
1238     /*
1239      * Translate as cDNA with sub-menu of translation tables
1240      */
1241     showTranslation.setText(MessageManager
1242             .getString("label.translate_cDNA"));
1243     boolean first = true;
1244     for (final GeneticCodeI table : GeneticCodes.getInstance()
1245             .getCodeTables())
1246     {
1247       JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
1248       showTranslation.add(item);
1249       item.addActionListener(new ActionListener()
1250       {
1251         @Override
1252         public void actionPerformed(ActionEvent e)
1253         {
1254           showTranslation_actionPerformed(table);
1255         }
1256       });
1257       if (first)
1258       {
1259         showTranslation.addSeparator();
1260       }
1261       first = false;
1262     }
1263
1264     showReverse.setText(MessageManager.getString("label.reverse"));
1265     showReverse.addActionListener(new ActionListener()
1266     {
1267       @Override
1268       public void actionPerformed(ActionEvent e)
1269       {
1270         showReverse_actionPerformed(false);
1271       }
1272     });
1273     showReverseComplement
1274             .setText(MessageManager.getString("label.reverse_complement"));
1275     showReverseComplement.addActionListener(new ActionListener()
1276     {
1277       @Override
1278       public void actionPerformed(ActionEvent e)
1279       {
1280         showReverse_actionPerformed(true);
1281       }
1282     });
1283
1284     JMenuItem extractScores = new JMenuItem(
1285             MessageManager.getString("label.extract_scores"));
1286     extractScores.addActionListener(new ActionListener()
1287     {
1288       @Override
1289       public void actionPerformed(ActionEvent e)
1290       {
1291         extractScores_actionPerformed(e);
1292       }
1293     });
1294     extractScores.setVisible(true);
1295     // JBPNote: TODO: make gui for regex based score extraction
1296
1297     // for show products actions see AlignFrame.canShowProducts
1298     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1299
1300     runGroovy.setText(MessageManager.getString("label.run_groovy"));
1301     runGroovy.setToolTipText(
1302             MessageManager.getString("label.run_groovy_tip"));
1303     runGroovy.addActionListener(new ActionListener()
1304     {
1305       @Override
1306       public void actionPerformed(ActionEvent e)
1307       {
1308         runGroovy_actionPerformed();
1309       }
1310     });
1311
1312     JMenuItem openFeatureSettings = new JMenuItem(
1313             MessageManager.getString("action.feature_settings"));
1314     openFeatureSettings.addActionListener(new ActionListener()
1315     {
1316       @Override
1317       public void actionPerformed(ActionEvent e)
1318       {
1319         featureSettings_actionPerformed(e);
1320       }
1321     });
1322     JMenuItem fetchSequence = new JMenuItem(
1323             MessageManager.getString("label.fetch_sequences"));
1324     fetchSequence.addActionListener(new ActionListener()
1325     {
1326       @Override
1327       public void actionPerformed(ActionEvent e)
1328       {
1329         fetchSequence_actionPerformed(e);
1330       }
1331     });
1332
1333     JMenuItem associatedData = new JMenuItem(
1334             MessageManager.getString("label.load_features_annotations"));
1335     associatedData.addActionListener(new ActionListener()
1336     {
1337       @Override
1338       public void actionPerformed(ActionEvent e)
1339       {
1340         associatedData_actionPerformed(e);
1341       }
1342     });
1343     loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
1344     loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
1345     loadVcf.addActionListener(new ActionListener()
1346     {
1347       @Override
1348       public void actionPerformed(ActionEvent e)
1349       {
1350         loadVcf_actionPerformed();
1351       }
1352     });
1353     autoCalculate.setText(
1354             MessageManager.getString("label.autocalculate_consensus"));
1355     autoCalculate.setState(
1356             jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1357     autoCalculate.addActionListener(new ActionListener()
1358     {
1359       @Override
1360       public void actionPerformed(ActionEvent e)
1361       {
1362         autoCalculate_actionPerformed(e);
1363       }
1364     });
1365     sortByTree.setText(
1366             MessageManager.getString("label.sort_alignment_new_tree"));
1367     sortByTree.setToolTipText("<html>" + MessageManager.getString(
1368             "label.enable_automatically_sort_alignment_when_open_new_tree"));
1369     sortByTree
1370             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1371     sortByTree.addActionListener(new ActionListener()
1372     {
1373       @Override
1374       public void actionPerformed(ActionEvent e)
1375       {
1376         sortByTreeOption_actionPerformed(e);
1377       }
1378     });
1379
1380     listenToViewSelections.setText(
1381             MessageManager.getString("label.listen_for_selections"));
1382     listenToViewSelections
1383             .setToolTipText("<html>" + MessageManager.getString(
1384                     "label.selections_mirror_selections_made_same_sequences_other_views"));
1385     listenToViewSelections.setState(false);
1386     listenToViewSelections.addActionListener(new ActionListener()
1387     {
1388       @Override
1389       public void actionPerformed(ActionEvent e)
1390       {
1391         listenToViewSelections_actionPerformed(e);
1392       }
1393     });
1394
1395     JMenu addSequenceMenu = new JMenu(
1396             MessageManager.getString("label.add_sequences"));
1397     JMenuItem addFromFile = new JMenuItem(
1398             MessageManager.getString("label.from_file"));
1399     addFromFile.addActionListener(new ActionListener()
1400     {
1401       @Override
1402       public void actionPerformed(ActionEvent e)
1403       {
1404         addFromFile_actionPerformed(e);
1405       }
1406     });
1407     JMenuItem addFromText = new JMenuItem(
1408             MessageManager.getString("label.from_textbox"));
1409     addFromText.addActionListener(new ActionListener()
1410     {
1411       @Override
1412       public void actionPerformed(ActionEvent e)
1413       {
1414         addFromText_actionPerformed(e);
1415       }
1416     });
1417     JMenuItem addFromURL = new JMenuItem(
1418             MessageManager.getString("label.from_url"));
1419     addFromURL.addActionListener(new ActionListener()
1420     {
1421       @Override
1422       public void actionPerformed(ActionEvent e)
1423       {
1424         addFromURL_actionPerformed(e);
1425       }
1426     });
1427     JMenuItem exportFeatures = new JMenuItem(
1428             MessageManager.getString("label.export_features"));
1429     exportFeatures.addActionListener(new ActionListener()
1430     {
1431       @Override
1432       public void actionPerformed(ActionEvent e)
1433       {
1434         exportFeatures_actionPerformed(e);
1435       }
1436     });
1437     JMenuItem exportAnnotations = new JMenuItem(
1438             MessageManager.getString("label.export_annotations"));
1439     exportAnnotations.addActionListener(new ActionListener()
1440     {
1441       @Override
1442       public void actionPerformed(ActionEvent e)
1443       {
1444         exportAnnotations_actionPerformed(e);
1445       }
1446     });
1447     statusPanel.setLayout(new GridLayout());
1448     JMenuItem showAllSeqs = new JMenuItem(
1449             MessageManager.getString("label.all_sequences"));
1450     showAllSeqs.setToolTipText(
1451             MessageManager.getString("label.toggle_sequence_visibility"));
1452     showAllSeqs.addActionListener(new ActionListener()
1453     {
1454       @Override
1455       public void actionPerformed(ActionEvent e)
1456       {
1457         showAllSeqs_actionPerformed(e);
1458       }
1459     });
1460     JMenuItem showAllColumns = new JMenuItem(
1461             MessageManager.getString("label.all_columns"));
1462     showAllColumns.setToolTipText(
1463             MessageManager.getString("label.toggle_columns_visibility"));
1464     showAllColumns.addActionListener(new ActionListener()
1465     {
1466       @Override
1467       public void actionPerformed(ActionEvent e)
1468       {
1469         showAllColumns_actionPerformed(e);
1470       }
1471     });
1472     JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1473     JMenuItem hideSelSequences = new JMenuItem(
1474             MessageManager.getString("label.selected_sequences"));
1475     hideSelSequences.setToolTipText(
1476             MessageManager.getString("label.toggle_sequence_visibility"));
1477     hideSelSequences.addActionListener(new ActionListener()
1478     {
1479       @Override
1480       public void actionPerformed(ActionEvent e)
1481       {
1482         hideSelSequences_actionPerformed(e);
1483       }
1484     });
1485     JMenuItem hideSelColumns = new JMenuItem(
1486             MessageManager.getString("label.selected_columns"));
1487     hideSelColumns.setToolTipText(
1488             MessageManager.getString("label.toggle_columns_visibility"));
1489     hideSelColumns.addActionListener(new ActionListener()
1490     {
1491       @Override
1492       public void actionPerformed(ActionEvent e)
1493       {
1494         hideSelColumns_actionPerformed(e);
1495       }
1496     });
1497     JMenuItem hideAllSelection = new JMenuItem(
1498             MessageManager.getString("label.selected_region"));
1499     hideAllSelection.addActionListener(new ActionListener()
1500     {
1501       @Override
1502       public void actionPerformed(ActionEvent e)
1503       {
1504         hideAllSelection_actionPerformed(e);
1505       }
1506     });
1507     // TODO: should be hidden if no selection exists.
1508     JMenuItem hideAllButSelection = new JMenuItem(
1509             MessageManager.getString("label.all_but_selected_region"));
1510     hideAllButSelection.addActionListener(new ActionListener()
1511     {
1512       @Override
1513       public void actionPerformed(ActionEvent e)
1514       {
1515         hideAllButSelection_actionPerformed(e);
1516       }
1517     });
1518     JMenuItem showAllhidden = new JMenuItem(
1519             MessageManager.getString("label.all_sequences_columns"));
1520     showAllhidden.setToolTipText(MessageManager
1521             .getString("label.toggles_visibility_hidden_selected_regions"));
1522     showAllhidden.addActionListener(new ActionListener()
1523     {
1524       @Override
1525       public void actionPerformed(ActionEvent e)
1526       {
1527         showAllhidden_actionPerformed(e);
1528       }
1529     });
1530     hiddenMarkers.setText(
1531             MessageManager.getString("action.show_hidden_markers"));
1532     hiddenMarkers.addActionListener(new ActionListener()
1533     {
1534       @Override
1535       public void actionPerformed(ActionEvent e)
1536       {
1537         hiddenMarkers_actionPerformed(e);
1538       }
1539     });
1540
1541     JMenuItem invertColSel = new JMenuItem(
1542             MessageManager.getString("action.invert_column_selection"));
1543     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1544             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1545                     | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
1546             false);
1547     al = new ActionListener()
1548     {
1549       @Override
1550       public void actionPerformed(ActionEvent e)
1551       {
1552         invertColSel_actionPerformed(e);
1553       }
1554     };
1555     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1556
1557     showComplementMenuItem.setVisible(false);
1558     showComplementMenuItem.addActionListener(new ActionListener()
1559     {
1560       @Override
1561       public void actionPerformed(ActionEvent e)
1562       {
1563         showComplement_actionPerformed(showComplementMenuItem.getState());
1564       }
1565     });
1566
1567     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1568     {
1569       @Override
1570       public void stateChanged(ChangeEvent evt)
1571       {
1572         JTabbedPane pane = (JTabbedPane) evt.getSource();
1573         int sel = pane.getSelectedIndex();
1574         tabSelectionChanged(sel);
1575       }
1576     });
1577     tabbedPane.addMouseListener(new MouseAdapter()
1578     {
1579       @Override
1580       public void mousePressed(MouseEvent e)
1581       {
1582         if (e.isPopupTrigger()) // Mac
1583         {
1584           tabbedPane_mousePressed(e);
1585         }
1586       }
1587
1588       @Override
1589       public void mouseReleased(MouseEvent e)
1590       {
1591         if (e.isPopupTrigger()) // Windows
1592         {
1593           tabbedPane_mousePressed(e);
1594         }
1595       }
1596     });
1597     tabbedPane.addFocusListener(new FocusAdapter()
1598     {
1599       @Override
1600       public void focusGained(FocusEvent e)
1601       {
1602         tabbedPane_focusGained(e);
1603       }
1604     });
1605
1606     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1607     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1608             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
1609     al = new ActionListener()
1610     {
1611       @Override
1612       public void actionPerformed(ActionEvent e)
1613       {
1614         save_actionPerformed(e);
1615       }
1616     };
1617     addMenuActionAndAccelerator(keyStroke, save, al);
1618
1619     reload.setEnabled(false);
1620     reload.setText(MessageManager.getString("action.reload"));
1621     reload.addActionListener(new ActionListener()
1622     {
1623       @Override
1624       public void actionPerformed(ActionEvent e)
1625       {
1626         reload_actionPerformed(e);
1627       }
1628     });
1629
1630     JMenuItem newView = new JMenuItem(
1631             MessageManager.getString("action.new_view"));
1632     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1633             jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
1634     al = new ActionListener()
1635     {
1636       @Override
1637       public void actionPerformed(ActionEvent e)
1638       {
1639         newView_actionPerformed(e);
1640       }
1641     };
1642     addMenuActionAndAccelerator(keyStroke, newView, al);
1643
1644     tabbedPane.setToolTipText("<html><i>"
1645             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1646             + "</i></html>");
1647
1648     formatMenu.setText(MessageManager.getString("action.format"));
1649     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1650
1651     idRightAlign.setText(
1652             MessageManager.getString("label.right_align_sequence_id"));
1653     idRightAlign.addActionListener(new ActionListener()
1654     {
1655       @Override
1656       public void actionPerformed(ActionEvent e)
1657       {
1658         idRightAlign_actionPerformed(e);
1659       }
1660     });
1661
1662     gatherViews.setEnabled(false);
1663     gatherViews.setText(MessageManager.getString("action.gather_views"));
1664     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1665     al = new ActionListener()
1666     {
1667       @Override
1668       public void actionPerformed(ActionEvent e)
1669       {
1670         gatherViews_actionPerformed(e);
1671       }
1672     };
1673     addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1674
1675     expandViews.setEnabled(false);
1676     expandViews.setText(MessageManager.getString("action.expand_views"));
1677     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1678     al = new ActionListener()
1679     {
1680       @Override
1681       public void actionPerformed(ActionEvent e)
1682       {
1683         expandViews_actionPerformed(e);
1684       }
1685     };
1686     addMenuActionAndAccelerator(keyStroke, expandViews, al);
1687
1688     JMenuItem pageSetup = new JMenuItem(
1689             MessageManager.getString("action.page_setup"));
1690     pageSetup.addActionListener(new ActionListener()
1691     {
1692       @Override
1693       public void actionPerformed(ActionEvent e)
1694       {
1695         pageSetup_actionPerformed(e);
1696       }
1697     });
1698     JMenuItem alignmentProperties = new JMenuItem(
1699             MessageManager.getString("label.alignment_props"));
1700     alignmentProperties.addActionListener(new ActionListener()
1701     {
1702       @Override
1703       public void actionPerformed(ActionEvent actionEvent)
1704       {
1705         alignmentProperties();
1706       }
1707     });
1708     JMenuItem selectHighlighted = new JMenuItem(
1709             MessageManager.getString("action.select_highlighted_columns"));
1710     selectHighlighted.setToolTipText(
1711             MessageManager.getString("tooltip.select_highlighted_columns"));
1712     al = new ActionListener()
1713     {
1714       @Override
1715       public void actionPerformed(ActionEvent actionEvent)
1716       {
1717         selectHighlightedColumns_actionPerformed(actionEvent);
1718       }
1719     };
1720     selectHighlighted.addActionListener(al);
1721     JMenu tooltipSettingsMenu = new JMenu(
1722             MessageManager.getString("label.sequence_id_tooltip"));
1723     JMenu autoAnnMenu = new JMenu(
1724             MessageManager.getString("label.autocalculated_annotation"));
1725
1726     JMenu exportImageMenu = new JMenu(
1727             MessageManager.getString("label.export_image"));
1728     JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1729     alignFrameMenuBar.add(fileMenu);
1730     alignFrameMenuBar.add(editMenu);
1731     alignFrameMenuBar.add(selectMenu);
1732     alignFrameMenuBar.add(viewMenu);
1733     alignFrameMenuBar.add(annotationsMenu);
1734     alignFrameMenuBar.add(formatMenu);
1735     alignFrameMenuBar.add(colourMenu);
1736     alignFrameMenuBar.add(calculateMenu);
1737     alignFrameMenuBar.add(webService);
1738
1739     fileMenu.add(fetchSequence);
1740     fileMenu.add(addSequenceMenu);
1741     fileMenu.add(reload);
1742     fileMenu.addSeparator();
1743     fileMenu.add(vamsasStore);
1744     fileMenu.add(save);
1745     fileMenu.add(saveAs);
1746     fileMenu.add(outputTextboxMenu);
1747     fileMenu.add(pageSetup);
1748     fileMenu.add(printMenuItem);
1749     fileMenu.addSeparator();
1750     fileMenu.add(exportImageMenu);
1751     fileMenu.add(exportFeatures);
1752     fileMenu.add(exportAnnotations);
1753     fileMenu.add(loadTreeMenuItem);
1754     fileMenu.add(associatedData);
1755     fileMenu.add(loadVcf);
1756     fileMenu.addSeparator();
1757     fileMenu.add(closeMenuItem);
1758
1759     pasteMenu.add(pasteNew);
1760     pasteMenu.add(pasteThis);
1761     editMenu.add(undoMenuItem);
1762     editMenu.add(redoMenuItem);
1763     editMenu.add(cut);
1764     editMenu.add(copy);
1765     editMenu.add(pasteMenu);
1766     editMenu.add(delete);
1767     editMenu.addSeparator();
1768     editMenu.add(remove2LeftMenuItem);
1769     editMenu.add(remove2RightMenuItem);
1770     editMenu.add(removeGappedColumnMenuItem);
1771     editMenu.add(removeAllGapsMenuItem);
1772     editMenu.add(removeRedundancyMenuItem);
1773     editMenu.addSeparator();
1774     // dont add these yet in the CVS build - they cannot be undone!
1775     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1776     // editMenu.add(justifyLeftMenuItem);
1777     // editMenu.add(justifyRightMenuItem);
1778     // editMenu.addSeparator();
1779     editMenu.add(padGapsMenuitem);
1780
1781     showMenu.add(showAllColumns);
1782     showMenu.add(showAllSeqs);
1783     showMenu.add(showAllhidden);
1784     hideMenu.add(hideSelColumns);
1785     hideMenu.add(hideSelSequences);
1786     hideMenu.add(hideAllSelection);
1787     hideMenu.add(hideAllButSelection);
1788     viewMenu.add(newView);
1789     viewMenu.add(expandViews);
1790     viewMenu.add(gatherViews);
1791     viewMenu.addSeparator();
1792     viewMenu.add(showMenu);
1793     viewMenu.add(hideMenu);
1794     viewMenu.add(showComplementMenuItem);
1795     viewMenu.addSeparator();
1796     viewMenu.add(followHighlightMenuItem);
1797     viewMenu.addSeparator();
1798     viewMenu.add(showSeqFeatures);
1799     // viewMenu.add(showSeqFeaturesHeight);
1800     viewMenu.add(openFeatureSettings);
1801     tooltipSettingsMenu.add(showDbRefsMenuitem);
1802     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1803     viewMenu.add(tooltipSettingsMenu);
1804     viewMenu.addSeparator();
1805     viewMenu.add(alignmentProperties);
1806     viewMenu.addSeparator();
1807     viewMenu.add(overviewMenuItem);
1808
1809     annotationsMenu.add(annotationPanelMenuItem);
1810     annotationsMenu.addSeparator();
1811     annotationsMenu.add(showAllAlAnnotations);
1812     annotationsMenu.add(hideAllAlAnnotations);
1813     annotationsMenu.addSeparator();
1814     annotationsMenu.add(showAllSeqAnnotations);
1815     annotationsMenu.add(hideAllSeqAnnotations);
1816     annotationsMenu.add(sortAnnBySequence);
1817     annotationsMenu.add(sortAnnByLabel);
1818     annotationsMenu.addSeparator();
1819     autoAnnMenu.add(showAutoFirst);
1820     autoAnnMenu.add(showAutoLast);
1821     autoAnnMenu.addSeparator();
1822     autoAnnMenu.add(applyAutoAnnotationSettings);
1823     autoAnnMenu.add(showConsensusHistogram);
1824     autoAnnMenu.add(showSequenceLogo);
1825     autoAnnMenu.add(normaliseSequenceLogo);
1826     autoAnnMenu.addSeparator();
1827     autoAnnMenu.add(showGroupConservation);
1828     autoAnnMenu.add(showGroupConsensus);
1829     annotationsMenu.add(autoAnnMenu);
1830
1831     sort.add(sortIDMenuItem);
1832     sort.add(sortLengthMenuItem);
1833     sort.add(sortGroupMenuItem);
1834     sort.add(sortPairwiseMenuItem);
1835     sort.add(sortByTreeMenu);
1836     calculateMenu.add(sort);
1837     calculateMenu.add(calculateTree);
1838     calculateMenu.addSeparator();
1839     calculateMenu.add(pairwiseAlignmentMenuItem);
1840     calculateMenu.addSeparator();
1841     calculateMenu.add(showTranslation);
1842     calculateMenu.add(showReverse);
1843     calculateMenu.add(showReverseComplement);
1844     calculateMenu.add(showProducts);
1845     calculateMenu.add(autoCalculate);
1846     calculateMenu.add(sortByTree);
1847     calculateMenu.addSeparator();
1848     calculateMenu.add(expandAlignment);
1849     calculateMenu.add(extractScores);
1850     calculateMenu.addSeparator();
1851     calculateMenu.add(runGroovy);
1852
1853     webServiceNoServices = new JMenuItem(
1854             MessageManager.getString("label.no_services"));
1855     webService.add(webServiceNoServices);
1856     exportImageMenu.add(htmlMenuItem);
1857     exportImageMenu.add(epsFile);
1858     exportImageMenu.add(createPNG);
1859     exportImageMenu.add(createBioJS);
1860     exportImageMenu.add(createSVG);
1861     addSequenceMenu.add(addFromFile);
1862     addSequenceMenu.add(addFromText);
1863     addSequenceMenu.add(addFromURL);
1864     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1865     statusPanel.add(statusBar, null);
1866     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1867
1868     formatMenu.add(font);
1869     formatMenu.addSeparator();
1870     formatMenu.add(wrapMenuItem);
1871     formatMenu.add(scaleAbove);
1872     formatMenu.add(scaleLeft);
1873     formatMenu.add(scaleRight);
1874     formatMenu.add(seqLimits);
1875     formatMenu.add(idRightAlign);
1876     formatMenu.add(hiddenMarkers);
1877     formatMenu.add(viewBoxesMenuItem);
1878     formatMenu.add(viewTextMenuItem);
1879     formatMenu.add(colourTextMenuItem);
1880     formatMenu.add(renderGapsMenuItem);
1881     formatMenu.add(colourGapsMenuItem);
1882     formatMenu.add(centreColumnLabelsMenuItem);
1883     formatMenu.add(showNonconservedMenuItem);
1884     selectMenu.add(findMenuItem);
1885     selectMenu.addSeparator();
1886     selectMenu.add(selectAllSequenceMenuItem);
1887     selectMenu.add(deselectAllSequenceMenuItem);
1888     selectMenu.add(invertSequenceMenuItem);
1889     selectMenu.add(invertColSel);
1890     selectMenu.add(createGroup);
1891     selectMenu.add(unGroup);
1892     selectMenu.add(grpsFromSelection);
1893     selectMenu.add(deleteGroups);
1894     selectMenu.add(annotationColumn);
1895     selectMenu.add(selectHighlighted);
1896     // TODO - determine if the listenToViewSelections button is needed : see bug
1897     // JAL-574
1898     // selectMenu.addSeparator();
1899     // selectMenu.add(listenToViewSelections);
1900   }
1901
1902   protected void colourGapsMenuItem_actionPerformed(ActionEvent e)
1903   {
1904     // TODO Auto-generated method stub
1905
1906   }
1907
1908   protected void loadVcf_actionPerformed()
1909   {
1910   }
1911
1912   /**
1913    * Constructs the entries on the Colour menu (but does not add them to the
1914    * menu).
1915    */
1916   protected void initColourMenu()
1917   {
1918     applyToAllGroups = new JCheckBoxMenuItem(
1919             MessageManager.getString("label.apply_colour_to_all_groups"));
1920     applyToAllGroups.addActionListener(new ActionListener()
1921     {
1922       @Override
1923       public void actionPerformed(ActionEvent e)
1924       {
1925         applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1926       }
1927     });
1928
1929     textColour = new JMenuItem(
1930             MessageManager.getString("label.text_colour"));
1931     textColour.addActionListener(new ActionListener()
1932     {
1933       @Override
1934       public void actionPerformed(ActionEvent e)
1935       {
1936         textColour_actionPerformed();
1937       }
1938     });
1939
1940     conservationMenuItem = new JCheckBoxMenuItem(
1941             MessageManager.getString("action.by_conservation"));
1942     conservationMenuItem.addActionListener(new ActionListener()
1943     {
1944       @Override
1945       public void actionPerformed(ActionEvent e)
1946       {
1947         conservationMenuItem_actionPerformed(
1948                 conservationMenuItem.isSelected());
1949       }
1950     });
1951
1952     abovePIDThreshold = new JCheckBoxMenuItem(
1953             MessageManager.getString("label.above_identity_threshold"));
1954     abovePIDThreshold.addActionListener(new ActionListener()
1955     {
1956       @Override
1957       public void actionPerformed(ActionEvent e)
1958       {
1959         abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
1960       }
1961     });
1962     modifyPID = new JMenuItem(
1963             MessageManager.getString("label.modify_identity_threshold"));
1964     modifyPID.addActionListener(new ActionListener()
1965     {
1966       @Override
1967       public void actionPerformed(ActionEvent e)
1968       {
1969         modifyPID_actionPerformed();
1970       }
1971     });
1972     modifyConservation = new JMenuItem(MessageManager
1973             .getString("label.modify_conservation_threshold"));
1974     modifyConservation.addActionListener(new ActionListener()
1975     {
1976       @Override
1977       public void actionPerformed(ActionEvent e)
1978       {
1979         modifyConservation_actionPerformed();
1980       }
1981     });
1982
1983     annotationColour = new JRadioButtonMenuItem(
1984             MessageManager.getString("action.by_annotation"));
1985     annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
1986     annotationColour.addActionListener(new ActionListener()
1987     {
1988       @Override
1989       public void actionPerformed(ActionEvent e)
1990       {
1991         annotationColour_actionPerformed();
1992       }
1993     });
1994   }
1995
1996   protected void selectHighlightedColumns_actionPerformed(
1997           ActionEvent actionEvent)
1998   {
1999     // TODO Auto-generated method stub
2000
2001   }
2002
2003   /**
2004    * Generate the reverse sequence (or reverse complement if the flag is true)
2005    * and add it to the alignment
2006    *
2007    * @param complement
2008    */
2009   protected void showReverse_actionPerformed(boolean complement)
2010   {
2011   }
2012
2013   /**
2014    * Try to run script in a Groovy console, having first ensured that this
2015    * alignframe is set as currentAlignFrame in Desktop
2016    */
2017   protected void runGroovy_actionPerformed()
2018   {
2019
2020   }
2021
2022   /**
2023    * Adds the given action listener and key accelerator to the given menu item.
2024    * Also saves in a lookup table to support lookup of action by key stroke.
2025    *
2026    * @param keyStroke
2027    * @param menuItem
2028    * @param actionListener
2029    */
2030   protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2031           JMenuItem menuItem, ActionListener actionListener)
2032   {
2033     menuItem.setAccelerator(keyStroke);
2034     accelerators.put(keyStroke, menuItem);
2035     menuItem.addActionListener(actionListener);
2036   }
2037
2038   /**
2039    * Action on clicking sort annotations by type.
2040    *
2041    * @param sortOrder
2042    */
2043   protected void sortAnnotations_actionPerformed()
2044   {
2045   }
2046
2047   /**
2048    * Action on clicking Show all annotations.
2049    *
2050    * @param forSequences
2051    *          update sequence-related annotations
2052    * @param forAlignment
2053    *          update non-sequence-related annotations
2054    */
2055   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2056           boolean forAlignment)
2057   {
2058     setAnnotationsVisibility(true, forSequences, forAlignment);
2059   }
2060
2061   /**
2062    * Action on clicking Hide all annotations.
2063    *
2064    * @param forSequences
2065    *          update sequence-related annotations
2066    * @param forAlignment
2067    *          update non-sequence-related annotations
2068    */
2069   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2070           boolean forAlignment)
2071   {
2072     setAnnotationsVisibility(false, forSequences, forAlignment);
2073   }
2074
2075   /**
2076    * Set the visibility of annotations to true or false. Can act on
2077    * sequence-related annotations, or alignment-related, or both.
2078    *
2079    * @param visible
2080    * @param forSequences
2081    *          update sequence-related annotations
2082    * @param forAlignment
2083    *          update non-sequence-related annotations
2084    */
2085   protected void setAnnotationsVisibility(boolean visible,
2086           boolean forSequences, boolean forAlignment)
2087   {
2088
2089   }
2090
2091   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2092   {
2093     // TODO Auto-generated method stub
2094
2095   }
2096
2097   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2098   {
2099     // TODO Auto-generated method stub
2100
2101   }
2102
2103   protected void showAllhidden_actionPerformed(ActionEvent e)
2104   {
2105     // TODO Auto-generated method stub
2106
2107   }
2108
2109   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2110   {
2111     // TODO Auto-generated method stub
2112
2113   }
2114
2115   protected void hideAllSelection_actionPerformed(ActionEvent e)
2116   {
2117     // TODO Auto-generated method stub
2118
2119   }
2120
2121   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2122   {
2123     // TODO Auto-generated method stub
2124
2125   }
2126
2127   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2128   {
2129     // TODO Auto-generated method stub
2130
2131   }
2132
2133   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2134   {
2135     // TODO Auto-generated method stub
2136
2137   }
2138
2139   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2140   {
2141     // TODO Auto-generated method stub
2142
2143   }
2144
2145   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2146   {
2147     // TODO Auto-generated method stub
2148
2149   }
2150
2151   protected void showGroupConservation_actionPerformed(ActionEvent e)
2152   {
2153     // TODO Auto-generated method stub
2154
2155   }
2156
2157   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2158   {
2159     // TODO Auto-generated method stub
2160
2161   }
2162
2163   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2164   {
2165     // TODO Auto-generated method stub
2166
2167   }
2168
2169   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2170   {
2171     // TODO Auto-generated method stub
2172
2173   }
2174
2175   protected void followHighlight_actionPerformed()
2176   {
2177     // TODO Auto-generated method stub
2178
2179   }
2180
2181   protected void showNpFeats_actionPerformed(ActionEvent e)
2182   {
2183     // TODO Auto-generated method stub
2184
2185   }
2186
2187   protected void showDbRefs_actionPerformed(ActionEvent e)
2188   {
2189     // TODO Auto-generated method stub
2190
2191   }
2192
2193   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2194   {
2195   }
2196
2197   protected void buildSortByAnnotationScoresMenu()
2198   {
2199   }
2200
2201   protected void extractScores_actionPerformed(ActionEvent e)
2202   {
2203   }
2204
2205   protected void outputText_actionPerformed(ActionEvent e)
2206   {
2207   }
2208
2209   public void addFromFile_actionPerformed(ActionEvent e)
2210   {
2211
2212   }
2213
2214   public void addFromText_actionPerformed(ActionEvent e)
2215   {
2216
2217   }
2218
2219   public void addFromURL_actionPerformed(ActionEvent e)
2220   {
2221
2222   }
2223
2224   public void exportFeatures_actionPerformed(ActionEvent e)
2225   {
2226
2227   }
2228
2229   public void exportAnnotations_actionPerformed(ActionEvent e)
2230   {
2231
2232   }
2233
2234   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2235   {
2236   }
2237
2238   protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2239   {
2240
2241   }
2242
2243   protected void closeMenuItem_actionPerformed(boolean b)
2244   {
2245   }
2246
2247   protected void redoMenuItem_actionPerformed(ActionEvent e)
2248   {
2249   }
2250
2251   protected void undoMenuItem_actionPerformed(ActionEvent e)
2252   {
2253   }
2254
2255   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2256   {
2257   }
2258
2259   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2260   {
2261   }
2262
2263   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2264   {
2265   }
2266
2267   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2268   {
2269   }
2270
2271   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2272   {
2273   }
2274
2275   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2276   {
2277   }
2278
2279   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2280   {
2281   }
2282
2283   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2284   {
2285   }
2286
2287   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2288   {
2289   }
2290
2291   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2292   {
2293   }
2294
2295   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2296   {
2297   }
2298
2299   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2300   {
2301   }
2302
2303   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2304   {
2305   }
2306
2307   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2308   {
2309   }
2310
2311   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2312   {
2313   }
2314
2315   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2316   {
2317   }
2318
2319   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2320   {
2321   }
2322
2323   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2324   {
2325   }
2326
2327   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2328   {
2329   }
2330
2331   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2332   {
2333   }
2334
2335   protected void conservationMenuItem_actionPerformed(boolean selected)
2336   {
2337   }
2338
2339   protected void printMenuItem_actionPerformed(ActionEvent e)
2340   {
2341   }
2342
2343   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2344   {
2345   }
2346
2347   protected void findMenuItem_actionPerformed(ActionEvent e)
2348   {
2349   }
2350
2351   protected void abovePIDThreshold_actionPerformed(boolean selected)
2352   {
2353   }
2354
2355   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2356   {
2357   }
2358
2359   protected void deleteGroups_actionPerformed(ActionEvent e)
2360   {
2361   }
2362
2363   protected void createGroup_actionPerformed(ActionEvent e)
2364   {
2365   }
2366
2367   protected void unGroup_actionPerformed(ActionEvent e)
2368   {
2369   }
2370
2371   protected void copy_actionPerformed(ActionEvent e)
2372   {
2373   }
2374
2375   protected void cut_actionPerformed(ActionEvent e)
2376   {
2377   }
2378
2379   protected void delete_actionPerformed(ActionEvent e)
2380   {
2381   }
2382
2383   protected void pasteNew_actionPerformed(ActionEvent e)
2384   {
2385   }
2386
2387   protected void pasteThis_actionPerformed(ActionEvent e)
2388   {
2389   }
2390
2391   protected void applyToAllGroups_actionPerformed(boolean selected)
2392   {
2393   }
2394
2395   public void createPNG(java.io.File f)
2396   {
2397   }
2398
2399   protected void font_actionPerformed(ActionEvent e)
2400   {
2401   }
2402
2403   protected void seqLimit_actionPerformed(ActionEvent e)
2404   {
2405   }
2406
2407   public void seqDBRef_actionPerformed(ActionEvent e)
2408   {
2409
2410   }
2411
2412   public void createEPS(java.io.File f)
2413   {
2414   }
2415
2416   public void createSVG(java.io.File f)
2417   {
2418
2419   }
2420
2421   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2422   {
2423
2424   }
2425
2426   /**
2427    * Template method to handle the 'load T-Coffee scores' menu event.
2428    * <p>
2429    * Subclasses override this method to provide a custom action.
2430    *
2431    * @param event
2432    *          The raised event
2433    */
2434   protected void loadScores_actionPerformed(ActionEvent event)
2435   {
2436
2437   }
2438
2439   protected void jpred_actionPerformed(ActionEvent e)
2440   {
2441   }
2442
2443   protected void scaleAbove_actionPerformed(ActionEvent e)
2444   {
2445   }
2446
2447   protected void scaleLeft_actionPerformed(ActionEvent e)
2448   {
2449   }
2450
2451   protected void scaleRight_actionPerformed(ActionEvent e)
2452   {
2453   }
2454
2455   protected void modifyPID_actionPerformed()
2456   {
2457   }
2458
2459   protected void modifyConservation_actionPerformed()
2460   {
2461   }
2462
2463   protected void saveAs_actionPerformed(ActionEvent e)
2464   {
2465   }
2466
2467   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2468   {
2469   }
2470
2471   public void vamsasStore_actionPerformed(ActionEvent e)
2472   {
2473
2474   }
2475
2476   public void vamsasLoad_actionPerformed(ActionEvent e)
2477   {
2478
2479   }
2480
2481   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
2482   {
2483
2484   }
2485
2486   public void featureSettings_actionPerformed(ActionEvent e)
2487   {
2488
2489   }
2490
2491   public void fetchSequence_actionPerformed(ActionEvent e)
2492   {
2493
2494   }
2495
2496   public void smoothFont_actionPerformed(ActionEvent e)
2497   {
2498
2499   }
2500
2501   public void annotationColour_actionPerformed()
2502   {
2503   }
2504
2505   public void annotationColumn_actionPerformed(ActionEvent e)
2506   {
2507   }
2508
2509   public void associatedData_actionPerformed(ActionEvent e)
2510   {
2511
2512   }
2513
2514   public void autoCalculate_actionPerformed(ActionEvent e)
2515   {
2516
2517   }
2518
2519   public void sortByTreeOption_actionPerformed(ActionEvent e)
2520   {
2521
2522   }
2523
2524   public void showAllSeqs_actionPerformed(ActionEvent e)
2525   {
2526
2527   }
2528
2529   public void showAllColumns_actionPerformed(ActionEvent e)
2530   {
2531
2532   }
2533
2534   public void hideSelSequences_actionPerformed(ActionEvent e)
2535   {
2536
2537   }
2538
2539   public void hideSelColumns_actionPerformed(ActionEvent e)
2540   {
2541
2542   }
2543
2544   public void hiddenMarkers_actionPerformed(ActionEvent e)
2545   {
2546
2547   }
2548
2549   public void findPdbId_actionPerformed(ActionEvent e)
2550   {
2551
2552   }
2553
2554   public void enterPdbId_actionPerformed(ActionEvent e)
2555   {
2556
2557   }
2558
2559   public void pdbFile_actionPerformed(ActionEvent e)
2560   {
2561
2562   }
2563
2564   public void invertColSel_actionPerformed(ActionEvent e)
2565   {
2566
2567   }
2568
2569   public void tabSelectionChanged(int sel)
2570   {
2571
2572   }
2573
2574   public void tabbedPane_mousePressed(MouseEvent e)
2575   {
2576
2577   }
2578
2579   public void tabbedPane_focusGained(FocusEvent e)
2580   {
2581     requestFocus();
2582   }
2583
2584   public void save_actionPerformed(ActionEvent e)
2585   {
2586
2587   }
2588
2589   public void reload_actionPerformed(ActionEvent e)
2590   {
2591
2592   }
2593
2594   public void newView_actionPerformed(ActionEvent e)
2595   {
2596
2597   }
2598
2599   public void textColour_actionPerformed()
2600   {
2601
2602   }
2603
2604   public void idRightAlign_actionPerformed(ActionEvent e)
2605   {
2606
2607   }
2608
2609   public void expandViews_actionPerformed(ActionEvent e)
2610   {
2611
2612   }
2613
2614   public void gatherViews_actionPerformed(ActionEvent e)
2615   {
2616
2617   }
2618
2619   public void buildTreeSortMenu()
2620   {
2621
2622   }
2623
2624   public void pageSetup_actionPerformed(ActionEvent e)
2625   {
2626
2627   }
2628
2629   public void alignmentProperties()
2630   {
2631
2632   }
2633
2634   protected void expand_newalign(ActionEvent e)
2635   {
2636     // TODO Auto-generated method stub
2637
2638   }
2639
2640   protected boolean isShowAutoCalculatedAbove()
2641   {
2642     return showAutoCalculatedAbove;
2643   }
2644
2645   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2646   {
2647     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2648   }
2649
2650   protected SequenceAnnotationOrder getAnnotationSortOrder()
2651   {
2652     return annotationSortOrder;
2653   }
2654
2655   protected void setAnnotationSortOrder(
2656           SequenceAnnotationOrder annotationSortOrder)
2657   {
2658     this.annotationSortOrder = annotationSortOrder;
2659   }
2660
2661   public Map<KeyStroke, JMenuItem> getAccelerators()
2662   {
2663     return this.accelerators;
2664   }
2665
2666   /**
2667    * Returns the selected index of the tabbed pane, or -1 if none selected
2668    * (including the case where the tabbed pane has not been made visible).
2669    *
2670    * @return
2671    */
2672   public int getTabIndex()
2673   {
2674     return tabbedPane.getSelectedIndex();
2675   }
2676
2677   public JPanel getStatusPanel()
2678   {
2679     return statusPanel;
2680   }
2681
2682   /**
2683    * Sets a reference to the containing split frame. Also makes the 'toggle
2684    * split view' menu item visible and checked.
2685    *
2686    * @param sf
2687    */
2688   public void setSplitFrame(SplitContainerI sf)
2689   {
2690     this.splitFrame = sf;
2691     if (sf != null)
2692     {
2693       this.showComplementMenuItem.setVisible(true);
2694       this.showComplementMenuItem.setState(true);
2695     }
2696   }
2697
2698   public SplitContainerI getSplitViewContainer()
2699   {
2700     return this.splitFrame;
2701   }
2702
2703   protected void showComplement_actionPerformed(boolean complement)
2704   {
2705   }
2706 }