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.io.IOException;
  44 import java.util.HashMap;
  45 import java.util.Map;
  46
  47 import javax.swing.BorderFactory;
  48 import javax.swing.ButtonGroup;
  49 import javax.swing.JCheckBoxMenuItem;
  50 import javax.swing.JInternalFrame;
  51 import javax.swing.JLabel;
  52 import javax.swing.JMenu;
  53 import javax.swing.JMenuBar;
  54 import javax.swing.JMenuItem;
  55 import javax.swing.JPanel;
  56 import javax.swing.JRadioButtonMenuItem;
  57 import javax.swing.JTabbedPane;
  58 import javax.swing.KeyStroke;
  59 import javax.swing.event.ChangeEvent;
  60 import javax.swing.event.MenuEvent;
  61 import javax.swing.event.MenuListener;
  62
  63 public class GAlignFrame extends JInternalFrame
  64 {
  65   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  66
  67   protected JMenuItem closeMenuItem = new JMenuItem();
  68
  69   protected JMenu webService = new JMenu();
  70
  71   protected JMenu hmmerMenu = new JMenu();
  72
  73   protected JMenuItem hmmAlign = new JMenuItem();
  74
  75   protected JMenuItem hmmSearch = new JMenuItem();
  76
  77   protected JMenuItem hmmBuild = new JCheckBoxMenuItem();
  78
  79   protected JMenuItem webServiceNoServices;
  80
  81   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  82
  83   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  84
  85   protected JMenu sortByAnnotScore = new JMenu();
  86
  87   public JLabel statusBar = new JLabel();
  88
  89   protected JMenu outputTextboxMenu = new JMenu();
  90
  91   protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
  92
  93   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
  94
  95   protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
  96
  97   protected JMenuItem undoMenuItem = new JMenuItem();
  98
  99   protected JMenuItem redoMenuItem = new JMenuItem();
 100
 101   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 102
 103   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 104
 105   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 106
 107   JMenuItem copy = new JMenuItem();
 108
 109   JMenuItem cut = new JMenuItem();
 110
 111   JMenu pasteMenu = new JMenu();
 112
 113   protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 114
 115   protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 116
 117   protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 118
 119   protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 120
 121   protected JCheckBoxMenuItem applyToAllGroups;
 122
 123   protected JMenu colourMenu = new JMenu();
 124
 125   protected JMenuItem textColour;
 126
 127   protected JCheckBoxMenuItem conservationMenuItem;
 128
 129   protected JMenuItem modifyConservation;
 130
 131   protected JCheckBoxMenuItem abovePIDThreshold;
 132
 133   protected JMenuItem modifyPID;
 134
 135   protected JMenuItem annotationColour;
 136
 137   protected JMenu sortByTreeMenu = new JMenu();
 138
 139   protected JMenu sort = new JMenu();
 140
 141   protected JMenuItem calculateTree = new JMenuItem();
 142
 143   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 144
 145   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 146
 147   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 148
 149   protected JMenuItem showTranslation = new JMenuItem();
 150
 151   protected JMenuItem showReverse = new JMenuItem();
 152
 153   protected JMenuItem showReverseComplement = new JMenuItem();
 154
 155   protected JMenu showProducts = new JMenu();
 156
 157   protected JMenuItem runGroovy = new JMenuItem();
 158
 159   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 160
 161   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 162
 163   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 164
 165   protected JPanel statusPanel = new JPanel();
 166
 167   protected JMenuItem showAllSeqAnnotations = new JMenuItem();
 168
 169   protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
 170
 171   protected JMenuItem showAllAlAnnotations = new JMenuItem();
 172
 173   protected JMenuItem hideAllAlAnnotations = new JMenuItem();
 174
 175   protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
 176
 177   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 178
 179   protected JTabbedPane tabbedPane = new JTabbedPane();
 180
 181   protected JMenuItem reload = new JMenuItem();
 182
 183   protected JMenu formatMenu = new JMenu();
 184
 185   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 186
 187   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 188
 189   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 190
 191   protected JMenuItem gatherViews = new JMenuItem();
 192
 193   protected JMenuItem expandViews = new JMenuItem();
 194
 195   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 196
 197   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 198
 199   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 200
 201   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 202
 203   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 204
 205   protected JCheckBoxMenuItem showInformationHistogram = new JCheckBoxMenuItem();
 206
 207   protected JCheckBoxMenuItem showHMMSequenceLogo = new JCheckBoxMenuItem();
 208
 209   protected JCheckBoxMenuItem normaliseHMMSequenceLogo = new JCheckBoxMenuItem();
 210
 211   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 212
 213   private SequenceAnnotationOrder annotationSortOrder;
 214
 215   private boolean showAutoCalculatedAbove = false;
 216
 217   private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
 218
 219   private SplitContainerI splitFrame;
 220
 221   public GAlignFrame()
 222   {
 223     try
 224     {
 225       jbInit();
 226       setJMenuBar(alignFrameMenuBar);
 227
 228       // dynamically fill save as menu with available formats
 229       for (String ff : FileFormats.getInstance().getWritableFormats(true))
 230       {
 231         JMenuItem item = new JMenuItem(ff);
 232
 233         item.addActionListener(new ActionListener()
 234         {
 235           @Override
 236           public void actionPerformed(ActionEvent e)
 237           {
 238             outputText_actionPerformed(e);
 239           }
 240         });
 241
 242         outputTextboxMenu.add(item);
 243       }
 244     } catch (Exception e)
 245     {
 246       System.err.println(e.toString());
 247     }
 248
 249     if (!Platform.isAMac())
 250     {
 251       closeMenuItem.setMnemonic('C');
 252       outputTextboxMenu.setMnemonic('T');
 253       undoMenuItem.setMnemonic('Z');
 254       redoMenuItem.setMnemonic('0');
 255       copy.setMnemonic('C');
 256       cut.setMnemonic('U');
 257       pasteMenu.setMnemonic('P');
 258       reload.setMnemonic('R');
 259     }
 260   }
 261
 262   private void jbInit() throws Exception
 263   {
 264     initColourMenu();
 265     initHMMERMenu();
 266
 267     JMenuItem saveAs = new JMenuItem(
 268             MessageManager.getString("action.save_as"));
 269     ActionListener al = new ActionListener()
 270     {
 271       @Override
 272       public void actionPerformed(ActionEvent e)
 273       {
 274         saveAs_actionPerformed(e);
 275       }
 276     };
 277
 278     // FIXME getDefaultToolkit throws an exception in Headless mode
 279     KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
 280             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
 281                     | KeyEvent.SHIFT_MASK,
 282             false);
 283     addMenuActionAndAccelerator(keyStroke, saveAs, al);
 284
 285     closeMenuItem.setText(MessageManager.getString("action.close"));
 286     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
 287             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 288     al = new ActionListener()
 289     {
 290       @Override
 291       public void actionPerformed(ActionEvent e)
 292       {
 293         closeMenuItem_actionPerformed(false);
 294       }
 295     };
 296     addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
 297
 298     JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
 299     JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
 300     JMenu annotationsMenu = new JMenu(
 301             MessageManager.getString("action.annotations"));
 302     JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
 303     colourMenu.setText(MessageManager.getString("action.colour"));
 304     JMenu calculateMenu = new JMenu(
 305             MessageManager.getString("action.calculate"));
 306     webService.setText(MessageManager.getString("action.web_service"));
 307     hmmerMenu.setText(MessageManager.getString("action.hmmer"));
 308     String status = Cache.getProperty("HMMER_FUNCTIONING");
 309     if ("false".equals(status) || status == null)
 310     {
 311       hmmerMenu.setEnabled(false);
 312     }
 313     else
 314     {
 315       hmmerMenu.setEnabled(true);
 316     }
 317     hmmerMenu.addActionListener(new ActionListener()
 318     {
 319       @Override
 320       public void actionPerformed(ActionEvent e)
 321       {
 322         hmmerMenu_actionPerformed(e);
 323       }
 324     });
 325     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
 326             MessageManager.getString("action.select_all"));
 327     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
 328             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 329     al = new ActionListener()
 330     {
 331       @Override
 332       public void actionPerformed(ActionEvent e)
 333       {
 334         selectAllSequenceMenuItem_actionPerformed(e);
 335       }
 336     };
 337     addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
 338
 339     JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
 340             MessageManager.getString("action.deselect_all"));
 341     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
 342     al = new ActionListener()
 343     {
 344       @Override
 345       public void actionPerformed(ActionEvent e)
 346       {
 347         deselectAllSequenceMenuItem_actionPerformed(e);
 348       }
 349     };
 350     addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
 351
 352     JMenuItem invertSequenceMenuItem = new JMenuItem(
 353             MessageManager.getString("action.invert_sequence_selection"));
 354     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
 355             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 356     al = new ActionListener()
 357     {
 358       @Override
 359       public void actionPerformed(ActionEvent e)
 360       {
 361         invertSequenceMenuItem_actionPerformed(e);
 362       }
 363     };
 364     addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
 365
 366     JMenuItem grpsFromSelection = new JMenuItem(
 367             MessageManager.getString("action.make_groups_selection"));
 368     grpsFromSelection.addActionListener(new ActionListener()
 369     {
 370       @Override
 371       public void actionPerformed(ActionEvent e)
 372       {
 373         makeGrpsFromSelection_actionPerformed(e);
 374       }
 375     });
 376     JMenuItem expandAlignment = new JMenuItem(
 377             MessageManager.getString("action.view_flanking_regions"));
 378     expandAlignment.setToolTipText(
 379             MessageManager.getString("label.view_flanking_regions"));
 380     expandAlignment.addActionListener(new ActionListener()
 381     {
 382       @Override
 383       public void actionPerformed(ActionEvent e)
 384       {
 385         expand_newalign(e);
 386       }
 387     });
 388     JMenuItem remove2LeftMenuItem = new JMenuItem(
 389             MessageManager.getString("action.remove_left"));
 390     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
 391             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 392     al = new ActionListener()
 393     {
 394       @Override
 395       public void actionPerformed(ActionEvent e)
 396       {
 397         remove2LeftMenuItem_actionPerformed(e);
 398       }
 399     };
 400     addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
 401
 402     JMenuItem remove2RightMenuItem = new JMenuItem(
 403             MessageManager.getString("action.remove_right"));
 404     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
 405             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 406     al = new ActionListener()
 407     {
 408       @Override
 409       public void actionPerformed(ActionEvent e)
 410       {
 411         remove2RightMenuItem_actionPerformed(e);
 412       }
 413     };
 414     addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
 415
 416     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
 417             MessageManager.getString("action.remove_empty_columns"));
 418     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
 419             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 420     al = new ActionListener()
 421     {
 422       @Override
 423       public void actionPerformed(ActionEvent e)
 424       {
 425         removeGappedColumnMenuItem_actionPerformed(e);
 426       }
 427     };
 428     addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
 429
 430     JMenuItem removeAllGapsMenuItem = new JMenuItem(
 431             MessageManager.getString("action.remove_all_gaps"));
 432     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
 433             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
 434                     | KeyEvent.SHIFT_MASK,
 435             false);
 436     al = new ActionListener()
 437     {
 438       @Override
 439       public void actionPerformed(ActionEvent e)
 440       {
 441         removeAllGapsMenuItem_actionPerformed(e);
 442       }
 443     };
 444     addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
 445
 446     JMenuItem justifyLeftMenuItem = new JMenuItem(
 447             MessageManager.getString("action.left_justify_alignment"));
 448     justifyLeftMenuItem.addActionListener(new ActionListener()
 449     {
 450       @Override
 451       public void actionPerformed(ActionEvent e)
 452       {
 453         justifyLeftMenuItem_actionPerformed(e);
 454       }
 455     });
 456     JMenuItem justifyRightMenuItem = new JMenuItem(
 457             MessageManager.getString("action.right_justify_alignment"));
 458     justifyRightMenuItem.addActionListener(new ActionListener()
 459     {
 460       @Override
 461       public void actionPerformed(ActionEvent e)
 462       {
 463         justifyRightMenuItem_actionPerformed(e);
 464       }
 465     });
 466     viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
 467     viewBoxesMenuItem.setState(true);
 468     viewBoxesMenuItem.addActionListener(new ActionListener()
 469     {
 470       @Override
 471       public void actionPerformed(ActionEvent e)
 472       {
 473         viewBoxesMenuItem_actionPerformed(e);
 474       }
 475     });
 476     viewTextMenuItem.setText(MessageManager.getString("action.text"));
 477     viewTextMenuItem.setState(true);
 478     viewTextMenuItem.addActionListener(new ActionListener()
 479     {
 480       @Override
 481       public void actionPerformed(ActionEvent e)
 482       {
 483         viewTextMenuItem_actionPerformed(e);
 484       }
 485     });
 486     showNonconservedMenuItem
 487             .setText(MessageManager.getString("label.show_non_conserved"));
 488     showNonconservedMenuItem.setState(false);
 489     showNonconservedMenuItem.addActionListener(new ActionListener()
 490     {
 491       @Override
 492       public void actionPerformed(ActionEvent e)
 493       {
 494         showUnconservedMenuItem_actionPerformed(e);
 495       }
 496     });
 497     JMenuItem sortPairwiseMenuItem = new JMenuItem(
 498             MessageManager.getString("action.by_pairwise_id"));
 499     sortPairwiseMenuItem.addActionListener(new ActionListener()
 500     {
 501       @Override
 502       public void actionPerformed(ActionEvent e)
 503       {
 504         sortPairwiseMenuItem_actionPerformed(e);
 505       }
 506     });
 507     JMenuItem sortIDMenuItem = new JMenuItem(
 508             MessageManager.getString("action.by_id"));
 509     sortIDMenuItem.addActionListener(new ActionListener()
 510     {
 511       @Override
 512       public void actionPerformed(ActionEvent e)
 513       {
 514         sortIDMenuItem_actionPerformed(e);
 515       }
 516     });
 517     JMenuItem sortLengthMenuItem = new JMenuItem(
 518             MessageManager.getString("action.by_length"));
 519     sortLengthMenuItem.addActionListener(new ActionListener()
 520     {
 521       @Override
 522       public void actionPerformed(ActionEvent e)
 523       {
 524         sortLengthMenuItem_actionPerformed(e);
 525       }
 526     });
 527     JMenuItem sortGroupMenuItem = new JMenuItem(
 528             MessageManager.getString("action.by_group"));
 529     sortGroupMenuItem.addActionListener(new ActionListener()
 530     {
 531       @Override
 532       public void actionPerformed(ActionEvent e)
 533       {
 534         sortGroupMenuItem_actionPerformed(e);
 535       }
 536     });
 537
 538     JMenuItem removeRedundancyMenuItem = new JMenuItem(
 539             MessageManager.getString("action.remove_redundancy"));
 540     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
 541             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 542     al = new ActionListener()
 543     {
 544       @Override
 545       public void actionPerformed(ActionEvent e)
 546       {
 547         removeRedundancyMenuItem_actionPerformed(e);
 548       }
 549     };
 550     addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
 551
 552     JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
 553             MessageManager.getString("action.pairwise_alignment"));
 554     pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
 555     {
 556       @Override
 557       public void actionPerformed(ActionEvent e)
 558       {
 559         pairwiseAlignmentMenuItem_actionPerformed(e);
 560       }
 561     });
 562
 563     this.getContentPane().setLayout(new BorderLayout());
 564     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 565     statusBar.setBackground(Color.white);
 566     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 567     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 568     statusBar.setText(MessageManager.getString("label.status_bar"));
 569
 570     outputTextboxMenu
 571             .setText(MessageManager.getString("label.out_to_textbox"));
 572
 573
 574     annotationPanelMenuItem.setActionCommand("");
 575     annotationPanelMenuItem
 576             .setText(MessageManager.getString("label.show_annotations"));
 577     annotationPanelMenuItem
 578             .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
 579     annotationPanelMenuItem.addActionListener(new ActionListener()
 580     {
 581       @Override
 582       public void actionPerformed(ActionEvent e)
 583       {
 584         annotationPanelMenuItem_actionPerformed(e);
 585       }
 586     });
 587     showAllAlAnnotations.setText(
 588             MessageManager.getString("label.show_all_al_annotations"));
 589     final boolean isAnnotationPanelShown = annotationPanelMenuItem
 590             .getState();
 591     showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 592     showAllAlAnnotations.addActionListener(new ActionListener()
 593     {
 594       @Override
 595       public void actionPerformed(ActionEvent e)
 596       {
 597         showAllAnnotations_actionPerformed(false, true);
 598       }
 599     });
 600     hideAllAlAnnotations.setText(
 601             MessageManager.getString("label.hide_all_al_annotations"));
 602     hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 603     hideAllAlAnnotations.addActionListener(new ActionListener()
 604     {
 605       @Override
 606       public void actionPerformed(ActionEvent e)
 607       {
 608         hideAllAnnotations_actionPerformed(false, true);
 609       }
 610     });
 611     showAllSeqAnnotations.setText(
 612             MessageManager.getString("label.show_all_seq_annotations"));
 613     showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 614     showAllSeqAnnotations.addActionListener(new ActionListener()
 615     {
 616       @Override
 617       public void actionPerformed(ActionEvent e)
 618       {
 619         showAllAnnotations_actionPerformed(true, false);
 620       }
 621     });
 622     hideAllSeqAnnotations.setText(
 623             MessageManager.getString("label.hide_all_seq_annotations"));
 624     hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 625     hideAllSeqAnnotations.addActionListener(new ActionListener()
 626     {
 627       @Override
 628       public void actionPerformed(ActionEvent e)
 629       {
 630         hideAllAnnotations_actionPerformed(true, false);
 631       }
 632     });
 633     SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
 634             .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
 635                     SequenceAnnotationOrder.NONE.name()));
 636     final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
 637             MessageManager.getString("label.sort_annotations_by_sequence"));
 638     final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
 639             MessageManager.getString("label.sort_annotations_by_label"));
 640
 641
 642     sortAnnBySequence.setSelected(
 643             sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
 644     sortAnnBySequence.addActionListener(new ActionListener()
 645     {
 646       @Override
 647       public void actionPerformed(ActionEvent e)
 648       {
 649         boolean newState = sortAnnBySequence.getState();
 650         sortAnnByLabel.setSelected(false);
 651         setAnnotationSortOrder(
 652                 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 653                         : SequenceAnnotationOrder.NONE);
 654         sortAnnotations_actionPerformed();
 655       }
 656     });
 657     sortAnnByLabel.setSelected(
 658             sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
 659     sortAnnByLabel.addActionListener(new ActionListener()
 660     {
 661       @Override
 662       public void actionPerformed(ActionEvent e)
 663       {
 664         boolean newState = sortAnnByLabel.getState();
 665         sortAnnBySequence.setSelected(false);
 666         setAnnotationSortOrder(
 667                 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 668                         : SequenceAnnotationOrder.NONE);
 669         sortAnnotations_actionPerformed();
 670       }
 671     });
 672     colourTextMenuItem = new JCheckBoxMenuItem(
 673             MessageManager.getString("label.colour_text"));
 674     colourTextMenuItem.addActionListener(new ActionListener()
 675     {
 676       @Override
 677       public void actionPerformed(ActionEvent e)
 678       {
 679         colourTextMenuItem_actionPerformed(e);
 680       }
 681     });
 682
 683     JMenuItem htmlMenuItem = new JMenuItem(
 684             MessageManager.getString("label.html"));
 685     htmlMenuItem.addActionListener(new ActionListener()
 686     {
 687       @Override
 688       public void actionPerformed(ActionEvent e)
 689       {
 690         htmlMenuItem_actionPerformed(e);
 691       }
 692     });
 693
 694     JMenuItem createBioJS = new JMenuItem(
 695             MessageManager.getString("label.biojs_html_export"));
 696     createBioJS.addActionListener(new java.awt.event.ActionListener()
 697     {
 698       @Override
 699       public void actionPerformed(ActionEvent e)
 700       {
 701         bioJSMenuItem_actionPerformed(e);
 702       }
 703     });
 704
 705     JMenuItem overviewMenuItem = new JMenuItem(
 706             MessageManager.getString("label.overview_window"));
 707     overviewMenuItem.addActionListener(new ActionListener()
 708     {
 709       @Override
 710       public void actionPerformed(ActionEvent e)
 711       {
 712         overviewMenuItem_actionPerformed(e);
 713       }
 714     });
 715
 716     undoMenuItem.setEnabled(false);
 717     undoMenuItem.setText(MessageManager.getString("action.undo"));
 718     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
 719             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 720     al = new ActionListener()
 721     {
 722       @Override
 723       public void actionPerformed(ActionEvent e)
 724       {
 725         undoMenuItem_actionPerformed(e);
 726       }
 727     };
 728     addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
 729
 730     redoMenuItem.setEnabled(false);
 731     redoMenuItem.setText(MessageManager.getString("action.redo"));
 732     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
 733             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 734     al = new ActionListener()
 735     {
 736       @Override
 737       public void actionPerformed(ActionEvent e)
 738       {
 739         redoMenuItem_actionPerformed(e);
 740       }
 741     };
 742     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
 743
 744     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
 745     wrapMenuItem.addActionListener(new ActionListener()
 746     {
 747       @Override
 748       public void actionPerformed(ActionEvent e)
 749       {
 750         wrapMenuItem_actionPerformed(e);
 751       }
 752     });
 753
 754     JMenuItem printMenuItem = new JMenuItem(
 755             MessageManager.getString("action.print"));
 756     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
 757             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 758     al = new ActionListener()
 759     {
 760       @Override
 761       public void actionPerformed(ActionEvent e)
 762       {
 763         printMenuItem_actionPerformed(e);
 764       }
 765     };
 766     addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
 767
 768     renderGapsMenuItem
 769             .setText(MessageManager.getString("action.show_gaps"));
 770     renderGapsMenuItem.setState(true);
 771     renderGapsMenuItem.addActionListener(new ActionListener()
 772     {
 773       @Override
 774       public void actionPerformed(ActionEvent e)
 775       {
 776         renderGapsMenuItem_actionPerformed(e);
 777       }
 778     });
 779
 780     JMenuItem findMenuItem = new JMenuItem(
 781             MessageManager.getString("action.find"));
 782     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
 783             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 784     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
 785             MessageManager.getString("label.find_tip")));
 786     al = new ActionListener()
 787     {
 788       @Override
 789       public void actionPerformed(ActionEvent e)
 790       {
 791         findMenuItem_actionPerformed(e);
 792       }
 793     };
 794     addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
 795
 796     showSeqFeatures.setText(
 797             MessageManager.getString("label.show_sequence_features"));
 798
 799     showSeqFeatures.addActionListener(new ActionListener()
 800     {
 801       @Override
 802       public void actionPerformed(ActionEvent actionEvent)
 803       {
 804         showSeqFeatures_actionPerformed(actionEvent);
 805       }
 806     });
 807     /*
 808      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
 809      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
 810      * void actionPerformed(ActionEvent actionEvent) {
 811      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
 812      */
 813     showDbRefsMenuitem
 814             .setText(MessageManager.getString("label.show_database_refs"));
 815     showDbRefsMenuitem.addActionListener(new ActionListener()
 816     {
 817
 818       @Override
 819       public void actionPerformed(ActionEvent e)
 820       {
 821         showDbRefs_actionPerformed(e);
 822       }
 823
 824     });
 825     showNpFeatsMenuitem.setText(
 826             MessageManager.getString("label.show_non_positional_features"));
 827     showNpFeatsMenuitem.addActionListener(new ActionListener()
 828     {
 829
 830       @Override
 831       public void actionPerformed(ActionEvent e)
 832       {
 833         showNpFeats_actionPerformed(e);
 834       }
 835
 836     });
 837     showGroupConservation
 838             .setText(MessageManager.getString("label.group_conservation"));
 839     showGroupConservation.addActionListener(new ActionListener()
 840     {
 841
 842       @Override
 843       public void actionPerformed(ActionEvent e)
 844       {
 845         showGroupConservation_actionPerformed(e);
 846       }
 847
 848     });
 849
 850     showGroupConsensus
 851             .setText(MessageManager.getString("label.group_consensus"));
 852     showGroupConsensus.addActionListener(new ActionListener()
 853     {
 854
 855       @Override
 856       public void actionPerformed(ActionEvent e)
 857       {
 858         showGroupConsensus_actionPerformed(e);
 859       }
 860
 861     });
 862     showConsensusHistogram.setText(
 863             MessageManager.getString("label.show_consensus_histogram"));
 864     showConsensusHistogram.addActionListener(new ActionListener()
 865     {
 866
 867       @Override
 868       public void actionPerformed(ActionEvent e)
 869       {
 870         showConsensusHistogram_actionPerformed(e);
 871       }
 872
 873     });
 874     showSequenceLogo
 875             .setText(MessageManager.getString("label.show_consensus_logo"));
 876     showSequenceLogo.addActionListener(new ActionListener()
 877     {
 878
 879       @Override
 880       public void actionPerformed(ActionEvent e)
 881       {
 882         showSequenceLogo_actionPerformed(e);
 883       }
 884
 885     });
 886     normaliseSequenceLogo
 887             .setText(MessageManager.getString("label.norm_consensus_logo"));
 888     normaliseSequenceLogo.addActionListener(new ActionListener()
 889     {
 890
 891       @Override
 892       public void actionPerformed(ActionEvent e)
 893       {
 894         normaliseSequenceLogo_actionPerformed(e);
 895       }
 896
 897     });
 898     applyAutoAnnotationSettings
 899             .setText(MessageManager.getString("label.apply_all_groups"));
 900     applyAutoAnnotationSettings.setState(false);
 901     applyAutoAnnotationSettings.setVisible(true);
 902     applyAutoAnnotationSettings.addActionListener(new ActionListener()
 903     {
 904       @Override
 905       public void actionPerformed(ActionEvent e)
 906       {
 907         applyAutoAnnotationSettings_actionPerformed(e);
 908       }
 909     });
 910
 911     ButtonGroup buttonGroup = new ButtonGroup();
 912     final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
 913             MessageManager.getString("label.show_first"));
 914     final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
 915             MessageManager.getString("label.show_last"));
 916     buttonGroup.add(showAutoFirst);
 917     buttonGroup.add(showAutoLast);
 918     final boolean autoFirst = Cache
 919             .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
 920     showAutoFirst.setSelected(autoFirst);
 921     setShowAutoCalculatedAbove(autoFirst);
 922     showAutoFirst.addActionListener(new ActionListener()
 923     {
 924       @Override
 925       public void actionPerformed(ActionEvent e)
 926       {
 927         setShowAutoCalculatedAbove(showAutoFirst.isSelected());
 928         sortAnnotations_actionPerformed();
 929       }
 930     });
 931     showAutoLast.setSelected(!showAutoFirst.isSelected());
 932     showAutoLast.addActionListener(new ActionListener()
 933     {
 934       @Override
 935       public void actionPerformed(ActionEvent e)
 936       {
 937         setShowAutoCalculatedAbove(!showAutoLast.isSelected());
 938         sortAnnotations_actionPerformed();
 939       }
 940     });
 941
 942     JMenuItem deleteGroups = new JMenuItem(
 943             MessageManager.getString("action.undefine_groups"));
 944     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
 945             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 946     al = new ActionListener()
 947     {
 948       @Override
 949       public void actionPerformed(ActionEvent e)
 950       {
 951         deleteGroups_actionPerformed(e);
 952       }
 953     };
 954     addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
 955
 956     JMenuItem annotationColumn = new JMenuItem(
 957             MessageManager.getString("action.select_by_annotation"));
 958     annotationColumn.addActionListener(new ActionListener()
 959     {
 960       @Override
 961       public void actionPerformed(ActionEvent e)
 962       {
 963         annotationColumn_actionPerformed(e);
 964       }
 965     });
 966
 967     JMenuItem createGroup = new JMenuItem(
 968             MessageManager.getString("action.create_group"));
 969     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
 970             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 971     al = new ActionListener()
 972     {
 973       @Override
 974       public void actionPerformed(ActionEvent e)
 975       {
 976         createGroup_actionPerformed(e);
 977       }
 978     };
 979     addMenuActionAndAccelerator(keyStroke, createGroup, al);
 980
 981     JMenuItem unGroup = new JMenuItem(
 982             MessageManager.getString("action.remove_group"));
 983     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
 984             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
 985                     | KeyEvent.SHIFT_MASK,
 986             false);
 987     al = new ActionListener()
 988     {
 989       @Override
 990       public void actionPerformed(ActionEvent e)
 991       {
 992         unGroup_actionPerformed(e);
 993       }
 994     };
 995     addMenuActionAndAccelerator(keyStroke, unGroup, al);
 996
 997     copy.setText(MessageManager.getString("action.copy"));
 998     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
 999             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1000
1001     al = new ActionListener()
1002     {
1003       @Override
1004       public void actionPerformed(ActionEvent e)
1005       {
1006         copy_actionPerformed(e);
1007       }
1008     };
1009     addMenuActionAndAccelerator(keyStroke, copy, al);
1010
1011     cut.setText(MessageManager.getString("action.cut"));
1012     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
1013             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1014     al = new ActionListener()
1015     {
1016       @Override
1017       public void actionPerformed(ActionEvent e)
1018       {
1019         cut_actionPerformed(e);
1020       }
1021     };
1022     addMenuActionAndAccelerator(keyStroke, cut, al);
1023
1024     JMenuItem delete = new JMenuItem(
1025             MessageManager.getString("action.delete"));
1026     delete.addActionListener(new ActionListener()
1027     {
1028       @Override
1029       public void actionPerformed(ActionEvent e)
1030       {
1031         delete_actionPerformed(e);
1032       }
1033     });
1034
1035     pasteMenu.setText(MessageManager.getString("action.paste"));
1036     JMenuItem pasteNew = new JMenuItem(
1037             MessageManager.getString("label.to_new_alignment"));
1038     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1039             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1040                     | KeyEvent.SHIFT_MASK,
1041             false);
1042     al = new ActionListener()
1043     {
1044       @Override
1045       public void actionPerformed(ActionEvent e)
1046       {
1047         try
1048         {
1049           pasteNew_actionPerformed(e);
1050         } catch (IOException | InterruptedException e1)
1051         {
1052           // TODO Auto-generated catch block
1053           e1.printStackTrace();
1054         }
1055       }
1056     };
1057     addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1058
1059     JMenuItem pasteThis = new JMenuItem(
1060             MessageManager.getString("label.to_this_alignment"));
1061     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1062             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1063     al = new ActionListener()
1064     {
1065       @Override
1066       public void actionPerformed(ActionEvent e)
1067       {
1068         try
1069         {
1070           pasteThis_actionPerformed(e);
1071         } catch (IOException | InterruptedException e1)
1072         {
1073           // TODO Auto-generated catch block
1074           e1.printStackTrace();
1075         }
1076       }
1077     };
1078     addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1079
1080     JMenuItem createPNG = new JMenuItem("PNG");
1081     createPNG.addActionListener(new ActionListener()
1082     {
1083       @Override
1084       public void actionPerformed(ActionEvent e)
1085       {
1086         createPNG(null);
1087       }
1088     });
1089     createPNG.setActionCommand(
1090             MessageManager.getString("label.save_png_image"));
1091     JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1092     font.addActionListener(new ActionListener()
1093     {
1094       @Override
1095       public void actionPerformed(ActionEvent e)
1096       {
1097         font_actionPerformed(e);
1098       }
1099     });
1100     seqLimits.setText(
1101             MessageManager.getString("label.show_sequence_limits"));
1102     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1103     seqLimits.addActionListener(new ActionListener()
1104     {
1105       @Override
1106       public void actionPerformed(ActionEvent e)
1107       {
1108         seqLimit_actionPerformed(e);
1109       }
1110     });
1111     JMenuItem epsFile = new JMenuItem("EPS");
1112     epsFile.addActionListener(new ActionListener()
1113     {
1114       @Override
1115       public void actionPerformed(ActionEvent e)
1116       {
1117         createEPS(null);
1118       }
1119     });
1120
1121     JMenuItem createSVG = new JMenuItem("SVG");
1122     createSVG.addActionListener(new ActionListener()
1123     {
1124       @Override
1125       public void actionPerformed(ActionEvent e)
1126       {
1127         createSVG(null);
1128       }
1129     });
1130
1131     JMenuItem loadTreeMenuItem = new JMenuItem(
1132             MessageManager.getString("label.load_associated_tree"));
1133     loadTreeMenuItem.setActionCommand(
1134             MessageManager.getString("label.load_tree_for_sequence_set"));
1135     loadTreeMenuItem.addActionListener(new ActionListener()
1136     {
1137       @Override
1138       public void actionPerformed(ActionEvent e)
1139       {
1140         loadTreeMenuItem_actionPerformed(e);
1141       }
1142     });
1143
1144     scaleAbove.setVisible(false);
1145     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1146     scaleAbove.addActionListener(new ActionListener()
1147     {
1148       @Override
1149       public void actionPerformed(ActionEvent e)
1150       {
1151         scaleAbove_actionPerformed(e);
1152       }
1153     });
1154     scaleLeft.setVisible(false);
1155     scaleLeft.setSelected(true);
1156     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1157     scaleLeft.addActionListener(new ActionListener()
1158     {
1159       @Override
1160       public void actionPerformed(ActionEvent e)
1161       {
1162         scaleLeft_actionPerformed(e);
1163       }
1164     });
1165     scaleRight.setVisible(false);
1166     scaleRight.setSelected(true);
1167     scaleRight.setText(MessageManager.getString("action.scale_right"));
1168     scaleRight.addActionListener(new ActionListener()
1169     {
1170       @Override
1171       public void actionPerformed(ActionEvent e)
1172       {
1173         scaleRight_actionPerformed(e);
1174       }
1175     });
1176     centreColumnLabelsMenuItem.setVisible(true);
1177     centreColumnLabelsMenuItem.setState(false);
1178     centreColumnLabelsMenuItem.setText(
1179             MessageManager.getString("label.centre_column_labels"));
1180     centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1181     {
1182       @Override
1183       public void actionPerformed(ActionEvent e)
1184       {
1185         centreColumnLabels_actionPerformed(e);
1186       }
1187     });
1188     followHighlightMenuItem.setVisible(true);
1189     followHighlightMenuItem.setState(true);
1190     followHighlightMenuItem
1191             .setText(MessageManager.getString("label.automatic_scrolling"));
1192     followHighlightMenuItem.addActionListener(new ActionListener()
1193     {
1194
1195       @Override
1196       public void actionPerformed(ActionEvent e)
1197       {
1198         followHighlight_actionPerformed();
1199       }
1200
1201     });
1202
1203     sortByTreeMenu
1204             .setText(MessageManager.getString("action.by_tree_order"));
1205     sort.setText(MessageManager.getString("action.sort"));
1206     sort.addMenuListener(new MenuListener()
1207     {
1208       @Override
1209       public void menuSelected(MenuEvent e)
1210       {
1211         buildTreeSortMenu();
1212       }
1213
1214       @Override
1215       public void menuDeselected(MenuEvent e)
1216       {
1217       }
1218
1219       @Override
1220       public void menuCanceled(MenuEvent e)
1221       {
1222       }
1223     });
1224     sortByAnnotScore
1225             .setText(MessageManager.getString("label.sort_by_score"));
1226     sort.add(sortByAnnotScore);
1227     sort.addMenuListener(new javax.swing.event.MenuListener()
1228     {
1229
1230       @Override
1231       public void menuCanceled(MenuEvent e)
1232       {
1233       }
1234
1235       @Override
1236       public void menuDeselected(MenuEvent e)
1237       {
1238       }
1239
1240       @Override
1241       public void menuSelected(MenuEvent e)
1242       {
1243         buildSortByAnnotationScoresMenu();
1244       }
1245     });
1246     sortByAnnotScore.setVisible(false);
1247
1248     calculateTree
1249             .setText(MessageManager.getString("action.calculate_tree_pca"));
1250
1251     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1252     padGapsMenuitem
1253             .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
1254     padGapsMenuitem.addActionListener(new ActionListener()
1255     {
1256       @Override
1257       public void actionPerformed(ActionEvent e)
1258       {
1259         padGapsMenuitem_actionPerformed(e);
1260       }
1261     });
1262     JMenuItem vamsasStore = new JMenuItem(
1263             MessageManager.getString("label.vamsas_store"));
1264     vamsasStore.setVisible(false);
1265     vamsasStore.addActionListener(new ActionListener()
1266     {
1267       @Override
1268       public void actionPerformed(ActionEvent e)
1269       {
1270         vamsasStore_actionPerformed(e);
1271       }
1272     });
1273     showTranslation
1274             .setText(MessageManager.getString("label.translate_cDNA"));
1275     showTranslation.addActionListener(new ActionListener()
1276     {
1277       @Override
1278       public void actionPerformed(ActionEvent e)
1279       {
1280         showTranslation_actionPerformed(e);
1281       }
1282     });
1283     showReverse.setText(MessageManager.getString("label.reverse"));
1284     showReverse.addActionListener(new ActionListener()
1285     {
1286       @Override
1287       public void actionPerformed(ActionEvent e)
1288       {
1289         showReverse_actionPerformed(false);
1290       }
1291     });
1292     showReverseComplement
1293             .setText(MessageManager.getString("label.reverse_complement"));
1294     showReverseComplement.addActionListener(new ActionListener()
1295     {
1296       @Override
1297       public void actionPerformed(ActionEvent e)
1298       {
1299         showReverse_actionPerformed(true);
1300       }
1301     });
1302
1303     JMenuItem extractScores = new JMenuItem(
1304             MessageManager.getString("label.extract_scores"));
1305     extractScores.addActionListener(new ActionListener()
1306     {
1307       @Override
1308       public void actionPerformed(ActionEvent e)
1309       {
1310         extractScores_actionPerformed(e);
1311       }
1312     });
1313     extractScores.setVisible(true);
1314     // JBPNote: TODO: make gui for regex based score extraction
1315
1316     // for show products actions see AlignFrame.canShowProducts
1317     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1318
1319     runGroovy.setText(MessageManager.getString("label.run_groovy"));
1320     runGroovy.setToolTipText(
1321             MessageManager.getString("label.run_groovy_tip"));
1322     runGroovy.addActionListener(new ActionListener()
1323     {
1324       @Override
1325       public void actionPerformed(ActionEvent e)
1326       {
1327         runGroovy_actionPerformed();
1328       }
1329     });
1330
1331     JMenuItem openFeatureSettings = new JMenuItem(
1332             MessageManager.getString("action.feature_settings"));
1333     openFeatureSettings.addActionListener(new ActionListener()
1334     {
1335       @Override
1336       public void actionPerformed(ActionEvent e)
1337       {
1338         featureSettings_actionPerformed(e);
1339       }
1340     });
1341     JMenuItem fetchSequence = new JMenuItem(
1342             MessageManager.getString("label.fetch_sequences"));
1343     fetchSequence.addActionListener(new ActionListener()
1344     {
1345       @Override
1346       public void actionPerformed(ActionEvent e)
1347       {
1348         fetchSequence_actionPerformed(e);
1349       }
1350     });
1351
1352     JMenuItem associatedData = new JMenuItem(
1353             MessageManager.getString("label.load_features_annotations"));
1354     associatedData.addActionListener(new ActionListener()
1355     {
1356       @Override
1357       public void actionPerformed(ActionEvent e)
1358       {
1359         try
1360         {
1361           associatedData_actionPerformed(e);
1362         } catch (IOException | InterruptedException e1)
1363         {
1364           // TODO Auto-generated catch block
1365           e1.printStackTrace();
1366         }
1367       }
1368     });
1369     autoCalculate.setText(
1370             MessageManager.getString("label.autocalculate_consensus"));
1371     autoCalculate.setState(
1372             jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1373     autoCalculate.addActionListener(new ActionListener()
1374     {
1375       @Override
1376       public void actionPerformed(ActionEvent e)
1377       {
1378         autoCalculate_actionPerformed(e);
1379       }
1380     });
1381     sortByTree.setText(
1382             MessageManager.getString("label.sort_alignment_new_tree"));
1383     sortByTree.setToolTipText("<html>" + MessageManager.getString(
1384             "label.enable_automatically_sort_alignment_when_open_new_tree"));
1385     sortByTree
1386             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1387     sortByTree.addActionListener(new ActionListener()
1388     {
1389       @Override
1390       public void actionPerformed(ActionEvent e)
1391       {
1392         sortByTreeOption_actionPerformed(e);
1393       }
1394     });
1395
1396     listenToViewSelections.setText(
1397             MessageManager.getString("label.listen_for_selections"));
1398     listenToViewSelections
1399             .setToolTipText("<html>" + MessageManager.getString(
1400                     "label.selections_mirror_selections_made_same_sequences_other_views"));
1401     listenToViewSelections.setState(false);
1402     listenToViewSelections.addActionListener(new ActionListener()
1403     {
1404       @Override
1405       public void actionPerformed(ActionEvent e)
1406       {
1407         listenToViewSelections_actionPerformed(e);
1408       }
1409     });
1410
1411     JMenu addSequenceMenu = new JMenu(
1412             MessageManager.getString("label.add_sequences"));
1413     JMenuItem addFromFile = new JMenuItem(
1414             MessageManager.getString("label.from_file"));
1415     addFromFile.addActionListener(new ActionListener()
1416     {
1417       @Override
1418       public void actionPerformed(ActionEvent e)
1419       {
1420         addFromFile_actionPerformed(e);
1421       }
1422     });
1423     JMenuItem addFromText = new JMenuItem(
1424             MessageManager.getString("label.from_textbox"));
1425     addFromText.addActionListener(new ActionListener()
1426     {
1427       @Override
1428       public void actionPerformed(ActionEvent e)
1429       {
1430         addFromText_actionPerformed(e);
1431       }
1432     });
1433     JMenuItem addFromURL = new JMenuItem(
1434             MessageManager.getString("label.from_url"));
1435     addFromURL.addActionListener(new ActionListener()
1436     {
1437       @Override
1438       public void actionPerformed(ActionEvent e)
1439       {
1440         addFromURL_actionPerformed(e);
1441       }
1442     });
1443     JMenuItem exportFeatures = new JMenuItem(
1444             MessageManager.getString("label.export_features"));
1445     exportFeatures.addActionListener(new ActionListener()
1446     {
1447       @Override
1448       public void actionPerformed(ActionEvent e)
1449       {
1450         exportFeatures_actionPerformed(e);
1451       }
1452     });
1453     JMenuItem exportAnnotations = new JMenuItem(
1454             MessageManager.getString("label.export_annotations"));
1455     exportAnnotations.addActionListener(new ActionListener()
1456     {
1457       @Override
1458       public void actionPerformed(ActionEvent e)
1459       {
1460         exportAnnotations_actionPerformed(e);
1461       }
1462     });
1463     statusPanel.setLayout(new GridLayout());
1464     JMenuItem showAllSeqs = new JMenuItem(
1465             MessageManager.getString("label.all_sequences"));
1466     showAllSeqs.setToolTipText(
1467             MessageManager.getString("label.toggle_sequence_visibility"));
1468     showAllSeqs.addActionListener(new ActionListener()
1469     {
1470       @Override
1471       public void actionPerformed(ActionEvent e)
1472       {
1473         showAllSeqs_actionPerformed(e);
1474       }
1475     });
1476     JMenuItem showAllColumns = new JMenuItem(
1477             MessageManager.getString("label.all_columns"));
1478     showAllColumns.setToolTipText(
1479             MessageManager.getString("label.toggle_columns_visibility"));
1480     showAllColumns.addActionListener(new ActionListener()
1481     {
1482       @Override
1483       public void actionPerformed(ActionEvent e)
1484       {
1485         showAllColumns_actionPerformed(e);
1486       }
1487     });
1488     JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1489     JMenuItem hideSelSequences = new JMenuItem(
1490             MessageManager.getString("label.selected_sequences"));
1491     hideSelSequences.setToolTipText(
1492             MessageManager.getString("label.toggle_sequence_visibility"));
1493     hideSelSequences.addActionListener(new ActionListener()
1494     {
1495       @Override
1496       public void actionPerformed(ActionEvent e)
1497       {
1498         hideSelSequences_actionPerformed(e);
1499       }
1500     });
1501     JMenuItem hideSelColumns = new JMenuItem(
1502             MessageManager.getString("label.selected_columns"));
1503     hideSelColumns.setToolTipText(
1504             MessageManager.getString("label.toggle_columns_visibility"));
1505     hideSelColumns.addActionListener(new ActionListener()
1506     {
1507       @Override
1508       public void actionPerformed(ActionEvent e)
1509       {
1510         hideSelColumns_actionPerformed(e);
1511       }
1512     });
1513     JMenuItem hideAllSelection = new JMenuItem(
1514             MessageManager.getString("label.selected_region"));
1515     hideAllSelection.addActionListener(new ActionListener()
1516     {
1517       @Override
1518       public void actionPerformed(ActionEvent e)
1519       {
1520         hideAllSelection_actionPerformed(e);
1521       }
1522     });
1523     // TODO: should be hidden if no selection exists.
1524     JMenuItem hideAllButSelection = new JMenuItem(
1525             MessageManager.getString("label.all_but_selected_region"));
1526     hideAllButSelection.addActionListener(new ActionListener()
1527     {
1528       @Override
1529       public void actionPerformed(ActionEvent e)
1530       {
1531         hideAllButSelection_actionPerformed(e);
1532       }
1533     });
1534     JMenuItem showAllhidden = new JMenuItem(
1535             MessageManager.getString("label.all_sequences_columns"));
1536     showAllhidden.setToolTipText(MessageManager
1537             .getString("label.toggles_visibility_hidden_selected_regions"));
1538     showAllhidden.addActionListener(new ActionListener()
1539     {
1540       @Override
1541       public void actionPerformed(ActionEvent e)
1542       {
1543         showAllhidden_actionPerformed(e);
1544       }
1545     });
1546     hiddenMarkers.setText(
1547             MessageManager.getString("action.show_hidden_markers"));
1548     hiddenMarkers.addActionListener(new ActionListener()
1549     {
1550       @Override
1551       public void actionPerformed(ActionEvent e)
1552       {
1553         hiddenMarkers_actionPerformed(e);
1554       }
1555     });
1556
1557     JMenuItem invertColSel = new JMenuItem(
1558             MessageManager.getString("action.invert_column_selection"));
1559     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1560             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1561                     | KeyEvent.ALT_MASK,
1562             false);
1563     al = new ActionListener()
1564     {
1565       @Override
1566       public void actionPerformed(ActionEvent e)
1567       {
1568         invertColSel_actionPerformed(e);
1569       }
1570     };
1571     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1572
1573     showComplementMenuItem.setVisible(false);
1574     showComplementMenuItem.addActionListener(new ActionListener()
1575     {
1576       @Override
1577       public void actionPerformed(ActionEvent e)
1578       {
1579         showComplement_actionPerformed(showComplementMenuItem.getState());
1580       }
1581     });
1582
1583     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1584     {
1585       @Override
1586       public void stateChanged(ChangeEvent evt)
1587       {
1588         JTabbedPane pane = (JTabbedPane) evt.getSource();
1589         int sel = pane.getSelectedIndex();
1590         tabSelectionChanged(sel);
1591       }
1592     });
1593     tabbedPane.addMouseListener(new MouseAdapter()
1594     {
1595       @Override
1596       public void mousePressed(MouseEvent e)
1597       {
1598         if (e.isPopupTrigger()) // Mac
1599         {
1600           tabbedPane_mousePressed(e);
1601         }
1602       }
1603
1604       @Override
1605       public void mouseReleased(MouseEvent e)
1606       {
1607         if (e.isPopupTrigger()) // Windows
1608         {
1609           tabbedPane_mousePressed(e);
1610         }
1611       }
1612     });
1613     tabbedPane.addFocusListener(new FocusAdapter()
1614     {
1615       @Override
1616       public void focusGained(FocusEvent e)
1617       {
1618         tabbedPane_focusGained(e);
1619       }
1620     });
1621
1622     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1623     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1624             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1625     al = new ActionListener()
1626     {
1627       @Override
1628       public void actionPerformed(ActionEvent e)
1629       {
1630         save_actionPerformed(e);
1631       }
1632     };
1633     addMenuActionAndAccelerator(keyStroke, save, al);
1634
1635     reload.setEnabled(false);
1636     reload.setText(MessageManager.getString("action.reload"));
1637     reload.addActionListener(new ActionListener()
1638     {
1639       @Override
1640       public void actionPerformed(ActionEvent e)
1641       {
1642         reload_actionPerformed(e);
1643       }
1644     });
1645
1646     JMenuItem newView = new JMenuItem(
1647             MessageManager.getString("action.new_view"));
1648     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1649             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1650     al = new ActionListener()
1651     {
1652       @Override
1653       public void actionPerformed(ActionEvent e)
1654       {
1655         newView_actionPerformed(e);
1656       }
1657     };
1658     addMenuActionAndAccelerator(keyStroke, newView, al);
1659
1660     tabbedPane.setToolTipText("<html><i>"
1661             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1662             + "</i></html>");
1663
1664     formatMenu.setText(MessageManager.getString("action.format"));
1665     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1666
1667     idRightAlign.setText(
1668             MessageManager.getString("label.right_align_sequence_id"));
1669     idRightAlign.addActionListener(new ActionListener()
1670     {
1671       @Override
1672       public void actionPerformed(ActionEvent e)
1673       {
1674         idRightAlign_actionPerformed(e);
1675       }
1676     });
1677
1678     gatherViews.setEnabled(false);
1679     gatherViews.setText(MessageManager.getString("action.gather_views"));
1680     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1681     al = new ActionListener()
1682     {
1683       @Override
1684       public void actionPerformed(ActionEvent e)
1685       {
1686         gatherViews_actionPerformed(e);
1687       }
1688     };
1689     addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1690
1691     expandViews.setEnabled(false);
1692     expandViews.setText(MessageManager.getString("action.expand_views"));
1693     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1694     al = new ActionListener()
1695     {
1696       @Override
1697       public void actionPerformed(ActionEvent e)
1698       {
1699         expandViews_actionPerformed(e);
1700       }
1701     };
1702     addMenuActionAndAccelerator(keyStroke, expandViews, al);
1703
1704     JMenuItem pageSetup = new JMenuItem(
1705             MessageManager.getString("action.page_setup"));
1706     pageSetup.addActionListener(new ActionListener()
1707     {
1708       @Override
1709       public void actionPerformed(ActionEvent e)
1710       {
1711         pageSetup_actionPerformed(e);
1712       }
1713     });
1714     JMenuItem alignmentProperties = new JMenuItem(
1715             MessageManager.getString("label.alignment_props"));
1716     alignmentProperties.addActionListener(new ActionListener()
1717     {
1718       @Override
1719       public void actionPerformed(ActionEvent actionEvent)
1720       {
1721         alignmentProperties();
1722       }
1723     });
1724     JMenuItem selectHighlighted = new JMenuItem(
1725             MessageManager.getString("action.select_highlighted_columns"));
1726     selectHighlighted.setToolTipText(
1727             MessageManager.getString("tooltip.select_highlighted_columns"));
1728     al = new ActionListener()
1729     {
1730       @Override
1731       public void actionPerformed(ActionEvent actionEvent)
1732       {
1733         selectHighlightedColumns_actionPerformed(actionEvent);
1734       }
1735     };
1736     hmmBuild.setText(MessageManager.getString("label.hmmbuild"));
1737     hmmBuild.addActionListener(new ActionListener()
1738     {
1739
1740       @Override
1741       public void actionPerformed(ActionEvent e)
1742       {
1743         try
1744         {
1745           hmmBuild_actionPerformed(e);
1746         } catch (IOException e1)
1747         {
1748           // TODO Auto-generated catch block
1749           e1.printStackTrace();
1750         } catch (InterruptedException e1)
1751         {
1752           // TODO Auto-generated catch block
1753           e1.printStackTrace();
1754         }
1755       }
1756
1757     });
1758     hmmAlign.setText(MessageManager.getString("label.hmmalign"));
1759     hmmAlign.addActionListener(new ActionListener()
1760     {
1761
1762       @Override
1763       public void actionPerformed(ActionEvent e)
1764       {
1765         try
1766         {
1767           hmmAlign_actionPerformed(e);
1768         } catch (IOException e1)
1769         {
1770           // TODO Auto-generated catch block
1771           e1.printStackTrace();
1772         } catch (InterruptedException e1)
1773         {
1774           // TODO Auto-generated catch block
1775           e1.printStackTrace();
1776         }
1777       }
1778
1779     });
1780     selectHighlighted.addActionListener(al);
1781     JMenu tooltipSettingsMenu = new JMenu(
1782             MessageManager.getString("label.sequence_id_tooltip"));
1783     JMenu autoAnnMenu = new JMenu(
1784             MessageManager.getString("label.autocalculated_annotation"));
1785
1786     JMenu exportImageMenu = new JMenu(
1787             MessageManager.getString("label.export_image"));
1788     JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
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     alignFrameMenuBar.add(hmmerMenu);
1799
1800     fileMenu.add(fetchSequence);
1801     fileMenu.add(addSequenceMenu);
1802     fileMenu.add(reload);
1803     fileMenu.addSeparator();
1804     fileMenu.add(vamsasStore);
1805     fileMenu.add(save);
1806     fileMenu.add(saveAs);
1807     fileMenu.add(outputTextboxMenu);
1808     fileMenu.add(pageSetup);
1809     fileMenu.add(printMenuItem);
1810     fileMenu.addSeparator();
1811     fileMenu.add(exportImageMenu);
1812     fileMenu.add(exportFeatures);
1813     fileMenu.add(exportAnnotations);
1814     fileMenu.add(loadTreeMenuItem);
1815     fileMenu.add(associatedData);
1816     fileMenu.addSeparator();
1817     fileMenu.add(closeMenuItem);
1818
1819     pasteMenu.add(pasteNew);
1820     pasteMenu.add(pasteThis);
1821     editMenu.add(undoMenuItem);
1822     editMenu.add(redoMenuItem);
1823     editMenu.add(cut);
1824     editMenu.add(copy);
1825     editMenu.add(pasteMenu);
1826     editMenu.add(delete);
1827     editMenu.addSeparator();
1828     editMenu.add(remove2LeftMenuItem);
1829     editMenu.add(remove2RightMenuItem);
1830     editMenu.add(removeGappedColumnMenuItem);
1831     editMenu.add(removeAllGapsMenuItem);
1832     editMenu.add(removeRedundancyMenuItem);
1833     editMenu.addSeparator();
1834     // dont add these yet in the CVS build - they cannot be undone!
1835     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1836     // editMenu.add(justifyLeftMenuItem);
1837     // editMenu.add(justifyRightMenuItem);
1838     // editMenu.addSeparator();
1839     editMenu.add(padGapsMenuitem);
1840
1841     showMenu.add(showAllColumns);
1842     showMenu.add(showAllSeqs);
1843     showMenu.add(showAllhidden);
1844     hideMenu.add(hideSelColumns);
1845     hideMenu.add(hideSelSequences);
1846     hideMenu.add(hideAllSelection);
1847     hideMenu.add(hideAllButSelection);
1848     viewMenu.add(newView);
1849     viewMenu.add(expandViews);
1850     viewMenu.add(gatherViews);
1851     viewMenu.addSeparator();
1852     viewMenu.add(showMenu);
1853     viewMenu.add(hideMenu);
1854     viewMenu.add(showComplementMenuItem);
1855     viewMenu.addSeparator();
1856     viewMenu.add(followHighlightMenuItem);
1857     viewMenu.addSeparator();
1858     viewMenu.add(showSeqFeatures);
1859     // viewMenu.add(showSeqFeaturesHeight);
1860     viewMenu.add(openFeatureSettings);
1861     tooltipSettingsMenu.add(showDbRefsMenuitem);
1862     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1863     viewMenu.add(tooltipSettingsMenu);
1864     viewMenu.addSeparator();
1865     viewMenu.add(alignmentProperties);
1866     viewMenu.addSeparator();
1867     viewMenu.add(overviewMenuItem);
1868
1869     annotationsMenu.add(annotationPanelMenuItem);
1870     annotationsMenu.addSeparator();
1871     annotationsMenu.add(showAllAlAnnotations);
1872     annotationsMenu.add(hideAllAlAnnotations);
1873     annotationsMenu.addSeparator();
1874     annotationsMenu.add(showAllSeqAnnotations);
1875     annotationsMenu.add(hideAllSeqAnnotations);
1876     annotationsMenu.add(sortAnnBySequence);
1877     annotationsMenu.add(sortAnnByLabel);
1878     annotationsMenu.addSeparator();
1879     autoAnnMenu.add(showAutoFirst);
1880     autoAnnMenu.add(showAutoLast);
1881     autoAnnMenu.addSeparator();
1882     autoAnnMenu.add(applyAutoAnnotationSettings);
1883     autoAnnMenu.add(showConsensusHistogram);
1884     autoAnnMenu.add(showSequenceLogo);
1885     autoAnnMenu.add(normaliseSequenceLogo);
1886     autoAnnMenu.addSeparator();
1887     autoAnnMenu.add(showGroupConservation);
1888     autoAnnMenu.add(showGroupConsensus);
1889     annotationsMenu.add(autoAnnMenu);
1890
1891     sort.add(sortIDMenuItem);
1892     sort.add(sortLengthMenuItem);
1893     sort.add(sortGroupMenuItem);
1894     sort.add(sortPairwiseMenuItem);
1895     sort.add(sortByTreeMenu);
1896     calculateMenu.add(sort);
1897     calculateMenu.add(calculateTree);
1898     calculateMenu.addSeparator();
1899     calculateMenu.add(pairwiseAlignmentMenuItem);
1900     calculateMenu.addSeparator();
1901     calculateMenu.add(showTranslation);
1902     calculateMenu.add(showReverse);
1903     calculateMenu.add(showReverseComplement);
1904     calculateMenu.add(showProducts);
1905     calculateMenu.add(autoCalculate);
1906     calculateMenu.add(sortByTree);
1907     calculateMenu.addSeparator();
1908     calculateMenu.add(expandAlignment);
1909     calculateMenu.add(extractScores);
1910     calculateMenu.addSeparator();
1911     calculateMenu.add(runGroovy);
1912
1913     webServiceNoServices = new JMenuItem(
1914             MessageManager.getString("label.no_services"));
1915     webService.add(webServiceNoServices);
1916     exportImageMenu.add(htmlMenuItem);
1917     exportImageMenu.add(epsFile);
1918     exportImageMenu.add(createPNG);
1919     exportImageMenu.add(createBioJS);
1920     exportImageMenu.add(createSVG);
1921     addSequenceMenu.add(addFromFile);
1922     addSequenceMenu.add(addFromText);
1923     addSequenceMenu.add(addFromURL);
1924     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1925     statusPanel.add(statusBar, null);
1926     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1927
1928     formatMenu.add(font);
1929     formatMenu.addSeparator();
1930     formatMenu.add(wrapMenuItem);
1931     formatMenu.add(scaleAbove);
1932     formatMenu.add(scaleLeft);
1933     formatMenu.add(scaleRight);
1934     formatMenu.add(seqLimits);
1935     formatMenu.add(idRightAlign);
1936     formatMenu.add(hiddenMarkers);
1937     formatMenu.add(viewBoxesMenuItem);
1938     formatMenu.add(viewTextMenuItem);
1939     formatMenu.add(colourTextMenuItem);
1940     formatMenu.add(renderGapsMenuItem);
1941     formatMenu.add(centreColumnLabelsMenuItem);
1942     formatMenu.add(showNonconservedMenuItem);
1943     selectMenu.add(findMenuItem);
1944     selectMenu.addSeparator();
1945     selectMenu.add(selectAllSequenceMenuItem);
1946     selectMenu.add(deselectAllSequenceMenuItem);
1947     selectMenu.add(invertSequenceMenuItem);
1948     selectMenu.add(invertColSel);
1949     selectMenu.add(createGroup);
1950     selectMenu.add(unGroup);
1951     selectMenu.add(grpsFromSelection);
1952     selectMenu.add(deleteGroups);
1953     selectMenu.add(annotationColumn);
1954     selectMenu.add(selectHighlighted);
1955     // TODO - determine if the listenToViewSelections button is needed : see bug
1956     // JAL-574
1957     // selectMenu.addSeparator();
1958     // selectMenu.add(listenToViewSelections);
1959   }
1960
1961   public void hmmerMenu_actionPerformed(ActionEvent e)
1962   {
1963
1964   }
1965
1966   /**
1967    * Constructs the entries on the HMMER menu (does not add them to the menu).
1968    */
1969   protected void initHMMERMenu()
1970   {
1971     hmmAlign = new JMenuItem(MessageManager.getString("label.hmmalign"));
1972     hmmBuild = new JMenuItem(MessageManager.getString("label.hmmbuild"));
1973     hmmSearch = new JMenuItem(MessageManager.getString("label.hmmsearch"));
1974   }
1975
1976   /**
1977    * Constructs the entries on the Colour menu (but does not add them to the
1978    * menu).
1979    */
1980   protected void initColourMenu()
1981   {
1982     applyToAllGroups = new JCheckBoxMenuItem(
1983             MessageManager.getString("label.apply_colour_to_all_groups"));
1984     applyToAllGroups.addActionListener(new ActionListener()
1985     {
1986       @Override
1987       public void actionPerformed(ActionEvent e)
1988       {
1989         applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1990       }
1991     });
1992
1993     textColour = new JMenuItem(
1994             MessageManager.getString("label.text_colour"));
1995     textColour.addActionListener(new ActionListener()
1996     {
1997       @Override
1998       public void actionPerformed(ActionEvent e)
1999       {
2000         textColour_actionPerformed();
2001       }
2002     });
2003
2004     conservationMenuItem = new JCheckBoxMenuItem(
2005             MessageManager.getString("action.by_conservation"));
2006     conservationMenuItem.addActionListener(new ActionListener()
2007     {
2008       @Override
2009       public void actionPerformed(ActionEvent e)
2010       {
2011         conservationMenuItem_actionPerformed(
2012                 conservationMenuItem.isSelected());
2013       }
2014     });
2015
2016     abovePIDThreshold = new JCheckBoxMenuItem(
2017             MessageManager.getString("label.above_identity_threshold"));
2018     abovePIDThreshold.addActionListener(new ActionListener()
2019     {
2020       @Override
2021       public void actionPerformed(ActionEvent e)
2022       {
2023         abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
2024       }
2025     });
2026     modifyPID = new JMenuItem(
2027             MessageManager.getString("label.modify_identity_threshold"));
2028     modifyPID.addActionListener(new ActionListener()
2029     {
2030       @Override
2031       public void actionPerformed(ActionEvent e)
2032       {
2033         modifyPID_actionPerformed();
2034       }
2035     });
2036     modifyConservation = new JMenuItem(MessageManager
2037             .getString("label.modify_conservation_threshold"));
2038     modifyConservation.addActionListener(new ActionListener()
2039     {
2040       @Override
2041       public void actionPerformed(ActionEvent e)
2042       {
2043         modifyConservation_actionPerformed();
2044       }
2045     });
2046
2047     annotationColour = new JMenuItem(
2048             MessageManager.getString("action.by_annotation"));
2049     annotationColour.addActionListener(new ActionListener()
2050     {
2051       @Override
2052       public void actionPerformed(ActionEvent e)
2053       {
2054         annotationColour_actionPerformed();
2055       }
2056     });
2057   }
2058
2059   protected void selectHighlightedColumns_actionPerformed(
2060           ActionEvent actionEvent)
2061   {
2062     // TODO Auto-generated method stub
2063
2064   }
2065
2066   /**
2067    * Generate the reverse sequence (or reverse complement if the flag is true)
2068    * and add it to the alignment
2069    *
2070    * @param complement
2071    */
2072   protected void showReverse_actionPerformed(boolean complement)
2073   {
2074   }
2075
2076   /**
2077    * Try to run script in a Groovy console, having first ensured that this
2078    * alignframe is set as currentAlignFrame in Desktop
2079    */
2080   protected void runGroovy_actionPerformed()
2081   {
2082
2083   }
2084
2085   /**
2086    * Adds the given action listener and key accelerator to the given menu item.
2087    * Also saves in a lookup table to support lookup of action by key stroke.
2088    *
2089    * @param keyStroke
2090    * @param menuItem
2091    * @param actionListener
2092    */
2093   protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2094           JMenuItem menuItem, ActionListener actionListener)
2095   {
2096     menuItem.setAccelerator(keyStroke);
2097     accelerators.put(keyStroke, menuItem);
2098     menuItem.addActionListener(actionListener);
2099   }
2100
2101   /**
2102    * Action on clicking sort annotations by type.
2103    *
2104    * @param sortOrder
2105    */
2106   protected void sortAnnotations_actionPerformed()
2107   {
2108   }
2109
2110   /**
2111    * Action on clicking Show all annotations.
2112    *
2113    * @param forSequences
2114    *          update sequence-related annotations
2115    * @param forAlignment
2116    *          update non-sequence-related annotations
2117    */
2118   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2119           boolean forAlignment)
2120   {
2121     setAnnotationsVisibility(true, forSequences, forAlignment);
2122   }
2123
2124   /**
2125    * Action on clicking Hide all annotations.
2126    *
2127    * @param forSequences
2128    *          update sequence-related annotations
2129    * @param forAlignment
2130    *          update non-sequence-related annotations
2131    */
2132   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2133           boolean forAlignment)
2134   {
2135     setAnnotationsVisibility(false, forSequences, forAlignment);
2136   }
2137
2138   /**
2139    * Set the visibility of annotations to true or false. Can act on
2140    * sequence-related annotations, or alignment-related, or both.
2141    *
2142    * @param visible
2143    * @param forSequences
2144    *          update sequence-related annotations
2145    * @param forAlignment
2146    *          update non-sequence-related annotations
2147    */
2148   protected void setAnnotationsVisibility(boolean visible,
2149           boolean forSequences, boolean forAlignment)
2150   {
2151
2152   }
2153
2154   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2155   {
2156     // TODO Auto-generated method stub
2157
2158   }
2159
2160   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2161   {
2162     // TODO Auto-generated method stub
2163
2164   }
2165
2166   protected void showAllhidden_actionPerformed(ActionEvent e)
2167   {
2168     // TODO Auto-generated method stub
2169
2170   }
2171
2172   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2173   {
2174     // TODO Auto-generated method stub
2175
2176   }
2177
2178   protected void hideAllSelection_actionPerformed(ActionEvent e)
2179   {
2180     // TODO Auto-generated method stub
2181
2182   }
2183
2184   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2185   {
2186     // TODO Auto-generated method stub
2187
2188   }
2189
2190   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2191   {
2192     // TODO Auto-generated method stub
2193
2194   }
2195
2196   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2197   {
2198     // TODO Auto-generated method stub
2199
2200   }
2201
2202   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2203   {
2204     // TODO Auto-generated method stub
2205
2206   }
2207
2208   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2209   {
2210     // TODO Auto-generated method stub
2211
2212   }
2213
2214   protected void showGroupConservation_actionPerformed(ActionEvent e)
2215   {
2216     // TODO Auto-generated method stub
2217
2218   }
2219
2220   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2221   {
2222     // TODO Auto-generated method stub
2223
2224   }
2225
2226   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2227   {
2228     // TODO Auto-generated method stub
2229
2230   }
2231
2232   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2233   {
2234     // TODO Auto-generated method stub
2235
2236   }
2237
2238   protected void followHighlight_actionPerformed()
2239   {
2240     // TODO Auto-generated method stub
2241
2242   }
2243
2244   protected void showNpFeats_actionPerformed(ActionEvent e)
2245   {
2246     // TODO Auto-generated method stub
2247
2248   }
2249
2250   protected void showDbRefs_actionPerformed(ActionEvent e)
2251   {
2252     // TODO Auto-generated method stub
2253
2254   }
2255
2256   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2257   {
2258   }
2259
2260   protected void buildSortByAnnotationScoresMenu()
2261   {
2262   }
2263
2264   protected void extractScores_actionPerformed(ActionEvent e)
2265   {
2266   }
2267
2268   protected void outputText_actionPerformed(ActionEvent e)
2269   {
2270   }
2271
2272   public void addFromFile_actionPerformed(ActionEvent e)
2273   {
2274
2275   }
2276
2277   public void addFromText_actionPerformed(ActionEvent e)
2278   {
2279
2280   }
2281
2282   public void addFromURL_actionPerformed(ActionEvent e)
2283   {
2284
2285   }
2286
2287   public void exportFeatures_actionPerformed(ActionEvent e)
2288   {
2289
2290   }
2291
2292   public void exportAnnotations_actionPerformed(ActionEvent e)
2293   {
2294
2295   }
2296
2297   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2298   {
2299   }
2300
2301   protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2302   {
2303
2304   }
2305
2306   protected void closeMenuItem_actionPerformed(boolean b)
2307   {
2308   }
2309
2310   protected void redoMenuItem_actionPerformed(ActionEvent e)
2311   {
2312   }
2313
2314   protected void undoMenuItem_actionPerformed(ActionEvent e)
2315   {
2316   }
2317
2318   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2319   {
2320   }
2321
2322   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2323   {
2324   }
2325
2326   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2327   {
2328   }
2329
2330   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2331   {
2332   }
2333
2334   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2335   {
2336   }
2337
2338   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2339   {
2340   }
2341
2342   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2343   {
2344   }
2345
2346   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2347   {
2348   }
2349
2350   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2351   {
2352   }
2353
2354   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2355   {
2356   }
2357
2358   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2359   {
2360   }
2361
2362   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2363   {
2364   }
2365
2366   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2367   {
2368   }
2369
2370   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2371   {
2372   }
2373
2374   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2375   {
2376   }
2377
2378   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2379   {
2380   }
2381
2382   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2383   {
2384   }
2385
2386   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2387   {
2388   }
2389
2390   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2391   {
2392   }
2393
2394   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2395   {
2396   }
2397
2398   protected void conservationMenuItem_actionPerformed(boolean selected)
2399   {
2400   }
2401
2402   protected void printMenuItem_actionPerformed(ActionEvent e)
2403   {
2404   }
2405
2406   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2407   {
2408   }
2409
2410   protected void findMenuItem_actionPerformed(ActionEvent e)
2411   {
2412   }
2413
2414   protected void abovePIDThreshold_actionPerformed(boolean selected)
2415   {
2416   }
2417
2418   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2419   {
2420   }
2421
2422   protected void deleteGroups_actionPerformed(ActionEvent e)
2423   {
2424   }
2425
2426   protected void createGroup_actionPerformed(ActionEvent e)
2427   {
2428   }
2429
2430   protected void unGroup_actionPerformed(ActionEvent e)
2431   {
2432   }
2433
2434   protected void copy_actionPerformed(ActionEvent e)
2435   {
2436   }
2437
2438   protected void cut_actionPerformed(ActionEvent e)
2439   {
2440   }
2441
2442   protected void delete_actionPerformed(ActionEvent e)
2443   {
2444   }
2445
2446   protected void pasteNew_actionPerformed(ActionEvent e)
2447           throws IOException, InterruptedException
2448   {
2449   }
2450
2451   protected void pasteThis_actionPerformed(ActionEvent e)
2452           throws IOException, InterruptedException
2453   {
2454   }
2455
2456   protected void applyToAllGroups_actionPerformed(boolean selected)
2457   {
2458   }
2459
2460   protected void autoAlignSeqs_actionPerformed(boolean selected)
2461   {
2462   }
2463
2464   protected void hmmAlign_actionPerformed(ActionEvent e)
2465           throws IOException, InterruptedException
2466   {
2467   }
2468
2469   protected void changeHMMERLocation_actionPerformed(ActionEvent e)
2470   {
2471   }
2472
2473   protected void hmmBuild_actionPerformed(ActionEvent e)
2474           throws IOException, InterruptedException
2475   {
2476   }
2477
2478   protected void hmmSearch_actionPerformed(ActionEvent e)
2479   {
2480   }
2481
2482   public void createPNG(java.io.File f)
2483   {
2484   }
2485
2486   protected void font_actionPerformed(ActionEvent e)
2487   {
2488   }
2489
2490   protected void seqLimit_actionPerformed(ActionEvent e)
2491   {
2492   }
2493
2494   public void seqDBRef_actionPerformed(ActionEvent e)
2495   {
2496
2497   }
2498
2499   public void createEPS(java.io.File f)
2500   {
2501   }
2502
2503   public void createSVG(java.io.File f)
2504   {
2505
2506   }
2507
2508   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2509   {
2510
2511   }
2512
2513   /**
2514    * Template method to handle the 'load T-Coffee scores' menu event.
2515    * <p>
2516    * Subclasses override this method to provide a custom action.
2517    *
2518    * @param event
2519    *          The raised event
2520    */
2521   protected void loadScores_actionPerformed(ActionEvent event)
2522   {
2523
2524   }
2525
2526   protected void jpred_actionPerformed(ActionEvent e)
2527   {
2528   }
2529
2530   protected void scaleAbove_actionPerformed(ActionEvent e)
2531   {
2532   }
2533
2534   protected void scaleLeft_actionPerformed(ActionEvent e)
2535   {
2536   }
2537
2538   protected void scaleRight_actionPerformed(ActionEvent e)
2539   {
2540   }
2541
2542   protected void modifyPID_actionPerformed()
2543   {
2544   }
2545
2546   protected void modifyConservation_actionPerformed()
2547   {
2548   }
2549
2550   protected void saveAs_actionPerformed(ActionEvent e)
2551   {
2552   }
2553
2554   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2555   {
2556   }
2557
2558   public void vamsasStore_actionPerformed(ActionEvent e)
2559   {
2560
2561   }
2562
2563   public void vamsasLoad_actionPerformed(ActionEvent e)
2564   {
2565
2566   }
2567
2568   public void showTranslation_actionPerformed(ActionEvent e)
2569   {
2570
2571   }
2572
2573   public void featureSettings_actionPerformed(ActionEvent e)
2574   {
2575
2576   }
2577
2578   public void fetchSequence_actionPerformed(ActionEvent e)
2579   {
2580
2581   }
2582
2583   public void smoothFont_actionPerformed(ActionEvent e)
2584   {
2585
2586   }
2587
2588   public void annotationColour_actionPerformed()
2589   {
2590   }
2591
2592   public void annotationColumn_actionPerformed(ActionEvent e)
2593   {
2594   }
2595
2596   public void associatedData_actionPerformed(ActionEvent e)
2597           throws IOException, InterruptedException
2598   {
2599
2600   }
2601
2602   public void autoCalculate_actionPerformed(ActionEvent e)
2603   {
2604
2605   }
2606
2607   public void sortByTreeOption_actionPerformed(ActionEvent e)
2608   {
2609
2610   }
2611
2612   public void showAllSeqs_actionPerformed(ActionEvent e)
2613   {
2614
2615   }
2616
2617   public void showAllColumns_actionPerformed(ActionEvent e)
2618   {
2619
2620   }
2621
2622   public void hideSelSequences_actionPerformed(ActionEvent e)
2623   {
2624
2625   }
2626
2627   public void hideSelColumns_actionPerformed(ActionEvent e)
2628   {
2629
2630   }
2631
2632   public void hiddenMarkers_actionPerformed(ActionEvent e)
2633   {
2634
2635   }
2636
2637   public void findPdbId_actionPerformed(ActionEvent e)
2638   {
2639
2640   }
2641
2642   public void enterPdbId_actionPerformed(ActionEvent e)
2643   {
2644
2645   }
2646
2647   public void pdbFile_actionPerformed(ActionEvent e)
2648   {
2649
2650   }
2651
2652   public void invertColSel_actionPerformed(ActionEvent e)
2653   {
2654
2655   }
2656
2657   public void tabSelectionChanged(int sel)
2658   {
2659
2660   }
2661
2662   public void tabbedPane_mousePressed(MouseEvent e)
2663   {
2664
2665   }
2666
2667   public void tabbedPane_focusGained(FocusEvent e)
2668   {
2669     requestFocus();
2670   }
2671
2672   public void save_actionPerformed(ActionEvent e)
2673   {
2674
2675   }
2676
2677   public void reload_actionPerformed(ActionEvent e)
2678   {
2679
2680   }
2681
2682   public void newView_actionPerformed(ActionEvent e)
2683   {
2684
2685   }
2686
2687   public void textColour_actionPerformed()
2688   {
2689
2690   }
2691
2692   public void idRightAlign_actionPerformed(ActionEvent e)
2693   {
2694
2695   }
2696
2697   public void expandViews_actionPerformed(ActionEvent e)
2698   {
2699
2700   }
2701
2702   public void gatherViews_actionPerformed(ActionEvent e)
2703   {
2704
2705   }
2706
2707   public void buildTreeSortMenu()
2708   {
2709
2710   }
2711
2712   public void pageSetup_actionPerformed(ActionEvent e)
2713   {
2714
2715   }
2716
2717   public void alignmentProperties()
2718   {
2719
2720   }
2721
2722   protected void expand_newalign(ActionEvent e)
2723   {
2724     // TODO Auto-generated method stub
2725
2726   }
2727
2728   protected boolean isShowAutoCalculatedAbove()
2729   {
2730     return showAutoCalculatedAbove;
2731   }
2732
2733   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2734   {
2735     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2736   }
2737
2738   protected SequenceAnnotationOrder getAnnotationSortOrder()
2739   {
2740     return annotationSortOrder;
2741   }
2742
2743   protected void setAnnotationSortOrder(
2744           SequenceAnnotationOrder annotationSortOrder)
2745   {
2746     this.annotationSortOrder = annotationSortOrder;
2747   }
2748
2749   public Map<KeyStroke, JMenuItem> getAccelerators()
2750   {
2751     return this.accelerators;
2752   }
2753
2754   /**
2755    * Returns the selected index of the tabbed pane, or -1 if none selected
2756    * (including the case where the tabbed pane has not been made visible).
2757    *
2758    * @return
2759    */
2760   public int getTabIndex()
2761   {
2762     return tabbedPane.getSelectedIndex();
2763   }
2764
2765   public JPanel getStatusPanel()
2766   {
2767     return statusPanel;
2768   }
2769
2770   /**
2771    * Sets a reference to the containing split frame. Also makes the 'toggle
2772    * split view' menu item visible and checked.
2773    *
2774    * @param sf
2775    */
2776   public void setSplitFrame(SplitContainerI sf)
2777   {
2778     this.splitFrame = sf;
2779     if (sf != null)
2780     {
2781       this.showComplementMenuItem.setVisible(true);
2782       this.showComplementMenuItem.setState(true);
2783     }
2784   }
2785
2786   public SplitContainerI getSplitViewContainer()
2787   {
2788     return this.splitFrame;
2789   }
2790
2791   protected void showComplement_actionPerformed(boolean complement)
2792   {
2793   }
2794
2795   protected void showInformationHistogram_actionPerformed(ActionEvent e)
2796   {
2797     // TODO Auto-generated method stub
2798
2799   }
2800
2801   protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
2802   {
2803
2804   }
2805
2806   protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
2807   {
2808
2809   }
2810 }