src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.jbgui;
  22
  23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  24 import jalview.api.SplitContainerI;
  25 import jalview.bin.Cache;
  26 import jalview.gui.JvSwingUtils;
  27 import jalview.gui.Preferences;
  28 import jalview.io.FileFormats;
  29 import jalview.util.MessageManager;
  30 import jalview.util.Platform;
  31
  32 import java.awt.BorderLayout;
  33 import java.awt.Color;
  34 import java.awt.GridLayout;
  35 import java.awt.Toolkit;
  36 import java.awt.event.ActionEvent;
  37 import java.awt.event.ActionListener;
  38 import java.awt.event.FocusAdapter;
  39 import java.awt.event.FocusEvent;
  40 import java.awt.event.KeyEvent;
  41 import java.awt.event.MouseAdapter;
  42 import java.awt.event.MouseEvent;
  43 import java.util.HashMap;
  44 import java.util.Map;
  45
  46 import javax.swing.BorderFactory;
  47 import javax.swing.ButtonGroup;
  48 import javax.swing.JCheckBoxMenuItem;
  49 import javax.swing.JInternalFrame;
  50 import javax.swing.JLabel;
  51 import javax.swing.JMenu;
  52 import javax.swing.JMenuBar;
  53 import javax.swing.JMenuItem;
  54 import javax.swing.JPanel;
  55 import javax.swing.JRadioButtonMenuItem;
  56 import javax.swing.JTabbedPane;
  57 import javax.swing.KeyStroke;
  58 import javax.swing.event.ChangeEvent;
  59 import javax.swing.event.MenuEvent;
  60 import javax.swing.event.MenuListener;
  61
  62 public class GAlignFrame extends JInternalFrame
  63 {
  64   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  65
  66   protected JMenuItem closeMenuItem = new JMenuItem();
  67
  68   protected JMenu webService = new JMenu();
  69
  70   protected JMenuItem webServiceNoServices;
  71
  72   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  73
  74   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  75
  76   protected JMenu sortByAnnotScore = new JMenu();
  77
  78   public JLabel statusBar = new JLabel();
  79
  80   protected JMenu outputTextboxMenu = new JMenu();
  81
  82   protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
  83
  84   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
  85
  86   protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
  87
  88   protected JMenuItem undoMenuItem = new JMenuItem();
  89
  90   protected JMenuItem redoMenuItem = new JMenuItem();
  91
  92   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
  93
  94   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
  95
  96   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
  97
  98   JMenuItem copy = new JMenuItem();
  99
 100   JMenuItem cut = new JMenuItem();
 101
 102   JMenu pasteMenu = new JMenu();
 103
 104   protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 105
 106   protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 107
 108   protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 109
 110   protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 111
 112   protected JCheckBoxMenuItem applyToAllGroups;
 113
 114   protected JMenu colourMenu = new JMenu();
 115
 116   protected JMenuItem textColour;
 117
 118   protected JCheckBoxMenuItem conservationMenuItem;
 119
 120   protected JMenuItem modifyConservation;
 121
 122   protected JCheckBoxMenuItem abovePIDThreshold;
 123
 124   protected JMenuItem modifyPID;
 125
 126   protected JMenuItem annotationColour;
 127
 128   protected JMenu sortByTreeMenu = new JMenu();
 129
 130   protected JMenu sort = new JMenu();
 131
 132   protected JMenuItem calculateTree = new JMenuItem();
 133
 134   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 135
 136   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 137
 138   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 139
 140   protected JMenuItem showTranslation = new JMenuItem();
 141
 142   protected JMenuItem showReverse = new JMenuItem();
 143
 144   protected JMenuItem showReverseComplement = new JMenuItem();
 145
 146   protected JMenu showProducts = new JMenu();
 147
 148   protected JMenuItem runGroovy = new JMenuItem();
 149
 150   protected JMenuItem loadVcf;
 151
 152   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 153
 154   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 155
 156   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 157
 158   protected JPanel statusPanel = new JPanel();
 159
 160   protected JMenuItem showAllSeqAnnotations = new JMenuItem();
 161
 162   protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
 163
 164   protected JMenuItem showAllAlAnnotations = new JMenuItem();
 165
 166   protected JMenuItem hideAllAlAnnotations = new JMenuItem();
 167
 168   protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
 169
 170   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 171
 172   protected JTabbedPane tabbedPane = jalview.jbgui.swing.JTabbedPane.createTabbedPane();
 173
 174   protected JMenuItem reload = new JMenuItem();
 175
 176   protected JMenu formatMenu = new JMenu();
 177
 178   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 179
 180   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 181
 182   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 183
 184   protected JMenuItem gatherViews = new JMenuItem();
 185
 186   protected JMenuItem expandViews = new JMenuItem();
 187
 188   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 189
 190   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 191
 192   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 193
 194   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 195
 196   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 197
 198   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 199
 200   protected JMenuItem openFeatureSettings;
 201
 202   private SequenceAnnotationOrder annotationSortOrder;
 203
 204   private boolean showAutoCalculatedAbove = false;
 205
 206   private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
 207
 208   private SplitContainerI splitFrame;
 209
 210   public GAlignFrame()
 211   {
 212     try
 213     {
 214       jbInit();
 215       setJMenuBar(alignFrameMenuBar);
 216
 217       // dynamically fill save as menu with available formats
 218       for (String ff : FileFormats.getInstance().getWritableFormats(true))
 219       {
 220         JMenuItem item = new JMenuItem(ff);
 221
 222         item.addActionListener(new ActionListener()
 223         {
 224           @Override
 225           public void actionPerformed(ActionEvent e)
 226           {
 227             outputText_actionPerformed(e);
 228           }
 229         });
 230
 231         outputTextboxMenu.add(item);
 232       }
 233     } catch (Exception e)
 234     {
 235       System.err.println(e.toString());
 236     }
 237
 238     if (!Platform.isAMac())
 239     {
 240       closeMenuItem.setMnemonic('C');
 241       outputTextboxMenu.setMnemonic('T');
 242       undoMenuItem.setMnemonic('Z');
 243       redoMenuItem.setMnemonic('0');
 244       copy.setMnemonic('C');
 245       cut.setMnemonic('U');
 246       pasteMenu.setMnemonic('P');
 247       reload.setMnemonic('R');
 248     }
 249   }
 250
 251   private void jbInit() throws Exception
 252   {
 253     initColourMenu();
 254
 255     JMenuItem saveAs = new JMenuItem(
 256             MessageManager.getString("action.save_as"));
 257     ActionListener al = new ActionListener()
 258     {
 259       @Override
 260       public void actionPerformed(ActionEvent e)
 261       {
 262         saveAs_actionPerformed(e);
 263       }
 264     };
 265
 266     // FIXME getDefaultToolkit throws an exception in Headless mode
 267     KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
 268             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
 269                     | KeyEvent.SHIFT_MASK,
 270             false);
 271     addMenuActionAndAccelerator(keyStroke, saveAs, al);
 272
 273     closeMenuItem.setText(MessageManager.getString("action.close"));
 274     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
 275             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 276     al = new ActionListener()
 277     {
 278       @Override
 279       public void actionPerformed(ActionEvent e)
 280       {
 281         closeMenuItem_actionPerformed(false);
 282       }
 283     };
 284     addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
 285
 286     JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
 287     JMenu viewMenu = new JMenu(MessageManager.getString("action.view")) {
 288
 289       public void setPopupMenuVisible(boolean b) {
 290         if (b) {
 291           openFeatureSettings.setEnabled(haveAlignmentFeatures());
 292         }
 293         super.setPopupMenuVisible(b);
 294       }
 295
 296     };
 297     JMenu annotationsMenu = new JMenu(
 298             MessageManager.getString("action.annotations"));
 299     JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
 300     colourMenu.setText(MessageManager.getString("action.colour"));
 301     JMenu calculateMenu = new JMenu(
 302             MessageManager.getString("action.calculate"));
 303     webService.setText(MessageManager.getString("action.web_service"));
 304     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
 305             MessageManager.getString("action.select_all"));
 306     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
 307             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 308     al = new ActionListener()
 309     {
 310       @Override
 311       public void actionPerformed(ActionEvent e)
 312       {
 313         selectAllSequenceMenuItem_actionPerformed(e);
 314       }
 315     };
 316     addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
 317
 318     JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
 319             MessageManager.getString("action.deselect_all"));
 320     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
 321     al = new ActionListener()
 322     {
 323       @Override
 324       public void actionPerformed(ActionEvent e)
 325       {
 326         deselectAllSequenceMenuItem_actionPerformed(e);
 327       }
 328     };
 329     addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
 330
 331     JMenuItem invertSequenceMenuItem = new JMenuItem(
 332             MessageManager.getString("action.invert_sequence_selection"));
 333     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
 334             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 335     al = new ActionListener()
 336     {
 337       @Override
 338       public void actionPerformed(ActionEvent e)
 339       {
 340         invertSequenceMenuItem_actionPerformed(e);
 341       }
 342     };
 343     addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
 344
 345     JMenuItem grpsFromSelection = new JMenuItem(
 346             MessageManager.getString("action.make_groups_selection"));
 347     grpsFromSelection.addActionListener(new ActionListener()
 348     {
 349       @Override
 350       public void actionPerformed(ActionEvent e)
 351       {
 352         makeGrpsFromSelection_actionPerformed(e);
 353       }
 354     });
 355     JMenuItem expandAlignment = new JMenuItem(
 356             MessageManager.getString("action.view_flanking_regions"));
 357     expandAlignment.setToolTipText(
 358             MessageManager.getString("label.view_flanking_regions"));
 359     expandAlignment.addActionListener(new ActionListener()
 360     {
 361       @Override
 362       public void actionPerformed(ActionEvent e)
 363       {
 364         expand_newalign(e);
 365       }
 366     });
 367     JMenuItem remove2LeftMenuItem = new JMenuItem(
 368             MessageManager.getString("action.remove_left"));
 369     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
 370             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 371     al = new ActionListener()
 372     {
 373       @Override
 374       public void actionPerformed(ActionEvent e)
 375       {
 376         remove2LeftMenuItem_actionPerformed(e);
 377       }
 378     };
 379     addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
 380
 381     JMenuItem remove2RightMenuItem = new JMenuItem(
 382             MessageManager.getString("action.remove_right"));
 383     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
 384             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 385     al = new ActionListener()
 386     {
 387       @Override
 388       public void actionPerformed(ActionEvent e)
 389       {
 390         remove2RightMenuItem_actionPerformed(e);
 391       }
 392     };
 393     addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
 394
 395     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
 396             MessageManager.getString("action.remove_empty_columns"));
 397     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
 398             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 399     al = new ActionListener()
 400     {
 401       @Override
 402       public void actionPerformed(ActionEvent e)
 403       {
 404         removeGappedColumnMenuItem_actionPerformed(e);
 405       }
 406     };
 407     addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
 408
 409     JMenuItem removeAllGapsMenuItem = new JMenuItem(
 410             MessageManager.getString("action.remove_all_gaps"));
 411     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
 412             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
 413                     | KeyEvent.SHIFT_MASK,
 414             false);
 415     al = new ActionListener()
 416     {
 417       @Override
 418       public void actionPerformed(ActionEvent e)
 419       {
 420         removeAllGapsMenuItem_actionPerformed(e);
 421       }
 422     };
 423     addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
 424
 425     JMenuItem justifyLeftMenuItem = new JMenuItem(
 426             MessageManager.getString("action.left_justify_alignment"));
 427     justifyLeftMenuItem.addActionListener(new ActionListener()
 428     {
 429       @Override
 430       public void actionPerformed(ActionEvent e)
 431       {
 432         justifyLeftMenuItem_actionPerformed(e);
 433       }
 434     });
 435     JMenuItem justifyRightMenuItem = new JMenuItem(
 436             MessageManager.getString("action.right_justify_alignment"));
 437     justifyRightMenuItem.addActionListener(new ActionListener()
 438     {
 439       @Override
 440       public void actionPerformed(ActionEvent e)
 441       {
 442         justifyRightMenuItem_actionPerformed(e);
 443       }
 444     });
 445     viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
 446     viewBoxesMenuItem.setState(true);
 447     viewBoxesMenuItem.addActionListener(new ActionListener()
 448     {
 449       @Override
 450       public void actionPerformed(ActionEvent e)
 451       {
 452         viewBoxesMenuItem_actionPerformed(e);
 453       }
 454     });
 455     viewTextMenuItem.setText(MessageManager.getString("action.text"));
 456     viewTextMenuItem.setState(true);
 457     viewTextMenuItem.addActionListener(new ActionListener()
 458     {
 459       @Override
 460       public void actionPerformed(ActionEvent e)
 461       {
 462         viewTextMenuItem_actionPerformed(e);
 463       }
 464     });
 465     showNonconservedMenuItem
 466             .setText(MessageManager.getString("label.show_non_conserved"));
 467     showNonconservedMenuItem.setState(false);
 468     showNonconservedMenuItem.addActionListener(new ActionListener()
 469     {
 470       @Override
 471       public void actionPerformed(ActionEvent e)
 472       {
 473         showUnconservedMenuItem_actionPerformed(e);
 474       }
 475     });
 476     JMenuItem sortPairwiseMenuItem = new JMenuItem(
 477             MessageManager.getString("action.by_pairwise_id"));
 478     sortPairwiseMenuItem.addActionListener(new ActionListener()
 479     {
 480       @Override
 481       public void actionPerformed(ActionEvent e)
 482       {
 483         sortPairwiseMenuItem_actionPerformed(e);
 484       }
 485     });
 486     JMenuItem sortIDMenuItem = new JMenuItem(
 487             MessageManager.getString("action.by_id"));
 488     sortIDMenuItem.addActionListener(new ActionListener()
 489     {
 490       @Override
 491       public void actionPerformed(ActionEvent e)
 492       {
 493         sortIDMenuItem_actionPerformed(e);
 494       }
 495     });
 496     JMenuItem sortLengthMenuItem = new JMenuItem(
 497             MessageManager.getString("action.by_length"));
 498     sortLengthMenuItem.addActionListener(new ActionListener()
 499     {
 500       @Override
 501       public void actionPerformed(ActionEvent e)
 502       {
 503         sortLengthMenuItem_actionPerformed(e);
 504       }
 505     });
 506     JMenuItem sortGroupMenuItem = new JMenuItem(
 507             MessageManager.getString("action.by_group"));
 508     sortGroupMenuItem.addActionListener(new ActionListener()
 509     {
 510       @Override
 511       public void actionPerformed(ActionEvent e)
 512       {
 513         sortGroupMenuItem_actionPerformed(e);
 514       }
 515     });
 516
 517     JMenuItem removeRedundancyMenuItem = new JMenuItem(
 518             MessageManager.getString("action.remove_redundancy"));
 519     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
 520             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 521     al = new ActionListener()
 522     {
 523       @Override
 524       public void actionPerformed(ActionEvent e)
 525       {
 526         removeRedundancyMenuItem_actionPerformed(e);
 527       }
 528     };
 529     addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
 530
 531     JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
 532             MessageManager.getString("action.pairwise_alignment"));
 533     pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
 534     {
 535       @Override
 536       public void actionPerformed(ActionEvent e)
 537       {
 538         pairwiseAlignmentMenuItem_actionPerformed(e);
 539       }
 540     });
 541
 542     this.getContentPane().setLayout(new BorderLayout());
 543     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 544     statusBar.setBackground(Color.white);
 545     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 546     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 547     statusBar.setText(MessageManager.getString("label.status_bar"));
 548     outputTextboxMenu
 549             .setText(MessageManager.getString("label.out_to_textbox"));
 550
 551     annotationPanelMenuItem.setActionCommand("");
 552     annotationPanelMenuItem
 553             .setText(MessageManager.getString("label.show_annotations"));
 554     annotationPanelMenuItem
 555             .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
 556     annotationPanelMenuItem.addActionListener(new ActionListener()
 557     {
 558       @Override
 559       public void actionPerformed(ActionEvent e)
 560       {
 561         annotationPanelMenuItem_actionPerformed(e);
 562       }
 563     });
 564     showAllAlAnnotations.setText(
 565             MessageManager.getString("label.show_all_al_annotations"));
 566     final boolean isAnnotationPanelShown = annotationPanelMenuItem
 567             .getState();
 568     showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 569     showAllAlAnnotations.addActionListener(new ActionListener()
 570     {
 571       @Override
 572       public void actionPerformed(ActionEvent e)
 573       {
 574         showAllAnnotations_actionPerformed(false, true);
 575       }
 576     });
 577     hideAllAlAnnotations.setText(
 578             MessageManager.getString("label.hide_all_al_annotations"));
 579     hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 580     hideAllAlAnnotations.addActionListener(new ActionListener()
 581     {
 582       @Override
 583       public void actionPerformed(ActionEvent e)
 584       {
 585         hideAllAnnotations_actionPerformed(false, true);
 586       }
 587     });
 588     showAllSeqAnnotations.setText(
 589             MessageManager.getString("label.show_all_seq_annotations"));
 590     showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 591     showAllSeqAnnotations.addActionListener(new ActionListener()
 592     {
 593       @Override
 594       public void actionPerformed(ActionEvent e)
 595       {
 596         showAllAnnotations_actionPerformed(true, false);
 597       }
 598     });
 599     hideAllSeqAnnotations.setText(
 600             MessageManager.getString("label.hide_all_seq_annotations"));
 601     hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 602     hideAllSeqAnnotations.addActionListener(new ActionListener()
 603     {
 604       @Override
 605       public void actionPerformed(ActionEvent e)
 606       {
 607         hideAllAnnotations_actionPerformed(true, false);
 608       }
 609     });
 610     SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
 611             .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
 612                     SequenceAnnotationOrder.NONE.name()));
 613     final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
 614             MessageManager.getString("label.sort_annotations_by_sequence"));
 615     final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
 616             MessageManager.getString("label.sort_annotations_by_label"));
 617
 618     sortAnnBySequence.setSelected(
 619             sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
 620     sortAnnBySequence.addActionListener(new ActionListener()
 621     {
 622       @Override
 623       public void actionPerformed(ActionEvent e)
 624       {
 625         boolean newState = sortAnnBySequence.getState();
 626         sortAnnByLabel.setSelected(false);
 627         setAnnotationSortOrder(
 628                 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 629                         : SequenceAnnotationOrder.NONE);
 630         sortAnnotations_actionPerformed();
 631       }
 632     });
 633     sortAnnByLabel.setSelected(
 634             sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
 635     sortAnnByLabel.addActionListener(new ActionListener()
 636     {
 637       @Override
 638       public void actionPerformed(ActionEvent e)
 639       {
 640         boolean newState = sortAnnByLabel.getState();
 641         sortAnnBySequence.setSelected(false);
 642         setAnnotationSortOrder(
 643                 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 644                         : SequenceAnnotationOrder.NONE);
 645         sortAnnotations_actionPerformed();
 646       }
 647     });
 648     colourTextMenuItem = new JCheckBoxMenuItem(
 649             MessageManager.getString("label.colour_text"));
 650     colourTextMenuItem.addActionListener(new ActionListener()
 651     {
 652       @Override
 653       public void actionPerformed(ActionEvent e)
 654       {
 655         colourTextMenuItem_actionPerformed(e);
 656       }
 657     });
 658
 659     JMenuItem htmlMenuItem = new JMenuItem(
 660             MessageManager.getString("label.html"));
 661     htmlMenuItem.addActionListener(new ActionListener()
 662     {
 663       @Override
 664       public void actionPerformed(ActionEvent e)
 665       {
 666         htmlMenuItem_actionPerformed(e);
 667       }
 668     });
 669
 670     JMenuItem createBioJS = new JMenuItem(
 671             MessageManager.getString("label.biojs_html_export"));
 672     createBioJS.addActionListener(new java.awt.event.ActionListener()
 673     {
 674       @Override
 675       public void actionPerformed(ActionEvent e)
 676       {
 677         bioJSMenuItem_actionPerformed(e);
 678       }
 679     });
 680
 681     JMenuItem overviewMenuItem = new JMenuItem(
 682             MessageManager.getString("label.overview_window"));
 683     overviewMenuItem.addActionListener(new ActionListener()
 684     {
 685       @Override
 686       public void actionPerformed(ActionEvent e)
 687       {
 688         overviewMenuItem_actionPerformed(e);
 689       }
 690     });
 691
 692     undoMenuItem.setEnabled(false);
 693     undoMenuItem.setText(MessageManager.getString("action.undo"));
 694     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
 695             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 696     al = new ActionListener()
 697     {
 698       @Override
 699       public void actionPerformed(ActionEvent e)
 700       {
 701         undoMenuItem_actionPerformed(e);
 702       }
 703     };
 704     addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
 705
 706     redoMenuItem.setEnabled(false);
 707     redoMenuItem.setText(MessageManager.getString("action.redo"));
 708     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
 709             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 710     al = new ActionListener()
 711     {
 712       @Override
 713       public void actionPerformed(ActionEvent e)
 714       {
 715         redoMenuItem_actionPerformed(e);
 716       }
 717     };
 718     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
 719
 720     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
 721     wrapMenuItem.addActionListener(new ActionListener()
 722     {
 723       @Override
 724       public void actionPerformed(ActionEvent e)
 725       {
 726         wrapMenuItem_actionPerformed(e);
 727       }
 728     });
 729
 730     JMenuItem printMenuItem = new JMenuItem(
 731             MessageManager.getString("action.print"));
 732     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
 733             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 734     al = new ActionListener()
 735     {
 736       @Override
 737       public void actionPerformed(ActionEvent e)
 738       {
 739         printMenuItem_actionPerformed(e);
 740       }
 741     };
 742     addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
 743
 744     renderGapsMenuItem
 745             .setText(MessageManager.getString("action.show_gaps"));
 746     renderGapsMenuItem.setState(true);
 747     renderGapsMenuItem.addActionListener(new ActionListener()
 748     {
 749       @Override
 750       public void actionPerformed(ActionEvent e)
 751       {
 752         renderGapsMenuItem_actionPerformed(e);
 753       }
 754     });
 755
 756     JMenuItem findMenuItem = new JMenuItem(
 757             MessageManager.getString("action.find"));
 758     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
 759             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 760     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
 761             MessageManager.getString("label.find_tip")));
 762     al = new ActionListener()
 763     {
 764       @Override
 765       public void actionPerformed(ActionEvent e)
 766       {
 767         findMenuItem_actionPerformed(e);
 768       }
 769     };
 770     addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
 771
 772     showSeqFeatures.setText(
 773             MessageManager.getString("label.show_sequence_features"));
 774     showSeqFeatures.addActionListener(new ActionListener()
 775     {
 776       @Override
 777       public void actionPerformed(ActionEvent actionEvent)
 778       {
 779         showSeqFeatures_actionPerformed(actionEvent);
 780       }
 781     });
 782     /*
 783      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
 784      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
 785      * void actionPerformed(ActionEvent actionEvent) {
 786      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
 787      */
 788     showDbRefsMenuitem
 789             .setText(MessageManager.getString("label.show_database_refs"));
 790     showDbRefsMenuitem.addActionListener(new ActionListener()
 791     {
 792
 793       @Override
 794       public void actionPerformed(ActionEvent e)
 795       {
 796         showDbRefs_actionPerformed(e);
 797       }
 798
 799     });
 800     showNpFeatsMenuitem.setText(
 801             MessageManager.getString("label.show_non_positional_features"));
 802     showNpFeatsMenuitem.addActionListener(new ActionListener()
 803     {
 804
 805       @Override
 806       public void actionPerformed(ActionEvent e)
 807       {
 808         showNpFeats_actionPerformed(e);
 809       }
 810
 811     });
 812     showGroupConservation
 813             .setText(MessageManager.getString("label.group_conservation"));
 814     showGroupConservation.addActionListener(new ActionListener()
 815     {
 816
 817       @Override
 818       public void actionPerformed(ActionEvent e)
 819       {
 820         showGroupConservation_actionPerformed(e);
 821       }
 822
 823     });
 824
 825     showGroupConsensus
 826             .setText(MessageManager.getString("label.group_consensus"));
 827     showGroupConsensus.addActionListener(new ActionListener()
 828     {
 829
 830       @Override
 831       public void actionPerformed(ActionEvent e)
 832       {
 833         showGroupConsensus_actionPerformed(e);
 834       }
 835
 836     });
 837     showConsensusHistogram.setText(
 838             MessageManager.getString("label.show_consensus_histogram"));
 839     showConsensusHistogram.addActionListener(new ActionListener()
 840     {
 841
 842       @Override
 843       public void actionPerformed(ActionEvent e)
 844       {
 845         showConsensusHistogram_actionPerformed(e);
 846       }
 847
 848     });
 849     showSequenceLogo
 850             .setText(MessageManager.getString("label.show_consensus_logo"));
 851     showSequenceLogo.addActionListener(new ActionListener()
 852     {
 853
 854       @Override
 855       public void actionPerformed(ActionEvent e)
 856       {
 857         showSequenceLogo_actionPerformed(e);
 858       }
 859
 860     });
 861     normaliseSequenceLogo
 862             .setText(MessageManager.getString("label.norm_consensus_logo"));
 863     normaliseSequenceLogo.addActionListener(new ActionListener()
 864     {
 865
 866       @Override
 867       public void actionPerformed(ActionEvent e)
 868       {
 869         normaliseSequenceLogo_actionPerformed(e);
 870       }
 871
 872     });
 873     applyAutoAnnotationSettings
 874             .setText(MessageManager.getString("label.apply_all_groups"));
 875     applyAutoAnnotationSettings.setState(false);
 876     applyAutoAnnotationSettings.setVisible(true);
 877     applyAutoAnnotationSettings.addActionListener(new ActionListener()
 878     {
 879       @Override
 880       public void actionPerformed(ActionEvent e)
 881       {
 882         applyAutoAnnotationSettings_actionPerformed(e);
 883       }
 884     });
 885
 886     ButtonGroup buttonGroup = new ButtonGroup();
 887     final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
 888             MessageManager.getString("label.show_first"));
 889     final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
 890             MessageManager.getString("label.show_last"));
 891     buttonGroup.add(showAutoFirst);
 892     buttonGroup.add(showAutoLast);
 893     final boolean autoFirst = Cache
 894             .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
 895     showAutoFirst.setSelected(autoFirst);
 896     setShowAutoCalculatedAbove(autoFirst);
 897     showAutoFirst.addActionListener(new ActionListener()
 898     {
 899       @Override
 900       public void actionPerformed(ActionEvent e)
 901       {
 902         setShowAutoCalculatedAbove(showAutoFirst.isSelected());
 903         sortAnnotations_actionPerformed();
 904       }
 905     });
 906     showAutoLast.setSelected(!showAutoFirst.isSelected());
 907     showAutoLast.addActionListener(new ActionListener()
 908     {
 909       @Override
 910       public void actionPerformed(ActionEvent e)
 911       {
 912         setShowAutoCalculatedAbove(!showAutoLast.isSelected());
 913         sortAnnotations_actionPerformed();
 914       }
 915     });
 916
 917     JMenuItem deleteGroups = new JMenuItem(
 918             MessageManager.getString("action.undefine_groups"));
 919     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
 920             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 921     al = new ActionListener()
 922     {
 923       @Override
 924       public void actionPerformed(ActionEvent e)
 925       {
 926         deleteGroups_actionPerformed(e);
 927       }
 928     };
 929     addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
 930
 931     JMenuItem annotationColumn = new JMenuItem(
 932             MessageManager.getString("action.select_by_annotation"));
 933     annotationColumn.addActionListener(new ActionListener()
 934     {
 935       @Override
 936       public void actionPerformed(ActionEvent e)
 937       {
 938         annotationColumn_actionPerformed(e);
 939       }
 940     });
 941
 942     JMenuItem createGroup = new JMenuItem(
 943             MessageManager.getString("action.create_group"));
 944     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
 945             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 946     al = new ActionListener()
 947     {
 948       @Override
 949       public void actionPerformed(ActionEvent e)
 950       {
 951         createGroup_actionPerformed(e);
 952       }
 953     };
 954     addMenuActionAndAccelerator(keyStroke, createGroup, al);
 955
 956     JMenuItem unGroup = new JMenuItem(
 957             MessageManager.getString("action.remove_group"));
 958     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
 959             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
 960                     | KeyEvent.SHIFT_MASK,
 961             false);
 962     al = new ActionListener()
 963     {
 964       @Override
 965       public void actionPerformed(ActionEvent e)
 966       {
 967         unGroup_actionPerformed(e);
 968       }
 969     };
 970     addMenuActionAndAccelerator(keyStroke, unGroup, al);
 971
 972     copy.setText(MessageManager.getString("action.copy"));
 973     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
 974             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 975
 976     al = new ActionListener()
 977     {
 978       @Override
 979       public void actionPerformed(ActionEvent e)
 980       {
 981         copy_actionPerformed(e);
 982       }
 983     };
 984     addMenuActionAndAccelerator(keyStroke, copy, al);
 985
 986     cut.setText(MessageManager.getString("action.cut"));
 987     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
 988             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
 989     al = new ActionListener()
 990     {
 991       @Override
 992       public void actionPerformed(ActionEvent e)
 993       {
 994         cut_actionPerformed(e);
 995       }
 996     };
 997     addMenuActionAndAccelerator(keyStroke, cut, al);
 998
 999     JMenuItem delete = new JMenuItem(
1000             MessageManager.getString("action.delete"));
1001     delete.addActionListener(new ActionListener()
1002     {
1003       @Override
1004       public void actionPerformed(ActionEvent e)
1005       {
1006         delete_actionPerformed(e);
1007       }
1008     });
1009
1010     pasteMenu.setText(MessageManager.getString("action.paste"));
1011     JMenuItem pasteNew = new JMenuItem(
1012             MessageManager.getString("label.to_new_alignment"));
1013     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1014             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1015                     | KeyEvent.SHIFT_MASK,
1016             false);
1017     al = new ActionListener()
1018     {
1019       @Override
1020       public void actionPerformed(ActionEvent e)
1021       {
1022         pasteNew_actionPerformed(e);
1023       }
1024     };
1025     addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1026
1027     JMenuItem pasteThis = new JMenuItem(
1028             MessageManager.getString("label.to_this_alignment"));
1029     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1030             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1031     al = new ActionListener()
1032     {
1033       @Override
1034       public void actionPerformed(ActionEvent e)
1035       {
1036         pasteThis_actionPerformed(e);
1037       }
1038     };
1039     addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1040
1041     JMenuItem createPNG = new JMenuItem("PNG");
1042     createPNG.addActionListener(new ActionListener()
1043     {
1044       @Override
1045       public void actionPerformed(ActionEvent e)
1046       {
1047         createPNG(null);
1048       }
1049     });
1050     createPNG.setActionCommand(
1051             MessageManager.getString("label.save_png_image"));
1052
1053     JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1054     font.addActionListener(new ActionListener()
1055     {
1056       @Override
1057       public void actionPerformed(ActionEvent e)
1058       {
1059         font_actionPerformed(e);
1060       }
1061     });
1062     seqLimits.setText(
1063             MessageManager.getString("label.show_sequence_limits"));
1064     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1065     seqLimits.addActionListener(new ActionListener()
1066     {
1067       @Override
1068       public void actionPerformed(ActionEvent e)
1069       {
1070         seqLimit_actionPerformed(e);
1071       }
1072     });
1073     JMenuItem epsFile = new JMenuItem("EPS");
1074     epsFile.addActionListener(new ActionListener()
1075     {
1076       @Override
1077       public void actionPerformed(ActionEvent e)
1078       {
1079         createEPS(null);
1080       }
1081     });
1082
1083     JMenuItem createSVG = new JMenuItem("SVG");
1084     createSVG.addActionListener(new ActionListener()
1085     {
1086       @Override
1087       public void actionPerformed(ActionEvent e)
1088       {
1089         createSVG(null);
1090       }
1091     });
1092
1093     JMenuItem loadTreeMenuItem = new JMenuItem(
1094             MessageManager.getString("label.load_associated_tree"));
1095     loadTreeMenuItem.setActionCommand(
1096             MessageManager.getString("label.load_tree_for_sequence_set"));
1097     loadTreeMenuItem.addActionListener(new ActionListener()
1098     {
1099       @Override
1100       public void actionPerformed(ActionEvent e)
1101       {
1102         loadTreeMenuItem_actionPerformed(e);
1103       }
1104     });
1105
1106     scaleAbove.setVisible(false);
1107     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1108     scaleAbove.addActionListener(new ActionListener()
1109     {
1110       @Override
1111       public void actionPerformed(ActionEvent e)
1112       {
1113         scaleAbove_actionPerformed(e);
1114       }
1115     });
1116     scaleLeft.setVisible(false);
1117     scaleLeft.setSelected(true);
1118     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1119     scaleLeft.addActionListener(new ActionListener()
1120     {
1121       @Override
1122       public void actionPerformed(ActionEvent e)
1123       {
1124         scaleLeft_actionPerformed(e);
1125       }
1126     });
1127     scaleRight.setVisible(false);
1128     scaleRight.setSelected(true);
1129     scaleRight.setText(MessageManager.getString("action.scale_right"));
1130     scaleRight.addActionListener(new ActionListener()
1131     {
1132       @Override
1133       public void actionPerformed(ActionEvent e)
1134       {
1135         scaleRight_actionPerformed(e);
1136       }
1137     });
1138     centreColumnLabelsMenuItem.setVisible(true);
1139     centreColumnLabelsMenuItem.setState(false);
1140     centreColumnLabelsMenuItem.setText(
1141             MessageManager.getString("label.centre_column_labels"));
1142     centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1143     {
1144       @Override
1145       public void actionPerformed(ActionEvent e)
1146       {
1147         centreColumnLabels_actionPerformed(e);
1148       }
1149     });
1150     followHighlightMenuItem.setVisible(true);
1151     followHighlightMenuItem.setState(true);
1152     followHighlightMenuItem
1153             .setText(MessageManager.getString("label.automatic_scrolling"));
1154     followHighlightMenuItem.addActionListener(new ActionListener()
1155     {
1156
1157       @Override
1158       public void actionPerformed(ActionEvent e)
1159       {
1160         followHighlight_actionPerformed();
1161       }
1162
1163     });
1164
1165     sortByTreeMenu
1166             .setText(MessageManager.getString("action.by_tree_order"));
1167     sort.setText(MessageManager.getString("action.sort"));
1168     sort.addMenuListener(new MenuListener()
1169     {
1170       @Override
1171       public void menuSelected(MenuEvent e)
1172       {
1173         buildTreeSortMenu();
1174       }
1175
1176       @Override
1177       public void menuDeselected(MenuEvent e)
1178       {
1179       }
1180
1181       @Override
1182       public void menuCanceled(MenuEvent e)
1183       {
1184       }
1185     });
1186     sortByAnnotScore
1187             .setText(MessageManager.getString("label.sort_by_score"));
1188     sort.add(sortByAnnotScore);
1189     sort.addMenuListener(new javax.swing.event.MenuListener()
1190     {
1191
1192       @Override
1193       public void menuCanceled(MenuEvent e)
1194       {
1195       }
1196
1197       @Override
1198       public void menuDeselected(MenuEvent e)
1199       {
1200       }
1201
1202       @Override
1203       public void menuSelected(MenuEvent e)
1204       {
1205         buildSortByAnnotationScoresMenu();
1206       }
1207     });
1208     sortByAnnotScore.setVisible(false);
1209
1210     calculateTree
1211             .setText(MessageManager.getString("action.calculate_tree_pca"));
1212
1213     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1214     padGapsMenuitem
1215             .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
1216     padGapsMenuitem.addActionListener(new ActionListener()
1217     {
1218       @Override
1219       public void actionPerformed(ActionEvent e)
1220       {
1221         padGapsMenuitem_actionPerformed(e);
1222       }
1223     });
1224     JMenuItem vamsasStore = new JMenuItem(
1225             MessageManager.getString("label.vamsas_store"));
1226     vamsasStore.setVisible(false);
1227     vamsasStore.addActionListener(new ActionListener()
1228     {
1229       @Override
1230       public void actionPerformed(ActionEvent e)
1231       {
1232         vamsasStore_actionPerformed(e);
1233       }
1234     });
1235     showTranslation
1236             .setText(MessageManager.getString("label.translate_cDNA"));
1237     showTranslation.addActionListener(new ActionListener()
1238     {
1239       @Override
1240       public void actionPerformed(ActionEvent e)
1241       {
1242         showTranslation_actionPerformed(e);
1243       }
1244     });
1245     showReverse.setText(MessageManager.getString("label.reverse"));
1246     showReverse.addActionListener(new ActionListener()
1247     {
1248       @Override
1249       public void actionPerformed(ActionEvent e)
1250       {
1251         showReverse_actionPerformed(false);
1252       }
1253     });
1254     showReverseComplement
1255             .setText(MessageManager.getString("label.reverse_complement"));
1256     showReverseComplement.addActionListener(new ActionListener()
1257     {
1258       @Override
1259       public void actionPerformed(ActionEvent e)
1260       {
1261         showReverse_actionPerformed(true);
1262       }
1263     });
1264
1265     JMenuItem extractScores = new JMenuItem(
1266             MessageManager.getString("label.extract_scores"));
1267     extractScores.addActionListener(new ActionListener()
1268     {
1269       @Override
1270       public void actionPerformed(ActionEvent e)
1271       {
1272         extractScores_actionPerformed(e);
1273       }
1274     });
1275     extractScores.setVisible(true);
1276     // JBPNote: TODO: make gui for regex based score extraction
1277
1278     // for show products actions see AlignFrame.canShowProducts
1279     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1280
1281     runGroovy.setText(MessageManager.getString("label.run_groovy"));
1282     runGroovy.setToolTipText(
1283             MessageManager.getString("label.run_groovy_tip"));
1284     runGroovy.addActionListener(new ActionListener()
1285     {
1286       @Override
1287       public void actionPerformed(ActionEvent e)
1288       {
1289         runGroovy_actionPerformed();
1290       }
1291     });
1292
1293     openFeatureSettings = new JMenuItem(
1294             MessageManager.getString("action.feature_settings"));
1295     openFeatureSettings.setEnabled(false);
1296     openFeatureSettings.addActionListener(new ActionListener()
1297     {
1298       @Override
1299       public void actionPerformed(ActionEvent e)
1300       {
1301         featureSettings_actionPerformed(e);
1302       }
1303     });
1304     JMenuItem fetchSequence = new JMenuItem(
1305             MessageManager.getString("label.fetch_sequences"));
1306     fetchSequence.addActionListener(new ActionListener()
1307     {
1308       @Override
1309       public void actionPerformed(ActionEvent e)
1310       {
1311         fetchSequence_actionPerformed(e);
1312       }
1313     });
1314
1315     JMenuItem associatedData = new JMenuItem(
1316             MessageManager.getString("label.load_features_annotations"));
1317     associatedData.addActionListener(new ActionListener()
1318     {
1319       @Override
1320       public void actionPerformed(ActionEvent e)
1321       {
1322         associatedData_actionPerformed(e);
1323       }
1324     });
1325     loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
1326     loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
1327     loadVcf.addActionListener(new ActionListener()
1328     {
1329       @Override
1330       public void actionPerformed(ActionEvent e)
1331       {
1332         loadVcf_actionPerformed();
1333       }
1334     });
1335     autoCalculate.setText(
1336             MessageManager.getString("label.autocalculate_consensus"));
1337     autoCalculate.setState(
1338             jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1339     autoCalculate.addActionListener(new ActionListener()
1340     {
1341       @Override
1342       public void actionPerformed(ActionEvent e)
1343       {
1344         autoCalculate_actionPerformed(e);
1345       }
1346     });
1347     sortByTree.setText(
1348             MessageManager.getString("label.sort_alignment_new_tree"));
1349     sortByTree.setToolTipText("<html>" + MessageManager.getString(
1350             "label.enable_automatically_sort_alignment_when_open_new_tree"));
1351     sortByTree
1352             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1353     sortByTree.addActionListener(new ActionListener()
1354     {
1355       @Override
1356       public void actionPerformed(ActionEvent e)
1357       {
1358         sortByTreeOption_actionPerformed(e);
1359       }
1360     });
1361
1362     listenToViewSelections.setText(
1363             MessageManager.getString("label.listen_for_selections"));
1364     listenToViewSelections
1365             .setToolTipText("<html>" + MessageManager.getString(
1366                     "label.selections_mirror_selections_made_same_sequences_other_views"));
1367     listenToViewSelections.setState(false);
1368     listenToViewSelections.addActionListener(new ActionListener()
1369     {
1370       @Override
1371       public void actionPerformed(ActionEvent e)
1372       {
1373         listenToViewSelections_actionPerformed(e);
1374       }
1375     });
1376
1377     JMenu addSequenceMenu = new JMenu(
1378             MessageManager.getString("label.add_sequences"));
1379     JMenuItem addFromFile = new JMenuItem(
1380             MessageManager.getString("label.from_file"));
1381     addFromFile.addActionListener(new ActionListener()
1382     {
1383       @Override
1384       public void actionPerformed(ActionEvent e)
1385       {
1386         addFromFile_actionPerformed(e);
1387       }
1388     });
1389     JMenuItem addFromText = new JMenuItem(
1390             MessageManager.getString("label.from_textbox"));
1391     addFromText.addActionListener(new ActionListener()
1392     {
1393       @Override
1394       public void actionPerformed(ActionEvent e)
1395       {
1396         addFromText_actionPerformed(e);
1397       }
1398     });
1399     JMenuItem addFromURL = new JMenuItem(
1400             MessageManager.getString("label.from_url"));
1401     addFromURL.addActionListener(new ActionListener()
1402     {
1403       @Override
1404       public void actionPerformed(ActionEvent e)
1405       {
1406         addFromURL_actionPerformed(e);
1407       }
1408     });
1409     JMenuItem exportFeatures = new JMenuItem(
1410             MessageManager.getString("label.export_features"));
1411     exportFeatures.addActionListener(new ActionListener()
1412     {
1413       @Override
1414       public void actionPerformed(ActionEvent e)
1415       {
1416         exportFeatures_actionPerformed(e);
1417       }
1418     });
1419     JMenuItem exportAnnotations = new JMenuItem(
1420             MessageManager.getString("label.export_annotations"));
1421     exportAnnotations.addActionListener(new ActionListener()
1422     {
1423       @Override
1424       public void actionPerformed(ActionEvent e)
1425       {
1426         exportAnnotations_actionPerformed(e);
1427       }
1428     });
1429     statusPanel.setLayout(new GridLayout());
1430     JMenuItem showAllSeqs = new JMenuItem(
1431             MessageManager.getString("label.all_sequences"));
1432     showAllSeqs.setToolTipText(
1433             MessageManager.getString("label.toggle_sequence_visibility"));
1434     showAllSeqs.addActionListener(new ActionListener()
1435     {
1436       @Override
1437       public void actionPerformed(ActionEvent e)
1438       {
1439         showAllSeqs_actionPerformed(e);
1440       }
1441     });
1442     JMenuItem showAllColumns = new JMenuItem(
1443             MessageManager.getString("label.all_columns"));
1444     showAllColumns.setToolTipText(
1445             MessageManager.getString("label.toggle_columns_visibility"));
1446     showAllColumns.addActionListener(new ActionListener()
1447     {
1448       @Override
1449       public void actionPerformed(ActionEvent e)
1450       {
1451         showAllColumns_actionPerformed(e);
1452       }
1453     });
1454     JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1455     JMenuItem hideSelSequences = new JMenuItem(
1456             MessageManager.getString("label.selected_sequences"));
1457     hideSelSequences.setToolTipText(
1458             MessageManager.getString("label.toggle_sequence_visibility"));
1459     hideSelSequences.addActionListener(new ActionListener()
1460     {
1461       @Override
1462       public void actionPerformed(ActionEvent e)
1463       {
1464         hideSelSequences_actionPerformed(e);
1465       }
1466     });
1467     JMenuItem hideSelColumns = new JMenuItem(
1468             MessageManager.getString("label.selected_columns"));
1469     hideSelColumns.setToolTipText(
1470             MessageManager.getString("label.toggle_columns_visibility"));
1471     hideSelColumns.addActionListener(new ActionListener()
1472     {
1473       @Override
1474       public void actionPerformed(ActionEvent e)
1475       {
1476         hideSelColumns_actionPerformed(e);
1477       }
1478     });
1479     JMenuItem hideAllSelection = new JMenuItem(
1480             MessageManager.getString("label.selected_region"));
1481     hideAllSelection.addActionListener(new ActionListener()
1482     {
1483       @Override
1484       public void actionPerformed(ActionEvent e)
1485       {
1486         hideAllSelection_actionPerformed(e);
1487       }
1488     });
1489     // TODO: should be hidden if no selection exists.
1490     JMenuItem hideAllButSelection = new JMenuItem(
1491             MessageManager.getString("label.all_but_selected_region"));
1492     hideAllButSelection.addActionListener(new ActionListener()
1493     {
1494       @Override
1495       public void actionPerformed(ActionEvent e)
1496       {
1497         hideAllButSelection_actionPerformed(e);
1498       }
1499     });
1500     JMenuItem showAllhidden = new JMenuItem(
1501             MessageManager.getString("label.all_sequences_columns"));
1502     showAllhidden.setToolTipText(MessageManager
1503             .getString("label.toggles_visibility_hidden_selected_regions"));
1504     showAllhidden.addActionListener(new ActionListener()
1505     {
1506       @Override
1507       public void actionPerformed(ActionEvent e)
1508       {
1509         showAllhidden_actionPerformed(e);
1510       }
1511     });
1512     hiddenMarkers.setText(
1513             MessageManager.getString("action.show_hidden_markers"));
1514     hiddenMarkers.addActionListener(new ActionListener()
1515     {
1516       @Override
1517       public void actionPerformed(ActionEvent e)
1518       {
1519         hiddenMarkers_actionPerformed(e);
1520       }
1521     });
1522
1523     JMenuItem invertColSel = new JMenuItem(
1524             MessageManager.getString("action.invert_column_selection"));
1525     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1526             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1527                     | KeyEvent.ALT_MASK,
1528             false);
1529     al = new ActionListener()
1530     {
1531       @Override
1532       public void actionPerformed(ActionEvent e)
1533       {
1534         invertColSel_actionPerformed(e);
1535       }
1536     };
1537     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1538
1539     showComplementMenuItem.setVisible(false);
1540     showComplementMenuItem.addActionListener(new ActionListener()
1541     {
1542       @Override
1543       public void actionPerformed(ActionEvent e)
1544       {
1545         showComplement_actionPerformed(showComplementMenuItem.getState());
1546       }
1547     });
1548
1549     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1550     {
1551       @Override
1552       public void stateChanged(ChangeEvent evt)
1553       {
1554         JTabbedPane pane = (JTabbedPane) evt.getSource();
1555         int sel = pane.getSelectedIndex();
1556         tabSelectionChanged(sel);
1557       }
1558     });
1559     tabbedPane.addMouseListener(new MouseAdapter()
1560     {
1561       @Override
1562       public void mousePressed(MouseEvent e)
1563       {
1564         if (e.isPopupTrigger()) // Mac
1565         {
1566           tabbedPane_mousePressed(e);
1567         }
1568       }
1569
1570       @Override
1571       public void mouseReleased(MouseEvent e)
1572       {
1573         if (e.isPopupTrigger()) // Windows
1574         {
1575           tabbedPane_mousePressed(e);
1576         }
1577       }
1578     });
1579     tabbedPane.addFocusListener(new FocusAdapter()
1580     {
1581       @Override
1582       public void focusGained(FocusEvent e)
1583       {
1584         tabbedPane_focusGained(e);
1585       }
1586     });
1587
1588     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1589     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1590             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1591     al = new ActionListener()
1592     {
1593       @Override
1594       public void actionPerformed(ActionEvent e)
1595       {
1596         save_actionPerformed(e);
1597       }
1598     };
1599     addMenuActionAndAccelerator(keyStroke, save, al);
1600
1601     reload.setEnabled(false);
1602     reload.setText(MessageManager.getString("action.reload"));
1603     reload.addActionListener(new ActionListener()
1604     {
1605       @Override
1606       public void actionPerformed(ActionEvent e)
1607       {
1608         reload_actionPerformed(e);
1609       }
1610     });
1611
1612     JMenuItem newView = new JMenuItem(
1613             MessageManager.getString("action.new_view"));
1614     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1615             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1616     al = new ActionListener()
1617     {
1618       @Override
1619       public void actionPerformed(ActionEvent e)
1620       {
1621         newView_actionPerformed(e);
1622       }
1623     };
1624     addMenuActionAndAccelerator(keyStroke, newView, al);
1625
1626     tabbedPane.setToolTipText("<html><i>"
1627             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1628             + "</i></html>");
1629
1630     formatMenu.setText(MessageManager.getString("action.format"));
1631     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1632
1633     idRightAlign.setText(
1634             MessageManager.getString("label.right_align_sequence_id"));
1635     idRightAlign.addActionListener(new ActionListener()
1636     {
1637       @Override
1638       public void actionPerformed(ActionEvent e)
1639       {
1640         idRightAlign_actionPerformed(e);
1641       }
1642     });
1643
1644     gatherViews.setEnabled(false);
1645     gatherViews.setText(MessageManager.getString("action.gather_views"));
1646     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1647     al = new ActionListener()
1648     {
1649       @Override
1650       public void actionPerformed(ActionEvent e)
1651       {
1652         gatherViews_actionPerformed(e);
1653       }
1654     };
1655     addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1656
1657     expandViews.setEnabled(false);
1658     expandViews.setText(MessageManager.getString("action.expand_views"));
1659     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1660     al = new ActionListener()
1661     {
1662       @Override
1663       public void actionPerformed(ActionEvent e)
1664       {
1665         expandViews_actionPerformed(e);
1666       }
1667     };
1668     addMenuActionAndAccelerator(keyStroke, expandViews, al);
1669
1670     JMenuItem pageSetup = new JMenuItem(
1671             MessageManager.getString("action.page_setup"));
1672     pageSetup.addActionListener(new ActionListener()
1673     {
1674       @Override
1675       public void actionPerformed(ActionEvent e)
1676       {
1677         pageSetup_actionPerformed(e);
1678       }
1679     });
1680     JMenuItem alignmentProperties = new JMenuItem(
1681             MessageManager.getString("label.alignment_props"));
1682     alignmentProperties.addActionListener(new ActionListener()
1683     {
1684       @Override
1685       public void actionPerformed(ActionEvent actionEvent)
1686       {
1687         alignmentProperties();
1688       }
1689     });
1690     JMenuItem selectHighlighted = new JMenuItem(
1691             MessageManager.getString("action.select_highlighted_columns"));
1692     selectHighlighted.setToolTipText(
1693             MessageManager.getString("tooltip.select_highlighted_columns"));
1694     al = new ActionListener()
1695     {
1696       @Override
1697       public void actionPerformed(ActionEvent actionEvent)
1698       {
1699         selectHighlightedColumns_actionPerformed(actionEvent);
1700       }
1701     };
1702     selectHighlighted.addActionListener(al);
1703     JMenu tooltipSettingsMenu = new JMenu(
1704             MessageManager.getString("label.sequence_id_tooltip"));
1705     JMenu autoAnnMenu = new JMenu(
1706             MessageManager.getString("label.autocalculated_annotation"));
1707
1708     JMenu exportImageMenu = new JMenu(
1709             MessageManager.getString("label.export_image"));
1710     JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1711     alignFrameMenuBar.add(fileMenu);
1712     alignFrameMenuBar.add(editMenu);
1713     alignFrameMenuBar.add(selectMenu);
1714     alignFrameMenuBar.add(viewMenu);
1715     alignFrameMenuBar.add(annotationsMenu);
1716     alignFrameMenuBar.add(formatMenu);
1717     alignFrameMenuBar.add(colourMenu);
1718     alignFrameMenuBar.add(calculateMenu);
1719     alignFrameMenuBar.add(webService);
1720
1721     fileMenu.add(fetchSequence);
1722     fileMenu.add(addSequenceMenu);
1723     fileMenu.add(reload);
1724     fileMenu.addSeparator();
1725     fileMenu.add(vamsasStore);
1726     fileMenu.add(save);
1727     fileMenu.add(saveAs);
1728     fileMenu.add(outputTextboxMenu);
1729     fileMenu.add(pageSetup);
1730     fileMenu.add(printMenuItem);
1731     fileMenu.addSeparator();
1732     fileMenu.add(exportImageMenu);
1733     fileMenu.add(exportFeatures);
1734     fileMenu.add(exportAnnotations);
1735     fileMenu.add(loadTreeMenuItem);
1736     fileMenu.add(associatedData);
1737     /*
1738      * No VCF import in Jalview-JS
1739      * @j2sNative
1740      */
1741     {
1742       fileMenu.add(loadVcf);
1743     }
1744     fileMenu.addSeparator();
1745     fileMenu.add(closeMenuItem);
1746
1747     pasteMenu.add(pasteNew);
1748     pasteMenu.add(pasteThis);
1749     editMenu.add(undoMenuItem);
1750     editMenu.add(redoMenuItem);
1751     editMenu.add(cut);
1752     editMenu.add(copy);
1753     editMenu.add(pasteMenu);
1754     editMenu.add(delete);
1755     editMenu.addSeparator();
1756     editMenu.add(remove2LeftMenuItem);
1757     editMenu.add(remove2RightMenuItem);
1758     editMenu.add(removeGappedColumnMenuItem);
1759     editMenu.add(removeAllGapsMenuItem);
1760     editMenu.add(removeRedundancyMenuItem);
1761     editMenu.addSeparator();
1762     // dont add these yet in the CVS build - they cannot be undone!
1763     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1764     // editMenu.add(justifyLeftMenuItem);
1765     // editMenu.add(justifyRightMenuItem);
1766     // editMenu.addSeparator();
1767     editMenu.add(padGapsMenuitem);
1768
1769     showMenu.add(showAllColumns);
1770     showMenu.add(showAllSeqs);
1771     showMenu.add(showAllhidden);
1772     hideMenu.add(hideSelColumns);
1773     hideMenu.add(hideSelSequences);
1774     hideMenu.add(hideAllSelection);
1775     hideMenu.add(hideAllButSelection);
1776     viewMenu.add(newView);
1777     viewMenu.add(expandViews);
1778     viewMenu.add(gatherViews);
1779     viewMenu.addSeparator();
1780     viewMenu.add(showMenu);
1781     viewMenu.add(hideMenu);
1782     viewMenu.add(showComplementMenuItem);
1783     viewMenu.addSeparator();
1784     viewMenu.add(followHighlightMenuItem);
1785     viewMenu.addSeparator();
1786     viewMenu.add(showSeqFeatures);
1787     // viewMenu.add(showSeqFeaturesHeight);
1788     viewMenu.add(openFeatureSettings);
1789     tooltipSettingsMenu.add(showDbRefsMenuitem);
1790     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1791     viewMenu.add(tooltipSettingsMenu);
1792     viewMenu.addSeparator();
1793     viewMenu.add(alignmentProperties);
1794     viewMenu.addSeparator();
1795     viewMenu.add(overviewMenuItem);
1796
1797     annotationsMenu.add(annotationPanelMenuItem);
1798     annotationsMenu.addSeparator();
1799     annotationsMenu.add(showAllAlAnnotations);
1800     annotationsMenu.add(hideAllAlAnnotations);
1801     annotationsMenu.addSeparator();
1802     annotationsMenu.add(showAllSeqAnnotations);
1803     annotationsMenu.add(hideAllSeqAnnotations);
1804     annotationsMenu.add(sortAnnBySequence);
1805     annotationsMenu.add(sortAnnByLabel);
1806     annotationsMenu.addSeparator();
1807     autoAnnMenu.add(showAutoFirst);
1808     autoAnnMenu.add(showAutoLast);
1809     autoAnnMenu.addSeparator();
1810     autoAnnMenu.add(applyAutoAnnotationSettings);
1811     autoAnnMenu.add(showConsensusHistogram);
1812     autoAnnMenu.add(showSequenceLogo);
1813     autoAnnMenu.add(normaliseSequenceLogo);
1814     autoAnnMenu.addSeparator();
1815     autoAnnMenu.add(showGroupConservation);
1816     autoAnnMenu.add(showGroupConsensus);
1817     annotationsMenu.add(autoAnnMenu);
1818
1819     sort.add(sortIDMenuItem);
1820     sort.add(sortLengthMenuItem);
1821     sort.add(sortGroupMenuItem);
1822     sort.add(sortPairwiseMenuItem);
1823     sort.add(sortByTreeMenu);
1824     calculateMenu.add(sort);
1825     calculateMenu.add(calculateTree);
1826     calculateMenu.addSeparator();
1827     calculateMenu.add(pairwiseAlignmentMenuItem);
1828     calculateMenu.addSeparator();
1829     calculateMenu.add(showTranslation);
1830     calculateMenu.add(showReverse);
1831     calculateMenu.add(showReverseComplement);
1832     calculateMenu.add(showProducts);
1833     calculateMenu.add(autoCalculate);
1834     calculateMenu.add(sortByTree);
1835     calculateMenu.addSeparator();
1836     calculateMenu.add(expandAlignment);
1837     calculateMenu.add(extractScores);
1838     calculateMenu.addSeparator();
1839     calculateMenu.add(runGroovy);
1840
1841     webServiceNoServices = new JMenuItem(
1842             MessageManager.getString("label.no_services"));
1843     webService.add(webServiceNoServices);
1844     exportImageMenu.add(htmlMenuItem);
1845     exportImageMenu.add(epsFile);
1846     exportImageMenu.add(createPNG);
1847     exportImageMenu.add(createBioJS);
1848     exportImageMenu.add(createSVG);
1849     addSequenceMenu.add(addFromFile);
1850     addSequenceMenu.add(addFromText);
1851     addSequenceMenu.add(addFromURL);
1852     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1853     statusPanel.add(statusBar, null);
1854     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1855
1856     formatMenu.add(font);
1857     formatMenu.addSeparator();
1858     formatMenu.add(wrapMenuItem);
1859     formatMenu.add(scaleAbove);
1860     formatMenu.add(scaleLeft);
1861     formatMenu.add(scaleRight);
1862     formatMenu.add(seqLimits);
1863     formatMenu.add(idRightAlign);
1864     formatMenu.add(hiddenMarkers);
1865     formatMenu.add(viewBoxesMenuItem);
1866     formatMenu.add(viewTextMenuItem);
1867     formatMenu.add(colourTextMenuItem);
1868     formatMenu.add(renderGapsMenuItem);
1869     formatMenu.add(centreColumnLabelsMenuItem);
1870     formatMenu.add(showNonconservedMenuItem);
1871     selectMenu.add(findMenuItem);
1872     selectMenu.addSeparator();
1873     selectMenu.add(selectAllSequenceMenuItem);
1874     selectMenu.add(deselectAllSequenceMenuItem);
1875     selectMenu.add(invertSequenceMenuItem);
1876     selectMenu.add(invertColSel);
1877     selectMenu.add(createGroup);
1878     selectMenu.add(unGroup);
1879     selectMenu.add(grpsFromSelection);
1880     selectMenu.add(deleteGroups);
1881     selectMenu.add(annotationColumn);
1882     selectMenu.add(selectHighlighted);
1883     // TODO - determine if the listenToViewSelections button is needed : see bug
1884     // JAL-574
1885     // selectMenu.addSeparator();
1886     // selectMenu.add(listenToViewSelections);
1887   }
1888
1889   protected boolean haveAlignmentFeatures()
1890   {
1891     // because gAlignFrame is not an abstract class  -- see AlignFrame
1892     return false;
1893   }
1894
1895   protected void loadVcf_actionPerformed()
1896   {
1897   }
1898
1899   /**
1900    * Constructs the entries on the Colour menu (but does not add them to the
1901    * menu).
1902    */
1903   protected void initColourMenu()
1904   {
1905     applyToAllGroups = new JCheckBoxMenuItem(
1906             MessageManager.getString("label.apply_colour_to_all_groups"));
1907     applyToAllGroups.addActionListener(new ActionListener()
1908     {
1909       @Override
1910       public void actionPerformed(ActionEvent e)
1911       {
1912         applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1913       }
1914     });
1915
1916     textColour = new JMenuItem(
1917             MessageManager.getString("label.text_colour"));
1918     textColour.addActionListener(new ActionListener()
1919     {
1920       @Override
1921       public void actionPerformed(ActionEvent e)
1922       {
1923         textColour_actionPerformed();
1924       }
1925     });
1926
1927     conservationMenuItem = new JCheckBoxMenuItem(
1928             MessageManager.getString("action.by_conservation"));
1929     conservationMenuItem.addActionListener(new ActionListener()
1930     {
1931       @Override
1932       public void actionPerformed(ActionEvent e)
1933       {
1934         conservationMenuItem_actionPerformed(
1935                 conservationMenuItem.isSelected());
1936       }
1937     });
1938
1939     abovePIDThreshold = new JCheckBoxMenuItem(
1940             MessageManager.getString("label.above_identity_threshold"));
1941     abovePIDThreshold.addActionListener(new ActionListener()
1942     {
1943       @Override
1944       public void actionPerformed(ActionEvent e)
1945       {
1946         abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
1947       }
1948     });
1949     modifyPID = new JMenuItem(
1950             MessageManager.getString("label.modify_identity_threshold"));
1951     modifyPID.addActionListener(new ActionListener()
1952     {
1953       @Override
1954       public void actionPerformed(ActionEvent e)
1955       {
1956         modifyPID_actionPerformed();
1957       }
1958     });
1959     modifyConservation = new JMenuItem(MessageManager
1960             .getString("label.modify_conservation_threshold"));
1961     modifyConservation.addActionListener(new ActionListener()
1962     {
1963       @Override
1964       public void actionPerformed(ActionEvent e)
1965       {
1966         modifyConservation_actionPerformed();
1967       }
1968     });
1969
1970     annotationColour = new JMenuItem(
1971             MessageManager.getString("action.by_annotation"));
1972     annotationColour.addActionListener(new ActionListener()
1973     {
1974       @Override
1975       public void actionPerformed(ActionEvent e)
1976       {
1977         annotationColour_actionPerformed();
1978       }
1979     });
1980   }
1981
1982   protected void selectHighlightedColumns_actionPerformed(
1983           ActionEvent actionEvent)
1984   {
1985     // TODO Auto-generated method stub
1986
1987   }
1988
1989   /**
1990    * Generate the reverse sequence (or reverse complement if the flag is true)
1991    * and add it to the alignment
1992    *
1993    * @param complement
1994    */
1995   protected void showReverse_actionPerformed(boolean complement)
1996   {
1997   }
1998
1999   /**
2000    * Try to run script in a Groovy console, having first ensured that this
2001    * alignframe is set as currentAlignFrame in Desktop
2002    */
2003   protected void runGroovy_actionPerformed()
2004   {
2005
2006   }
2007
2008   /**
2009    * Adds the given action listener and key accelerator to the given menu item.
2010    * Also saves in a lookup table to support lookup of action by key stroke.
2011    *
2012    * @param keyStroke
2013    * @param menuItem
2014    * @param actionListener
2015    */
2016   protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2017           JMenuItem menuItem, ActionListener actionListener)
2018   {
2019     menuItem.setAccelerator(keyStroke);
2020     accelerators.put(keyStroke, menuItem);
2021     menuItem.addActionListener(actionListener);
2022   }
2023
2024   /**
2025    * Action on clicking sort annotations by type.
2026    *
2027    * @param sortOrder
2028    */
2029   protected void sortAnnotations_actionPerformed()
2030   {
2031   }
2032
2033   /**
2034    * Action on clicking Show all annotations.
2035    *
2036    * @param forSequences
2037    *          update sequence-related annotations
2038    * @param forAlignment
2039    *          update non-sequence-related annotations
2040    */
2041   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2042           boolean forAlignment)
2043   {
2044     setAnnotationsVisibility(true, forSequences, forAlignment);
2045   }
2046
2047   /**
2048    * Action on clicking Hide all annotations.
2049    *
2050    * @param forSequences
2051    *          update sequence-related annotations
2052    * @param forAlignment
2053    *          update non-sequence-related annotations
2054    */
2055   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2056           boolean forAlignment)
2057   {
2058     setAnnotationsVisibility(false, forSequences, forAlignment);
2059   }
2060
2061   /**
2062    * Set the visibility of annotations to true or false. Can act on
2063    * sequence-related annotations, or alignment-related, or both.
2064    *
2065    * @param visible
2066    * @param forSequences
2067    *          update sequence-related annotations
2068    * @param forAlignment
2069    *          update non-sequence-related annotations
2070    */
2071   protected void setAnnotationsVisibility(boolean visible,
2072           boolean forSequences, boolean forAlignment)
2073   {
2074
2075   }
2076
2077   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2078   {
2079     // TODO Auto-generated method stub
2080
2081   }
2082
2083   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2084   {
2085     // TODO Auto-generated method stub
2086
2087   }
2088
2089   protected void showAllhidden_actionPerformed(ActionEvent e)
2090   {
2091     // TODO Auto-generated method stub
2092
2093   }
2094
2095   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2096   {
2097     // TODO Auto-generated method stub
2098
2099   }
2100
2101   protected void hideAllSelection_actionPerformed(ActionEvent e)
2102   {
2103     // TODO Auto-generated method stub
2104
2105   }
2106
2107   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2108   {
2109     // TODO Auto-generated method stub
2110
2111   }
2112
2113   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2114   {
2115     // TODO Auto-generated method stub
2116
2117   }
2118
2119   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2120   {
2121     // TODO Auto-generated method stub
2122
2123   }
2124
2125   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2126   {
2127     // TODO Auto-generated method stub
2128
2129   }
2130
2131   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2132   {
2133     // TODO Auto-generated method stub
2134
2135   }
2136
2137   protected void showGroupConservation_actionPerformed(ActionEvent e)
2138   {
2139     // TODO Auto-generated method stub
2140
2141   }
2142
2143   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2144   {
2145     // TODO Auto-generated method stub
2146
2147   }
2148
2149   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2150   {
2151     // TODO Auto-generated method stub
2152
2153   }
2154
2155   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2156   {
2157     // TODO Auto-generated method stub
2158
2159   }
2160
2161   protected void followHighlight_actionPerformed()
2162   {
2163     // TODO Auto-generated method stub
2164
2165   }
2166
2167   protected void showNpFeats_actionPerformed(ActionEvent e)
2168   {
2169     // TODO Auto-generated method stub
2170
2171   }
2172
2173   protected void showDbRefs_actionPerformed(ActionEvent e)
2174   {
2175     // TODO Auto-generated method stub
2176
2177   }
2178
2179   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2180   {
2181   }
2182
2183   protected void buildSortByAnnotationScoresMenu()
2184   {
2185   }
2186
2187   protected void extractScores_actionPerformed(ActionEvent e)
2188   {
2189   }
2190
2191   protected void outputText_actionPerformed(ActionEvent e)
2192   {
2193   }
2194
2195   public void addFromFile_actionPerformed(ActionEvent e)
2196   {
2197
2198   }
2199
2200   public void addFromText_actionPerformed(ActionEvent e)
2201   {
2202
2203   }
2204
2205   public void addFromURL_actionPerformed(ActionEvent e)
2206   {
2207
2208   }
2209
2210   public void exportFeatures_actionPerformed(ActionEvent e)
2211   {
2212
2213   }
2214
2215   public void exportAnnotations_actionPerformed(ActionEvent e)
2216   {
2217
2218   }
2219
2220   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2221   {
2222   }
2223
2224   protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2225   {
2226
2227   }
2228
2229   protected void closeMenuItem_actionPerformed(boolean b)
2230   {
2231   }
2232
2233   protected void redoMenuItem_actionPerformed(ActionEvent e)
2234   {
2235   }
2236
2237   protected void undoMenuItem_actionPerformed(ActionEvent e)
2238   {
2239   }
2240
2241   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2242   {
2243   }
2244
2245   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2246   {
2247   }
2248
2249   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2250   {
2251   }
2252
2253   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2254   {
2255   }
2256
2257   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2258   {
2259   }
2260
2261   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2262   {
2263   }
2264
2265   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2266   {
2267   }
2268
2269   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2270   {
2271   }
2272
2273   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2274   {
2275   }
2276
2277   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2278   {
2279   }
2280
2281   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2282   {
2283   }
2284
2285   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2286   {
2287   }
2288
2289   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2290   {
2291   }
2292
2293   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2294   {
2295   }
2296
2297   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2298   {
2299   }
2300
2301   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2302   {
2303   }
2304
2305   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2306   {
2307   }
2308
2309   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2310   {
2311   }
2312
2313   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2314   {
2315   }
2316
2317   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2318   {
2319   }
2320
2321   protected void conservationMenuItem_actionPerformed(boolean selected)
2322   {
2323   }
2324
2325   protected void printMenuItem_actionPerformed(ActionEvent e)
2326   {
2327   }
2328
2329   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2330   {
2331   }
2332
2333   protected void findMenuItem_actionPerformed(ActionEvent e)
2334   {
2335   }
2336
2337   protected void abovePIDThreshold_actionPerformed(boolean selected)
2338   {
2339   }
2340
2341   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2342   {
2343   }
2344
2345   protected void deleteGroups_actionPerformed(ActionEvent e)
2346   {
2347   }
2348
2349   protected void createGroup_actionPerformed(ActionEvent e)
2350   {
2351   }
2352
2353   protected void unGroup_actionPerformed(ActionEvent e)
2354   {
2355   }
2356
2357   protected void copy_actionPerformed(ActionEvent e)
2358   {
2359   }
2360
2361   protected void cut_actionPerformed(ActionEvent e)
2362   {
2363   }
2364
2365   protected void delete_actionPerformed(ActionEvent e)
2366   {
2367   }
2368
2369   protected void pasteNew_actionPerformed(ActionEvent e)
2370   {
2371   }
2372
2373   protected void pasteThis_actionPerformed(ActionEvent e)
2374   {
2375   }
2376
2377   protected void applyToAllGroups_actionPerformed(boolean selected)
2378   {
2379   }
2380
2381   public void createPNG(java.io.File f)
2382   {
2383   }
2384
2385   protected void font_actionPerformed(ActionEvent e)
2386   {
2387   }
2388
2389   protected void seqLimit_actionPerformed(ActionEvent e)
2390   {
2391   }
2392
2393   public void seqDBRef_actionPerformed(ActionEvent e)
2394   {
2395
2396   }
2397
2398   public void createEPS(java.io.File f)
2399   {
2400   }
2401
2402   public void createSVG(java.io.File f)
2403   {
2404
2405   }
2406
2407   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2408   {
2409
2410   }
2411
2412   /**
2413    * Template method to handle the 'load T-Coffee scores' menu event.
2414    * <p>
2415    * Subclasses override this method to provide a custom action.
2416    *
2417    * @param event
2418    *          The raised event
2419    */
2420   protected void loadScores_actionPerformed(ActionEvent event)
2421   {
2422
2423   }
2424
2425   protected void jpred_actionPerformed(ActionEvent e)
2426   {
2427   }
2428
2429   protected void scaleAbove_actionPerformed(ActionEvent e)
2430   {
2431   }
2432
2433   protected void scaleLeft_actionPerformed(ActionEvent e)
2434   {
2435   }
2436
2437   protected void scaleRight_actionPerformed(ActionEvent e)
2438   {
2439   }
2440
2441   protected void modifyPID_actionPerformed()
2442   {
2443   }
2444
2445   protected void modifyConservation_actionPerformed()
2446   {
2447   }
2448
2449   protected void saveAs_actionPerformed(ActionEvent e)
2450   {
2451   }
2452
2453   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2454   {
2455   }
2456
2457   public void vamsasStore_actionPerformed(ActionEvent e)
2458   {
2459
2460   }
2461
2462   public void vamsasLoad_actionPerformed(ActionEvent e)
2463   {
2464
2465   }
2466
2467   public void showTranslation_actionPerformed(ActionEvent e)
2468   {
2469
2470   }
2471
2472   public void featureSettings_actionPerformed(ActionEvent e)
2473   {
2474
2475   }
2476
2477   public void fetchSequence_actionPerformed(ActionEvent e)
2478   {
2479
2480   }
2481
2482   public void smoothFont_actionPerformed(ActionEvent e)
2483   {
2484
2485   }
2486
2487   public void annotationColour_actionPerformed()
2488   {
2489   }
2490
2491   public void annotationColumn_actionPerformed(ActionEvent e)
2492   {
2493   }
2494
2495   public void associatedData_actionPerformed(ActionEvent e)
2496   {
2497
2498   }
2499
2500   public void autoCalculate_actionPerformed(ActionEvent e)
2501   {
2502
2503   }
2504
2505   public void sortByTreeOption_actionPerformed(ActionEvent e)
2506   {
2507
2508   }
2509
2510   public void showAllSeqs_actionPerformed(ActionEvent e)
2511   {
2512
2513   }
2514
2515   public void showAllColumns_actionPerformed(ActionEvent e)
2516   {
2517
2518   }
2519
2520   public void hideSelSequences_actionPerformed(ActionEvent e)
2521   {
2522
2523   }
2524
2525   public void hideSelColumns_actionPerformed(ActionEvent e)
2526   {
2527
2528   }
2529
2530   public void hiddenMarkers_actionPerformed(ActionEvent e)
2531   {
2532
2533   }
2534
2535   public void findPdbId_actionPerformed(ActionEvent e)
2536   {
2537
2538   }
2539
2540   public void enterPdbId_actionPerformed(ActionEvent e)
2541   {
2542
2543   }
2544
2545   public void pdbFile_actionPerformed(ActionEvent e)
2546   {
2547
2548   }
2549
2550   public void invertColSel_actionPerformed(ActionEvent e)
2551   {
2552
2553   }
2554
2555   public void tabSelectionChanged(int sel)
2556   {
2557
2558   }
2559
2560   public void tabbedPane_mousePressed(MouseEvent e)
2561   {
2562
2563   }
2564
2565   public void tabbedPane_focusGained(FocusEvent e)
2566   {
2567     requestFocus();
2568   }
2569
2570   public void save_actionPerformed(ActionEvent e)
2571   {
2572
2573   }
2574
2575   public void reload_actionPerformed(ActionEvent e)
2576   {
2577
2578   }
2579
2580   public void newView_actionPerformed(ActionEvent e)
2581   {
2582
2583   }
2584
2585   public void textColour_actionPerformed()
2586   {
2587
2588   }
2589
2590   public void idRightAlign_actionPerformed(ActionEvent e)
2591   {
2592
2593   }
2594
2595   public void expandViews_actionPerformed(ActionEvent e)
2596   {
2597
2598   }
2599
2600   public void gatherViews_actionPerformed(ActionEvent e)
2601   {
2602
2603   }
2604
2605   public void buildTreeSortMenu()
2606   {
2607
2608   }
2609
2610   public void pageSetup_actionPerformed(ActionEvent e)
2611   {
2612
2613   }
2614
2615   public void alignmentProperties()
2616   {
2617
2618   }
2619
2620   protected void expand_newalign(ActionEvent e)
2621   {
2622     // TODO Auto-generated method stub
2623
2624   }
2625
2626   protected boolean isShowAutoCalculatedAbove()
2627   {
2628     return showAutoCalculatedAbove;
2629   }
2630
2631   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2632   {
2633     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2634   }
2635
2636   protected SequenceAnnotationOrder getAnnotationSortOrder()
2637   {
2638     return annotationSortOrder;
2639   }
2640
2641   protected void setAnnotationSortOrder(
2642           SequenceAnnotationOrder annotationSortOrder)
2643   {
2644     this.annotationSortOrder = annotationSortOrder;
2645   }
2646
2647   public Map<KeyStroke, JMenuItem> getAccelerators()
2648   {
2649     return this.accelerators;
2650   }
2651
2652   /**
2653    * Returns the selected index of the tabbed pane, or -1 if none selected
2654    * (including the case where the tabbed pane has not been made visible).
2655    *
2656    * @return
2657    */
2658   public int getTabIndex()
2659   {
2660     return tabbedPane.getSelectedIndex();
2661   }
2662
2663   public JPanel getStatusPanel()
2664   {
2665     return statusPanel;
2666   }
2667
2668   /**
2669    * Sets a reference to the containing split frame. Also makes the 'toggle
2670    * split view' menu item visible and checked.
2671    *
2672    * @param sf
2673    */
2674   public void setSplitFrame(SplitContainerI sf)
2675   {
2676     this.splitFrame = sf;
2677     if (sf != null)
2678     {
2679       this.showComplementMenuItem.setVisible(true);
2680       this.showComplementMenuItem.setState(true);
2681     }
2682   }
2683
2684   public SplitContainerI getSplitViewContainer()
2685   {
2686     return this.splitFrame;
2687   }
2688
2689   protected void showComplement_actionPerformed(boolean complement)
2690   {
2691   }
2692 }