src/jalview/jbgui/GAlignFrame.java

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