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 JRadioButtonMenuItem 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 JMenu calculateTree = new JMenu();
 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     JMenuItem averageDistanceTreeMenuItem = new JMenuItem(
 537             MessageManager.getString("label.average_distance_identity"));
 538     averageDistanceTreeMenuItem.addActionListener(new ActionListener()
 539     {
 540       @Override
 541       public void actionPerformed(ActionEvent e)
 542       {
 543         averageDistanceTreeMenuItem_actionPerformed(e);
 544       }
 545     });
 546     JMenuItem neighbourTreeMenuItem = new JMenuItem(
 547             MessageManager.getString("label.neighbour_joining_identity"));
 548     neighbourTreeMenuItem.addActionListener(new ActionListener()
 549     {
 550       @Override
 551       public void actionPerformed(ActionEvent e)
 552       {
 553         neighbourTreeMenuItem_actionPerformed(e);
 554       }
 555     });
 556
 557     this.getContentPane().setLayout(new BorderLayout());
 558     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 559     statusBar.setBackground(Color.white);
 560     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 561     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 562     statusBar.setText(MessageManager.getString("label.status_bar"));
 563     outputTextboxMenu.setText(MessageManager
 564             .getString("label.out_to_textbox"));
 565
 566
 567     JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(
 568             MessageManager.getString("label.average_distance_blosum62"));
 569     avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
 570     {
 571       @Override
 572       public void actionPerformed(ActionEvent e)
 573       {
 574         avTreeBlosumMenuItem_actionPerformed(e);
 575       }
 576     });
 577     JMenuItem njTreeBlosumMenuItem = new JMenuItem(
 578             MessageManager.getString("label.neighbour_blosum62"));
 579     njTreeBlosumMenuItem.addActionListener(new ActionListener()
 580     {
 581       @Override
 582       public void actionPerformed(ActionEvent e)
 583       {
 584         njTreeBlosumMenuItem_actionPerformed(e);
 585       }
 586     });
 587     annotationPanelMenuItem.setActionCommand("");
 588     annotationPanelMenuItem.setText(MessageManager
 589             .getString("label.show_annotations"));
 590     annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
 591             true));
 592     annotationPanelMenuItem.addActionListener(new ActionListener()
 593     {
 594       @Override
 595       public void actionPerformed(ActionEvent e)
 596       {
 597         annotationPanelMenuItem_actionPerformed(e);
 598       }
 599     });
 600     showAllAlAnnotations.setText(MessageManager
 601             .getString("label.show_all_al_annotations"));
 602     final boolean isAnnotationPanelShown = annotationPanelMenuItem
 603             .getState();
 604     showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 605     showAllAlAnnotations.addActionListener(new ActionListener()
 606     {
 607       @Override
 608       public void actionPerformed(ActionEvent e)
 609       {
 610         showAllAnnotations_actionPerformed(false, true);
 611       }
 612     });
 613     hideAllAlAnnotations.setText(MessageManager
 614             .getString("label.hide_all_al_annotations"));
 615     hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 616     hideAllAlAnnotations.addActionListener(new ActionListener()
 617     {
 618       @Override
 619       public void actionPerformed(ActionEvent e)
 620       {
 621         hideAllAnnotations_actionPerformed(false, true);
 622       }
 623     });
 624     showAllSeqAnnotations.setText(MessageManager
 625             .getString("label.show_all_seq_annotations"));
 626     showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 627     showAllSeqAnnotations.addActionListener(new ActionListener()
 628     {
 629       @Override
 630       public void actionPerformed(ActionEvent e)
 631       {
 632         showAllAnnotations_actionPerformed(true, false);
 633       }
 634     });
 635     hideAllSeqAnnotations.setText(MessageManager
 636             .getString("label.hide_all_seq_annotations"));
 637     hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 638     hideAllSeqAnnotations.addActionListener(new ActionListener()
 639     {
 640       @Override
 641       public void actionPerformed(ActionEvent e)
 642       {
 643         hideAllAnnotations_actionPerformed(true, false);
 644       }
 645     });
 646     SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
 647             .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
 648                     SequenceAnnotationOrder.NONE.name()));
 649     final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
 650             MessageManager.getString("label.sort_annotations_by_sequence"));
 651     final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
 652             MessageManager.getString("label.sort_annotations_by_label"));
 653
 654     sortAnnBySequence
 655             .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
 656     sortAnnBySequence.addActionListener(new ActionListener()
 657     {
 658       @Override
 659       public void actionPerformed(ActionEvent e)
 660       {
 661         boolean newState = sortAnnBySequence.getState();
 662         sortAnnByLabel.setSelected(false);
 663         setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 664                 : SequenceAnnotationOrder.NONE);
 665         sortAnnotations_actionPerformed();
 666       }
 667     });
 668     sortAnnByLabel
 669             .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
 670     sortAnnByLabel.addActionListener(new ActionListener()
 671     {
 672       @Override
 673       public void actionPerformed(ActionEvent e)
 674       {
 675         boolean newState = sortAnnByLabel.getState();
 676         sortAnnBySequence.setSelected(false);
 677         setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 678                 : SequenceAnnotationOrder.NONE);
 679         sortAnnotations_actionPerformed();
 680       }
 681     });
 682     colourTextMenuItem = new JCheckBoxMenuItem(
 683             MessageManager
 684             .getString("label.colour_text"));
 685     colourTextMenuItem.addActionListener(new ActionListener()
 686     {
 687       @Override
 688       public void actionPerformed(ActionEvent e)
 689       {
 690         colourTextMenuItem_actionPerformed(e);
 691       }
 692     });
 693
 694     JMenuItem htmlMenuItem = new JMenuItem(
 695             MessageManager.getString("label.html"));
 696     htmlMenuItem.addActionListener(new ActionListener()
 697     {
 698       @Override
 699       public void actionPerformed(ActionEvent e)
 700       {
 701         htmlMenuItem_actionPerformed(e);
 702       }
 703     });
 704
 705     JMenuItem createBioJS = new JMenuItem(
 706             MessageManager.getString("label.biojs_html_export"));
 707     createBioJS.addActionListener(new java.awt.event.ActionListener()
 708     {
 709       @Override
 710       public void actionPerformed(ActionEvent e)
 711       {
 712         bioJSMenuItem_actionPerformed(e);
 713       }
 714     });
 715
 716     JMenuItem overviewMenuItem = new JMenuItem(
 717             MessageManager.getString("label.overview_window"));
 718     overviewMenuItem.addActionListener(new ActionListener()
 719     {
 720       @Override
 721       public void actionPerformed(ActionEvent e)
 722       {
 723         overviewMenuItem_actionPerformed(e);
 724       }
 725     });
 726
 727     undoMenuItem.setEnabled(false);
 728     undoMenuItem.setText(MessageManager.getString("action.undo"));
 729     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
 730             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 731     al = new ActionListener()
 732     {
 733       @Override
 734       public void actionPerformed(ActionEvent e)
 735       {
 736         undoMenuItem_actionPerformed(e);
 737       }
 738     };
 739     addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
 740
 741     redoMenuItem.setEnabled(false);
 742     redoMenuItem.setText(MessageManager.getString("action.redo"));
 743     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
 744             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 745     al = new ActionListener()
 746     {
 747       @Override
 748       public void actionPerformed(ActionEvent e)
 749       {
 750         redoMenuItem_actionPerformed(e);
 751       }
 752     };
 753     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
 754
 755     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
 756     wrapMenuItem.addActionListener(new ActionListener()
 757     {
 758       @Override
 759       public void actionPerformed(ActionEvent e)
 760       {
 761         wrapMenuItem_actionPerformed(e);
 762       }
 763     });
 764
 765     JMenuItem printMenuItem = new JMenuItem(
 766             MessageManager.getString("action.print"));
 767     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
 768             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 769     al = new ActionListener()
 770     {
 771       @Override
 772       public void actionPerformed(ActionEvent e)
 773       {
 774         printMenuItem_actionPerformed(e);
 775       }
 776     };
 777     addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
 778
 779     renderGapsMenuItem
 780             .setText(MessageManager.getString("action.show_gaps"));
 781     renderGapsMenuItem.setState(true);
 782     renderGapsMenuItem.addActionListener(new ActionListener()
 783     {
 784       @Override
 785       public void actionPerformed(ActionEvent e)
 786       {
 787         renderGapsMenuItem_actionPerformed(e);
 788       }
 789     });
 790
 791     JMenuItem findMenuItem = new JMenuItem(
 792             MessageManager.getString("action.find"));
 793     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
 794             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 795     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
 796             MessageManager.getString("label.find_tip")));
 797     al = new ActionListener()
 798     {
 799       @Override
 800       public void actionPerformed(ActionEvent e)
 801       {
 802         findMenuItem_actionPerformed(e);
 803       }
 804     };
 805     addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
 806
 807     showSeqFeatures.setText(MessageManager
 808             .getString("label.show_sequence_features"));
 809     showSeqFeatures.addActionListener(new ActionListener()
 810     {
 811       @Override
 812       public void actionPerformed(ActionEvent actionEvent)
 813       {
 814         showSeqFeatures_actionPerformed(actionEvent);
 815       }
 816     });
 817     /*
 818      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
 819      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
 820      * void actionPerformed(ActionEvent actionEvent) {
 821      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
 822      */
 823     showDbRefsMenuitem.setText(MessageManager
 824             .getString("label.show_database_refs"));
 825     showDbRefsMenuitem.addActionListener(new ActionListener()
 826     {
 827
 828       @Override
 829       public void actionPerformed(ActionEvent e)
 830       {
 831         showDbRefs_actionPerformed(e);
 832       }
 833
 834     });
 835     showNpFeatsMenuitem.setText(MessageManager
 836             .getString("label.show_non_positional_features"));
 837     showNpFeatsMenuitem.addActionListener(new ActionListener()
 838     {
 839
 840       @Override
 841       public void actionPerformed(ActionEvent e)
 842       {
 843         showNpFeats_actionPerformed(e);
 844       }
 845
 846     });
 847     showGroupConservation.setText(MessageManager
 848             .getString("label.group_conservation"));
 849     showGroupConservation.addActionListener(new ActionListener()
 850     {
 851
 852       @Override
 853       public void actionPerformed(ActionEvent e)
 854       {
 855         showGroupConservation_actionPerformed(e);
 856       }
 857
 858     });
 859
 860     showGroupConsensus.setText(MessageManager
 861             .getString("label.group_consensus"));
 862     showGroupConsensus.addActionListener(new ActionListener()
 863     {
 864
 865       @Override
 866       public void actionPerformed(ActionEvent e)
 867       {
 868         showGroupConsensus_actionPerformed(e);
 869       }
 870
 871     });
 872     showConsensusHistogram.setText(MessageManager
 873             .getString("label.show_consensus_histogram"));
 874     showConsensusHistogram.addActionListener(new ActionListener()
 875     {
 876
 877       @Override
 878       public void actionPerformed(ActionEvent e)
 879       {
 880         showConsensusHistogram_actionPerformed(e);
 881       }
 882
 883     });
 884     showSequenceLogo.setText(MessageManager
 885             .getString("label.show_consensus_logo"));
 886     showSequenceLogo.addActionListener(new ActionListener()
 887     {
 888
 889       @Override
 890       public void actionPerformed(ActionEvent e)
 891       {
 892         showSequenceLogo_actionPerformed(e);
 893       }
 894
 895     });
 896     normaliseSequenceLogo.setText(MessageManager
 897             .getString("label.norm_consensus_logo"));
 898     normaliseSequenceLogo.addActionListener(new ActionListener()
 899     {
 900
 901       @Override
 902       public void actionPerformed(ActionEvent e)
 903       {
 904         normaliseSequenceLogo_actionPerformed(e);
 905       }
 906
 907     });
 908     applyAutoAnnotationSettings.setText(MessageManager
 909             .getString("label.apply_all_groups"));
 910     applyAutoAnnotationSettings.setState(false);
 911     applyAutoAnnotationSettings.setVisible(true);
 912     applyAutoAnnotationSettings.addActionListener(new ActionListener()
 913     {
 914       @Override
 915       public void actionPerformed(ActionEvent e)
 916       {
 917         applyAutoAnnotationSettings_actionPerformed(e);
 918       }
 919     });
 920
 921     ButtonGroup buttonGroup = new ButtonGroup();
 922     final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
 923             MessageManager.getString("label.show_first"));
 924     final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
 925             MessageManager.getString("label.show_last"));
 926     buttonGroup.add(showAutoFirst);
 927     buttonGroup.add(showAutoLast);
 928     final boolean autoFirst = Cache.getDefault(
 929             Preferences.SHOW_AUTOCALC_ABOVE, false);
 930     showAutoFirst.setSelected(autoFirst);
 931     setShowAutoCalculatedAbove(autoFirst);
 932     showAutoFirst.addActionListener(new ActionListener()
 933     {
 934       @Override
 935       public void actionPerformed(ActionEvent e)
 936       {
 937         setShowAutoCalculatedAbove(showAutoFirst.isSelected());
 938         sortAnnotations_actionPerformed();
 939       }
 940     });
 941     showAutoLast.setSelected(!showAutoFirst.isSelected());
 942     showAutoLast.addActionListener(new ActionListener()
 943     {
 944       @Override
 945       public void actionPerformed(ActionEvent e)
 946       {
 947         setShowAutoCalculatedAbove(!showAutoLast.isSelected());
 948         sortAnnotations_actionPerformed();
 949       }
 950     });
 951
 952     JMenuItem deleteGroups = new JMenuItem(
 953             MessageManager.getString("action.undefine_groups"));
 954     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
 955             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 956     al = new ActionListener()
 957     {
 958       @Override
 959       public void actionPerformed(ActionEvent e)
 960       {
 961         deleteGroups_actionPerformed(e);
 962       }
 963     };
 964     addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
 965
 966     JMenuItem annotationColumn = new JMenuItem(
 967             MessageManager.getString("action.select_by_annotation"));
 968     annotationColumn.addActionListener(new ActionListener()
 969     {
 970       @Override
 971       public void actionPerformed(ActionEvent e)
 972       {
 973         annotationColumn_actionPerformed(e);
 974       }
 975     });
 976
 977     JMenuItem createGroup = new JMenuItem(
 978             MessageManager.getString("action.create_groups"));
 979     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
 980             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 981     al = new ActionListener()
 982     {
 983       @Override
 984       public void actionPerformed(ActionEvent e)
 985       {
 986         createGroup_actionPerformed(e);
 987       }
 988     };
 989     addMenuActionAndAccelerator(keyStroke, createGroup, al);
 990
 991     JMenuItem unGroup = new JMenuItem(
 992             MessageManager.getString("action.remove_group"));
 993     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
 994             .getDefaultToolkit().getMenuShortcutKeyMask()
 995             | KeyEvent.SHIFT_MASK, false);
 996     al = new ActionListener()
 997     {
 998       @Override
 999       public void actionPerformed(ActionEvent e)
1000       {
1001         unGroup_actionPerformed(e);
1002       }
1003     };
1004     addMenuActionAndAccelerator(keyStroke, unGroup, al);
1005
1006     copy.setText(MessageManager.getString("action.copy"));
1007     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
1008             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1009
1010     al = new ActionListener()
1011     {
1012       @Override
1013       public void actionPerformed(ActionEvent e)
1014       {
1015         copy_actionPerformed(e);
1016       }
1017     };
1018     addMenuActionAndAccelerator(keyStroke, copy, al);
1019
1020     cut.setText(MessageManager.getString("action.cut"));
1021     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
1022             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1023     al = new ActionListener()
1024     {
1025       @Override
1026       public void actionPerformed(ActionEvent e)
1027       {
1028         cut_actionPerformed(e);
1029       }
1030     };
1031     addMenuActionAndAccelerator(keyStroke, cut, al);
1032
1033     JMenuItem delete = new JMenuItem(
1034             MessageManager.getString("action.delete"));
1035     delete.addActionListener(new ActionListener()
1036     {
1037       @Override
1038       public void actionPerformed(ActionEvent e)
1039       {
1040         delete_actionPerformed(e);
1041       }
1042     });
1043
1044     pasteMenu.setText(MessageManager.getString("action.paste"));
1045     JMenuItem pasteNew = new JMenuItem(
1046             MessageManager.getString("label.to_new_alignment"));
1047     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1048             .getDefaultToolkit().getMenuShortcutKeyMask()
1049             | KeyEvent.SHIFT_MASK, false);
1050     al = new ActionListener()
1051     {
1052       @Override
1053       public void actionPerformed(ActionEvent e)
1054       {
1055         pasteNew_actionPerformed(e);
1056       }
1057     };
1058     addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1059
1060     JMenuItem pasteThis = new JMenuItem(
1061             MessageManager.getString("label.to_this_alignment"));
1062     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1063             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1064     al = new ActionListener()
1065     {
1066       @Override
1067       public void actionPerformed(ActionEvent e)
1068       {
1069         pasteThis_actionPerformed(e);
1070       }
1071     };
1072     addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1073
1074     JMenuItem createPNG = new JMenuItem("PNG");
1075     createPNG.addActionListener(new ActionListener()
1076     {
1077       @Override
1078       public void actionPerformed(ActionEvent e)
1079       {
1080         createPNG(null);
1081       }
1082     });
1083     createPNG.setActionCommand(MessageManager
1084             .getString("label.save_png_image"));
1085
1086     JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1087     font.addActionListener(new ActionListener()
1088     {
1089       @Override
1090       public void actionPerformed(ActionEvent e)
1091       {
1092         font_actionPerformed(e);
1093       }
1094     });
1095     seqLimits.setText(MessageManager
1096             .getString("label.show_sequence_limits"));
1097     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1098     seqLimits.addActionListener(new ActionListener()
1099     {
1100       @Override
1101       public void actionPerformed(ActionEvent e)
1102       {
1103         seqLimit_actionPerformed(e);
1104       }
1105     });
1106     JMenuItem epsFile = new JMenuItem("EPS");
1107     epsFile.addActionListener(new ActionListener()
1108     {
1109       @Override
1110       public void actionPerformed(ActionEvent e)
1111       {
1112         createEPS(null);
1113       }
1114     });
1115
1116     JMenuItem createSVG = new JMenuItem("SVG");
1117     createSVG.addActionListener(new ActionListener()
1118     {
1119       @Override
1120       public void actionPerformed(ActionEvent e)
1121       {
1122         createSVG(null);
1123       }
1124     });
1125
1126     JMenuItem loadTreeMenuItem = new JMenuItem(
1127             MessageManager.getString("label.load_associated_tree"));
1128     loadTreeMenuItem.setActionCommand(MessageManager
1129             .getString("label.load_tree_for_sequence_set"));
1130     loadTreeMenuItem.addActionListener(new ActionListener()
1131     {
1132       @Override
1133       public void actionPerformed(ActionEvent e)
1134       {
1135         loadTreeMenuItem_actionPerformed(e);
1136       }
1137     });
1138
1139     scaleAbove.setVisible(false);
1140     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1141     scaleAbove.addActionListener(new ActionListener()
1142     {
1143       @Override
1144       public void actionPerformed(ActionEvent e)
1145       {
1146         scaleAbove_actionPerformed(e);
1147       }
1148     });
1149     scaleLeft.setVisible(false);
1150     scaleLeft.setSelected(true);
1151     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1152     scaleLeft.addActionListener(new ActionListener()
1153     {
1154       @Override
1155       public void actionPerformed(ActionEvent e)
1156       {
1157         scaleLeft_actionPerformed(e);
1158       }
1159     });
1160     scaleRight.setVisible(false);
1161     scaleRight.setSelected(true);
1162     scaleRight.setText(MessageManager.getString("action.scale_right"));
1163     scaleRight.addActionListener(new ActionListener()
1164     {
1165       @Override
1166       public void actionPerformed(ActionEvent e)
1167       {
1168         scaleRight_actionPerformed(e);
1169       }
1170     });
1171     centreColumnLabelsMenuItem.setVisible(true);
1172     centreColumnLabelsMenuItem.setState(false);
1173     centreColumnLabelsMenuItem.setText(MessageManager
1174             .getString("label.centre_column_labels"));
1175     centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1176     {
1177       @Override
1178       public void actionPerformed(ActionEvent e)
1179       {
1180         centreColumnLabels_actionPerformed(e);
1181       }
1182     });
1183     followHighlightMenuItem.setVisible(true);
1184     followHighlightMenuItem.setState(true);
1185     followHighlightMenuItem.setText(MessageManager
1186             .getString("label.automatic_scrolling"));
1187     followHighlightMenuItem.addActionListener(new ActionListener()
1188     {
1189
1190       @Override
1191       public void actionPerformed(ActionEvent e)
1192       {
1193         followHighlight_actionPerformed();
1194       }
1195
1196     });
1197
1198     sortByTreeMenu
1199             .setText(MessageManager.getString("action.by_tree_order"));
1200     sort.setText(MessageManager.getString("action.sort"));
1201     sort.addMenuListener(new MenuListener()
1202     {
1203       @Override
1204       public void menuSelected(MenuEvent e)
1205       {
1206         buildTreeMenu();
1207       }
1208
1209       @Override
1210       public void menuDeselected(MenuEvent e)
1211       {
1212       }
1213
1214       @Override
1215       public void menuCanceled(MenuEvent e)
1216       {
1217       }
1218     });
1219     sortByAnnotScore.setText(MessageManager
1220             .getString("label.sort_by_score"));
1221     sort.add(sortByAnnotScore);
1222     sort.addMenuListener(new javax.swing.event.MenuListener()
1223     {
1224
1225       @Override
1226       public void menuCanceled(MenuEvent e)
1227       {
1228       }
1229
1230       @Override
1231       public void menuDeselected(MenuEvent e)
1232       {
1233       }
1234
1235       @Override
1236       public void menuSelected(MenuEvent e)
1237       {
1238         buildSortByAnnotationScoresMenu();
1239       }
1240     });
1241     sortByAnnotScore.setVisible(false);
1242
1243     calculateTree
1244             .setText(MessageManager.getString("action.calculate_tree"));
1245
1246     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1247     padGapsMenuitem.setState(jalview.bin.Cache
1248             .getDefault("PAD_GAPS", false));
1249     padGapsMenuitem.addActionListener(new ActionListener()
1250     {
1251       @Override
1252       public void actionPerformed(ActionEvent e)
1253       {
1254         padGapsMenuitem_actionPerformed(e);
1255       }
1256     });
1257     JMenuItem vamsasStore = new JMenuItem(
1258             MessageManager.getString("label.vamsas_store"));
1259     vamsasStore.setVisible(false);
1260     vamsasStore.addActionListener(new ActionListener()
1261     {
1262       @Override
1263       public void actionPerformed(ActionEvent e)
1264       {
1265         vamsasStore_actionPerformed(e);
1266       }
1267     });
1268     showTranslation.setText(MessageManager
1269             .getString("label.translate_cDNA"));
1270     showTranslation.addActionListener(new ActionListener()
1271     {
1272       @Override
1273       public void actionPerformed(ActionEvent e)
1274       {
1275         showTranslation_actionPerformed(e);
1276       }
1277     });
1278     showReverse.setText(MessageManager.getString("label.reverse"));
1279     showReverse.addActionListener(new ActionListener()
1280     {
1281       @Override
1282       public void actionPerformed(ActionEvent e)
1283       {
1284         showReverse_actionPerformed(false);
1285       }
1286     });
1287     showReverseComplement.setText(MessageManager
1288             .getString("label.reverse_complement"));
1289     showReverseComplement.addActionListener(new ActionListener()
1290     {
1291       @Override
1292       public void actionPerformed(ActionEvent e)
1293       {
1294         showReverse_actionPerformed(true);
1295       }
1296     });
1297
1298     JMenuItem extractScores = new JMenuItem(
1299             MessageManager.getString("label.extract_scores"));
1300     extractScores.addActionListener(new ActionListener()
1301     {
1302       @Override
1303       public void actionPerformed(ActionEvent e)
1304       {
1305         extractScores_actionPerformed(e);
1306       }
1307     });
1308     extractScores.setVisible(true);
1309     // JBPNote: TODO: make gui for regex based score extraction
1310
1311     // for show products actions see AlignFrame.canShowProducts
1312     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1313
1314     runGroovy.setText(MessageManager.getString("label.run_groovy"));
1315     runGroovy.setToolTipText(MessageManager
1316             .getString("label.run_groovy_tip"));
1317     runGroovy.addActionListener(new ActionListener()
1318     {
1319       @Override
1320       public void actionPerformed(ActionEvent e)
1321       {
1322         runGroovy_actionPerformed();
1323       }
1324     });
1325
1326     JMenuItem openFeatureSettings = new JMenuItem(
1327             MessageManager.getString("action.feature_settings"));
1328     openFeatureSettings.addActionListener(new ActionListener()
1329     {
1330       @Override
1331       public void actionPerformed(ActionEvent e)
1332       {
1333         featureSettings_actionPerformed(e);
1334       }
1335     });
1336     JMenuItem fetchSequence = new JMenuItem(
1337             MessageManager.getString("label.fetch_sequences"));
1338     fetchSequence.addActionListener(new ActionListener()
1339     {
1340       @Override
1341       public void actionPerformed(ActionEvent e)
1342       {
1343         fetchSequence_actionPerformed(e);
1344       }
1345     });
1346
1347     JMenuItem associatedData = new JMenuItem(
1348             MessageManager.getString("label.load_features_annotations"));
1349     associatedData.addActionListener(new ActionListener()
1350     {
1351       @Override
1352       public void actionPerformed(ActionEvent e)
1353       {
1354         associatedData_actionPerformed(e);
1355       }
1356     });
1357     autoCalculate.setText(MessageManager
1358             .getString("label.autocalculate_consensus"));
1359     autoCalculate.setState(jalview.bin.Cache.getDefault(
1360             "AUTO_CALC_CONSENSUS", true));
1361     autoCalculate.addActionListener(new ActionListener()
1362     {
1363       @Override
1364       public void actionPerformed(ActionEvent e)
1365       {
1366         autoCalculate_actionPerformed(e);
1367       }
1368     });
1369     sortByTree.setText(MessageManager
1370             .getString("label.sort_alignment_new_tree"));
1371     sortByTree
1372             .setToolTipText("<html>"
1373                     + MessageManager
1374                             .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1375     sortByTree
1376             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1377     sortByTree.addActionListener(new ActionListener()
1378     {
1379       @Override
1380       public void actionPerformed(ActionEvent e)
1381       {
1382         sortByTreeOption_actionPerformed(e);
1383       }
1384     });
1385
1386     listenToViewSelections.setText(MessageManager
1387             .getString("label.listen_for_selections"));
1388     listenToViewSelections
1389             .setToolTipText("<html>"
1390                     + MessageManager
1391                             .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1392     listenToViewSelections.setState(false);
1393     listenToViewSelections.addActionListener(new ActionListener()
1394     {
1395       @Override
1396       public void actionPerformed(ActionEvent e)
1397       {
1398         listenToViewSelections_actionPerformed(e);
1399       }
1400     });
1401
1402     JMenu addSequenceMenu = new JMenu(
1403             MessageManager.getString("label.add_sequences"));
1404     JMenuItem addFromFile = new JMenuItem(
1405             MessageManager.getString("label.from_file"));
1406     addFromFile.addActionListener(new ActionListener()
1407     {
1408       @Override
1409       public void actionPerformed(ActionEvent e)
1410       {
1411         addFromFile_actionPerformed(e);
1412       }
1413     });
1414     JMenuItem addFromText = new JMenuItem(
1415             MessageManager.getString("label.from_textbox"));
1416     addFromText.addActionListener(new ActionListener()
1417     {
1418       @Override
1419       public void actionPerformed(ActionEvent e)
1420       {
1421         addFromText_actionPerformed(e);
1422       }
1423     });
1424     JMenuItem addFromURL = new JMenuItem(
1425             MessageManager.getString("label.from_url"));
1426     addFromURL.addActionListener(new ActionListener()
1427     {
1428       @Override
1429       public void actionPerformed(ActionEvent e)
1430       {
1431         addFromURL_actionPerformed(e);
1432       }
1433     });
1434     JMenuItem exportFeatures = new JMenuItem(
1435             MessageManager.getString("label.export_features"));
1436     exportFeatures.addActionListener(new ActionListener()
1437     {
1438       @Override
1439       public void actionPerformed(ActionEvent e)
1440       {
1441         exportFeatures_actionPerformed(e);
1442       }
1443     });
1444     JMenuItem exportAnnotations = new JMenuItem(
1445             MessageManager.getString("label.export_annotations"));
1446     exportAnnotations.addActionListener(new ActionListener()
1447     {
1448       @Override
1449       public void actionPerformed(ActionEvent e)
1450       {
1451         exportAnnotations_actionPerformed(e);
1452       }
1453     });
1454     statusPanel.setLayout(new GridLayout());
1455     JMenuItem showAllSeqs = new JMenuItem(
1456             MessageManager.getString("label.all_sequences"));
1457     showAllSeqs.setToolTipText(MessageManager
1458             .getString("label.toggle_sequence_visibility"));
1459     showAllSeqs.addActionListener(new ActionListener()
1460     {
1461       @Override
1462       public void actionPerformed(ActionEvent e)
1463       {
1464         showAllSeqs_actionPerformed(e);
1465       }
1466     });
1467     JMenuItem showAllColumns = new JMenuItem(
1468             MessageManager.getString("label.all_columns"));
1469     showAllColumns.setToolTipText(MessageManager
1470             .getString("label.toggle_columns_visibility"));
1471     showAllColumns.addActionListener(new ActionListener()
1472     {
1473       @Override
1474       public void actionPerformed(ActionEvent e)
1475       {
1476         showAllColumns_actionPerformed(e);
1477       }
1478     });
1479     JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1480     JMenuItem hideSelSequences = new JMenuItem(
1481             MessageManager.getString("label.selected_sequences"));
1482     hideSelSequences.setToolTipText(MessageManager
1483             .getString("label.toggle_sequence_visibility"));
1484     hideSelSequences.addActionListener(new ActionListener()
1485     {
1486       @Override
1487       public void actionPerformed(ActionEvent e)
1488       {
1489         hideSelSequences_actionPerformed(e);
1490       }
1491     });
1492     JMenuItem hideSelColumns = new JMenuItem(
1493             MessageManager.getString("label.selected_columns"));
1494     hideSelColumns.setToolTipText(MessageManager
1495             .getString("label.toggle_columns_visibility"));
1496     hideSelColumns.addActionListener(new ActionListener()
1497     {
1498       @Override
1499       public void actionPerformed(ActionEvent e)
1500       {
1501         hideSelColumns_actionPerformed(e);
1502       }
1503     });
1504     JMenuItem hideAllSelection = new JMenuItem(
1505             MessageManager.getString("label.selected_region"));
1506     hideAllSelection.addActionListener(new ActionListener()
1507     {
1508       @Override
1509       public void actionPerformed(ActionEvent e)
1510       {
1511         hideAllSelection_actionPerformed(e);
1512       }
1513     });
1514     // TODO: should be hidden if no selection exists.
1515     JMenuItem hideAllButSelection = new JMenuItem(
1516             MessageManager.getString("label.all_but_selected_region"));
1517     hideAllButSelection.addActionListener(new ActionListener()
1518     {
1519       @Override
1520       public void actionPerformed(ActionEvent e)
1521       {
1522         hideAllButSelection_actionPerformed(e);
1523       }
1524     });
1525     JMenuItem showAllhidden = new JMenuItem(
1526             MessageManager.getString("label.all_sequences_columns"));
1527     showAllhidden.setToolTipText(MessageManager
1528             .getString("label.toggles_visibility_hidden_selected_regions"));
1529     showAllhidden.addActionListener(new ActionListener()
1530     {
1531       @Override
1532       public void actionPerformed(ActionEvent e)
1533       {
1534         showAllhidden_actionPerformed(e);
1535       }
1536     });
1537     hiddenMarkers.setText(MessageManager
1538             .getString("action.show_hidden_markers"));
1539     hiddenMarkers.addActionListener(new ActionListener()
1540     {
1541       @Override
1542       public void actionPerformed(ActionEvent e)
1543       {
1544         hiddenMarkers_actionPerformed(e);
1545       }
1546     });
1547
1548     JMenuItem invertColSel = new JMenuItem(
1549             MessageManager.getString("action.invert_column_selection"));
1550     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
1551             .getDefaultToolkit().getMenuShortcutKeyMask()
1552             | KeyEvent.ALT_MASK, false);
1553     al = new ActionListener()
1554     {
1555       @Override
1556       public void actionPerformed(ActionEvent e)
1557       {
1558         invertColSel_actionPerformed(e);
1559       }
1560     };
1561     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1562
1563     showComplementMenuItem.setVisible(false);
1564     showComplementMenuItem.addActionListener(new ActionListener()
1565     {
1566       @Override
1567       public void actionPerformed(ActionEvent e)
1568       {
1569         showComplement_actionPerformed(showComplementMenuItem.getState());
1570       }
1571     });
1572
1573     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1574     {
1575       @Override
1576       public void stateChanged(ChangeEvent evt)
1577       {
1578         JTabbedPane pane = (JTabbedPane) evt.getSource();
1579         int sel = pane.getSelectedIndex();
1580         tabSelectionChanged(sel);
1581       }
1582     });
1583     tabbedPane.addMouseListener(new MouseAdapter()
1584     {
1585       @Override
1586       public void mousePressed(MouseEvent e)
1587       {
1588         if (e.isPopupTrigger()) // Mac
1589         {
1590           tabbedPane_mousePressed(e);
1591         }
1592       }
1593
1594       @Override
1595       public void mouseReleased(MouseEvent e)
1596       {
1597         if (e.isPopupTrigger()) // Windows
1598         {
1599           tabbedPane_mousePressed(e);
1600         }
1601       }
1602     });
1603     tabbedPane.addFocusListener(new FocusAdapter()
1604     {
1605       @Override
1606       public void focusGained(FocusEvent e)
1607       {
1608         tabbedPane_focusGained(e);
1609       }
1610     });
1611
1612     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1613     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
1614             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1615     al = new ActionListener()
1616     {
1617       @Override
1618       public void actionPerformed(ActionEvent e)
1619       {
1620         save_actionPerformed(e);
1621       }
1622     };
1623     addMenuActionAndAccelerator(keyStroke, save, al);
1624
1625     reload.setEnabled(false);
1626     reload.setText(MessageManager.getString("action.reload"));
1627     reload.addActionListener(new ActionListener()
1628     {
1629       @Override
1630       public void actionPerformed(ActionEvent e)
1631       {
1632         reload_actionPerformed(e);
1633       }
1634     });
1635
1636     JMenuItem newView = new JMenuItem(
1637             MessageManager.getString("action.new_view"));
1638     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
1639             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1640     al = new ActionListener()
1641     {
1642       @Override
1643       public void actionPerformed(ActionEvent e)
1644       {
1645         newView_actionPerformed(e);
1646       }
1647     };
1648     addMenuActionAndAccelerator(keyStroke, newView, al);
1649
1650     tabbedPane.setToolTipText("<html><i>"
1651             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1652             + "</i></html>");
1653
1654     formatMenu.setText(MessageManager.getString("action.format"));
1655     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1656     idRightAlign.setText(MessageManager
1657             .getString("label.right_align_sequence_id"));
1658     idRightAlign.addActionListener(new ActionListener()
1659     {
1660       @Override
1661       public void actionPerformed(ActionEvent e)
1662       {
1663         idRightAlign_actionPerformed(e);
1664       }
1665     });
1666
1667     gatherViews.setEnabled(false);
1668     gatherViews.setText(MessageManager.getString("action.gather_views"));
1669     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1670     al = new ActionListener()
1671     {
1672       @Override
1673       public void actionPerformed(ActionEvent e)
1674       {
1675         gatherViews_actionPerformed(e);
1676       }
1677     };
1678     addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1679
1680     expandViews.setEnabled(false);
1681     expandViews.setText(MessageManager.getString("action.expand_views"));
1682     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1683     al = new ActionListener()
1684     {
1685       @Override
1686       public void actionPerformed(ActionEvent e)
1687       {
1688         expandViews_actionPerformed(e);
1689       }
1690     };
1691     addMenuActionAndAccelerator(keyStroke, expandViews, al);
1692
1693     JMenuItem pageSetup = new JMenuItem(
1694             MessageManager.getString("action.page_setup"));
1695     pageSetup.addActionListener(new ActionListener()
1696     {
1697       @Override
1698       public void actionPerformed(ActionEvent e)
1699       {
1700         pageSetup_actionPerformed(e);
1701       }
1702     });
1703     JMenuItem alignmentProperties = new JMenuItem(
1704             MessageManager.getString("label.alignment_props"));
1705     alignmentProperties.addActionListener(new ActionListener()
1706     {
1707       @Override
1708       public void actionPerformed(ActionEvent actionEvent)
1709       {
1710         alignmentProperties();
1711       }
1712     });
1713     JMenuItem selectHighlighted = new JMenuItem(
1714             MessageManager.getString("action.select_highlighted_columns"));
1715     selectHighlighted.setToolTipText(MessageManager
1716             .getString("tooltip.select_highlighted_columns"));
1717     al = new ActionListener()
1718     {
1719       @Override
1720       public void actionPerformed(ActionEvent actionEvent)
1721       {
1722         selectHighlightedColumns_actionPerformed(actionEvent);
1723       }
1724     };
1725     selectHighlighted.addActionListener(al);
1726     JMenu tooltipSettingsMenu = new JMenu(
1727             MessageManager.getString("label.sequence_id_tooltip"));
1728     JMenu autoAnnMenu = new JMenu(
1729             MessageManager.getString("label.autocalculated_annotation"));
1730
1731     JMenu exportImageMenu = new JMenu(
1732             MessageManager.getString("label.export_image"));
1733     JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1734     alignFrameMenuBar.add(fileMenu);
1735     alignFrameMenuBar.add(editMenu);
1736     alignFrameMenuBar.add(selectMenu);
1737     alignFrameMenuBar.add(viewMenu);
1738     alignFrameMenuBar.add(annotationsMenu);
1739     alignFrameMenuBar.add(formatMenu);
1740     alignFrameMenuBar.add(colourMenu);
1741     alignFrameMenuBar.add(calculateMenu);
1742     alignFrameMenuBar.add(webService);
1743
1744     fileMenu.add(fetchSequence);
1745     fileMenu.add(addSequenceMenu);
1746     fileMenu.add(reload);
1747     fileMenu.addSeparator();
1748     fileMenu.add(vamsasStore);
1749     fileMenu.add(save);
1750     fileMenu.add(saveAs);
1751     fileMenu.add(outputTextboxMenu);
1752     fileMenu.add(pageSetup);
1753     fileMenu.add(printMenuItem);
1754     fileMenu.addSeparator();
1755     fileMenu.add(exportImageMenu);
1756     fileMenu.add(exportFeatures);
1757     fileMenu.add(exportAnnotations);
1758     fileMenu.add(loadTreeMenuItem);
1759     fileMenu.add(associatedData);
1760     fileMenu.addSeparator();
1761     fileMenu.add(closeMenuItem);
1762
1763     pasteMenu.add(pasteNew);
1764     pasteMenu.add(pasteThis);
1765     editMenu.add(undoMenuItem);
1766     editMenu.add(redoMenuItem);
1767     editMenu.add(cut);
1768     editMenu.add(copy);
1769     editMenu.add(pasteMenu);
1770     editMenu.add(delete);
1771     editMenu.addSeparator();
1772     editMenu.add(remove2LeftMenuItem);
1773     editMenu.add(remove2RightMenuItem);
1774     editMenu.add(removeGappedColumnMenuItem);
1775     editMenu.add(removeAllGapsMenuItem);
1776     editMenu.add(removeRedundancyMenuItem);
1777     editMenu.addSeparator();
1778     // dont add these yet in the CVS build - they cannot be undone!
1779     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1780     // editMenu.add(justifyLeftMenuItem);
1781     // editMenu.add(justifyRightMenuItem);
1782     // editMenu.addSeparator();
1783     editMenu.add(padGapsMenuitem);
1784
1785     showMenu.add(showAllColumns);
1786     showMenu.add(showAllSeqs);
1787     showMenu.add(showAllhidden);
1788     hideMenu.add(hideSelColumns);
1789     hideMenu.add(hideSelSequences);
1790     hideMenu.add(hideAllSelection);
1791     hideMenu.add(hideAllButSelection);
1792     viewMenu.add(newView);
1793     viewMenu.add(expandViews);
1794     viewMenu.add(gatherViews);
1795     viewMenu.addSeparator();
1796     viewMenu.add(showMenu);
1797     viewMenu.add(hideMenu);
1798     viewMenu.add(showComplementMenuItem);
1799     viewMenu.addSeparator();
1800     viewMenu.add(followHighlightMenuItem);
1801     viewMenu.addSeparator();
1802     viewMenu.add(showSeqFeatures);
1803     // viewMenu.add(showSeqFeaturesHeight);
1804     viewMenu.add(openFeatureSettings);
1805     tooltipSettingsMenu.add(showDbRefsMenuitem);
1806     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1807     viewMenu.add(tooltipSettingsMenu);
1808     viewMenu.addSeparator();
1809     viewMenu.add(alignmentProperties);
1810     viewMenu.addSeparator();
1811     viewMenu.add(overviewMenuItem);
1812
1813     annotationsMenu.add(annotationPanelMenuItem);
1814     annotationsMenu.addSeparator();
1815     annotationsMenu.add(showAllAlAnnotations);
1816     annotationsMenu.add(hideAllAlAnnotations);
1817     annotationsMenu.addSeparator();
1818     annotationsMenu.add(showAllSeqAnnotations);
1819     annotationsMenu.add(hideAllSeqAnnotations);
1820     annotationsMenu.add(sortAnnBySequence);
1821     annotationsMenu.add(sortAnnByLabel);
1822     annotationsMenu.addSeparator();
1823     autoAnnMenu.add(showAutoFirst);
1824     autoAnnMenu.add(showAutoLast);
1825     autoAnnMenu.addSeparator();
1826     autoAnnMenu.add(applyAutoAnnotationSettings);
1827     autoAnnMenu.add(showConsensusHistogram);
1828     autoAnnMenu.add(showSequenceLogo);
1829     autoAnnMenu.add(normaliseSequenceLogo);
1830     autoAnnMenu.addSeparator();
1831     autoAnnMenu.add(showGroupConservation);
1832     autoAnnMenu.add(showGroupConsensus);
1833     annotationsMenu.add(autoAnnMenu);
1834
1835
1836     sort.add(sortIDMenuItem);
1837     sort.add(sortLengthMenuItem);
1838     sort.add(sortGroupMenuItem);
1839     sort.add(sortPairwiseMenuItem);
1840     sort.add(sortByTreeMenu);
1841     calculateMenu.add(sort);
1842     calculateMenu.add(calculateTree);
1843     calculateMenu.addSeparator();
1844     calculateMenu.add(pairwiseAlignmentMenuItem);
1845     calculateMenu.add(PCAMenuItem);
1846     calculateMenu.addSeparator();
1847     calculateMenu.add(showTranslation);
1848     calculateMenu.add(showReverse);
1849     calculateMenu.add(showReverseComplement);
1850     calculateMenu.add(showProducts);
1851     calculateMenu.add(autoCalculate);
1852     calculateMenu.add(sortByTree);
1853     calculateMenu.addSeparator();
1854     calculateMenu.add(expandAlignment);
1855     calculateMenu.add(extractScores);
1856     calculateMenu.addSeparator();
1857     calculateMenu.add(runGroovy);
1858
1859     webServiceNoServices = new JMenuItem(
1860             MessageManager.getString("label.no_services"));
1861     webService.add(webServiceNoServices);
1862     exportImageMenu.add(htmlMenuItem);
1863     exportImageMenu.add(epsFile);
1864     exportImageMenu.add(createPNG);
1865     exportImageMenu.add(createBioJS);
1866     exportImageMenu.add(createSVG);
1867     addSequenceMenu.add(addFromFile);
1868     addSequenceMenu.add(addFromText);
1869     addSequenceMenu.add(addFromURL);
1870     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1871     statusPanel.add(statusBar, null);
1872     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1873
1874     formatMenu.add(font);
1875     formatMenu.addSeparator();
1876     formatMenu.add(wrapMenuItem);
1877     formatMenu.add(scaleAbove);
1878     formatMenu.add(scaleLeft);
1879     formatMenu.add(scaleRight);
1880     formatMenu.add(seqLimits);
1881     formatMenu.add(idRightAlign);
1882     formatMenu.add(hiddenMarkers);
1883     formatMenu.add(viewBoxesMenuItem);
1884     formatMenu.add(viewTextMenuItem);
1885     formatMenu.add(colourTextMenuItem);
1886     formatMenu.add(renderGapsMenuItem);
1887     formatMenu.add(centreColumnLabelsMenuItem);
1888     formatMenu.add(showNonconservedMenuItem);
1889     selectMenu.add(findMenuItem);
1890     selectMenu.addSeparator();
1891     selectMenu.add(selectAllSequenceMenuItem);
1892     selectMenu.add(deselectAllSequenceMenuItem);
1893     selectMenu.add(invertSequenceMenuItem);
1894     selectMenu.add(invertColSel);
1895     selectMenu.add(createGroup);
1896     selectMenu.add(unGroup);
1897     selectMenu.add(grpsFromSelection);
1898     selectMenu.add(deleteGroups);
1899     selectMenu.add(annotationColumn);
1900     selectMenu.add(selectHighlighted);
1901     // TODO - determine if the listenToViewSelections button is needed : see bug
1902     // JAL-574
1903     // selectMenu.addSeparator();
1904     // selectMenu.add(listenToViewSelections);
1905   }
1906
1907   /**
1908    * Constructs the entries on the Colour menu (but does not add them to the
1909    * menu).
1910    */
1911   protected void initColourMenu()
1912   {
1913     applyToAllGroups = new JCheckBoxMenuItem(
1914             MessageManager.getString("label.apply_colour_to_all_groups"));
1915     applyToAllGroups.addActionListener(new ActionListener()
1916     {
1917       @Override
1918       public void actionPerformed(ActionEvent e)
1919       {
1920         applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1921       }
1922     });
1923
1924     textColour = new JRadioButtonMenuItem(
1925             MessageManager.getString("action.set_text_colour"));
1926     textColour.addActionListener(new ActionListener()
1927     {
1928       @Override
1929       public void actionPerformed(ActionEvent e)
1930       {
1931         textColour_actionPerformed();
1932       }
1933     });
1934
1935     conservationMenuItem = new JCheckBoxMenuItem(
1936             MessageManager.getString("action.by_conservation"));
1937     conservationMenuItem.addActionListener(new ActionListener()
1938     {
1939       @Override
1940       public void actionPerformed(ActionEvent e)
1941       {
1942         conservationMenuItem_actionPerformed(conservationMenuItem
1943                 .isSelected());
1944       }
1945     });
1946
1947     abovePIDThreshold = new JCheckBoxMenuItem(
1948             MessageManager.getString("label.above_identity_threshold"));
1949     abovePIDThreshold.addActionListener(new ActionListener()
1950     {
1951       @Override
1952       public void actionPerformed(ActionEvent e)
1953       {
1954         abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
1955       }
1956     });
1957     modifyPID = new JMenuItem(
1958             MessageManager.getString("label.modify_identity_threshold"));
1959     modifyPID.addActionListener(new ActionListener()
1960     {
1961       @Override
1962       public void actionPerformed(ActionEvent e)
1963       {
1964         modifyPID_actionPerformed();
1965       }
1966     });
1967     modifyConservation = new JMenuItem(
1968             MessageManager
1969             .getString("label.modify_conservation_threshold"));
1970     modifyConservation.addActionListener(new ActionListener()
1971     {
1972       @Override
1973       public void actionPerformed(ActionEvent e)
1974       {
1975         modifyConservation_actionPerformed();
1976       }
1977     });
1978
1979     annotationColour = new JMenuItem(
1980             MessageManager.getString("action.by_annotation"));
1981     annotationColour.addActionListener(new ActionListener()
1982     {
1983       @Override
1984       public void actionPerformed(ActionEvent e)
1985       {
1986         annotationColour_actionPerformed();
1987       }
1988     });
1989   }
1990
1991   protected void selectHighlightedColumns_actionPerformed(
1992           ActionEvent actionEvent)
1993   {
1994     // TODO Auto-generated method stub
1995
1996   }
1997
1998   /**
1999    * Generate the reverse sequence (or reverse complement if the flag is true)
2000    * and add it to the alignment
2001    *
2002    * @param complement
2003    */
2004   protected void showReverse_actionPerformed(boolean complement)
2005   {
2006   }
2007
2008   /**
2009    * Try to run script in a Groovy console, having first ensured that this
2010    * alignframe is set as currentAlignFrame in Desktop
2011    */
2012   protected void runGroovy_actionPerformed()
2013   {
2014
2015   }
2016
2017   /**
2018    * Adds the given action listener and key accelerator to the given menu item.
2019    * Also saves in a lookup table to support lookup of action by key stroke.
2020    *
2021    * @param keyStroke
2022    * @param menuItem
2023    * @param actionListener
2024    */
2025   protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2026           JMenuItem menuItem, ActionListener actionListener)
2027   {
2028     menuItem.setAccelerator(keyStroke);
2029     accelerators.put(keyStroke, menuItem);
2030     menuItem.addActionListener(actionListener);
2031   }
2032
2033   /**
2034    * Action on clicking sort annotations by type.
2035    *
2036    * @param sortOrder
2037    */
2038   protected void sortAnnotations_actionPerformed()
2039   {
2040   }
2041
2042   /**
2043    * Action on clicking Show all annotations.
2044    *
2045    * @param forSequences
2046    *          update sequence-related annotations
2047    * @param forAlignment
2048    *          update non-sequence-related annotations
2049    */
2050   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2051           boolean forAlignment)
2052   {
2053     setAnnotationsVisibility(true, forSequences, forAlignment);
2054   }
2055
2056   /**
2057    * Action on clicking Hide all annotations.
2058    *
2059    * @param forSequences
2060    *          update sequence-related annotations
2061    * @param forAlignment
2062    *          update non-sequence-related annotations
2063    */
2064   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2065           boolean forAlignment)
2066   {
2067     setAnnotationsVisibility(false, forSequences, forAlignment);
2068   }
2069
2070   /**
2071    * Set the visibility of annotations to true or false. Can act on
2072    * sequence-related annotations, or alignment-related, or both.
2073    *
2074    * @param visible
2075    * @param forSequences
2076    *          update sequence-related annotations
2077    * @param forAlignment
2078    *          update non-sequence-related annotations
2079    */
2080   protected void setAnnotationsVisibility(boolean visible,
2081           boolean forSequences, boolean forAlignment)
2082   {
2083
2084   }
2085
2086   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2087   {
2088     // TODO Auto-generated method stub
2089
2090   }
2091
2092   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2093   {
2094     // TODO Auto-generated method stub
2095
2096   }
2097
2098   protected void showAllhidden_actionPerformed(ActionEvent e)
2099   {
2100     // TODO Auto-generated method stub
2101
2102   }
2103
2104   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2105   {
2106     // TODO Auto-generated method stub
2107
2108   }
2109
2110   protected void hideAllSelection_actionPerformed(ActionEvent e)
2111   {
2112     // TODO Auto-generated method stub
2113
2114   }
2115
2116   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2117   {
2118     // TODO Auto-generated method stub
2119
2120   }
2121
2122   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2123   {
2124     // TODO Auto-generated method stub
2125
2126   }
2127
2128   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2129   {
2130     // TODO Auto-generated method stub
2131
2132   }
2133
2134   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2135   {
2136     // TODO Auto-generated method stub
2137
2138   }
2139
2140   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2141   {
2142     // TODO Auto-generated method stub
2143
2144   }
2145
2146   protected void showGroupConservation_actionPerformed(ActionEvent e)
2147   {
2148     // TODO Auto-generated method stub
2149
2150   }
2151
2152   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2153   {
2154     // TODO Auto-generated method stub
2155
2156   }
2157
2158   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2159   {
2160     // TODO Auto-generated method stub
2161
2162   }
2163
2164   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2165   {
2166     // TODO Auto-generated method stub
2167
2168   }
2169
2170   protected void followHighlight_actionPerformed()
2171   {
2172     // TODO Auto-generated method stub
2173
2174   }
2175
2176   protected void showNpFeats_actionPerformed(ActionEvent e)
2177   {
2178     // TODO Auto-generated method stub
2179
2180   }
2181
2182   protected void showDbRefs_actionPerformed(ActionEvent e)
2183   {
2184     // TODO Auto-generated method stub
2185
2186   }
2187
2188   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2189   {
2190   }
2191
2192   protected void buildSortByAnnotationScoresMenu()
2193   {
2194   }
2195
2196   protected void extractScores_actionPerformed(ActionEvent e)
2197   {
2198   }
2199
2200   protected void outputText_actionPerformed(ActionEvent e)
2201   {
2202   }
2203
2204   public void addFromFile_actionPerformed(ActionEvent e)
2205   {
2206
2207   }
2208
2209   public void addFromText_actionPerformed(ActionEvent e)
2210   {
2211
2212   }
2213
2214   public void addFromURL_actionPerformed(ActionEvent e)
2215   {
2216
2217   }
2218
2219   public void exportFeatures_actionPerformed(ActionEvent e)
2220   {
2221
2222   }
2223
2224   public void exportAnnotations_actionPerformed(ActionEvent e)
2225   {
2226
2227   }
2228
2229   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2230   {
2231   }
2232
2233   protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2234   {
2235
2236   }
2237
2238   protected void closeMenuItem_actionPerformed(boolean b)
2239   {
2240   }
2241
2242   protected void redoMenuItem_actionPerformed(ActionEvent e)
2243   {
2244   }
2245
2246   protected void undoMenuItem_actionPerformed(ActionEvent e)
2247   {
2248   }
2249
2250   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2251   {
2252   }
2253
2254   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2255   {
2256   }
2257
2258   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2259   {
2260   }
2261
2262   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2263   {
2264   }
2265
2266   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2267   {
2268   }
2269
2270   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2271   {
2272   }
2273
2274   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2275   {
2276   }
2277
2278   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2279   {
2280   }
2281
2282   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2283   {
2284   }
2285
2286   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2287   {
2288   }
2289
2290   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2291   {
2292   }
2293
2294   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2295   {
2296   }
2297
2298   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2299   {
2300   }
2301
2302   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2303   {
2304   }
2305
2306   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2307   {
2308   }
2309
2310   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2311   {
2312   }
2313
2314   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2315   {
2316   }
2317
2318   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2319   {
2320   }
2321
2322   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2323   {
2324   }
2325
2326   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2327   {
2328   }
2329
2330   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2331   {
2332   }
2333
2334   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2335   {
2336   }
2337
2338   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2339   {
2340   }
2341
2342   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2343   {
2344   }
2345
2346   protected void conservationMenuItem_actionPerformed(boolean selected)
2347   {
2348   }
2349
2350   protected void printMenuItem_actionPerformed(ActionEvent e)
2351   {
2352   }
2353
2354   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2355   {
2356   }
2357
2358   protected void findMenuItem_actionPerformed(ActionEvent e)
2359   {
2360   }
2361
2362   protected void abovePIDThreshold_actionPerformed(boolean selected)
2363   {
2364   }
2365
2366   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2367   {
2368   }
2369
2370   protected void deleteGroups_actionPerformed(ActionEvent e)
2371   {
2372   }
2373
2374   protected void createGroup_actionPerformed(ActionEvent e)
2375   {
2376   }
2377
2378   protected void unGroup_actionPerformed(ActionEvent e)
2379   {
2380   }
2381
2382   protected void copy_actionPerformed(ActionEvent e)
2383   {
2384   }
2385
2386   protected void cut_actionPerformed(ActionEvent e)
2387   {
2388   }
2389
2390   protected void delete_actionPerformed(ActionEvent e)
2391   {
2392   }
2393
2394   protected void pasteNew_actionPerformed(ActionEvent e)
2395   {
2396   }
2397
2398   protected void pasteThis_actionPerformed(ActionEvent e)
2399   {
2400   }
2401
2402   protected void applyToAllGroups_actionPerformed(boolean selected)
2403   {
2404   }
2405
2406   public void createPNG(java.io.File f)
2407   {
2408   }
2409
2410   protected void font_actionPerformed(ActionEvent e)
2411   {
2412   }
2413
2414   protected void seqLimit_actionPerformed(ActionEvent e)
2415   {
2416   }
2417
2418   public void seqDBRef_actionPerformed(ActionEvent e)
2419   {
2420
2421   }
2422
2423   public void createEPS(java.io.File f)
2424   {
2425   }
2426
2427   public void createSVG(java.io.File f)
2428   {
2429
2430   }
2431
2432   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2433   {
2434
2435   }
2436
2437   /**
2438    * Template method to handle the 'load T-Coffee scores' menu event.
2439    * <p>
2440    * Subclasses override this method to provide a custom action.
2441    *
2442    * @param event
2443    *          The raised event
2444    */
2445   protected void loadScores_actionPerformed(ActionEvent event)
2446   {
2447
2448   }
2449
2450   protected void jpred_actionPerformed(ActionEvent e)
2451   {
2452   }
2453
2454   protected void scaleAbove_actionPerformed(ActionEvent e)
2455   {
2456   }
2457
2458   protected void scaleLeft_actionPerformed(ActionEvent e)
2459   {
2460   }
2461
2462   protected void scaleRight_actionPerformed(ActionEvent e)
2463   {
2464   }
2465
2466   protected void modifyPID_actionPerformed()
2467   {
2468   }
2469
2470   protected void modifyConservation_actionPerformed()
2471   {
2472   }
2473
2474   protected void saveAs_actionPerformed(ActionEvent e)
2475   {
2476   }
2477
2478   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2479   {
2480   }
2481
2482   public void vamsasStore_actionPerformed(ActionEvent e)
2483   {
2484
2485   }
2486
2487   public void vamsasLoad_actionPerformed(ActionEvent e)
2488   {
2489
2490   }
2491
2492   public void showTranslation_actionPerformed(ActionEvent e)
2493   {
2494
2495   }
2496
2497   public void featureSettings_actionPerformed(ActionEvent e)
2498   {
2499
2500   }
2501
2502   public void fetchSequence_actionPerformed(ActionEvent e)
2503   {
2504
2505   }
2506
2507   public void smoothFont_actionPerformed(ActionEvent e)
2508   {
2509
2510   }
2511
2512   public void annotationColour_actionPerformed()
2513   {
2514   }
2515
2516   public void annotationColumn_actionPerformed(ActionEvent e)
2517   {
2518   }
2519
2520   public void associatedData_actionPerformed(ActionEvent e)
2521   {
2522
2523   }
2524
2525   public void autoCalculate_actionPerformed(ActionEvent e)
2526   {
2527
2528   }
2529
2530   public void sortByTreeOption_actionPerformed(ActionEvent e)
2531   {
2532
2533   }
2534
2535   public void showAllSeqs_actionPerformed(ActionEvent e)
2536   {
2537
2538   }
2539
2540   public void showAllColumns_actionPerformed(ActionEvent e)
2541   {
2542
2543   }
2544
2545   public void hideSelSequences_actionPerformed(ActionEvent e)
2546   {
2547
2548   }
2549
2550   public void hideSelColumns_actionPerformed(ActionEvent e)
2551   {
2552
2553   }
2554
2555   public void hiddenMarkers_actionPerformed(ActionEvent e)
2556   {
2557
2558   }
2559
2560   public void findPdbId_actionPerformed(ActionEvent e)
2561   {
2562
2563   }
2564
2565   public void enterPdbId_actionPerformed(ActionEvent e)
2566   {
2567
2568   }
2569
2570   public void pdbFile_actionPerformed(ActionEvent e)
2571   {
2572
2573   }
2574
2575   public void invertColSel_actionPerformed(ActionEvent e)
2576   {
2577
2578   }
2579
2580   public void tabSelectionChanged(int sel)
2581   {
2582
2583   }
2584
2585   public void tabbedPane_mousePressed(MouseEvent e)
2586   {
2587
2588   }
2589
2590   public void tabbedPane_focusGained(FocusEvent e)
2591   {
2592     requestFocus();
2593   }
2594
2595   public void save_actionPerformed(ActionEvent e)
2596   {
2597
2598   }
2599
2600   public void reload_actionPerformed(ActionEvent e)
2601   {
2602
2603   }
2604
2605   public void newView_actionPerformed(ActionEvent e)
2606   {
2607
2608   }
2609
2610   public void textColour_actionPerformed()
2611   {
2612
2613   }
2614
2615   public void idRightAlign_actionPerformed(ActionEvent e)
2616   {
2617
2618   }
2619
2620   public void expandViews_actionPerformed(ActionEvent e)
2621   {
2622
2623   }
2624
2625   public void gatherViews_actionPerformed(ActionEvent e)
2626   {
2627
2628   }
2629
2630   public void buildTreeMenu()
2631   {
2632
2633   }
2634
2635   public void pageSetup_actionPerformed(ActionEvent e)
2636   {
2637
2638   }
2639
2640   public void alignmentProperties()
2641   {
2642
2643   }
2644
2645   protected void expand_newalign(ActionEvent e)
2646   {
2647     // TODO Auto-generated method stub
2648
2649   }
2650
2651   protected boolean isShowAutoCalculatedAbove()
2652   {
2653     return showAutoCalculatedAbove;
2654   }
2655
2656   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2657   {
2658     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2659   }
2660
2661   protected SequenceAnnotationOrder getAnnotationSortOrder()
2662   {
2663     return annotationSortOrder;
2664   }
2665
2666   protected void setAnnotationSortOrder(
2667           SequenceAnnotationOrder annotationSortOrder)
2668   {
2669     this.annotationSortOrder = annotationSortOrder;
2670   }
2671
2672   public Map<KeyStroke, JMenuItem> getAccelerators()
2673   {
2674     return this.accelerators;
2675   }
2676
2677   /**
2678    * Returns the selected index of the tabbed pane, or -1 if none selected
2679    * (including the case where the tabbed pane has not been made visible).
2680    *
2681    * @return
2682    */
2683   public int getTabIndex()
2684   {
2685     return tabbedPane.getSelectedIndex();
2686   }
2687
2688   public JPanel getStatusPanel()
2689   {
2690     return statusPanel;
2691   }
2692
2693   /**
2694    * Sets a reference to the containing split frame. Also makes the 'toggle
2695    * split view' menu item visible and checked.
2696    *
2697    * @param sf
2698    */
2699   public void setSplitFrame(SplitContainerI sf)
2700   {
2701     this.splitFrame = sf;
2702     if (sf != null)
2703     {
2704       this.showComplementMenuItem.setVisible(true);
2705       this.showComplementMenuItem.setState(true);
2706     }
2707   }
2708
2709   public SplitContainerI getSplitViewContainer()
2710   {
2711     return this.splitFrame;
2712   }
2713
2714   protected void showComplement_actionPerformed(boolean complement)
2715   {
2716   }
2717 }