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.Desktop;
  27 import jalview.gui.JvOptionPane;
  28 import jalview.gui.JvSwingUtils;
  29 import jalview.gui.Preferences;
  30 import jalview.gui.UserDefinedColours;
  31 import jalview.io.FileFormat;
  32 import jalview.schemes.JalviewColourScheme;
  33 import jalview.schemes.ResidueColourScheme;
  34 import jalview.schemes.UserColourScheme;
  35 import jalview.util.MessageManager;
  36 import jalview.util.Platform;
  37
  38 import java.awt.BorderLayout;
  39 import java.awt.Color;
  40 import java.awt.Component;
  41 import java.awt.GridLayout;
  42 import java.awt.Toolkit;
  43 import java.awt.event.ActionEvent;
  44 import java.awt.event.ActionListener;
  45 import java.awt.event.FocusAdapter;
  46 import java.awt.event.FocusEvent;
  47 import java.awt.event.KeyEvent;
  48 import java.awt.event.MouseAdapter;
  49 import java.awt.event.MouseEvent;
  50 import java.util.HashMap;
  51 import java.util.Map;
  52
  53 import javax.swing.BorderFactory;
  54 import javax.swing.ButtonGroup;
  55 import javax.swing.JCheckBoxMenuItem;
  56 import javax.swing.JInternalFrame;
  57 import javax.swing.JLabel;
  58 import javax.swing.JMenu;
  59 import javax.swing.JMenuBar;
  60 import javax.swing.JMenuItem;
  61 import javax.swing.JPanel;
  62 import javax.swing.JRadioButtonMenuItem;
  63 import javax.swing.JTabbedPane;
  64 import javax.swing.KeyStroke;
  65 import javax.swing.event.ChangeEvent;
  66 import javax.swing.event.MenuEvent;
  67 import javax.swing.event.MenuListener;
  68
  69 public class GAlignFrame extends JInternalFrame
  70 {
  71   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  72
  73   protected JMenuItem closeMenuItem = new JMenuItem();
  74
  75   protected JMenu colourMenu = new JMenu();
  76
  77   protected JMenu webService = new JMenu();
  78
  79   protected JMenuItem webServiceNoServices;
  80
  81   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  82
  83   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  84
  85   protected JMenu sortByAnnotScore = new JMenu();
  86
  87   public JLabel statusBar = new JLabel();
  88
  89   protected JMenu outputTextboxMenu = new JMenu();
  90
  91   protected JRadioButtonMenuItem textColour;
  92
  93   protected JRadioButtonMenuItem clustalColour;
  94
  95   protected JRadioButtonMenuItem zappoColour;
  96
  97   protected JRadioButtonMenuItem taylorColour;
  98
  99   protected JRadioButtonMenuItem hydrophobicityColour;
 100
 101   protected JRadioButtonMenuItem helixColour;
 102
 103   protected JRadioButtonMenuItem strandColour;
 104
 105   protected JRadioButtonMenuItem turnColour;
 106
 107   protected JRadioButtonMenuItem buriedColour;
 108
 109   protected JRadioButtonMenuItem userDefinedColour;
 110
 111   protected JRadioButtonMenuItem PIDColour;
 112
 113   protected JRadioButtonMenuItem BLOSUM62Colour;
 114
 115   protected JRadioButtonMenuItem nucleotideColour;
 116
 117   protected JRadioButtonMenuItem purinePyrimidineColour;
 118
 119   protected JRadioButtonMenuItem RNAInteractionColour;
 120
 121   // protected JRadioButtonMenuItem covariationColour;
 122
 123   protected JRadioButtonMenuItem tcoffeeColour;
 124
 125   protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 126
 127   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 128
 129   protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
 130
 131   protected JMenuItem undoMenuItem = new JMenuItem();
 132
 133   protected JMenuItem redoMenuItem = new JMenuItem();
 134
 135   protected JCheckBoxMenuItem conservationMenuItem;
 136
 137   JRadioButtonMenuItem noColourmenuItem;
 138
 139   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 140
 141   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 142
 143   protected JCheckBoxMenuItem abovePIDThreshold;
 144
 145   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 146
 147   JMenuItem copy = new JMenuItem();
 148
 149   JMenuItem cut = new JMenuItem();
 150
 151   JMenu pasteMenu = new JMenu();
 152
 153   protected JCheckBoxMenuItem applyToAllGroups;
 154
 155   protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 156
 157   protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 158
 159   protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 160
 161   protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 162
 163   protected JMenuItem modifyPID;
 164
 165   protected JMenuItem modifyConservation;
 166
 167   protected JMenuItem annotationColour;
 168
 169   protected JMenu sortByTreeMenu = new JMenu();
 170
 171   protected JMenu sort = new JMenu();
 172
 173   protected JMenu calculateTree = new JMenu();
 174
 175   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 176
 177   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 178
 179   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 180
 181   protected ButtonGroup colours = new ButtonGroup();
 182
 183   protected JMenuItem showTranslation = new JMenuItem();
 184
 185   protected JMenuItem showReverse = new JMenuItem();
 186
 187   protected JMenuItem showReverseComplement = new JMenuItem();
 188
 189   protected JMenu showProducts = new JMenu();
 190
 191   protected JMenuItem runGroovy = new JMenuItem();
 192
 193   protected JMenuItem rnahelicesColour;
 194
 195   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 196
 197   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 198
 199   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 200
 201   protected JPanel statusPanel = new JPanel();
 202
 203   protected JMenuItem showAllSeqAnnotations = new JMenuItem();
 204
 205   protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
 206
 207   protected JMenuItem showAllAlAnnotations = new JMenuItem();
 208
 209   protected JMenuItem hideAllAlAnnotations = new JMenuItem();
 210
 211   protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
 212
 213   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 214
 215   protected JTabbedPane tabbedPane = new JTabbedPane();
 216
 217   protected JMenuItem reload = new JMenuItem();
 218
 219   protected JMenu formatMenu = new JMenu();
 220
 221   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 222
 223   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 224
 225   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 226
 227   protected JMenuItem gatherViews = new JMenuItem();
 228
 229   protected JMenuItem expandViews = new JMenuItem();
 230
 231   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 232
 233   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 234
 235   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 236
 237   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 238
 239   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 240
 241   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 242
 243   private SequenceAnnotationOrder annotationSortOrder;
 244
 245   private boolean showAutoCalculatedAbove = false;
 246
 247   private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
 248
 249   private SplitContainerI splitFrame;
 250
 251   public GAlignFrame()
 252   {
 253     try
 254     {
 255       jbInit();
 256       setJMenuBar(alignFrameMenuBar);
 257
 258       // dynamically fill save as menu with available formats
 259       for (String ff : FileFormat.getWritableFormats(true))
 260       {
 261         JMenuItem item = new JMenuItem(ff);
 262
 263         item.addActionListener(new ActionListener()
 264         {
 265           @Override
 266           public void actionPerformed(ActionEvent e)
 267           {
 268             outputText_actionPerformed(e);
 269           }
 270         });
 271
 272         outputTextboxMenu.add(item);
 273       }
 274     } catch (Exception e)
 275     {
 276       System.err.println(e.toString());
 277     }
 278
 279     if (!Platform.isAMac())
 280     {
 281       closeMenuItem.setMnemonic('C');
 282       outputTextboxMenu.setMnemonic('T');
 283       undoMenuItem.setMnemonic('Z');
 284       redoMenuItem.setMnemonic('0');
 285       copy.setMnemonic('C');
 286       cut.setMnemonic('U');
 287       pasteMenu.setMnemonic('P');
 288       reload.setMnemonic('R');
 289     }
 290   }
 291
 292   /**
 293    * Marks as selected the colour menu item matching the given name, or the
 294    * first item ('None') if no match is found
 295    *
 296    * @param colourName
 297    */
 298   protected void setColourSelected(String colourName)
 299   {
 300     noColourmenuItem.setSelected(true);
 301     if (colourName == null)
 302     {
 303       return;
 304     }
 305
 306     /*
 307      * look for a radio button with a name that matches the colour name
 308      * (note the button text may not as it may be internationalised)
 309      */
 310     for (Component menuItem : colourMenu.getMenuComponents())
 311     {
 312       if (menuItem instanceof JRadioButtonMenuItem)
 313       {
 314         if (colourName.equals(((JRadioButtonMenuItem) menuItem).getName()))
 315         {
 316           ((JRadioButtonMenuItem) menuItem).setSelected(true);
 317           return;
 318         }
 319       }
 320     }
 321   }
 322
 323   private void jbInit() throws Exception
 324   {
 325     initColourMenu();
 326     buildColourMenu();
 327
 328     JMenuItem saveAs = new JMenuItem(
 329             MessageManager.getString("action.save_as"));
 330     ActionListener al = new ActionListener()
 331     {
 332       @Override
 333       public void actionPerformed(ActionEvent e)
 334       {
 335         saveAs_actionPerformed(e);
 336       }
 337     };
 338
 339     // FIXME getDefaultToolkit throws an exception in Headless mode
 340     KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
 341             .getDefaultToolkit().getMenuShortcutKeyMask()
 342             | KeyEvent.SHIFT_MASK, false);
 343     addMenuActionAndAccelerator(keyStroke, saveAs, al);
 344
 345     closeMenuItem.setText(MessageManager.getString("action.close"));
 346     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
 347             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 348     al = new ActionListener()
 349     {
 350       @Override
 351       public void actionPerformed(ActionEvent e)
 352       {
 353         closeMenuItem_actionPerformed(false);
 354       }
 355     };
 356     addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
 357
 358     JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
 359     JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
 360     JMenu annotationsMenu = new JMenu(
 361             MessageManager.getString("action.annotations"));
 362     JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
 363     colourMenu.setText(MessageManager.getString("action.colour"));
 364     JMenu calculateMenu = new JMenu(
 365             MessageManager.getString("action.calculate"));
 366     webService.setText(MessageManager.getString("action.web_service"));
 367     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
 368             MessageManager.getString("action.select_all"));
 369     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
 370             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 371     al = new ActionListener()
 372     {
 373       @Override
 374       public void actionPerformed(ActionEvent e)
 375       {
 376         selectAllSequenceMenuItem_actionPerformed(e);
 377       }
 378     };
 379     addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
 380
 381     JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
 382             MessageManager.getString("action.deselect_all"));
 383     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
 384     al = new ActionListener()
 385     {
 386       @Override
 387       public void actionPerformed(ActionEvent e)
 388       {
 389         deselectAllSequenceMenuItem_actionPerformed(e);
 390       }
 391     };
 392     addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
 393
 394     JMenuItem invertSequenceMenuItem = new JMenuItem(
 395             MessageManager.getString("action.invert_sequence_selection"));
 396     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
 397             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 398     al = new ActionListener()
 399     {
 400       @Override
 401       public void actionPerformed(ActionEvent e)
 402       {
 403         invertSequenceMenuItem_actionPerformed(e);
 404       }
 405     };
 406     addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
 407
 408     JMenuItem grpsFromSelection = new JMenuItem(
 409             MessageManager.getString("action.make_groups_selection"));
 410     grpsFromSelection.addActionListener(new ActionListener()
 411     {
 412       @Override
 413       public void actionPerformed(ActionEvent e)
 414       {
 415         makeGrpsFromSelection_actionPerformed(e);
 416       }
 417     });
 418     JMenuItem expandAlignment = new JMenuItem(
 419             MessageManager.getString("action.view_flanking_regions"));
 420     expandAlignment.setToolTipText(MessageManager
 421             .getString("label.view_flanking_regions"));
 422     expandAlignment.addActionListener(new ActionListener()
 423     {
 424       @Override
 425       public void actionPerformed(ActionEvent e)
 426       {
 427         expand_newalign(e);
 428       }
 429     });
 430     JMenuItem remove2LeftMenuItem = new JMenuItem(
 431             MessageManager.getString("action.remove_left"));
 432     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
 433             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 434     al = new ActionListener()
 435     {
 436       @Override
 437       public void actionPerformed(ActionEvent e)
 438       {
 439         remove2LeftMenuItem_actionPerformed(e);
 440       }
 441     };
 442     addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
 443
 444     JMenuItem remove2RightMenuItem = new JMenuItem(
 445             MessageManager.getString("action.remove_right"));
 446     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
 447             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 448     al = new ActionListener()
 449     {
 450       @Override
 451       public void actionPerformed(ActionEvent e)
 452       {
 453         remove2RightMenuItem_actionPerformed(e);
 454       }
 455     };
 456     addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
 457
 458     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
 459             MessageManager.getString("action.remove_empty_columns"));
 460     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
 461             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 462     al = new ActionListener()
 463     {
 464       @Override
 465       public void actionPerformed(ActionEvent e)
 466       {
 467         removeGappedColumnMenuItem_actionPerformed(e);
 468       }
 469     };
 470     addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
 471
 472     JMenuItem removeAllGapsMenuItem = new JMenuItem(
 473             MessageManager.getString("action.remove_all_gaps"));
 474     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
 475             .getDefaultToolkit().getMenuShortcutKeyMask()
 476             | KeyEvent.SHIFT_MASK, false);
 477     al = new ActionListener()
 478     {
 479       @Override
 480       public void actionPerformed(ActionEvent e)
 481       {
 482         removeAllGapsMenuItem_actionPerformed(e);
 483       }
 484     };
 485     addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
 486
 487     JMenuItem justifyLeftMenuItem = new JMenuItem(
 488             MessageManager.getString("action.left_justify_alignment"));
 489     justifyLeftMenuItem.addActionListener(new ActionListener()
 490     {
 491       @Override
 492       public void actionPerformed(ActionEvent e)
 493       {
 494         justifyLeftMenuItem_actionPerformed(e);
 495       }
 496     });
 497     JMenuItem justifyRightMenuItem = new JMenuItem(
 498             MessageManager.getString("action.right_justify_alignment"));
 499     justifyRightMenuItem.addActionListener(new ActionListener()
 500     {
 501       @Override
 502       public void actionPerformed(ActionEvent e)
 503       {
 504         justifyRightMenuItem_actionPerformed(e);
 505       }
 506     });
 507     viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
 508     viewBoxesMenuItem.setState(true);
 509     viewBoxesMenuItem.addActionListener(new ActionListener()
 510     {
 511       @Override
 512       public void actionPerformed(ActionEvent e)
 513       {
 514         viewBoxesMenuItem_actionPerformed(e);
 515       }
 516     });
 517     viewTextMenuItem.setText(MessageManager.getString("action.text"));
 518     viewTextMenuItem.setState(true);
 519     viewTextMenuItem.addActionListener(new ActionListener()
 520     {
 521       @Override
 522       public void actionPerformed(ActionEvent e)
 523       {
 524         viewTextMenuItem_actionPerformed(e);
 525       }
 526     });
 527     showNonconservedMenuItem.setText(MessageManager
 528             .getString("label.show_non_conserved"));
 529     showNonconservedMenuItem.setState(false);
 530     showNonconservedMenuItem.addActionListener(new ActionListener()
 531     {
 532       @Override
 533       public void actionPerformed(ActionEvent e)
 534       {
 535         showUnconservedMenuItem_actionPerformed(e);
 536       }
 537     });
 538     JMenuItem sortPairwiseMenuItem = new JMenuItem(
 539             MessageManager.getString("action.by_pairwise_id"));
 540     sortPairwiseMenuItem.addActionListener(new ActionListener()
 541     {
 542       @Override
 543       public void actionPerformed(ActionEvent e)
 544       {
 545         sortPairwiseMenuItem_actionPerformed(e);
 546       }
 547     });
 548     JMenuItem sortIDMenuItem = new JMenuItem(
 549             MessageManager.getString("action.by_id"));
 550     sortIDMenuItem.addActionListener(new ActionListener()
 551     {
 552       @Override
 553       public void actionPerformed(ActionEvent e)
 554       {
 555         sortIDMenuItem_actionPerformed(e);
 556       }
 557     });
 558     JMenuItem sortLengthMenuItem = new JMenuItem(
 559             MessageManager.getString("action.by_length"));
 560     sortLengthMenuItem.addActionListener(new ActionListener()
 561     {
 562       @Override
 563       public void actionPerformed(ActionEvent e)
 564       {
 565         sortLengthMenuItem_actionPerformed(e);
 566       }
 567     });
 568     JMenuItem sortGroupMenuItem = new JMenuItem(
 569             MessageManager.getString("action.by_group"));
 570     sortGroupMenuItem.addActionListener(new ActionListener()
 571     {
 572       @Override
 573       public void actionPerformed(ActionEvent e)
 574       {
 575         sortGroupMenuItem_actionPerformed(e);
 576       }
 577     });
 578
 579     JMenuItem removeRedundancyMenuItem = new JMenuItem(
 580             MessageManager.getString("action.remove_redundancy"));
 581     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
 582             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 583     al = new ActionListener()
 584     {
 585       @Override
 586       public void actionPerformed(ActionEvent e)
 587       {
 588         removeRedundancyMenuItem_actionPerformed(e);
 589       }
 590     };
 591     addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
 592
 593     JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
 594             MessageManager.getString("action.pairwise_alignment"));
 595     pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
 596     {
 597       @Override
 598       public void actionPerformed(ActionEvent e)
 599       {
 600         pairwiseAlignmentMenuItem_actionPerformed(e);
 601       }
 602     });
 603     JMenuItem PCAMenuItem = new JMenuItem(
 604             MessageManager.getString("label.principal_component_analysis"));
 605     PCAMenuItem.addActionListener(new ActionListener()
 606     {
 607       @Override
 608       public void actionPerformed(ActionEvent e)
 609       {
 610         PCAMenuItem_actionPerformed(e);
 611       }
 612     });
 613     JMenuItem averageDistanceTreeMenuItem = new JMenuItem(
 614             MessageManager.getString("label.average_distance_identity"));
 615     averageDistanceTreeMenuItem.addActionListener(new ActionListener()
 616     {
 617       @Override
 618       public void actionPerformed(ActionEvent e)
 619       {
 620         averageDistanceTreeMenuItem_actionPerformed(e);
 621       }
 622     });
 623     JMenuItem neighbourTreeMenuItem = new JMenuItem(
 624             MessageManager.getString("label.neighbour_joining_identity"));
 625     neighbourTreeMenuItem.addActionListener(new ActionListener()
 626     {
 627       @Override
 628       public void actionPerformed(ActionEvent e)
 629       {
 630         neighbourTreeMenuItem_actionPerformed(e);
 631       }
 632     });
 633
 634     this.getContentPane().setLayout(new BorderLayout());
 635     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 636     statusBar.setBackground(Color.white);
 637     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 638     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 639     statusBar.setText(MessageManager.getString("label.status_bar"));
 640     outputTextboxMenu.setText(MessageManager
 641             .getString("label.out_to_textbox"));
 642
 643
 644     JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(
 645             MessageManager.getString("label.average_distance_bloslum62"));
 646     avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
 647     {
 648       @Override
 649       public void actionPerformed(ActionEvent e)
 650       {
 651         avTreeBlosumMenuItem_actionPerformed(e);
 652       }
 653     });
 654     JMenuItem njTreeBlosumMenuItem = new JMenuItem(
 655             MessageManager.getString("label.neighbour_blosum62"));
 656     njTreeBlosumMenuItem.addActionListener(new ActionListener()
 657     {
 658       @Override
 659       public void actionPerformed(ActionEvent e)
 660       {
 661         njTreeBlosumMenuItem_actionPerformed(e);
 662       }
 663     });
 664     annotationPanelMenuItem.setActionCommand("");
 665     annotationPanelMenuItem.setText(MessageManager
 666             .getString("label.show_annotations"));
 667     annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
 668             true));
 669     annotationPanelMenuItem.addActionListener(new ActionListener()
 670     {
 671       @Override
 672       public void actionPerformed(ActionEvent e)
 673       {
 674         annotationPanelMenuItem_actionPerformed(e);
 675       }
 676     });
 677     showAllAlAnnotations.setText(MessageManager
 678             .getString("label.show_all_al_annotations"));
 679     final boolean isAnnotationPanelShown = annotationPanelMenuItem
 680             .getState();
 681     showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 682     showAllAlAnnotations.addActionListener(new ActionListener()
 683     {
 684       @Override
 685       public void actionPerformed(ActionEvent e)
 686       {
 687         showAllAnnotations_actionPerformed(false, true);
 688       }
 689     });
 690     hideAllAlAnnotations.setText(MessageManager
 691             .getString("label.hide_all_al_annotations"));
 692     hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
 693     hideAllAlAnnotations.addActionListener(new ActionListener()
 694     {
 695       @Override
 696       public void actionPerformed(ActionEvent e)
 697       {
 698         hideAllAnnotations_actionPerformed(false, true);
 699       }
 700     });
 701     showAllSeqAnnotations.setText(MessageManager
 702             .getString("label.show_all_seq_annotations"));
 703     showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 704     showAllSeqAnnotations.addActionListener(new ActionListener()
 705     {
 706       @Override
 707       public void actionPerformed(ActionEvent e)
 708       {
 709         showAllAnnotations_actionPerformed(true, false);
 710       }
 711     });
 712     hideAllSeqAnnotations.setText(MessageManager
 713             .getString("label.hide_all_seq_annotations"));
 714     hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
 715     hideAllSeqAnnotations.addActionListener(new ActionListener()
 716     {
 717       @Override
 718       public void actionPerformed(ActionEvent e)
 719       {
 720         hideAllAnnotations_actionPerformed(true, false);
 721       }
 722     });
 723     SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
 724             .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
 725                     SequenceAnnotationOrder.NONE.name()));
 726     final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
 727             MessageManager.getString("label.sort_annotations_by_sequence"));
 728     final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
 729             MessageManager.getString("label.sort_annotations_by_label"));
 730
 731     sortAnnBySequence
 732             .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
 733     sortAnnBySequence.addActionListener(new ActionListener()
 734     {
 735       @Override
 736       public void actionPerformed(ActionEvent e)
 737       {
 738         boolean newState = sortAnnBySequence.getState();
 739         sortAnnByLabel.setSelected(false);
 740         setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 741                 : SequenceAnnotationOrder.NONE);
 742         sortAnnotations_actionPerformed();
 743       }
 744     });
 745     sortAnnByLabel
 746             .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
 747     sortAnnByLabel.addActionListener(new ActionListener()
 748     {
 749       @Override
 750       public void actionPerformed(ActionEvent e)
 751       {
 752         boolean newState = sortAnnByLabel.getState();
 753         sortAnnBySequence.setSelected(false);
 754         setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 755                 : SequenceAnnotationOrder.NONE);
 756         sortAnnotations_actionPerformed();
 757       }
 758     });
 759     colourTextMenuItem = new JCheckBoxMenuItem(
 760             MessageManager
 761             .getString("label.colour_text"));
 762     colourTextMenuItem.addActionListener(new ActionListener()
 763     {
 764       @Override
 765       public void actionPerformed(ActionEvent e)
 766       {
 767         colourTextMenuItem_actionPerformed(e);
 768       }
 769     });
 770
 771     JMenuItem htmlMenuItem = new JMenuItem(
 772             MessageManager.getString("label.html"));
 773     htmlMenuItem.addActionListener(new ActionListener()
 774     {
 775       @Override
 776       public void actionPerformed(ActionEvent e)
 777       {
 778         htmlMenuItem_actionPerformed(e);
 779       }
 780     });
 781
 782     JMenuItem createBioJS = new JMenuItem(
 783             MessageManager.getString("label.biojs_html_export"));
 784     createBioJS.addActionListener(new java.awt.event.ActionListener()
 785     {
 786       @Override
 787       public void actionPerformed(ActionEvent e)
 788       {
 789         bioJSMenuItem_actionPerformed(e);
 790       }
 791     });
 792
 793     JMenuItem overviewMenuItem = new JMenuItem(
 794             MessageManager.getString("label.overview_window"));
 795     overviewMenuItem.addActionListener(new ActionListener()
 796     {
 797       @Override
 798       public void actionPerformed(ActionEvent e)
 799       {
 800         overviewMenuItem_actionPerformed(e);
 801       }
 802     });
 803
 804     undoMenuItem.setEnabled(false);
 805     undoMenuItem.setText(MessageManager.getString("action.undo"));
 806     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
 807             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 808     al = new ActionListener()
 809     {
 810       @Override
 811       public void actionPerformed(ActionEvent e)
 812       {
 813         undoMenuItem_actionPerformed(e);
 814       }
 815     };
 816     addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
 817
 818     redoMenuItem.setEnabled(false);
 819     redoMenuItem.setText(MessageManager.getString("action.redo"));
 820     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
 821             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 822     al = new ActionListener()
 823     {
 824       @Override
 825       public void actionPerformed(ActionEvent e)
 826       {
 827         redoMenuItem_actionPerformed(e);
 828       }
 829     };
 830     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
 831
 832     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
 833     wrapMenuItem.addActionListener(new ActionListener()
 834     {
 835       @Override
 836       public void actionPerformed(ActionEvent e)
 837       {
 838         wrapMenuItem_actionPerformed(e);
 839       }
 840     });
 841
 842     JMenuItem printMenuItem = new JMenuItem(
 843             MessageManager.getString("action.print"));
 844     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
 845             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 846     al = new ActionListener()
 847     {
 848       @Override
 849       public void actionPerformed(ActionEvent e)
 850       {
 851         printMenuItem_actionPerformed(e);
 852       }
 853     };
 854     addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
 855
 856     renderGapsMenuItem
 857             .setText(MessageManager.getString("action.show_gaps"));
 858     renderGapsMenuItem.setState(true);
 859     renderGapsMenuItem.addActionListener(new ActionListener()
 860     {
 861       @Override
 862       public void actionPerformed(ActionEvent e)
 863       {
 864         renderGapsMenuItem_actionPerformed(e);
 865       }
 866     });
 867
 868     JMenuItem findMenuItem = new JMenuItem(
 869             MessageManager.getString("action.find"));
 870     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
 871             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 872     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
 873             MessageManager.getString("label.find_tip")));
 874     al = new ActionListener()
 875     {
 876       @Override
 877       public void actionPerformed(ActionEvent e)
 878       {
 879         findMenuItem_actionPerformed(e);
 880       }
 881     };
 882     addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
 883
 884     showSeqFeatures.setText(MessageManager
 885             .getString("label.show_sequence_features"));
 886     showSeqFeatures.addActionListener(new ActionListener()
 887     {
 888       @Override
 889       public void actionPerformed(ActionEvent actionEvent)
 890       {
 891         showSeqFeatures_actionPerformed(actionEvent);
 892       }
 893     });
 894     /*
 895      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
 896      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
 897      * void actionPerformed(ActionEvent actionEvent) {
 898      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
 899      */
 900     showDbRefsMenuitem.setText(MessageManager
 901             .getString("label.show_database_refs"));
 902     showDbRefsMenuitem.addActionListener(new ActionListener()
 903     {
 904
 905       @Override
 906       public void actionPerformed(ActionEvent e)
 907       {
 908         showDbRefs_actionPerformed(e);
 909       }
 910
 911     });
 912     showNpFeatsMenuitem.setText(MessageManager
 913             .getString("label.show_non_positional_features"));
 914     showNpFeatsMenuitem.addActionListener(new ActionListener()
 915     {
 916
 917       @Override
 918       public void actionPerformed(ActionEvent e)
 919       {
 920         showNpFeats_actionPerformed(e);
 921       }
 922
 923     });
 924     showGroupConservation.setText(MessageManager
 925             .getString("label.group_conservation"));
 926     showGroupConservation.addActionListener(new ActionListener()
 927     {
 928
 929       @Override
 930       public void actionPerformed(ActionEvent e)
 931       {
 932         showGroupConservation_actionPerformed(e);
 933       }
 934
 935     });
 936
 937     showGroupConsensus.setText(MessageManager
 938             .getString("label.group_consensus"));
 939     showGroupConsensus.addActionListener(new ActionListener()
 940     {
 941
 942       @Override
 943       public void actionPerformed(ActionEvent e)
 944       {
 945         showGroupConsensus_actionPerformed(e);
 946       }
 947
 948     });
 949     showConsensusHistogram.setText(MessageManager
 950             .getString("label.show_consensus_histogram"));
 951     showConsensusHistogram.addActionListener(new ActionListener()
 952     {
 953
 954       @Override
 955       public void actionPerformed(ActionEvent e)
 956       {
 957         showConsensusHistogram_actionPerformed(e);
 958       }
 959
 960     });
 961     showSequenceLogo.setText(MessageManager
 962             .getString("label.show_consensus_logo"));
 963     showSequenceLogo.addActionListener(new ActionListener()
 964     {
 965
 966       @Override
 967       public void actionPerformed(ActionEvent e)
 968       {
 969         showSequenceLogo_actionPerformed(e);
 970       }
 971
 972     });
 973     normaliseSequenceLogo.setText(MessageManager
 974             .getString("label.norm_consensus_logo"));
 975     normaliseSequenceLogo.addActionListener(new ActionListener()
 976     {
 977
 978       @Override
 979       public void actionPerformed(ActionEvent e)
 980       {
 981         normaliseSequenceLogo_actionPerformed(e);
 982       }
 983
 984     });
 985     applyAutoAnnotationSettings.setText(MessageManager
 986             .getString("label.apply_all_groups"));
 987     applyAutoAnnotationSettings.setState(false);
 988     applyAutoAnnotationSettings.setVisible(true);
 989     applyAutoAnnotationSettings.addActionListener(new ActionListener()
 990     {
 991       @Override
 992       public void actionPerformed(ActionEvent e)
 993       {
 994         applyAutoAnnotationSettings_actionPerformed(e);
 995       }
 996     });
 997
 998     ButtonGroup buttonGroup = new ButtonGroup();
 999     final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
1000             MessageManager.getString("label.show_first"));
1001     final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
1002             MessageManager.getString("label.show_last"));
1003     buttonGroup.add(showAutoFirst);
1004     buttonGroup.add(showAutoLast);
1005     final boolean autoFirst = Cache.getDefault(
1006             Preferences.SHOW_AUTOCALC_ABOVE, false);
1007     showAutoFirst.setSelected(autoFirst);
1008     setShowAutoCalculatedAbove(autoFirst);
1009     showAutoFirst.addActionListener(new ActionListener()
1010     {
1011       @Override
1012       public void actionPerformed(ActionEvent e)
1013       {
1014         setShowAutoCalculatedAbove(showAutoFirst.isSelected());
1015         sortAnnotations_actionPerformed();
1016       }
1017     });
1018     showAutoLast.setSelected(!showAutoFirst.isSelected());
1019     showAutoLast.addActionListener(new ActionListener()
1020     {
1021       @Override
1022       public void actionPerformed(ActionEvent e)
1023       {
1024         setShowAutoCalculatedAbove(!showAutoLast.isSelected());
1025         sortAnnotations_actionPerformed();
1026       }
1027     });
1028
1029     JMenuItem deleteGroups = new JMenuItem(
1030             MessageManager.getString("action.undefine_groups"));
1031     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
1032             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1033     al = new ActionListener()
1034     {
1035       @Override
1036       public void actionPerformed(ActionEvent e)
1037       {
1038         deleteGroups_actionPerformed(e);
1039       }
1040     };
1041     addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
1042
1043     JMenuItem annotationColumn = new JMenuItem(
1044             MessageManager.getString("action.select_by_annotation"));
1045     annotationColumn.addActionListener(new ActionListener()
1046     {
1047       @Override
1048       public void actionPerformed(ActionEvent e)
1049       {
1050         annotationColumn_actionPerformed(e);
1051       }
1052     });
1053
1054     JMenuItem createGroup = new JMenuItem(
1055             MessageManager.getString("action.create_groups"));
1056     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
1057             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1058     al = new ActionListener()
1059     {
1060       @Override
1061       public void actionPerformed(ActionEvent e)
1062       {
1063         createGroup_actionPerformed(e);
1064       }
1065     };
1066     addMenuActionAndAccelerator(keyStroke, createGroup, al);
1067
1068     JMenuItem unGroup = new JMenuItem(
1069             MessageManager.getString("action.remove_group"));
1070     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
1071             .getDefaultToolkit().getMenuShortcutKeyMask()
1072             | KeyEvent.SHIFT_MASK, false);
1073     al = new ActionListener()
1074     {
1075       @Override
1076       public void actionPerformed(ActionEvent e)
1077       {
1078         unGroup_actionPerformed(e);
1079       }
1080     };
1081     addMenuActionAndAccelerator(keyStroke, unGroup, al);
1082
1083     copy.setText(MessageManager.getString("action.copy"));
1084     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
1085             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1086
1087     al = new ActionListener()
1088     {
1089       @Override
1090       public void actionPerformed(ActionEvent e)
1091       {
1092         copy_actionPerformed(e);
1093       }
1094     };
1095     addMenuActionAndAccelerator(keyStroke, copy, al);
1096
1097     cut.setText(MessageManager.getString("action.cut"));
1098     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
1099             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1100     al = new ActionListener()
1101     {
1102       @Override
1103       public void actionPerformed(ActionEvent e)
1104       {
1105         cut_actionPerformed(e);
1106       }
1107     };
1108     addMenuActionAndAccelerator(keyStroke, cut, al);
1109
1110     JMenuItem delete = new JMenuItem(
1111             MessageManager.getString("action.delete"));
1112     delete.addActionListener(new ActionListener()
1113     {
1114       @Override
1115       public void actionPerformed(ActionEvent e)
1116       {
1117         delete_actionPerformed(e);
1118       }
1119     });
1120
1121     pasteMenu.setText(MessageManager.getString("action.paste"));
1122     JMenuItem pasteNew = new JMenuItem(
1123             MessageManager.getString("label.to_new_alignment"));
1124     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1125             .getDefaultToolkit().getMenuShortcutKeyMask()
1126             | KeyEvent.SHIFT_MASK, false);
1127     al = new ActionListener()
1128     {
1129       @Override
1130       public void actionPerformed(ActionEvent e)
1131       {
1132         pasteNew_actionPerformed(e);
1133       }
1134     };
1135     addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1136
1137     JMenuItem pasteThis = new JMenuItem(
1138             MessageManager.getString("label.to_this_alignment"));
1139     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1140             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1141     al = new ActionListener()
1142     {
1143       @Override
1144       public void actionPerformed(ActionEvent e)
1145       {
1146         pasteThis_actionPerformed(e);
1147       }
1148     };
1149     addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1150
1151     JMenuItem createPNG = new JMenuItem("PNG");
1152     createPNG.addActionListener(new ActionListener()
1153     {
1154       @Override
1155       public void actionPerformed(ActionEvent e)
1156       {
1157         createPNG(null);
1158       }
1159     });
1160     createPNG.setActionCommand(MessageManager
1161             .getString("label.save_png_image"));
1162
1163     JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1164     font.addActionListener(new ActionListener()
1165     {
1166       @Override
1167       public void actionPerformed(ActionEvent e)
1168       {
1169         font_actionPerformed(e);
1170       }
1171     });
1172     seqLimits.setText(MessageManager
1173             .getString("label.show_sequence_limits"));
1174     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1175     seqLimits.addActionListener(new ActionListener()
1176     {
1177       @Override
1178       public void actionPerformed(ActionEvent e)
1179       {
1180         seqLimit_actionPerformed(e);
1181       }
1182     });
1183     JMenuItem epsFile = new JMenuItem("EPS");
1184     epsFile.addActionListener(new ActionListener()
1185     {
1186       @Override
1187       public void actionPerformed(ActionEvent e)
1188       {
1189         createEPS(null);
1190       }
1191     });
1192
1193     JMenuItem createSVG = new JMenuItem("SVG");
1194     createSVG.addActionListener(new ActionListener()
1195     {
1196       @Override
1197       public void actionPerformed(ActionEvent e)
1198       {
1199         createSVG(null);
1200       }
1201     });
1202
1203     JMenuItem loadTreeMenuItem = new JMenuItem(
1204             MessageManager.getString("label.load_associated_tree"));
1205     loadTreeMenuItem.setActionCommand(MessageManager
1206             .getString("label.load_tree_for_sequence_set"));
1207     loadTreeMenuItem.addActionListener(new ActionListener()
1208     {
1209       @Override
1210       public void actionPerformed(ActionEvent e)
1211       {
1212         loadTreeMenuItem_actionPerformed(e);
1213       }
1214     });
1215
1216     scaleAbove.setVisible(false);
1217     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1218     scaleAbove.addActionListener(new ActionListener()
1219     {
1220       @Override
1221       public void actionPerformed(ActionEvent e)
1222       {
1223         scaleAbove_actionPerformed(e);
1224       }
1225     });
1226     scaleLeft.setVisible(false);
1227     scaleLeft.setSelected(true);
1228     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1229     scaleLeft.addActionListener(new ActionListener()
1230     {
1231       @Override
1232       public void actionPerformed(ActionEvent e)
1233       {
1234         scaleLeft_actionPerformed(e);
1235       }
1236     });
1237     scaleRight.setVisible(false);
1238     scaleRight.setSelected(true);
1239     scaleRight.setText(MessageManager.getString("action.scale_right"));
1240     scaleRight.addActionListener(new ActionListener()
1241     {
1242       @Override
1243       public void actionPerformed(ActionEvent e)
1244       {
1245         scaleRight_actionPerformed(e);
1246       }
1247     });
1248     centreColumnLabelsMenuItem.setVisible(true);
1249     centreColumnLabelsMenuItem.setState(false);
1250     centreColumnLabelsMenuItem.setText(MessageManager
1251             .getString("label.centre_column_labels"));
1252     centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1253     {
1254       @Override
1255       public void actionPerformed(ActionEvent e)
1256       {
1257         centreColumnLabels_actionPerformed(e);
1258       }
1259     });
1260     followHighlightMenuItem.setVisible(true);
1261     followHighlightMenuItem.setState(true);
1262     followHighlightMenuItem.setText(MessageManager
1263             .getString("label.automatic_scrolling"));
1264     followHighlightMenuItem.addActionListener(new ActionListener()
1265     {
1266
1267       @Override
1268       public void actionPerformed(ActionEvent e)
1269       {
1270         followHighlight_actionPerformed();
1271       }
1272
1273     });
1274
1275     sortByTreeMenu
1276             .setText(MessageManager.getString("action.by_tree_order"));
1277     sort.setText(MessageManager.getString("action.sort"));
1278     sort.addMenuListener(new MenuListener()
1279     {
1280       @Override
1281       public void menuSelected(MenuEvent e)
1282       {
1283         buildTreeMenu();
1284       }
1285
1286       @Override
1287       public void menuDeselected(MenuEvent e)
1288       {
1289       }
1290
1291       @Override
1292       public void menuCanceled(MenuEvent e)
1293       {
1294       }
1295     });
1296     sortByAnnotScore.setText(MessageManager
1297             .getString("label.sort_by_score"));
1298     sort.add(sortByAnnotScore);
1299     sort.addMenuListener(new javax.swing.event.MenuListener()
1300     {
1301
1302       @Override
1303       public void menuCanceled(MenuEvent e)
1304       {
1305       }
1306
1307       @Override
1308       public void menuDeselected(MenuEvent e)
1309       {
1310       }
1311
1312       @Override
1313       public void menuSelected(MenuEvent e)
1314       {
1315         buildSortByAnnotationScoresMenu();
1316       }
1317     });
1318     sortByAnnotScore.setVisible(false);
1319
1320     calculateTree
1321             .setText(MessageManager.getString("action.calculate_tree"));
1322
1323     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1324     padGapsMenuitem.setState(jalview.bin.Cache
1325             .getDefault("PAD_GAPS", false));
1326     padGapsMenuitem.addActionListener(new ActionListener()
1327     {
1328       @Override
1329       public void actionPerformed(ActionEvent e)
1330       {
1331         padGapsMenuitem_actionPerformed(e);
1332       }
1333     });
1334     JMenuItem vamsasStore = new JMenuItem(
1335             MessageManager.getString("label.vamsas_store"));
1336     vamsasStore.setVisible(false);
1337     vamsasStore.addActionListener(new ActionListener()
1338     {
1339       @Override
1340       public void actionPerformed(ActionEvent e)
1341       {
1342         vamsasStore_actionPerformed(e);
1343       }
1344     });
1345     showTranslation.setText(MessageManager
1346             .getString("label.translate_cDNA"));
1347     showTranslation.addActionListener(new ActionListener()
1348     {
1349       @Override
1350       public void actionPerformed(ActionEvent e)
1351       {
1352         showTranslation_actionPerformed(e);
1353       }
1354     });
1355     showReverse.setText(MessageManager.getString("label.reverse"));
1356     showReverse.addActionListener(new ActionListener()
1357     {
1358       @Override
1359       public void actionPerformed(ActionEvent e)
1360       {
1361         showReverse_actionPerformed(false);
1362       }
1363     });
1364     showReverseComplement.setText(MessageManager
1365             .getString("label.reverse_complement"));
1366     showReverseComplement.addActionListener(new ActionListener()
1367     {
1368       @Override
1369       public void actionPerformed(ActionEvent e)
1370       {
1371         showReverse_actionPerformed(true);
1372       }
1373     });
1374
1375     JMenuItem extractScores = new JMenuItem(
1376             MessageManager.getString("label.extract_scores"));
1377     extractScores.addActionListener(new ActionListener()
1378     {
1379       @Override
1380       public void actionPerformed(ActionEvent e)
1381       {
1382         extractScores_actionPerformed(e);
1383       }
1384     });
1385     extractScores.setVisible(true);
1386     // JBPNote: TODO: make gui for regex based score extraction
1387
1388     // for show products actions see AlignFrame.canShowProducts
1389     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1390
1391     runGroovy.setText(MessageManager.getString("label.run_groovy"));
1392     runGroovy.setToolTipText(MessageManager
1393             .getString("label.run_groovy_tip"));
1394     runGroovy.addActionListener(new ActionListener()
1395     {
1396       @Override
1397       public void actionPerformed(ActionEvent e)
1398       {
1399         runGroovy_actionPerformed();
1400       }
1401     });
1402
1403     JMenuItem openFeatureSettings = new JMenuItem(
1404             MessageManager.getString("action.feature_settings"));
1405     openFeatureSettings.addActionListener(new ActionListener()
1406     {
1407       @Override
1408       public void actionPerformed(ActionEvent e)
1409       {
1410         featureSettings_actionPerformed(e);
1411       }
1412     });
1413     JMenuItem fetchSequence = new JMenuItem(
1414             MessageManager.getString("label.fetch_sequences"));
1415     fetchSequence.addActionListener(new ActionListener()
1416     {
1417       @Override
1418       public void actionPerformed(ActionEvent e)
1419       {
1420         fetchSequence_actionPerformed(e);
1421       }
1422     });
1423
1424     JMenuItem associatedData = new JMenuItem(
1425             MessageManager.getString("label.load_features_annotations"));
1426     associatedData.addActionListener(new ActionListener()
1427     {
1428       @Override
1429       public void actionPerformed(ActionEvent e)
1430       {
1431         associatedData_actionPerformed(e);
1432       }
1433     });
1434     autoCalculate.setText(MessageManager
1435             .getString("label.autocalculate_consensus"));
1436     autoCalculate.setState(jalview.bin.Cache.getDefault(
1437             "AUTO_CALC_CONSENSUS", true));
1438     autoCalculate.addActionListener(new ActionListener()
1439     {
1440       @Override
1441       public void actionPerformed(ActionEvent e)
1442       {
1443         autoCalculate_actionPerformed(e);
1444       }
1445     });
1446     sortByTree.setText(MessageManager
1447             .getString("label.sort_alignment_new_tree"));
1448     sortByTree
1449             .setToolTipText("<html>"
1450                     + MessageManager
1451                             .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1452     sortByTree
1453             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1454     sortByTree.addActionListener(new ActionListener()
1455     {
1456       @Override
1457       public void actionPerformed(ActionEvent e)
1458       {
1459         sortByTreeOption_actionPerformed(e);
1460       }
1461     });
1462
1463     listenToViewSelections.setText(MessageManager
1464             .getString("label.listen_for_selections"));
1465     listenToViewSelections
1466             .setToolTipText("<html>"
1467                     + MessageManager
1468                             .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1469     listenToViewSelections.setState(false);
1470     listenToViewSelections.addActionListener(new ActionListener()
1471     {
1472       @Override
1473       public void actionPerformed(ActionEvent e)
1474       {
1475         listenToViewSelections_actionPerformed(e);
1476       }
1477     });
1478
1479     JMenu addSequenceMenu = new JMenu(
1480             MessageManager.getString("label.add_sequences"));
1481     JMenuItem addFromFile = new JMenuItem(
1482             MessageManager.getString("label.from_file"));
1483     addFromFile.addActionListener(new ActionListener()
1484     {
1485       @Override
1486       public void actionPerformed(ActionEvent e)
1487       {
1488         addFromFile_actionPerformed(e);
1489       }
1490     });
1491     JMenuItem addFromText = new JMenuItem(
1492             MessageManager.getString("label.from_textbox"));
1493     addFromText.addActionListener(new ActionListener()
1494     {
1495       @Override
1496       public void actionPerformed(ActionEvent e)
1497       {
1498         addFromText_actionPerformed(e);
1499       }
1500     });
1501     JMenuItem addFromURL = new JMenuItem(
1502             MessageManager.getString("label.from_url"));
1503     addFromURL.addActionListener(new ActionListener()
1504     {
1505       @Override
1506       public void actionPerformed(ActionEvent e)
1507       {
1508         addFromURL_actionPerformed(e);
1509       }
1510     });
1511     JMenuItem exportFeatures = new JMenuItem(
1512             MessageManager.getString("label.export_features"));
1513     exportFeatures.addActionListener(new ActionListener()
1514     {
1515       @Override
1516       public void actionPerformed(ActionEvent e)
1517       {
1518         exportFeatures_actionPerformed(e);
1519       }
1520     });
1521     JMenuItem exportAnnotations = new JMenuItem(
1522             MessageManager.getString("label.export_annotations"));
1523     exportAnnotations.addActionListener(new ActionListener()
1524     {
1525       @Override
1526       public void actionPerformed(ActionEvent e)
1527       {
1528         exportAnnotations_actionPerformed(e);
1529       }
1530     });
1531     statusPanel.setLayout(new GridLayout());
1532     JMenuItem showAllSeqs = new JMenuItem(
1533             MessageManager.getString("label.all_sequences"));
1534     showAllSeqs.setToolTipText(MessageManager
1535             .getString("label.toggle_sequence_visibility"));
1536     showAllSeqs.addActionListener(new ActionListener()
1537     {
1538       @Override
1539       public void actionPerformed(ActionEvent e)
1540       {
1541         showAllSeqs_actionPerformed(e);
1542       }
1543     });
1544     JMenuItem showAllColumns = new JMenuItem(
1545             MessageManager.getString("label.all_columns"));
1546     showAllColumns.setToolTipText(MessageManager
1547             .getString("label.toggle_columns_visibility"));
1548     showAllColumns.addActionListener(new ActionListener()
1549     {
1550       @Override
1551       public void actionPerformed(ActionEvent e)
1552       {
1553         showAllColumns_actionPerformed(e);
1554       }
1555     });
1556     JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1557     JMenuItem hideSelSequences = new JMenuItem(
1558             MessageManager.getString("label.selected_sequences"));
1559     hideSelSequences.setToolTipText(MessageManager
1560             .getString("label.toggle_sequence_visibility"));
1561     hideSelSequences.addActionListener(new ActionListener()
1562     {
1563       @Override
1564       public void actionPerformed(ActionEvent e)
1565       {
1566         hideSelSequences_actionPerformed(e);
1567       }
1568     });
1569     JMenuItem hideSelColumns = new JMenuItem(
1570             MessageManager.getString("label.selected_columns"));
1571     hideSelColumns.setToolTipText(MessageManager
1572             .getString("label.toggle_columns_visibility"));
1573     hideSelColumns.addActionListener(new ActionListener()
1574     {
1575       @Override
1576       public void actionPerformed(ActionEvent e)
1577       {
1578         hideSelColumns_actionPerformed(e);
1579       }
1580     });
1581     JMenuItem hideAllSelection = new JMenuItem(
1582             MessageManager.getString("label.selected_region"));
1583     hideAllSelection.addActionListener(new ActionListener()
1584     {
1585       @Override
1586       public void actionPerformed(ActionEvent e)
1587       {
1588         hideAllSelection_actionPerformed(e);
1589       }
1590     });
1591     // TODO: should be hidden if no selection exists.
1592     JMenuItem hideAllButSelection = new JMenuItem(
1593             MessageManager.getString("label.all_but_selected_region"));
1594     hideAllButSelection.addActionListener(new ActionListener()
1595     {
1596       @Override
1597       public void actionPerformed(ActionEvent e)
1598       {
1599         hideAllButSelection_actionPerformed(e);
1600       }
1601     });
1602     JMenuItem showAllhidden = new JMenuItem(
1603             MessageManager.getString("label.all_sequences_columns"));
1604     showAllhidden.setToolTipText(MessageManager
1605             .getString("label.toggles_visibility_hidden_selected_regions"));
1606     showAllhidden.addActionListener(new ActionListener()
1607     {
1608       @Override
1609       public void actionPerformed(ActionEvent e)
1610       {
1611         showAllhidden_actionPerformed(e);
1612       }
1613     });
1614     hiddenMarkers.setText(MessageManager
1615             .getString("action.show_hidden_markers"));
1616     hiddenMarkers.addActionListener(new ActionListener()
1617     {
1618       @Override
1619       public void actionPerformed(ActionEvent e)
1620       {
1621         hiddenMarkers_actionPerformed(e);
1622       }
1623     });
1624
1625     JMenuItem invertColSel = new JMenuItem(
1626             MessageManager.getString("action.invert_column_selection"));
1627     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
1628             .getDefaultToolkit().getMenuShortcutKeyMask()
1629             | KeyEvent.ALT_MASK, false);
1630     al = new ActionListener()
1631     {
1632       @Override
1633       public void actionPerformed(ActionEvent e)
1634       {
1635         invertColSel_actionPerformed(e);
1636       }
1637     };
1638     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1639
1640     showComplementMenuItem.setVisible(false);
1641     showComplementMenuItem.addActionListener(new ActionListener()
1642     {
1643       @Override
1644       public void actionPerformed(ActionEvent e)
1645       {
1646         showComplement_actionPerformed(showComplementMenuItem.getState());
1647       }
1648     });
1649
1650     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1651     {
1652       @Override
1653       public void stateChanged(ChangeEvent evt)
1654       {
1655         JTabbedPane pane = (JTabbedPane) evt.getSource();
1656         int sel = pane.getSelectedIndex();
1657         tabSelectionChanged(sel);
1658       }
1659     });
1660     tabbedPane.addMouseListener(new MouseAdapter()
1661     {
1662       @Override
1663       public void mousePressed(MouseEvent e)
1664       {
1665         if (e.isPopupTrigger()) // Mac
1666         {
1667           tabbedPane_mousePressed(e);
1668         }
1669       }
1670
1671       @Override
1672       public void mouseReleased(MouseEvent e)
1673       {
1674         if (e.isPopupTrigger()) // Windows
1675         {
1676           tabbedPane_mousePressed(e);
1677         }
1678       }
1679     });
1680     tabbedPane.addFocusListener(new FocusAdapter()
1681     {
1682       @Override
1683       public void focusGained(FocusEvent e)
1684       {
1685         tabbedPane_focusGained(e);
1686       }
1687     });
1688
1689     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1690     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
1691             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1692     al = new ActionListener()
1693     {
1694       @Override
1695       public void actionPerformed(ActionEvent e)
1696       {
1697         save_actionPerformed(e);
1698       }
1699     };
1700     addMenuActionAndAccelerator(keyStroke, save, al);
1701
1702     reload.setEnabled(false);
1703     reload.setText(MessageManager.getString("action.reload"));
1704     reload.addActionListener(new ActionListener()
1705     {
1706       @Override
1707       public void actionPerformed(ActionEvent e)
1708       {
1709         reload_actionPerformed(e);
1710       }
1711     });
1712
1713     JMenuItem newView = new JMenuItem(
1714             MessageManager.getString("action.new_view"));
1715     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
1716             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1717     al = new ActionListener()
1718     {
1719       @Override
1720       public void actionPerformed(ActionEvent e)
1721       {
1722         newView_actionPerformed(e);
1723       }
1724     };
1725     addMenuActionAndAccelerator(keyStroke, newView, al);
1726
1727     tabbedPane.setToolTipText("<html><i>"
1728             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1729             + "</i></html>");
1730
1731     formatMenu.setText(MessageManager.getString("action.format"));
1732     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1733     idRightAlign.setText(MessageManager
1734             .getString("label.right_align_sequence_id"));
1735     idRightAlign.addActionListener(new ActionListener()
1736     {
1737       @Override
1738       public void actionPerformed(ActionEvent e)
1739       {
1740         idRightAlign_actionPerformed(e);
1741       }
1742     });
1743
1744     gatherViews.setEnabled(false);
1745     gatherViews.setText(MessageManager.getString("action.gather_views"));
1746     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1747     al = new ActionListener()
1748     {
1749       @Override
1750       public void actionPerformed(ActionEvent e)
1751       {
1752         gatherViews_actionPerformed(e);
1753       }
1754     };
1755     addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1756
1757     expandViews.setEnabled(false);
1758     expandViews.setText(MessageManager.getString("action.expand_views"));
1759     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1760     al = new ActionListener()
1761     {
1762       @Override
1763       public void actionPerformed(ActionEvent e)
1764       {
1765         expandViews_actionPerformed(e);
1766       }
1767     };
1768     addMenuActionAndAccelerator(keyStroke, expandViews, al);
1769
1770     JMenuItem pageSetup = new JMenuItem(
1771             MessageManager.getString("action.page_setup"));
1772     pageSetup.addActionListener(new ActionListener()
1773     {
1774       @Override
1775       public void actionPerformed(ActionEvent e)
1776       {
1777         pageSetup_actionPerformed(e);
1778       }
1779     });
1780     JMenuItem alignmentProperties = new JMenuItem(
1781             MessageManager.getString("label.alignment_props"));
1782     alignmentProperties.addActionListener(new ActionListener()
1783     {
1784       @Override
1785       public void actionPerformed(ActionEvent actionEvent)
1786       {
1787         alignmentProperties();
1788       }
1789     });
1790     JMenuItem selectHighlighted = new JMenuItem(
1791             MessageManager.getString("action.select_highlighted_columns"));
1792     selectHighlighted.setToolTipText(MessageManager
1793             .getString("tooltip.select_highlighted_columns"));
1794     al = new ActionListener()
1795     {
1796       @Override
1797       public void actionPerformed(ActionEvent actionEvent)
1798       {
1799         selectHighlightedColumns_actionPerformed(actionEvent);
1800       }
1801     };
1802     selectHighlighted.addActionListener(al);
1803     JMenu tooltipSettingsMenu = new JMenu(
1804             MessageManager.getString("label.sequence_id_tooltip"));
1805     JMenu autoAnnMenu = new JMenu(
1806             MessageManager.getString("label.autocalculated_annotation"));
1807
1808     JMenu exportImageMenu = new JMenu(
1809             MessageManager.getString("label.export_image"));
1810     JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1811     alignFrameMenuBar.add(fileMenu);
1812     alignFrameMenuBar.add(editMenu);
1813     alignFrameMenuBar.add(selectMenu);
1814     alignFrameMenuBar.add(viewMenu);
1815     alignFrameMenuBar.add(annotationsMenu);
1816     alignFrameMenuBar.add(formatMenu);
1817     alignFrameMenuBar.add(colourMenu);
1818     alignFrameMenuBar.add(calculateMenu);
1819     alignFrameMenuBar.add(webService);
1820
1821     fileMenu.add(fetchSequence);
1822     fileMenu.add(addSequenceMenu);
1823     fileMenu.add(reload);
1824     fileMenu.addSeparator();
1825     fileMenu.add(vamsasStore);
1826     fileMenu.add(save);
1827     fileMenu.add(saveAs);
1828     fileMenu.add(outputTextboxMenu);
1829     fileMenu.add(pageSetup);
1830     fileMenu.add(printMenuItem);
1831     fileMenu.addSeparator();
1832     fileMenu.add(exportImageMenu);
1833     fileMenu.add(exportFeatures);
1834     fileMenu.add(exportAnnotations);
1835     fileMenu.add(loadTreeMenuItem);
1836     fileMenu.add(associatedData);
1837     fileMenu.addSeparator();
1838     fileMenu.add(closeMenuItem);
1839
1840     pasteMenu.add(pasteNew);
1841     pasteMenu.add(pasteThis);
1842     editMenu.add(undoMenuItem);
1843     editMenu.add(redoMenuItem);
1844     editMenu.add(cut);
1845     editMenu.add(copy);
1846     editMenu.add(pasteMenu);
1847     editMenu.add(delete);
1848     editMenu.addSeparator();
1849     editMenu.add(remove2LeftMenuItem);
1850     editMenu.add(remove2RightMenuItem);
1851     editMenu.add(removeGappedColumnMenuItem);
1852     editMenu.add(removeAllGapsMenuItem);
1853     editMenu.add(removeRedundancyMenuItem);
1854     editMenu.addSeparator();
1855     // dont add these yet in the CVS build - they cannot be undone!
1856     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1857     // editMenu.add(justifyLeftMenuItem);
1858     // editMenu.add(justifyRightMenuItem);
1859     // editMenu.addSeparator();
1860     editMenu.add(padGapsMenuitem);
1861
1862     showMenu.add(showAllColumns);
1863     showMenu.add(showAllSeqs);
1864     showMenu.add(showAllhidden);
1865     hideMenu.add(hideSelColumns);
1866     hideMenu.add(hideSelSequences);
1867     hideMenu.add(hideAllSelection);
1868     hideMenu.add(hideAllButSelection);
1869     viewMenu.add(newView);
1870     viewMenu.add(expandViews);
1871     viewMenu.add(gatherViews);
1872     viewMenu.addSeparator();
1873     viewMenu.add(showMenu);
1874     viewMenu.add(hideMenu);
1875     viewMenu.add(showComplementMenuItem);
1876     viewMenu.addSeparator();
1877     viewMenu.add(followHighlightMenuItem);
1878     viewMenu.addSeparator();
1879     viewMenu.add(showSeqFeatures);
1880     // viewMenu.add(showSeqFeaturesHeight);
1881     viewMenu.add(openFeatureSettings);
1882     tooltipSettingsMenu.add(showDbRefsMenuitem);
1883     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1884     viewMenu.add(tooltipSettingsMenu);
1885     viewMenu.addSeparator();
1886     viewMenu.add(alignmentProperties);
1887     viewMenu.addSeparator();
1888     viewMenu.add(overviewMenuItem);
1889
1890     annotationsMenu.add(annotationPanelMenuItem);
1891     annotationsMenu.addSeparator();
1892     annotationsMenu.add(showAllAlAnnotations);
1893     annotationsMenu.add(hideAllAlAnnotations);
1894     annotationsMenu.addSeparator();
1895     annotationsMenu.add(showAllSeqAnnotations);
1896     annotationsMenu.add(hideAllSeqAnnotations);
1897     annotationsMenu.add(sortAnnBySequence);
1898     annotationsMenu.add(sortAnnByLabel);
1899     annotationsMenu.addSeparator();
1900     autoAnnMenu.add(showAutoFirst);
1901     autoAnnMenu.add(showAutoLast);
1902     autoAnnMenu.addSeparator();
1903     autoAnnMenu.add(applyAutoAnnotationSettings);
1904     autoAnnMenu.add(showConsensusHistogram);
1905     autoAnnMenu.add(showSequenceLogo);
1906     autoAnnMenu.add(normaliseSequenceLogo);
1907     autoAnnMenu.addSeparator();
1908     autoAnnMenu.add(showGroupConservation);
1909     autoAnnMenu.add(showGroupConsensus);
1910     annotationsMenu.add(autoAnnMenu);
1911
1912
1913     sort.add(sortIDMenuItem);
1914     sort.add(sortLengthMenuItem);
1915     sort.add(sortGroupMenuItem);
1916     sort.add(sortPairwiseMenuItem);
1917     sort.add(sortByTreeMenu);
1918     calculateMenu.add(sort);
1919     calculateMenu.add(calculateTree);
1920     calculateMenu.addSeparator();
1921     calculateMenu.add(pairwiseAlignmentMenuItem);
1922     calculateMenu.add(PCAMenuItem);
1923     calculateMenu.addSeparator();
1924     calculateMenu.add(showTranslation);
1925     calculateMenu.add(showReverse);
1926     calculateMenu.add(showReverseComplement);
1927     calculateMenu.add(showProducts);
1928     calculateMenu.add(autoCalculate);
1929     calculateMenu.add(sortByTree);
1930     calculateMenu.addSeparator();
1931     calculateMenu.add(expandAlignment);
1932     calculateMenu.add(extractScores);
1933     calculateMenu.addSeparator();
1934     calculateMenu.add(runGroovy);
1935
1936     webServiceNoServices = new JMenuItem(
1937             MessageManager.getString("label.no_services"));
1938     webService.add(webServiceNoServices);
1939     exportImageMenu.add(htmlMenuItem);
1940     exportImageMenu.add(epsFile);
1941     exportImageMenu.add(createPNG);
1942     exportImageMenu.add(createBioJS);
1943     exportImageMenu.add(createSVG);
1944     addSequenceMenu.add(addFromFile);
1945     addSequenceMenu.add(addFromText);
1946     addSequenceMenu.add(addFromURL);
1947     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1948     statusPanel.add(statusBar, null);
1949     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1950
1951     formatMenu.add(font);
1952     formatMenu.addSeparator();
1953     formatMenu.add(wrapMenuItem);
1954     formatMenu.add(scaleAbove);
1955     formatMenu.add(scaleLeft);
1956     formatMenu.add(scaleRight);
1957     formatMenu.add(seqLimits);
1958     formatMenu.add(idRightAlign);
1959     formatMenu.add(hiddenMarkers);
1960     formatMenu.add(viewBoxesMenuItem);
1961     formatMenu.add(viewTextMenuItem);
1962     formatMenu.add(colourTextMenuItem);
1963     formatMenu.add(renderGapsMenuItem);
1964     formatMenu.add(centreColumnLabelsMenuItem);
1965     formatMenu.add(showNonconservedMenuItem);
1966     selectMenu.add(findMenuItem);
1967     selectMenu.addSeparator();
1968     selectMenu.add(selectAllSequenceMenuItem);
1969     selectMenu.add(deselectAllSequenceMenuItem);
1970     selectMenu.add(invertSequenceMenuItem);
1971     selectMenu.add(invertColSel);
1972     selectMenu.add(createGroup);
1973     selectMenu.add(unGroup);
1974     selectMenu.add(grpsFromSelection);
1975     selectMenu.add(deleteGroups);
1976     selectMenu.add(annotationColumn);
1977     selectMenu.add(selectHighlighted);
1978     // TODO - determine if the listenToViewSelections button is needed : see bug
1979     // JAL-574
1980     // selectMenu.addSeparator();
1981     // selectMenu.add(listenToViewSelections);
1982   }
1983
1984   /**
1985    * Rebuilds the Colour menu, including any user-defined colours which have
1986    * been loaded either on startup or during the session
1987    */
1988   public void buildColourMenu()
1989   {
1990     colourMenu.removeAll();
1991     colours = new ButtonGroup();
1992
1993     colourMenu.add(applyToAllGroups);
1994     colourMenu.add(textColour);
1995     colourMenu.addSeparator();
1996     colourMenu.add(noColourmenuItem);
1997     colourMenu.add(clustalColour);
1998     colourMenu.add(BLOSUM62Colour);
1999     colourMenu.add(PIDColour);
2000     colourMenu.add(zappoColour);
2001     colourMenu.add(taylorColour);
2002     colourMenu.add(hydrophobicityColour);
2003     colourMenu.add(helixColour);
2004     colourMenu.add(strandColour);
2005     colourMenu.add(turnColour);
2006     colourMenu.add(buriedColour);
2007     colourMenu.add(nucleotideColour);
2008     colourMenu.add(purinePyrimidineColour);
2009     // colourMenu.add(RNAInteractionColour);
2010     // colourMenu.add(covariationColour);
2011     colourMenu.add(tcoffeeColour);
2012
2013     /*
2014      * add any user-defined colours
2015      */
2016     Map<String, UserColourScheme> userColourSchemes = UserDefinedColours
2017             .getUserColourSchemes();
2018     if (userColourSchemes != null)
2019     {
2020       for (String userColour : userColourSchemes.keySet())
2021       {
2022         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
2023                 userColour);
2024         radioItem.setName(userColour);
2025         radioItem.addMouseListener(new MouseAdapter()
2026         {
2027           @Override
2028           public void mousePressed(MouseEvent evt)
2029           {
2030             if (evt.isPopupTrigger()) // Mac
2031             {
2032               offerRemoval();
2033             }
2034           }
2035
2036           @Override
2037           public void mouseReleased(MouseEvent evt)
2038           {
2039             if (evt.isPopupTrigger()) // Windows
2040             {
2041               offerRemoval();
2042             }
2043           }
2044
2045           void offerRemoval()
2046           {
2047             radioItem.removeActionListener(radioItem.getActionListeners()[0]);
2048
2049             int option = JvOptionPane.showInternalConfirmDialog(
2050                     Desktop.desktop, MessageManager
2051                             .getString("label.remove_from_default_list"),
2052                     MessageManager
2053                             .getString("label.remove_user_defined_colour"),
2054                     JvOptionPane.YES_NO_OPTION);
2055             if (option == JvOptionPane.YES_OPTION)
2056             {
2057               UserDefinedColours.removeColourFromDefaults(radioItem
2058                       .getText());
2059               colourMenu.remove(radioItem);
2060             }
2061             else
2062             {
2063               radioItem.addActionListener(new ActionListener()
2064               {
2065                 @Override
2066                 public void actionPerformed(ActionEvent evt)
2067                 {
2068                   userDefinedColour_actionPerformed(evt);
2069                 }
2070               });
2071             }
2072           }
2073         });
2074         radioItem.addActionListener(new ActionListener()
2075         {
2076           @Override
2077           public void actionPerformed(ActionEvent evt)
2078           {
2079             userDefinedColour_actionPerformed(evt);
2080           }
2081         });
2082         colourMenu.add(radioItem);
2083         colours.add(radioItem);
2084       }
2085     }
2086
2087     colourMenu.add(userDefinedColour);
2088     colourMenu.addSeparator();
2089     colourMenu.add(conservationMenuItem);
2090     colourMenu.add(modifyConservation);
2091     colourMenu.add(abovePIDThreshold);
2092     colourMenu.add(modifyPID);
2093     colourMenu.add(annotationColour);
2094     colourMenu.add(rnahelicesColour);
2095
2096     /*
2097      * add colours to a ButtonGroup to make their
2098      * selection mutually exclusive
2099      */
2100     colours.add(noColourmenuItem);
2101     colours.add(clustalColour);
2102     colours.add(zappoColour);
2103     colours.add(taylorColour);
2104     colours.add(hydrophobicityColour);
2105     colours.add(helixColour);
2106     colours.add(strandColour);
2107     colours.add(turnColour);
2108     colours.add(buriedColour);
2109     colours.add(userDefinedColour);
2110     colours.add(PIDColour);
2111     colours.add(BLOSUM62Colour);
2112     colours.add(nucleotideColour);
2113     colours.add(purinePyrimidineColour);
2114     // colours.add(covariationColour);
2115     colours.add(tcoffeeColour);
2116     // colours.add(RNAInteractionColour);
2117     setColourSelected(Cache.getDefault(Preferences.DEFAULT_COLOUR,
2118             ResidueColourScheme.NONE));
2119
2120   }
2121
2122   /**
2123    * Constructs the entries on the Colour menu (but does not add them to the
2124    * menu). The 'name' property of each item is set to the canonical name of the
2125    * corresponding colour scheme (may not match the display name), to allow
2126    * selection of items by colour scheme name.
2127    */
2128   protected void initColourMenu()
2129   {
2130     applyToAllGroups = new JCheckBoxMenuItem(
2131             MessageManager.getString("label.apply_colour_to_all_groups"));
2132     applyToAllGroups.addActionListener(new ActionListener()
2133     {
2134       @Override
2135       public void actionPerformed(ActionEvent e)
2136       {
2137         applyToAllGroups_actionPerformed();
2138       }
2139     });
2140
2141     textColour = new JRadioButtonMenuItem(
2142             MessageManager.getString("action.set_text_colour"));
2143     textColour.addActionListener(new ActionListener()
2144     {
2145       @Override
2146       public void actionPerformed(ActionEvent e)
2147       {
2148         textColour_actionPerformed();
2149       }
2150     });
2151     clustalColour = new JRadioButtonMenuItem(
2152             MessageManager.getString("label.clustalx"));
2153     clustalColour.setName(JalviewColourScheme.Clustal.toString());
2154     clustalColour.addActionListener(new ActionListener()
2155     {
2156       @Override
2157       public void actionPerformed(ActionEvent e)
2158       {
2159         clustalColour_actionPerformed();
2160       }
2161     });
2162     zappoColour = new JRadioButtonMenuItem(
2163             MessageManager.getString("label.zappo"));
2164     zappoColour.setName(JalviewColourScheme.Zappo.toString());
2165     zappoColour.addActionListener(new ActionListener()
2166     {
2167       @Override
2168       public void actionPerformed(ActionEvent e)
2169       {
2170         zappoColour_actionPerformed();
2171       }
2172     });
2173     taylorColour = new JRadioButtonMenuItem(
2174             MessageManager.getString("label.taylor"));
2175     taylorColour.setName(JalviewColourScheme.Taylor.toString());
2176     taylorColour.addActionListener(new ActionListener()
2177     {
2178       @Override
2179       public void actionPerformed(ActionEvent e)
2180       {
2181         taylorColour_actionPerformed();
2182       }
2183     });
2184     hydrophobicityColour = new JRadioButtonMenuItem(
2185             MessageManager
2186             .getString("label.hydrophobicity"));
2187     hydrophobicityColour
2188             .setName(JalviewColourScheme.Hydrophobic.toString());
2189     hydrophobicityColour.addActionListener(new ActionListener()
2190     {
2191       @Override
2192       public void actionPerformed(ActionEvent e)
2193       {
2194         hydrophobicityColour_actionPerformed();
2195       }
2196     });
2197     helixColour = new JRadioButtonMenuItem(
2198             MessageManager.getString("label.helix_propensity"));
2199     helixColour.setName(JalviewColourScheme.Helix.toString());
2200     helixColour.addActionListener(new ActionListener()
2201     {
2202       @Override
2203       public void actionPerformed(ActionEvent e)
2204       {
2205         helixColour_actionPerformed();
2206       }
2207     });
2208     strandColour = new JRadioButtonMenuItem(
2209             MessageManager
2210             .getString("label.strand_propensity"));
2211     strandColour.setName(JalviewColourScheme.Strand.toString());
2212     strandColour.addActionListener(new ActionListener()
2213     {
2214       @Override
2215       public void actionPerformed(ActionEvent e)
2216       {
2217         strandColour_actionPerformed();
2218       }
2219     });
2220     turnColour = new JRadioButtonMenuItem(
2221             MessageManager.getString("label.turn_propensity"));
2222     turnColour.setName(JalviewColourScheme.Turn.toString());
2223     turnColour.addActionListener(new ActionListener()
2224     {
2225       @Override
2226       public void actionPerformed(ActionEvent e)
2227       {
2228         turnColour_actionPerformed();
2229       }
2230     });
2231     buriedColour = new JRadioButtonMenuItem(
2232             MessageManager.getString("label.buried_index"));
2233     buriedColour.setName(JalviewColourScheme.Buried.toString());
2234     buriedColour.addActionListener(new ActionListener()
2235     {
2236       @Override
2237       public void actionPerformed(ActionEvent e)
2238       {
2239         buriedColour_actionPerformed();
2240       }
2241     });
2242     userDefinedColour = new JRadioButtonMenuItem(
2243             MessageManager
2244             .getString("action.user_defined"));
2245     userDefinedColour.setName(JalviewColourScheme.UserDefined.toString());
2246     userDefinedColour.addActionListener(new ActionListener()
2247     {
2248       @Override
2249       public void actionPerformed(ActionEvent e)
2250       {
2251         userDefinedColour_actionPerformed(e);
2252       }
2253     });
2254     PIDColour = new JRadioButtonMenuItem(
2255             MessageManager.getString("label.percentage_identity"));
2256     PIDColour.setName(JalviewColourScheme.PID.toString());
2257     PIDColour.addActionListener(new ActionListener()
2258     {
2259       @Override
2260       public void actionPerformed(ActionEvent e)
2261       {
2262         PIDColour_actionPerformed();
2263       }
2264     });
2265     BLOSUM62Colour = new JRadioButtonMenuItem(
2266             MessageManager.getString("label.blosum62_score"));
2267     BLOSUM62Colour.setName(JalviewColourScheme.Blosum62.toString());
2268     BLOSUM62Colour.addActionListener(new ActionListener()
2269     {
2270       @Override
2271       public void actionPerformed(ActionEvent e)
2272       {
2273         BLOSUM62Colour_actionPerformed();
2274       }
2275     });
2276     nucleotideColour = new JRadioButtonMenuItem(
2277             MessageManager.getString("label.nucleotide"));
2278     nucleotideColour.setName(JalviewColourScheme.Nucleotide.toString());
2279     nucleotideColour.addActionListener(new ActionListener()
2280     {
2281       @Override
2282       public void actionPerformed(ActionEvent e)
2283       {
2284         nucleotideColour_actionPerformed();
2285       }
2286     });
2287     purinePyrimidineColour = new JRadioButtonMenuItem(
2288             MessageManager.getString("label.purine_pyrimidine"));
2289     purinePyrimidineColour.setName(JalviewColourScheme.PurinePyrimidine.toString());
2290     purinePyrimidineColour.addActionListener(new ActionListener()
2291     {
2292       @Override
2293       public void actionPerformed(ActionEvent e)
2294       {
2295         purinePyrimidineColour_actionPerformed();
2296       }
2297     });
2298
2299     tcoffeeColour = new JRadioButtonMenuItem(
2300             MessageManager.getString("label.tcoffee_scores"));
2301     tcoffeeColour.setName(JalviewColourScheme.TCoffee.toString());
2302     tcoffeeColour.setEnabled(false);
2303     tcoffeeColour.addActionListener(new ActionListener()
2304     {
2305
2306       @Override
2307       public void actionPerformed(ActionEvent e)
2308       {
2309         tcoffeeColorScheme_actionPerformed();
2310       }
2311     });
2312
2313     // RNAInteractionColour = new JRadioButtonMenuItem("RNA Interaction type");
2314     // RNAInteractionColour.setName("RNA Interaction");
2315     // RNAInteractionColour.addActionListener(new ActionListener()
2316     // {
2317     // @Override
2318     // public void actionPerformed(ActionEvent e)
2319     // {
2320     // RNAInteractionColour_actionPerformed();
2321     // }
2322     // });
2323     /*
2324      * covariationColour = new JRadioButtonMenuItem("Covariation");
2325      * covariationColour.addActionListener(new ActionListener() { public void
2326      * actionPerformed(ActionEvent e) { covariationColour_actionPerformed(); }
2327      * });
2328      */
2329
2330     conservationMenuItem = new JCheckBoxMenuItem(
2331             MessageManager.getString("action.by_conservation"));
2332     conservationMenuItem.addActionListener(new ActionListener()
2333     {
2334       @Override
2335       public void actionPerformed(ActionEvent e)
2336       {
2337         conservationMenuItem_actionPerformed();
2338       }
2339     });
2340     noColourmenuItem = new JRadioButtonMenuItem(
2341             MessageManager.getString("label.none"));
2342     noColourmenuItem.setName("None");
2343     noColourmenuItem.addActionListener(new ActionListener()
2344     {
2345       @Override
2346       public void actionPerformed(ActionEvent e)
2347       {
2348         noColourmenuItem_actionPerformed();
2349       }
2350     });
2351
2352     abovePIDThreshold = new JCheckBoxMenuItem(
2353             MessageManager.getString("label.above_identity_threshold"));
2354     abovePIDThreshold.addActionListener(new ActionListener()
2355     {
2356       @Override
2357       public void actionPerformed(ActionEvent e)
2358       {
2359         abovePIDThreshold_actionPerformed();
2360       }
2361     });
2362     modifyPID = new JMenuItem(
2363             MessageManager.getString("label.modify_identity_threshold"));
2364     modifyPID.addActionListener(new ActionListener()
2365     {
2366       @Override
2367       public void actionPerformed(ActionEvent e)
2368       {
2369         modifyPID_actionPerformed();
2370       }
2371     });
2372     modifyConservation = new JMenuItem(
2373             MessageManager
2374             .getString("label.modify_conservation_threshold"));
2375     modifyConservation.addActionListener(new ActionListener()
2376     {
2377       @Override
2378       public void actionPerformed(ActionEvent e)
2379       {
2380         modifyConservation_actionPerformed();
2381       }
2382     });
2383
2384     annotationColour = new JMenuItem(
2385             MessageManager.getString("action.by_annotation"));
2386     annotationColour.addActionListener(new ActionListener()
2387     {
2388       @Override
2389       public void actionPerformed(ActionEvent e)
2390       {
2391         annotationColour_actionPerformed();
2392       }
2393     });
2394
2395     rnahelicesColour = new JMenuItem(
2396             MessageManager.getString("action.by_rna_helixes"));
2397     rnahelicesColour.addActionListener(new ActionListener()
2398     {
2399       @Override
2400       public void actionPerformed(ActionEvent e)
2401       {
2402         rnahelicesColour_actionPerformed();
2403       }
2404     });
2405   }
2406
2407   protected void selectHighlightedColumns_actionPerformed(
2408           ActionEvent actionEvent)
2409   {
2410     // TODO Auto-generated method stub
2411
2412   }
2413
2414   /**
2415    * Generate the reverse sequence (or reverse complement if the flag is true)
2416    * and add it to the alignment
2417    *
2418    * @param complement
2419    */
2420   protected void showReverse_actionPerformed(boolean complement)
2421   {
2422   }
2423
2424   /**
2425    * Try to run script in a Groovy console, having first ensured that this
2426    * alignframe is set as currentAlignFrame in Desktop
2427    */
2428   protected void runGroovy_actionPerformed()
2429   {
2430
2431   }
2432
2433   /**
2434    * Adds the given action listener and key accelerator to the given menu item.
2435    * Also saves in a lookup table to support lookup of action by key stroke.
2436    *
2437    * @param keyStroke
2438    * @param menuItem
2439    * @param actionListener
2440    */
2441   protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2442           JMenuItem menuItem, ActionListener actionListener)
2443   {
2444     menuItem.setAccelerator(keyStroke);
2445     accelerators.put(keyStroke, menuItem);
2446     menuItem.addActionListener(actionListener);
2447   }
2448
2449   /**
2450    * Action on clicking sort annotations by type.
2451    *
2452    * @param sortOrder
2453    */
2454   protected void sortAnnotations_actionPerformed()
2455   {
2456   }
2457
2458   /**
2459    * Action on clicking Show all annotations.
2460    *
2461    * @param forSequences
2462    *          update sequence-related annotations
2463    * @param forAlignment
2464    *          update non-sequence-related annotations
2465    */
2466   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2467           boolean forAlignment)
2468   {
2469     setAnnotationsVisibility(true, forSequences, forAlignment);
2470   }
2471
2472   /**
2473    * Action on clicking Hide all annotations.
2474    *
2475    * @param forSequences
2476    *          update sequence-related annotations
2477    * @param forAlignment
2478    *          update non-sequence-related annotations
2479    */
2480   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2481           boolean forAlignment)
2482   {
2483     setAnnotationsVisibility(false, forSequences, forAlignment);
2484   }
2485
2486   /**
2487    * Set the visibility of annotations to true or false. Can act on
2488    * sequence-related annotations, or alignment-related, or both.
2489    *
2490    * @param visible
2491    * @param forSequences
2492    *          update sequence-related annotations
2493    * @param forAlignment
2494    *          update non-sequence-related annotations
2495    */
2496   protected void setAnnotationsVisibility(boolean visible,
2497           boolean forSequences, boolean forAlignment)
2498   {
2499
2500   }
2501
2502   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2503   {
2504     // TODO Auto-generated method stub
2505
2506   }
2507
2508   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2509   {
2510     // TODO Auto-generated method stub
2511
2512   }
2513
2514   protected void showAllhidden_actionPerformed(ActionEvent e)
2515   {
2516     // TODO Auto-generated method stub
2517
2518   }
2519
2520   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2521   {
2522     // TODO Auto-generated method stub
2523
2524   }
2525
2526   protected void hideAllSelection_actionPerformed(ActionEvent e)
2527   {
2528     // TODO Auto-generated method stub
2529
2530   }
2531
2532   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2533   {
2534     // TODO Auto-generated method stub
2535
2536   }
2537
2538   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2539   {
2540     // TODO Auto-generated method stub
2541
2542   }
2543
2544   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2545   {
2546     // TODO Auto-generated method stub
2547
2548   }
2549
2550   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2551   {
2552     // TODO Auto-generated method stub
2553
2554   }
2555
2556   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2557   {
2558     // TODO Auto-generated method stub
2559
2560   }
2561
2562   protected void showGroupConservation_actionPerformed(ActionEvent e)
2563   {
2564     // TODO Auto-generated method stub
2565
2566   }
2567
2568   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2569   {
2570     // TODO Auto-generated method stub
2571
2572   }
2573
2574   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2575   {
2576     // TODO Auto-generated method stub
2577
2578   }
2579
2580   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2581   {
2582     // TODO Auto-generated method stub
2583
2584   }
2585
2586   protected void followHighlight_actionPerformed()
2587   {
2588     // TODO Auto-generated method stub
2589
2590   }
2591
2592   protected void showNpFeats_actionPerformed(ActionEvent e)
2593   {
2594     // TODO Auto-generated method stub
2595
2596   }
2597
2598   protected void showDbRefs_actionPerformed(ActionEvent e)
2599   {
2600     // TODO Auto-generated method stub
2601
2602   }
2603
2604   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2605   {
2606   }
2607
2608   protected void buildSortByAnnotationScoresMenu()
2609   {
2610   }
2611
2612   protected void extractScores_actionPerformed(ActionEvent e)
2613   {
2614   }
2615
2616   protected void outputText_actionPerformed(ActionEvent e)
2617   {
2618   }
2619
2620   public void addFromFile_actionPerformed(ActionEvent e)
2621   {
2622
2623   }
2624
2625   public void addFromText_actionPerformed(ActionEvent e)
2626   {
2627
2628   }
2629
2630   public void addFromURL_actionPerformed(ActionEvent e)
2631   {
2632
2633   }
2634
2635   public void exportFeatures_actionPerformed(ActionEvent e)
2636   {
2637
2638   }
2639
2640   public void exportAnnotations_actionPerformed(ActionEvent e)
2641   {
2642
2643   }
2644
2645   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2646   {
2647   }
2648
2649   protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2650   {
2651
2652   }
2653
2654   protected void closeMenuItem_actionPerformed(boolean b)
2655   {
2656   }
2657
2658   protected void redoMenuItem_actionPerformed(ActionEvent e)
2659   {
2660   }
2661
2662   protected void undoMenuItem_actionPerformed(ActionEvent e)
2663   {
2664   }
2665
2666   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2667   {
2668   }
2669
2670   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2671   {
2672   }
2673
2674   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2675   {
2676   }
2677
2678   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2679   {
2680   }
2681
2682   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2683   {
2684   }
2685
2686   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2687   {
2688   }
2689
2690   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2691   {
2692   }
2693
2694   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2695   {
2696   }
2697
2698   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2699   {
2700   }
2701
2702   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2703   {
2704   }
2705
2706   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2707   {
2708   }
2709
2710   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2711   {
2712   }
2713
2714   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2715   {
2716   }
2717
2718   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2719   {
2720   }
2721
2722   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2723   {
2724   }
2725
2726   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2727   {
2728   }
2729
2730   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2731   {
2732   }
2733
2734   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2735   {
2736   }
2737
2738   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2739   {
2740   }
2741
2742   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2743   {
2744   }
2745
2746   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2747   {
2748   }
2749
2750   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2751   {
2752   }
2753
2754   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2755   {
2756   }
2757
2758   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2759   {
2760   }
2761
2762   protected void clustalColour_actionPerformed()
2763   {
2764   }
2765
2766   protected void zappoColour_actionPerformed()
2767   {
2768   }
2769
2770   protected void taylorColour_actionPerformed()
2771   {
2772   }
2773
2774   protected void hydrophobicityColour_actionPerformed()
2775   {
2776   }
2777
2778   protected void helixColour_actionPerformed()
2779   {
2780   }
2781
2782   protected void strandColour_actionPerformed()
2783   {
2784   }
2785
2786   protected void turnColour_actionPerformed()
2787   {
2788   }
2789
2790   protected void buriedColour_actionPerformed()
2791   {
2792   }
2793
2794   protected void userDefinedColour_actionPerformed(ActionEvent e)
2795   {
2796   }
2797
2798   protected void PIDColour_actionPerformed()
2799   {
2800   }
2801
2802   protected void BLOSUM62Colour_actionPerformed()
2803   {
2804   }
2805
2806   protected void purinePyrimidineColour_actionPerformed()
2807   {
2808   }
2809
2810   protected void RNAInteractionColour_actionPerformed()
2811   {
2812   }
2813
2814   /*
2815    * protected void covariationColour_actionPerformed() { }
2816    */
2817
2818   protected void noColourmenuItem_actionPerformed()
2819   {
2820   }
2821
2822   protected void conservationMenuItem_actionPerformed()
2823   {
2824   }
2825
2826   protected void printMenuItem_actionPerformed(ActionEvent e)
2827   {
2828   }
2829
2830   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2831   {
2832   }
2833
2834   protected void findMenuItem_actionPerformed(ActionEvent e)
2835   {
2836   }
2837
2838   protected void abovePIDThreshold_actionPerformed()
2839   {
2840   }
2841
2842   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2843   {
2844   }
2845
2846   protected void nucleotideColour_actionPerformed()
2847   {
2848   }
2849
2850   protected void deleteGroups_actionPerformed(ActionEvent e)
2851   {
2852   }
2853
2854   protected void createGroup_actionPerformed(ActionEvent e)
2855   {
2856   }
2857
2858   protected void unGroup_actionPerformed(ActionEvent e)
2859   {
2860   }
2861
2862   protected void copy_actionPerformed(ActionEvent e)
2863   {
2864   }
2865
2866   protected void cut_actionPerformed(ActionEvent e)
2867   {
2868   }
2869
2870   protected void delete_actionPerformed(ActionEvent e)
2871   {
2872   }
2873
2874   protected void pasteNew_actionPerformed(ActionEvent e)
2875   {
2876   }
2877
2878   protected void pasteThis_actionPerformed(ActionEvent e)
2879   {
2880   }
2881
2882   protected void applyToAllGroups_actionPerformed()
2883   {
2884   }
2885
2886   public void createPNG(java.io.File f)
2887   {
2888   }
2889
2890   protected void font_actionPerformed(ActionEvent e)
2891   {
2892   }
2893
2894   protected void seqLimit_actionPerformed(ActionEvent e)
2895   {
2896   }
2897
2898   public void seqDBRef_actionPerformed(ActionEvent e)
2899   {
2900
2901   }
2902
2903   public void createEPS(java.io.File f)
2904   {
2905   }
2906
2907   public void createSVG(java.io.File f)
2908   {
2909
2910   }
2911
2912   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2913   {
2914
2915   }
2916
2917   /**
2918    * Template method to handle the 'load T-Coffee scores' menu event.
2919    * <p>
2920    * Subclasses override this method to provide a custom action.
2921    *
2922    * @param event
2923    *          The raised event
2924    */
2925   protected void loadScores_actionPerformed(ActionEvent event)
2926   {
2927
2928   }
2929
2930   /**
2931    * Template method to handle the 'Color T-Coffee scores' menu event.
2932    * <p>
2933    * Subclasses override this method to provide a custom action.
2934    */
2935   protected void tcoffeeColorScheme_actionPerformed()
2936   {
2937
2938   }
2939
2940   protected void jpred_actionPerformed(ActionEvent e)
2941   {
2942   }
2943
2944   protected void scaleAbove_actionPerformed(ActionEvent e)
2945   {
2946   }
2947
2948   protected void scaleLeft_actionPerformed(ActionEvent e)
2949   {
2950   }
2951
2952   protected void scaleRight_actionPerformed(ActionEvent e)
2953   {
2954   }
2955
2956   protected void modifyPID_actionPerformed()
2957   {
2958   }
2959
2960   protected void modifyConservation_actionPerformed()
2961   {
2962   }
2963
2964   protected void saveAs_actionPerformed(ActionEvent e)
2965   {
2966   }
2967
2968   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2969   {
2970   }
2971
2972   public void vamsasStore_actionPerformed(ActionEvent e)
2973   {
2974
2975   }
2976
2977   public void vamsasLoad_actionPerformed(ActionEvent e)
2978   {
2979
2980   }
2981
2982   public void showTranslation_actionPerformed(ActionEvent e)
2983   {
2984
2985   }
2986
2987   public void featureSettings_actionPerformed(ActionEvent e)
2988   {
2989
2990   }
2991
2992   public void fetchSequence_actionPerformed(ActionEvent e)
2993   {
2994
2995   }
2996
2997   public void smoothFont_actionPerformed(ActionEvent e)
2998   {
2999
3000   }
3001
3002   public void annotationColour_actionPerformed()
3003   {
3004   }
3005
3006   public void annotationColumn_actionPerformed(ActionEvent e)
3007   {
3008   }
3009
3010   public void rnahelicesColour_actionPerformed()
3011   {
3012
3013   }
3014
3015   public void associatedData_actionPerformed(ActionEvent e)
3016   {
3017
3018   }
3019
3020   public void autoCalculate_actionPerformed(ActionEvent e)
3021   {
3022
3023   }
3024
3025   public void sortByTreeOption_actionPerformed(ActionEvent e)
3026   {
3027
3028   }
3029
3030   public void showAllSeqs_actionPerformed(ActionEvent e)
3031   {
3032
3033   }
3034
3035   public void showAllColumns_actionPerformed(ActionEvent e)
3036   {
3037
3038   }
3039
3040   public void hideSelSequences_actionPerformed(ActionEvent e)
3041   {
3042
3043   }
3044
3045   public void hideSelColumns_actionPerformed(ActionEvent e)
3046   {
3047
3048   }
3049
3050   public void hiddenMarkers_actionPerformed(ActionEvent e)
3051   {
3052
3053   }
3054
3055   public void findPdbId_actionPerformed(ActionEvent e)
3056   {
3057
3058   }
3059
3060   public void enterPdbId_actionPerformed(ActionEvent e)
3061   {
3062
3063   }
3064
3065   public void pdbFile_actionPerformed(ActionEvent e)
3066   {
3067
3068   }
3069
3070   public void invertColSel_actionPerformed(ActionEvent e)
3071   {
3072
3073   }
3074
3075   public void tabSelectionChanged(int sel)
3076   {
3077
3078   }
3079
3080   public void tabbedPane_mousePressed(MouseEvent e)
3081   {
3082
3083   }
3084
3085   public void tabbedPane_focusGained(FocusEvent e)
3086   {
3087     requestFocus();
3088   }
3089
3090   public void save_actionPerformed(ActionEvent e)
3091   {
3092
3093   }
3094
3095   public void reload_actionPerformed(ActionEvent e)
3096   {
3097
3098   }
3099
3100   public void newView_actionPerformed(ActionEvent e)
3101   {
3102
3103   }
3104
3105   public void textColour_actionPerformed()
3106   {
3107
3108   }
3109
3110   public void idRightAlign_actionPerformed(ActionEvent e)
3111   {
3112
3113   }
3114
3115   public void expandViews_actionPerformed(ActionEvent e)
3116   {
3117
3118   }
3119
3120   public void gatherViews_actionPerformed(ActionEvent e)
3121   {
3122
3123   }
3124
3125   public void buildTreeMenu()
3126   {
3127
3128   }
3129
3130   public void pageSetup_actionPerformed(ActionEvent e)
3131   {
3132
3133   }
3134
3135   public void alignmentProperties()
3136   {
3137
3138   }
3139
3140   protected void expand_newalign(ActionEvent e)
3141   {
3142     // TODO Auto-generated method stub
3143
3144   }
3145
3146   protected boolean isShowAutoCalculatedAbove()
3147   {
3148     return showAutoCalculatedAbove;
3149   }
3150
3151   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
3152   {
3153     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
3154   }
3155
3156   protected SequenceAnnotationOrder getAnnotationSortOrder()
3157   {
3158     return annotationSortOrder;
3159   }
3160
3161   protected void setAnnotationSortOrder(
3162           SequenceAnnotationOrder annotationSortOrder)
3163   {
3164     this.annotationSortOrder = annotationSortOrder;
3165   }
3166
3167   public Map<KeyStroke, JMenuItem> getAccelerators()
3168   {
3169     return this.accelerators;
3170   }
3171
3172   /**
3173    * Returns the selected index of the tabbed pane, or -1 if none selected
3174    * (including the case where the tabbed pane has not been made visible).
3175    *
3176    * @return
3177    */
3178   public int getTabIndex()
3179   {
3180     return tabbedPane.getSelectedIndex();
3181   }
3182
3183   public JPanel getStatusPanel()
3184   {
3185     return statusPanel;
3186   }
3187
3188   /**
3189    * Sets a reference to the containing split frame. Also makes the 'toggle
3190    * split view' menu item visible and checked.
3191    *
3192    * @param sf
3193    */
3194   public void setSplitFrame(SplitContainerI sf)
3195   {
3196     this.splitFrame = sf;
3197     if (sf != null)
3198     {
3199       this.showComplementMenuItem.setVisible(true);
3200       this.showComplementMenuItem.setState(true);
3201     }
3202   }
3203
3204   public SplitContainerI getSplitViewContainer()
3205   {
3206     return this.splitFrame;
3207   }
3208
3209   protected void showComplement_actionPerformed(boolean complement)
3210   {
3211   }
3212 }