src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 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.schemes.ColourSchemeProperty;
  24 import jalview.util.MessageManager;
  25
  26 import java.awt.BorderLayout;
  27 import java.awt.Color;
  28 import java.awt.GridLayout;
  29 import java.awt.Toolkit;
  30 import java.awt.event.ActionEvent;
  31 import java.awt.event.ActionListener;
  32 import java.awt.event.FocusAdapter;
  33 import java.awt.event.FocusEvent;
  34 import java.awt.event.MouseAdapter;
  35 import java.awt.event.MouseEvent;
  36
  37 import javax.swing.BorderFactory;
  38 import javax.swing.ButtonGroup;
  39 import javax.swing.JCheckBoxMenuItem;
  40 import javax.swing.JInternalFrame;
  41 import javax.swing.JLabel;
  42 import javax.swing.JMenu;
  43 import javax.swing.JMenuBar;
  44 import javax.swing.JMenuItem;
  45 import javax.swing.JOptionPane;
  46 import javax.swing.JPanel;
  47 import javax.swing.JRadioButtonMenuItem;
  48 import javax.swing.JTabbedPane;
  49 import javax.swing.SwingUtilities;
  50 import javax.swing.event.ChangeEvent;
  51 import javax.swing.event.MenuEvent;
  52 import javax.swing.event.MenuListener;
  53
  54 public class GAlignFrame extends JInternalFrame
  55 {
  56   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  57
  58   protected JMenu fileMenu = new JMenu();
  59
  60   protected JMenuItem closeMenuItem = new JMenuItem();
  61
  62   protected JMenu editMenu = new JMenu();
  63
  64   protected JMenu viewMenu = new JMenu();
  65
  66   protected JMenu colourMenu = new JMenu();
  67
  68   protected JMenu calculateMenu = new JMenu();
  69
  70   protected JMenu webService = new JMenu();
  71
  72   protected JMenuItem webServiceNoServices;
  73
  74   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  75
  76   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  77
  78   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  79
  80   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  81
  82   protected JMenuItem remove2RightMenuItem = new JMenuItem();
  83
  84   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  85
  86   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  87
  88   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  89
  90   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  91
  92   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  93
  94   protected JMenuItem sortIDMenuItem = new JMenuItem();
  95
  96   protected JMenuItem sortLengthMenuItem = new JMenuItem();
  97
  98   protected JMenuItem sortGroupMenuItem = new JMenuItem();
  99
 100   protected JMenu sortByAnnotScore = new JMenu();
 101
 102   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
 103
 104   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
 105
 106   protected JMenuItem PCAMenuItem = new JMenuItem();
 107
 108   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
 109
 110   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
 111
 112   BorderLayout borderLayout1 = new BorderLayout();
 113
 114   public JLabel statusBar = new JLabel();
 115
 116   protected JMenuItem saveAs = new JMenuItem();
 117
 118   protected JMenu outputTextboxMenu = new JMenu();
 119
 120   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
 121
 122   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
 123
 124   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
 125
 126   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
 127
 128   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
 129
 130   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
 131
 132   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
 133
 134   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 135
 136   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
 137
 138   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
 139
 140   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 141
 142   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
 143
 144   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
 145
 146   protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
 147
 148   // protected JRadioButtonMenuItem covariationColour = new
 149   // JRadioButtonMenuItem();
 150
 151   protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
 152
 153   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 154
 155   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
 156
 157   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 158
 159   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 160
 161   public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
 162
 163   JMenuItem htmlMenuItem = new JMenuItem();
 164
 165   JMenuItem overviewMenuItem = new JMenuItem();
 166
 167   protected JMenuItem undoMenuItem = new JMenuItem();
 168
 169   protected JMenuItem redoMenuItem = new JMenuItem();
 170
 171   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 172
 173   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 174
 175   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 176
 177   JMenuItem printMenuItem = new JMenuItem();
 178
 179   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 180
 181   JMenuItem findMenuItem = new JMenuItem();
 182
 183   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 184
 185   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 186
 187   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 188
 189   JMenuItem chooseAnnotations = new JMenuItem();
 190
 191   JMenuItem deleteGroups = new JMenuItem();
 192
 193   JMenuItem createGroup = new JMenuItem();
 194
 195   JMenuItem unGroup = new JMenuItem();
 196
 197   JMenuItem delete = new JMenuItem();
 198
 199   JMenuItem copy = new JMenuItem();
 200
 201   JMenuItem cut = new JMenuItem();
 202
 203   JMenu pasteMenu = new JMenu();
 204
 205   JMenuItem pasteNew = new JMenuItem();
 206
 207   JMenuItem pasteThis = new JMenuItem();
 208
 209   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
 210
 211   JMenuItem createPNG = new JMenuItem();
 212
 213   protected JMenuItem font = new JMenuItem();
 214
 215   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 216
 217   JMenuItem epsFile = new JMenuItem();
 218
 219   JMenuItem LoadtreeMenuItem = new JMenuItem();
 220
 221   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 222
 223   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 224
 225   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 226
 227   protected JMenuItem modifyPID = new JMenuItem();
 228
 229   protected JMenuItem modifyConservation = new JMenuItem();
 230
 231   protected JMenu sortByTreeMenu = new JMenu();
 232
 233   protected JMenu sort = new JMenu();
 234
 235   protected JMenu calculateTree = new JMenu();
 236
 237   JMenu jMenu2 = new JMenu();
 238
 239   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 240
 241   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 242
 243   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 244
 245   protected ButtonGroup colours = new ButtonGroup();
 246
 247   JMenuItem vamsasStore = new JMenuItem();
 248
 249   protected JMenuItem showTranslation = new JMenuItem();
 250
 251   protected JMenuItem extractScores = new JMenuItem();
 252
 253   protected JMenuItem expandAlignment = new JMenuItem();
 254
 255   protected JMenu showProducts = new JMenu();
 256
 257   public JMenuItem openFeatureSettings = new JMenuItem();
 258
 259   JMenuItem fetchSequence = new JMenuItem();
 260
 261   JMenuItem annotationColour = new JMenuItem();
 262
 263   protected JMenuItem rnahelicesColour = new JMenuItem();
 264
 265   JMenuItem associatedData = new JMenuItem();
 266
 267   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 268
 269   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 270
 271   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 272
 273   JMenu addSequenceMenu = new JMenu();
 274
 275   JMenuItem addFromFile = new JMenuItem();
 276
 277   JMenuItem addFromText = new JMenuItem();
 278
 279   JMenuItem addFromURL = new JMenuItem();
 280
 281   JMenuItem exportAnnotations = new JMenuItem();
 282
 283   JMenuItem exportFeatures = new JMenuItem();
 284
 285   protected JPanel statusPanel = new JPanel();
 286
 287   GridLayout gridLayout1 = new GridLayout();
 288
 289   JMenu jMenu3 = new JMenu();
 290
 291   JMenuItem showAllSeqs = new JMenuItem();
 292
 293   JMenuItem showAllColumns = new JMenuItem();
 294
 295   JMenu hideMenu = new JMenu();
 296
 297   JMenuItem hideSelSequences = new JMenuItem();
 298
 299   JMenuItem hideSelColumns = new JMenuItem();
 300
 301   JMenuItem hideAllButSelection = new JMenuItem();
 302
 303   JMenuItem hideAllSelection = new JMenuItem();
 304
 305   JMenuItem showAllhidden = new JMenuItem();
 306
 307   protected JMenu showAnnotations = new JMenu();
 308
 309   protected JMenu hideAnnotations = new JMenu();
 310
 311   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 312
 313   JMenuItem invertColSel = new JMenuItem();
 314
 315   protected JTabbedPane tabbedPane = new JTabbedPane();
 316
 317   JMenuItem save = new JMenuItem();
 318
 319   protected JMenuItem reload = new JMenuItem();
 320
 321   JMenuItem newView = new JMenuItem();
 322
 323   JMenuItem textColour = new JMenuItem();
 324
 325   JMenu formatMenu = new JMenu();
 326
 327   JMenu selectMenu = new JMenu();
 328
 329   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 330
 331   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 332
 333   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 334
 335   protected JMenuItem gatherViews = new JMenuItem();
 336
 337   protected JMenuItem expandViews = new JMenuItem();
 338
 339   JMenuItem pageSetup = new JMenuItem();
 340
 341   JMenuItem alignmentProperties = new JMenuItem();
 342
 343   JMenu tooltipSettingsMenu = new JMenu();
 344
 345   private JMenuItem justifyLeftMenuItem = new JMenuItem();
 346
 347   private JMenuItem justifyRightMenuItem = new JMenuItem();
 348
 349   JMenu autoAnnMenu = new JMenu();
 350
 351   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 352
 353   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 354
 355   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 356
 357   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 358
 359   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 360
 361   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 362
 363   private JMenuItem grpsFromSelection = new JMenuItem();
 364
 365   public GAlignFrame()
 366   {
 367     try
 368     {
 369       jbInit();
 370       setJMenuBar(alignFrameMenuBar);
 371
 372       // dynamically fill save as menu with available formats
 373       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 374       {
 375         JMenuItem item = new JMenuItem(
 376                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 377
 378         item.addActionListener(new java.awt.event.ActionListener()
 379         {
 380           @Override
 381           public void actionPerformed(ActionEvent e)
 382           {
 383             outputText_actionPerformed(e);
 384           }
 385         });
 386
 387         outputTextboxMenu.add(item);
 388       }
 389     } catch (Exception e)
 390     {
 391       System.err.println(e.toString());
 392     }
 393
 394     if (!new jalview.util.Platform().isAMac())
 395     {
 396       closeMenuItem.setMnemonic('C');
 397       outputTextboxMenu.setMnemonic('T');
 398       undoMenuItem.setMnemonic('Z');
 399       redoMenuItem.setMnemonic('0');
 400       copy.setMnemonic('C');
 401       cut.setMnemonic('U');
 402       pasteMenu.setMnemonic('P');
 403       reload.setMnemonic('R');
 404     }
 405
 406     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 407     {
 408       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 409               .getUserColourSchemes().keys();
 410
 411       while (userColours.hasMoreElements())
 412       {
 413         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 414                 userColours.nextElement().toString());
 415         radioItem.setName("USER_DEFINED");
 416         radioItem.addMouseListener(new MouseAdapter()
 417         {
 418           @Override
 419           public void mousePressed(MouseEvent evt)
 420           {
 421             if (evt.isControlDown()
 422                     || SwingUtilities.isRightMouseButton(evt))
 423             {
 424               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 425
 426               int option = JOptionPane.showInternalConfirmDialog(
 427                       jalview.gui.Desktop.desktop,
 428                       MessageManager
 429                               .getString("label.remove_from_default_list"),
 430                       MessageManager
 431                               .getString("label.remove_user_defined_colour"),
 432                       JOptionPane.YES_NO_OPTION);
 433               if (option == JOptionPane.YES_OPTION)
 434               {
 435                 jalview.gui.UserDefinedColours
 436                         .removeColourFromDefaults(radioItem.getText());
 437                 colourMenu.remove(radioItem);
 438               }
 439               else
 440               {
 441                 radioItem.addActionListener(new ActionListener()
 442                 {
 443                   @Override
 444                   public void actionPerformed(ActionEvent evt)
 445                   {
 446                     userDefinedColour_actionPerformed(evt);
 447                   }
 448                 });
 449               }
 450             }
 451           }
 452         });
 453         radioItem.addActionListener(new ActionListener()
 454         {
 455           @Override
 456           public void actionPerformed(ActionEvent evt)
 457           {
 458             userDefinedColour_actionPerformed(evt);
 459           }
 460         });
 461         colourMenu.insert(radioItem, 15);
 462         colours.add(radioItem);
 463       }
 464     }
 465     colours.add(noColourmenuItem);
 466     colours.add(clustalColour);
 467     colours.add(zappoColour);
 468     colours.add(taylorColour);
 469     colours.add(hydrophobicityColour);
 470     colours.add(helixColour);
 471     colours.add(strandColour);
 472     colours.add(turnColour);
 473     colours.add(buriedColour);
 474     colours.add(userDefinedColour);
 475     colours.add(PIDColour);
 476     colours.add(BLOSUM62Colour);
 477     colours.add(nucleotideColour);
 478     colours.add(purinePyrimidineColour);
 479     // colours.add(covariationColour);
 480     colours.add(tcoffeeColour);
 481     colours.add(RNAInteractionColour);
 482     setColourSelected(jalview.bin.Cache
 483             .getDefault("DEFAULT_COLOUR", "None"));
 484
 485   }
 486
 487   public void setColourSelected(String defaultColour)
 488   {
 489
 490     if (defaultColour != null)
 491     {
 492       int index = ColourSchemeProperty
 493               .getColourIndexFromName(defaultColour);
 494
 495       switch (index)
 496       {
 497       case ColourSchemeProperty.CLUSTAL:
 498         clustalColour.setSelected(true);
 499
 500         break;
 501
 502       case ColourSchemeProperty.BLOSUM:
 503         BLOSUM62Colour.setSelected(true);
 504
 505         break;
 506
 507       case ColourSchemeProperty.PID:
 508         PIDColour.setSelected(true);
 509
 510         break;
 511
 512       case ColourSchemeProperty.ZAPPO:
 513         zappoColour.setSelected(true);
 514
 515         break;
 516
 517       case ColourSchemeProperty.TAYLOR:
 518         taylorColour.setSelected(true);
 519         break;
 520
 521       case ColourSchemeProperty.HYDROPHOBIC:
 522         hydrophobicityColour.setSelected(true);
 523
 524         break;
 525
 526       case ColourSchemeProperty.HELIX:
 527         helixColour.setSelected(true);
 528
 529         break;
 530
 531       case ColourSchemeProperty.STRAND:
 532         strandColour.setSelected(true);
 533
 534         break;
 535
 536       case ColourSchemeProperty.TURN:
 537         turnColour.setSelected(true);
 538
 539         break;
 540
 541       case ColourSchemeProperty.BURIED:
 542         buriedColour.setSelected(true);
 543
 544         break;
 545
 546       case ColourSchemeProperty.NUCLEOTIDE:
 547         nucleotideColour.setSelected(true);
 548
 549         break;
 550
 551       case ColourSchemeProperty.TCOFFEE:
 552         tcoffeeColour.setSelected(true);
 553         break;
 554
 555       case ColourSchemeProperty.PURINEPYRIMIDINE:
 556         purinePyrimidineColour.setSelected(true);
 557
 558         break;
 559
 560       case ColourSchemeProperty.RNAINTERACTION:
 561         RNAInteractionColour.setSelected(true);
 562
 563         break;
 564       /*
 565        * case ColourSchemeProperty.COVARIATION:
 566        * covariationColour.setSelected(true);
 567        *
 568        * break;
 569        */
 570       case ColourSchemeProperty.USER_DEFINED:
 571         userDefinedColour.setSelected(true);
 572
 573         break;
 574       case ColourSchemeProperty.NONE:
 575       default:
 576         noColourmenuItem.setSelected(true);
 577         break;
 578
 579       }
 580     }
 581
 582   }
 583
 584   private void jbInit() throws Exception
 585   {
 586     fileMenu.setText(MessageManager.getString("action.file"));
 587     saveAs.setText(MessageManager.getString("action.save_as") + "...");
 588     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 589             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
 590                     .getMenuShortcutKeyMask()
 591                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 592     saveAs.addActionListener(new ActionListener()
 593     {
 594       @Override
 595       public void actionPerformed(ActionEvent e)
 596       {
 597         saveAs_actionPerformed(e);
 598       }
 599     });
 600     closeMenuItem.setText(MessageManager.getString("action.close"));
 601     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 602             java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
 603                     .getMenuShortcutKeyMask(), false));
 604     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 605     {
 606       @Override
 607       public void actionPerformed(ActionEvent e)
 608       {
 609         closeMenuItem_actionPerformed(false);
 610       }
 611     });
 612     editMenu.setText(MessageManager.getString("action.edit"));
 613     viewMenu.setText(MessageManager.getString("action.view"));
 614     colourMenu.setText(MessageManager.getString("action.colour"));
 615     calculateMenu.setText(MessageManager.getString("action.calculate"));
 616     webService.setText(MessageManager.getString("action.web_service"));
 617     selectAllSequenceMenuItem.setText(MessageManager
 618             .getString("action.select_all"));
 619     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 620             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
 621                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 622     selectAllSequenceMenuItem
 623             .addActionListener(new java.awt.event.ActionListener()
 624             {
 625               @Override
 626               public void actionPerformed(ActionEvent e)
 627               {
 628                 selectAllSequenceMenuItem_actionPerformed(e);
 629               }
 630             });
 631     deselectAllSequenceMenuItem.setText(MessageManager
 632             .getString("action.deselect_all"));
 633     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 634             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 635     deselectAllSequenceMenuItem
 636             .addActionListener(new java.awt.event.ActionListener()
 637             {
 638               @Override
 639               public void actionPerformed(ActionEvent e)
 640               {
 641                 deselectAllSequenceMenuItem_actionPerformed(e);
 642               }
 643             });
 644     invertSequenceMenuItem.setText(MessageManager
 645             .getString("action.invert_sequence_selection"));
 646     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 647             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
 648                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 649     invertSequenceMenuItem
 650             .addActionListener(new java.awt.event.ActionListener()
 651             {
 652               @Override
 653               public void actionPerformed(ActionEvent e)
 654               {
 655                 invertSequenceMenuItem_actionPerformed(e);
 656               }
 657             });
 658     grpsFromSelection.setText(MessageManager
 659             .getString("action.make_groups_selection"));
 660     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
 661     {
 662       @Override
 663       public void actionPerformed(ActionEvent e)
 664       {
 665         makeGrpsFromSelection_actionPerformed(e);
 666       }
 667     });
 668     expandAlignment.setText(MessageManager
 669             .getString("action.view_flanking_regions"));
 670     expandAlignment.setToolTipText(MessageManager
 671             .getString("label.view_flanking_regions"));
 672     expandAlignment.addActionListener(new java.awt.event.ActionListener()
 673     {
 674       @Override
 675       public void actionPerformed(ActionEvent e)
 676       {
 677         expand_newalign(e);
 678       }
 679     });
 680     remove2LeftMenuItem.setText(MessageManager
 681             .getString("action.remove_left"));
 682     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 683             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
 684                     .getMenuShortcutKeyMask(), false));
 685     remove2LeftMenuItem
 686             .addActionListener(new java.awt.event.ActionListener()
 687             {
 688               @Override
 689               public void actionPerformed(ActionEvent e)
 690               {
 691                 remove2LeftMenuItem_actionPerformed(e);
 692               }
 693             });
 694     remove2RightMenuItem.setText(MessageManager
 695             .getString("action.remove_right"));
 696     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 697             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
 698                     .getMenuShortcutKeyMask(), false));
 699     remove2RightMenuItem
 700             .addActionListener(new java.awt.event.ActionListener()
 701             {
 702               @Override
 703               public void actionPerformed(ActionEvent e)
 704               {
 705                 remove2RightMenuItem_actionPerformed(e);
 706               }
 707             });
 708     removeGappedColumnMenuItem.setText(MessageManager
 709             .getString("action.remove_empty_columns"));
 710     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
 711             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 712                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 713     removeGappedColumnMenuItem
 714             .addActionListener(new java.awt.event.ActionListener()
 715             {
 716               @Override
 717               public void actionPerformed(ActionEvent e)
 718               {
 719                 removeGappedColumnMenuItem_actionPerformed(e);
 720               }
 721             });
 722     removeAllGapsMenuItem.setText(MessageManager
 723             .getString("action.remove_all_gaps"));
 724     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
 725             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 726                     .getDefaultToolkit().getMenuShortcutKeyMask()
 727                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 728     removeAllGapsMenuItem
 729             .addActionListener(new java.awt.event.ActionListener()
 730             {
 731               @Override
 732               public void actionPerformed(ActionEvent e)
 733               {
 734                 removeAllGapsMenuItem_actionPerformed(e);
 735               }
 736             });
 737     justifyLeftMenuItem.setText(MessageManager
 738             .getString("action.left_justify_alignment"));
 739     justifyLeftMenuItem
 740             .addActionListener(new java.awt.event.ActionListener()
 741             {
 742               @Override
 743               public void actionPerformed(ActionEvent e)
 744               {
 745                 justifyLeftMenuItem_actionPerformed(e);
 746               }
 747             });
 748     justifyRightMenuItem.setText(MessageManager
 749             .getString("action.right_justify_alignment"));
 750     justifyRightMenuItem
 751             .addActionListener(new java.awt.event.ActionListener()
 752             {
 753               @Override
 754               public void actionPerformed(ActionEvent e)
 755               {
 756                 justifyRightMenuItem_actionPerformed(e);
 757               }
 758             });
 759     viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
 760     viewBoxesMenuItem.setState(true);
 761     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 762     {
 763       @Override
 764       public void actionPerformed(ActionEvent e)
 765       {
 766         viewBoxesMenuItem_actionPerformed(e);
 767       }
 768     });
 769     viewTextMenuItem.setText(MessageManager.getString("action.text"));
 770     viewTextMenuItem.setState(true);
 771     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 772     {
 773       @Override
 774       public void actionPerformed(ActionEvent e)
 775       {
 776         viewTextMenuItem_actionPerformed(e);
 777       }
 778     });
 779     showNonconservedMenuItem.setText(MessageManager
 780             .getString("label.show_non_conversed"));
 781     showNonconservedMenuItem.setState(false);
 782     showNonconservedMenuItem
 783             .addActionListener(new java.awt.event.ActionListener()
 784             {
 785               @Override
 786               public void actionPerformed(ActionEvent e)
 787               {
 788                 showUnconservedMenuItem_actionPerformed(e);
 789               }
 790             });
 791     sortPairwiseMenuItem.setText(MessageManager
 792             .getString("action.by_pairwise_id"));
 793     sortPairwiseMenuItem
 794             .addActionListener(new java.awt.event.ActionListener()
 795             {
 796               @Override
 797               public void actionPerformed(ActionEvent e)
 798               {
 799                 sortPairwiseMenuItem_actionPerformed(e);
 800               }
 801             });
 802     sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
 803     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 804     {
 805       @Override
 806       public void actionPerformed(ActionEvent e)
 807       {
 808         sortIDMenuItem_actionPerformed(e);
 809       }
 810     });
 811     sortLengthMenuItem
 812             .setText(MessageManager.getString("action.by_length"));
 813     sortLengthMenuItem
 814             .addActionListener(new java.awt.event.ActionListener()
 815             {
 816               @Override
 817               public void actionPerformed(ActionEvent e)
 818               {
 819                 sortLengthMenuItem_actionPerformed(e);
 820               }
 821             });
 822     sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
 823     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 824     {
 825       @Override
 826       public void actionPerformed(ActionEvent e)
 827       {
 828         sortGroupMenuItem_actionPerformed(e);
 829       }
 830     });
 831     removeRedundancyMenuItem.setText(MessageManager
 832             .getString("action.remove_redundancy"));
 833     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
 834             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
 835                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 836     removeRedundancyMenuItem
 837             .addActionListener(new java.awt.event.ActionListener()
 838             {
 839               @Override
 840               public void actionPerformed(ActionEvent e)
 841               {
 842                 removeRedundancyMenuItem_actionPerformed(e);
 843               }
 844             });
 845     pairwiseAlignmentMenuItem.setText(MessageManager
 846             .getString("action.pairwise_alignment"));
 847     pairwiseAlignmentMenuItem
 848             .addActionListener(new java.awt.event.ActionListener()
 849             {
 850               @Override
 851               public void actionPerformed(ActionEvent e)
 852               {
 853                 pairwiseAlignmentMenuItem_actionPerformed(e);
 854               }
 855             });
 856     PCAMenuItem.setText(MessageManager
 857             .getString("label.principal_component_analysis"));
 858     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 859     {
 860       @Override
 861       public void actionPerformed(ActionEvent e)
 862       {
 863         PCAMenuItem_actionPerformed(e);
 864       }
 865     });
 866     averageDistanceTreeMenuItem.setText(MessageManager
 867             .getString("label.average_distance_identity"));
 868     averageDistanceTreeMenuItem
 869             .addActionListener(new java.awt.event.ActionListener()
 870             {
 871               @Override
 872               public void actionPerformed(ActionEvent e)
 873               {
 874                 averageDistanceTreeMenuItem_actionPerformed(e);
 875               }
 876             });
 877     neighbourTreeMenuItem.setText(MessageManager
 878             .getString("label.neighbour_joining_identity"));
 879     neighbourTreeMenuItem
 880             .addActionListener(new java.awt.event.ActionListener()
 881             {
 882               @Override
 883               public void actionPerformed(ActionEvent e)
 884               {
 885                 neighbourTreeMenuItem_actionPerformed(e);
 886               }
 887             });
 888     this.getContentPane().setLayout(borderLayout1);
 889     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 890     statusBar.setBackground(Color.white);
 891     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 892     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 893     statusBar.setText(MessageManager.getString("label.status_bar"));
 894     outputTextboxMenu.setText(MessageManager
 895             .getString("label.out_to_textbox"));
 896     clustalColour.setText(MessageManager.getString("label.clustalx"));
 897
 898     clustalColour.addActionListener(new java.awt.event.ActionListener()
 899     {
 900       @Override
 901       public void actionPerformed(ActionEvent e)
 902       {
 903         clustalColour_actionPerformed(e);
 904       }
 905     });
 906     zappoColour.setText(MessageManager.getString("label.zappo"));
 907     zappoColour.addActionListener(new java.awt.event.ActionListener()
 908     {
 909       @Override
 910       public void actionPerformed(ActionEvent e)
 911       {
 912         zappoColour_actionPerformed(e);
 913       }
 914     });
 915     taylorColour.setText(MessageManager.getString("label.taylor"));
 916     taylorColour.addActionListener(new java.awt.event.ActionListener()
 917     {
 918       @Override
 919       public void actionPerformed(ActionEvent e)
 920       {
 921         taylorColour_actionPerformed(e);
 922       }
 923     });
 924     hydrophobicityColour.setText(MessageManager
 925             .getString("label.hydrophobicity"));
 926     hydrophobicityColour
 927             .addActionListener(new java.awt.event.ActionListener()
 928             {
 929               @Override
 930               public void actionPerformed(ActionEvent e)
 931               {
 932                 hydrophobicityColour_actionPerformed(e);
 933               }
 934             });
 935     helixColour.setText(MessageManager.getString("label.helix_propensity"));
 936     helixColour.addActionListener(new java.awt.event.ActionListener()
 937     {
 938       @Override
 939       public void actionPerformed(ActionEvent e)
 940       {
 941         helixColour_actionPerformed(e);
 942       }
 943     });
 944     strandColour.setText(MessageManager
 945             .getString("label.strand_propensity"));
 946     strandColour.addActionListener(new java.awt.event.ActionListener()
 947     {
 948       @Override
 949       public void actionPerformed(ActionEvent e)
 950       {
 951         strandColour_actionPerformed(e);
 952       }
 953     });
 954     turnColour.setText(MessageManager.getString("label.turn_propensity"));
 955     turnColour.addActionListener(new java.awt.event.ActionListener()
 956     {
 957       @Override
 958       public void actionPerformed(ActionEvent e)
 959       {
 960         turnColour_actionPerformed(e);
 961       }
 962     });
 963     buriedColour.setText(MessageManager.getString("label.buried_index"));
 964     buriedColour.addActionListener(new java.awt.event.ActionListener()
 965     {
 966       @Override
 967       public void actionPerformed(ActionEvent e)
 968       {
 969         buriedColour_actionPerformed(e);
 970       }
 971     });
 972     userDefinedColour.setText(MessageManager
 973             .getString("action.user_defined"));
 974     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 975     {
 976       @Override
 977       public void actionPerformed(ActionEvent e)
 978       {
 979         userDefinedColour_actionPerformed(e);
 980       }
 981     });
 982     PIDColour
 983             .setText(MessageManager.getString("label.percentage_identity"));
 984     PIDColour.addActionListener(new java.awt.event.ActionListener()
 985     {
 986       @Override
 987       public void actionPerformed(ActionEvent e)
 988       {
 989         PIDColour_actionPerformed(e);
 990       }
 991     });
 992     BLOSUM62Colour
 993             .setText(MessageManager.getString("label.blosum62_score"));
 994     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 995     {
 996       @Override
 997       public void actionPerformed(ActionEvent e)
 998       {
 999         BLOSUM62Colour_actionPerformed(e);
1000       }
1001     });
1002     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1003     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1004     {
1005       @Override
1006       public void actionPerformed(ActionEvent e)
1007       {
1008         nucleotideColour_actionPerformed(e);
1009       }
1010     });
1011
1012     purinePyrimidineColour.setText(MessageManager
1013             .getString("label.purine_pyrimidine"));
1014     purinePyrimidineColour
1015             .addActionListener(new java.awt.event.ActionListener()
1016             {
1017               @Override
1018               public void actionPerformed(ActionEvent e)
1019               {
1020                 purinePyrimidineColour_actionPerformed(e);
1021               }
1022             });
1023
1024     RNAInteractionColour.setText("RNA Interaction type");
1025     RNAInteractionColour
1026             .addActionListener(new java.awt.event.ActionListener()
1027             {
1028               @Override
1029               public void actionPerformed(ActionEvent e)
1030               {
1031                 RNAInteractionColour_actionPerformed(e);
1032               }
1033             });
1034     /*
1035      * covariationColour.setText("Covariation");
1036      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1037      * public void actionPerformed(ActionEvent e) {
1038      * covariationColour_actionPerformed(e); } });
1039      */
1040
1041     avDistanceTreeBlosumMenuItem.setText(MessageManager
1042             .getString("label.average_distance_bloslum62"));
1043     avDistanceTreeBlosumMenuItem
1044             .addActionListener(new java.awt.event.ActionListener()
1045             {
1046               @Override
1047               public void actionPerformed(ActionEvent e)
1048               {
1049                 avTreeBlosumMenuItem_actionPerformed(e);
1050               }
1051             });
1052     njTreeBlosumMenuItem.setText(MessageManager
1053             .getString("label.neighbour_blosum62"));
1054     njTreeBlosumMenuItem
1055             .addActionListener(new java.awt.event.ActionListener()
1056             {
1057               @Override
1058               public void actionPerformed(ActionEvent e)
1059               {
1060                 njTreeBlosumMenuItem_actionPerformed(e);
1061               }
1062             });
1063     annotationPanelMenuItem.setActionCommand("");
1064     annotationPanelMenuItem.setText(MessageManager
1065             .getString("label.show_annotations"));
1066     annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
1067             "SHOW_ANNOTATIONS", true));
1068     annotationPanelMenuItem
1069             .addActionListener(new java.awt.event.ActionListener()
1070             {
1071               @Override
1072               public void actionPerformed(ActionEvent e)
1073               {
1074                 annotationPanelMenuItem_actionPerformed(e);
1075               }
1076             });
1077     colourTextMenuItem.setText(MessageManager
1078             .getString("label.colour_text"));
1079     colourTextMenuItem
1080             .addActionListener(new java.awt.event.ActionListener()
1081             {
1082               @Override
1083               public void actionPerformed(ActionEvent e)
1084               {
1085                 colourTextMenuItem_actionPerformed(e);
1086               }
1087             });
1088     htmlMenuItem.setText(MessageManager.getString("label.html"));
1089     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
1090     {
1091       @Override
1092       public void actionPerformed(ActionEvent e)
1093       {
1094         htmlMenuItem_actionPerformed(e);
1095       }
1096     });
1097     overviewMenuItem.setText(MessageManager
1098             .getString("label.overview_window"));
1099     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
1100     {
1101       @Override
1102       public void actionPerformed(ActionEvent e)
1103       {
1104         overviewMenuItem_actionPerformed(e);
1105       }
1106     });
1107     undoMenuItem.setEnabled(false);
1108     undoMenuItem.setText(MessageManager.getString("action.undo"));
1109     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1110             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1111                     .getMenuShortcutKeyMask(), false));
1112     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1113     {
1114       @Override
1115       public void actionPerformed(ActionEvent e)
1116       {
1117         undoMenuItem_actionPerformed(e);
1118       }
1119     });
1120     redoMenuItem.setEnabled(false);
1121     redoMenuItem.setText(MessageManager.getString("action.redo"));
1122     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1123             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1124                     .getMenuShortcutKeyMask(), false));
1125     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1126     {
1127       @Override
1128       public void actionPerformed(ActionEvent e)
1129       {
1130         redoMenuItem_actionPerformed(e);
1131       }
1132     });
1133     conservationMenuItem.setText(MessageManager
1134             .getString("action.by_conservation"));
1135     conservationMenuItem
1136             .addActionListener(new java.awt.event.ActionListener()
1137             {
1138               @Override
1139               public void actionPerformed(ActionEvent e)
1140               {
1141                 conservationMenuItem_actionPerformed(e);
1142               }
1143             });
1144     noColourmenuItem.setText(MessageManager.getString("label.none"));
1145     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1146     {
1147       @Override
1148       public void actionPerformed(ActionEvent e)
1149       {
1150         noColourmenuItem_actionPerformed(e);
1151       }
1152     });
1153     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1154     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1155     {
1156       @Override
1157       public void actionPerformed(ActionEvent e)
1158       {
1159         wrapMenuItem_actionPerformed(e);
1160       }
1161     });
1162     printMenuItem.setText(MessageManager.getString("action.print") + "...");
1163     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1164             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1165                     .getMenuShortcutKeyMask(), false));
1166     printMenuItem.addActionListener(new java.awt.event.ActionListener()
1167     {
1168       @Override
1169       public void actionPerformed(ActionEvent e)
1170       {
1171         printMenuItem_actionPerformed(e);
1172       }
1173     });
1174     renderGapsMenuItem
1175             .setText(MessageManager.getString("action.show_gaps"));
1176     renderGapsMenuItem.setState(true);
1177     renderGapsMenuItem
1178             .addActionListener(new java.awt.event.ActionListener()
1179             {
1180               @Override
1181               public void actionPerformed(ActionEvent e)
1182               {
1183                 renderGapsMenuItem_actionPerformed(e);
1184               }
1185             });
1186     findMenuItem.setText(MessageManager.getString("action.find"));
1187     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1188             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1189                     .getMenuShortcutKeyMask(), false));
1190     findMenuItem.addActionListener(new java.awt.event.ActionListener()
1191     {
1192       @Override
1193       public void actionPerformed(ActionEvent e)
1194       {
1195         findMenuItem_actionPerformed(e);
1196       }
1197     });
1198     abovePIDThreshold.setText(MessageManager
1199             .getString("label.above_identity_threshold"));
1200     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1201     {
1202       @Override
1203       public void actionPerformed(ActionEvent e)
1204       {
1205         abovePIDThreshold_actionPerformed(e);
1206       }
1207     });
1208     showSeqFeatures.setText(MessageManager
1209             .getString("label.show_sequence_features"));
1210     showSeqFeatures.addActionListener(new ActionListener()
1211     {
1212       @Override
1213       public void actionPerformed(ActionEvent actionEvent)
1214       {
1215         showSeqFeatures_actionPerformed(actionEvent);
1216       }
1217     });
1218     chooseAnnotations.setText(MessageManager
1219             .getString("label.choose_annotations") + "...");
1220     chooseAnnotations.addActionListener(new ActionListener()
1221     {
1222       @Override
1223       public void actionPerformed(ActionEvent actionEvent)
1224       {
1225         chooseAnnotations_actionPerformed();
1226       }
1227     });
1228     /*
1229      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1230      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1231      * void actionPerformed(ActionEvent actionEvent) {
1232      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1233      */
1234     showDbRefsMenuitem.setText(MessageManager
1235             .getString("label.show_database_refs"));
1236     showDbRefsMenuitem.addActionListener(new ActionListener()
1237     {
1238
1239       @Override
1240       public void actionPerformed(ActionEvent e)
1241       {
1242         showDbRefs_actionPerformed(e);
1243       }
1244
1245     });
1246     showNpFeatsMenuitem.setText(MessageManager
1247             .getString("label.show_non_positional_features"));
1248     showNpFeatsMenuitem.addActionListener(new ActionListener()
1249     {
1250
1251       @Override
1252       public void actionPerformed(ActionEvent e)
1253       {
1254         showNpFeats_actionPerformed(e);
1255       }
1256
1257     });
1258     showGroupConservation.setText(MessageManager
1259             .getString("label.group_conservation"));
1260     showGroupConservation.addActionListener(new ActionListener()
1261     {
1262
1263       @Override
1264       public void actionPerformed(ActionEvent e)
1265       {
1266         showGroupConservation_actionPerformed(e);
1267       }
1268
1269     });
1270
1271     showGroupConsensus.setText(MessageManager
1272             .getString("label.group_consensus"));
1273     showGroupConsensus.addActionListener(new ActionListener()
1274     {
1275
1276       @Override
1277       public void actionPerformed(ActionEvent e)
1278       {
1279         showGroupConsensus_actionPerformed(e);
1280       }
1281
1282     });
1283     showConsensusHistogram.setText(MessageManager
1284             .getString("label.show_consensus_histogram"));
1285     showConsensusHistogram.addActionListener(new ActionListener()
1286     {
1287
1288       @Override
1289       public void actionPerformed(ActionEvent e)
1290       {
1291         showConsensusHistogram_actionPerformed(e);
1292       }
1293
1294     });
1295     showSequenceLogo.setText(MessageManager
1296             .getString("label.show_consensus_logo"));
1297     showSequenceLogo.addActionListener(new ActionListener()
1298     {
1299
1300       @Override
1301       public void actionPerformed(ActionEvent e)
1302       {
1303         showSequenceLogo_actionPerformed(e);
1304       }
1305
1306     });
1307     normaliseSequenceLogo.setText(MessageManager
1308             .getString("label.norm_consensus_logo"));
1309     normaliseSequenceLogo.addActionListener(new ActionListener()
1310     {
1311
1312       @Override
1313       public void actionPerformed(ActionEvent e)
1314       {
1315         normaliseSequenceLogo_actionPerformed(e);
1316       }
1317
1318     });
1319     applyAutoAnnotationSettings.setText(MessageManager
1320             .getString("label.apply_all_groups"));
1321     applyAutoAnnotationSettings.setState(false);
1322     applyAutoAnnotationSettings.setVisible(true);
1323     applyAutoAnnotationSettings.addActionListener(new ActionListener()
1324     {
1325
1326       @Override
1327       public void actionPerformed(ActionEvent e)
1328       {
1329         applyAutoAnnotationSettings_actionPerformed(e);
1330       }
1331
1332     });
1333
1334     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1335     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1336     {
1337       @Override
1338       public void actionPerformed(ActionEvent e)
1339       {
1340         nucleotideColour_actionPerformed(e);
1341       }
1342     });
1343
1344     tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1345     tcoffeeColour.setEnabled(false);
1346     tcoffeeColour.addActionListener(new ActionListener()
1347     {
1348
1349       @Override
1350       public void actionPerformed(ActionEvent e)
1351       {
1352         tcoffeeColorScheme_actionPerformed(e);
1353       }
1354     });
1355
1356     deleteGroups
1357             .setText(MessageManager.getString("action.undefine_groups"));
1358     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1359             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1360                     .getMenuShortcutKeyMask(), false));
1361     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1362     {
1363       @Override
1364       public void actionPerformed(ActionEvent e)
1365       {
1366         deleteGroups_actionPerformed(e);
1367       }
1368     });
1369     createGroup.setText(MessageManager.getString("action.create_groups"));
1370     createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1371             java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1372                     .getMenuShortcutKeyMask(), false));
1373     createGroup.addActionListener(new java.awt.event.ActionListener()
1374     {
1375       @Override
1376       public void actionPerformed(ActionEvent e)
1377       {
1378         createGroup_actionPerformed(e);
1379       }
1380     });
1381     unGroup.setText(MessageManager.getString("action.remove_group"));
1382     unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1383             java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1384                     .getMenuShortcutKeyMask()
1385                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1386     unGroup.addActionListener(new java.awt.event.ActionListener()
1387     {
1388       @Override
1389       public void actionPerformed(ActionEvent e)
1390       {
1391         unGroup_actionPerformed(e);
1392       }
1393     });
1394     copy.setText(MessageManager.getString("action.copy"));
1395     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1396             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1397                     .getMenuShortcutKeyMask(), false));
1398
1399     copy.addActionListener(new java.awt.event.ActionListener()
1400     {
1401       @Override
1402       public void actionPerformed(ActionEvent e)
1403       {
1404         copy_actionPerformed(e);
1405       }
1406     });
1407     cut.setText(MessageManager.getString("action.cut"));
1408     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1409             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1410                     .getMenuShortcutKeyMask(), false));
1411     cut.addActionListener(new java.awt.event.ActionListener()
1412     {
1413       @Override
1414       public void actionPerformed(ActionEvent e)
1415       {
1416         cut_actionPerformed(e);
1417       }
1418     });
1419     delete.setText(MessageManager.getString("action.delete"));
1420     delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1421             java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1422     delete.addActionListener(new java.awt.event.ActionListener()
1423     {
1424       @Override
1425       public void actionPerformed(ActionEvent e)
1426       {
1427         delete_actionPerformed(e);
1428       }
1429     });
1430     pasteMenu.setText(MessageManager.getString("action.paste"));
1431     pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1432     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1433             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1434                     .getMenuShortcutKeyMask()
1435                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1436     pasteNew.addActionListener(new java.awt.event.ActionListener()
1437     {
1438       @Override
1439       public void actionPerformed(ActionEvent e)
1440       {
1441         pasteNew_actionPerformed(e);
1442       }
1443     });
1444     pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1445     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1446             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1447                     .getMenuShortcutKeyMask(), false));
1448     pasteThis.addActionListener(new java.awt.event.ActionListener()
1449     {
1450       @Override
1451       public void actionPerformed(ActionEvent e)
1452       {
1453         pasteThis_actionPerformed(e);
1454       }
1455     });
1456     applyToAllGroups.setText(MessageManager
1457             .getString("label.apply_colour_to_all_groups"));
1458     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1459     {
1460       @Override
1461       public void actionPerformed(ActionEvent e)
1462       {
1463         applyToAllGroups_actionPerformed(e);
1464       }
1465     });
1466     createPNG.addActionListener(new java.awt.event.ActionListener()
1467     {
1468       @Override
1469       public void actionPerformed(ActionEvent e)
1470       {
1471         createPNG(null);
1472       }
1473     });
1474     createPNG.setActionCommand(MessageManager
1475             .getString("label.save_png_image"));
1476     createPNG.setText("PNG");
1477     font.setText(MessageManager.getString("action.font"));
1478     font.addActionListener(new java.awt.event.ActionListener()
1479     {
1480       @Override
1481       public void actionPerformed(ActionEvent e)
1482       {
1483         font_actionPerformed(e);
1484       }
1485     });
1486
1487     seqLimits.setText(MessageManager
1488             .getString("label.show_sequence_limits"));
1489     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1490     seqLimits.addActionListener(new java.awt.event.ActionListener()
1491     {
1492       @Override
1493       public void actionPerformed(ActionEvent e)
1494       {
1495         seqLimit_actionPerformed(e);
1496       }
1497     });
1498     epsFile.setText("EPS");
1499     epsFile.addActionListener(new java.awt.event.ActionListener()
1500     {
1501       @Override
1502       public void actionPerformed(ActionEvent e)
1503       {
1504         createEPS(null);
1505       }
1506     });
1507     LoadtreeMenuItem.setActionCommand(MessageManager
1508             .getString("label.load_tree_for_sequence_set"));
1509     LoadtreeMenuItem.setText(MessageManager
1510             .getString("label.load_associated_tree"));
1511     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1512     {
1513       @Override
1514       public void actionPerformed(ActionEvent e)
1515       {
1516         LoadtreeMenuItem_actionPerformed(e);
1517       }
1518     });
1519
1520     scaleAbove.setVisible(false);
1521     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1522     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1523     {
1524       @Override
1525       public void actionPerformed(ActionEvent e)
1526       {
1527         scaleAbove_actionPerformed(e);
1528       }
1529     });
1530     scaleLeft.setVisible(false);
1531     scaleLeft.setSelected(true);
1532     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1533     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1534     {
1535       @Override
1536       public void actionPerformed(ActionEvent e)
1537       {
1538         scaleLeft_actionPerformed(e);
1539       }
1540     });
1541     scaleRight.setVisible(false);
1542     scaleRight.setSelected(true);
1543     scaleRight.setText(MessageManager.getString("action.scale_right"));
1544     scaleRight.addActionListener(new java.awt.event.ActionListener()
1545     {
1546       @Override
1547       public void actionPerformed(ActionEvent e)
1548       {
1549         scaleRight_actionPerformed(e);
1550       }
1551     });
1552     centreColumnLabelsMenuItem.setVisible(true);
1553     centreColumnLabelsMenuItem.setState(false);
1554     centreColumnLabelsMenuItem.setText(MessageManager
1555             .getString("label.centre_column_labels"));
1556     centreColumnLabelsMenuItem
1557             .addActionListener(new java.awt.event.ActionListener()
1558             {
1559               @Override
1560               public void actionPerformed(ActionEvent e)
1561               {
1562                 centreColumnLabels_actionPerformed(e);
1563               }
1564             });
1565     followHighlightMenuItem.setVisible(true);
1566     followHighlightMenuItem.setState(true);
1567     followHighlightMenuItem.setText(MessageManager
1568             .getString("label.automatic_scrolling"));
1569     followHighlightMenuItem.addActionListener(new ActionListener()
1570     {
1571
1572       @Override
1573       public void actionPerformed(ActionEvent e)
1574       {
1575         followHighlight_actionPerformed();
1576       }
1577
1578     });
1579
1580     modifyPID.setText(MessageManager
1581             .getString("label.modify_identity_thereshold"));
1582     modifyPID.addActionListener(new java.awt.event.ActionListener()
1583     {
1584       @Override
1585       public void actionPerformed(ActionEvent e)
1586       {
1587         modifyPID_actionPerformed(e);
1588       }
1589     });
1590     modifyConservation.setText(MessageManager
1591             .getString("label.modify_conservation_thereshold"));
1592     modifyConservation
1593             .addActionListener(new java.awt.event.ActionListener()
1594             {
1595               @Override
1596               public void actionPerformed(ActionEvent e)
1597               {
1598                 modifyConservation_actionPerformed(e);
1599               }
1600             });
1601     sortByTreeMenu
1602             .setText(MessageManager.getString("action.by_tree_order"));
1603     sort.setText(MessageManager.getString("action.sort"));
1604     sort.addMenuListener(new MenuListener()
1605     {
1606       @Override
1607       public void menuSelected(MenuEvent e)
1608       {
1609         buildTreeMenu();
1610       }
1611
1612       @Override
1613       public void menuDeselected(MenuEvent e)
1614       {
1615       }
1616
1617       @Override
1618       public void menuCanceled(MenuEvent e)
1619       {
1620       }
1621     });
1622     sortByAnnotScore.setText(MessageManager
1623             .getString("label.sort_by_score"));
1624     sort.add(sortByAnnotScore);
1625     sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1626     {
1627
1628       @Override
1629       public void menuCanceled(MenuEvent e)
1630       {
1631       }
1632
1633       @Override
1634       public void menuDeselected(MenuEvent e)
1635       {
1636       }
1637
1638       @Override
1639       public void menuSelected(MenuEvent e)
1640       {
1641         buildSortByAnnotationScoresMenu();
1642       }
1643     });
1644     sortByAnnotScore.setVisible(false);
1645
1646     calculateTree
1647             .setText(MessageManager.getString("action.calculate_tree"));
1648
1649     jMenu2.setText(MessageManager.getString("label.export_image"));
1650     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1651     padGapsMenuitem.setState(jalview.bin.Cache
1652             .getDefault("PAD_GAPS", false));
1653     padGapsMenuitem.addActionListener(new ActionListener()
1654     {
1655       @Override
1656       public void actionPerformed(ActionEvent e)
1657       {
1658         padGapsMenuitem_actionPerformed(e);
1659       }
1660     });
1661     vamsasStore.setVisible(false);
1662     vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1663     vamsasStore.addActionListener(new ActionListener()
1664     {
1665       @Override
1666       public void actionPerformed(ActionEvent e)
1667       {
1668         vamsasStore_actionPerformed(e);
1669       }
1670     });
1671     showTranslation.setText(MessageManager
1672             .getString("label.translate_cDNA"));
1673     showTranslation.addActionListener(new ActionListener()
1674     {
1675       @Override
1676       public void actionPerformed(ActionEvent e)
1677       {
1678         showTranslation_actionPerformed(e);
1679       }
1680     });
1681     extractScores.setText(MessageManager.getString("label.extract_scores")
1682             + "...");
1683     extractScores.addActionListener(new ActionListener()
1684     {
1685       @Override
1686       public void actionPerformed(ActionEvent e)
1687       {
1688         extractScores_actionPerformed(e);
1689       }
1690     });
1691     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1692     // score extraction
1693     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1694     /*
1695      * showProducts.addActionListener(new ActionListener() {
1696      *
1697      * public void actionPerformed(ActionEvent e) {
1698      * showProducts_actionPerformed(e); } });
1699      */
1700     openFeatureSettings.setText(MessageManager
1701             .getString("label.feature_settings"));
1702     openFeatureSettings.addActionListener(new ActionListener()
1703     {
1704       @Override
1705       public void actionPerformed(ActionEvent e)
1706       {
1707         featureSettings_actionPerformed(e);
1708       }
1709     });
1710     fetchSequence
1711             .setText(MessageManager.getString("label.fetch_sequences"));
1712     fetchSequence.addActionListener(new ActionListener()
1713     {
1714       @Override
1715       public void actionPerformed(ActionEvent e)
1716       {
1717         fetchSequence_actionPerformed(e);
1718       }
1719     });
1720
1721     annotationColour.setText(MessageManager
1722             .getString("action.by_annotation"));
1723     annotationColour.addActionListener(new ActionListener()
1724     {
1725       @Override
1726       public void actionPerformed(ActionEvent e)
1727       {
1728         annotationColour_actionPerformed(e);
1729       }
1730     });
1731
1732     rnahelicesColour.setText(MessageManager
1733             .getString("action.by_rna_helixes"));
1734     rnahelicesColour.addActionListener(new ActionListener()
1735     {
1736       @Override
1737       public void actionPerformed(ActionEvent e)
1738       {
1739         rnahelicesColour_actionPerformed(e);
1740       }
1741     });
1742
1743     associatedData.setText(MessageManager
1744             .getString("label.load_features_annotations"));
1745     associatedData.addActionListener(new ActionListener()
1746     {
1747       @Override
1748       public void actionPerformed(ActionEvent e)
1749       {
1750         associatedData_actionPerformed(e);
1751       }
1752     });
1753     autoCalculate.setText(MessageManager
1754             .getString("label.autocalculate_consensus"));
1755     autoCalculate.setState(jalview.bin.Cache.getDefault(
1756             "AUTO_CALC_CONSENSUS", true));
1757     autoCalculate.addActionListener(new ActionListener()
1758     {
1759       @Override
1760       public void actionPerformed(ActionEvent e)
1761       {
1762         autoCalculate_actionPerformed(e);
1763       }
1764     });
1765     sortByTree.setText(MessageManager
1766             .getString("label.sort_alignment_new_tree"));
1767     sortByTree
1768             .setToolTipText("<html>"
1769                     + MessageManager
1770                             .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1771     sortByTree
1772             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1773     sortByTree.addActionListener(new ActionListener()
1774     {
1775       @Override
1776       public void actionPerformed(ActionEvent e)
1777       {
1778         sortByTreeOption_actionPerformed(e);
1779       }
1780     });
1781
1782     listenToViewSelections.setText(MessageManager
1783             .getString("label.listen_for_selections"));
1784     listenToViewSelections
1785             .setToolTipText("<html>"
1786                     + MessageManager
1787                             .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1788     listenToViewSelections.setState(false);
1789     listenToViewSelections.addActionListener(new ActionListener()
1790     {
1791       @Override
1792       public void actionPerformed(ActionEvent e)
1793       {
1794         listenToViewSelections_actionPerformed(e);
1795       }
1796     });
1797
1798     addSequenceMenu
1799             .setText(MessageManager.getString("label.add_sequences"));
1800     addFromFile.setText(MessageManager.getString("label.from_file"));
1801     addFromFile.addActionListener(new ActionListener()
1802     {
1803       @Override
1804       public void actionPerformed(ActionEvent e)
1805       {
1806         addFromFile_actionPerformed(e);
1807       }
1808     });
1809     addFromText.setText(MessageManager.getString("label.from_textbox"));
1810     addFromText.addActionListener(new ActionListener()
1811     {
1812       @Override
1813       public void actionPerformed(ActionEvent e)
1814       {
1815         addFromText_actionPerformed(e);
1816       }
1817     });
1818     addFromURL.setText(MessageManager.getString("label.from_url"));
1819     addFromURL.addActionListener(new ActionListener()
1820     {
1821       @Override
1822       public void actionPerformed(ActionEvent e)
1823       {
1824         addFromURL_actionPerformed(e);
1825       }
1826     });
1827     exportFeatures.setText(MessageManager
1828             .getString("label.export_features"));
1829     exportFeatures.addActionListener(new ActionListener()
1830     {
1831       @Override
1832       public void actionPerformed(ActionEvent e)
1833       {
1834         exportFeatures_actionPerformed(e);
1835       }
1836     });
1837     exportAnnotations.setText(MessageManager
1838             .getString("label.export_annotations"));
1839     exportAnnotations.addActionListener(new ActionListener()
1840     {
1841       @Override
1842       public void actionPerformed(ActionEvent e)
1843       {
1844         exportAnnotations_actionPerformed(e);
1845       }
1846     });
1847     statusPanel.setLayout(gridLayout1);
1848     jMenu3.setText(MessageManager.getString("action.show"));
1849     showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
1850     showAllSeqs.setToolTipText(MessageManager
1851             .getString("label.toggle_sequence_visibility"));
1852     showAllSeqs.addActionListener(new ActionListener()
1853     {
1854       @Override
1855       public void actionPerformed(ActionEvent e)
1856       {
1857         showAllSeqs_actionPerformed(e);
1858       }
1859     });
1860     showAllColumns.setText(MessageManager.getString("label.all_columns"));
1861     showAllColumns.setToolTipText(MessageManager
1862             .getString("label.toggle_columns_visibility"));
1863     showAllColumns.addActionListener(new ActionListener()
1864     {
1865       @Override
1866       public void actionPerformed(ActionEvent e)
1867       {
1868         showAllColumns_actionPerformed(e);
1869       }
1870     });
1871     hideMenu.setText(MessageManager.getString("action.hide"));
1872     hideSelSequences.setText(MessageManager
1873             .getString("label.selected_sequences"));
1874     hideSelSequences.setToolTipText(MessageManager
1875             .getString("label.toggle_sequence_visibility"));
1876     hideSelSequences.addActionListener(new ActionListener()
1877     {
1878       @Override
1879       public void actionPerformed(ActionEvent e)
1880       {
1881         hideSelSequences_actionPerformed(e);
1882       }
1883     });
1884     hideSelColumns.setText(MessageManager
1885             .getString("label.selected_columns"));
1886     hideSelColumns.setToolTipText(MessageManager
1887             .getString("label.toggle_columns_visibility"));
1888     hideSelColumns.addActionListener(new ActionListener()
1889     {
1890       @Override
1891       public void actionPerformed(ActionEvent e)
1892       {
1893         hideSelColumns_actionPerformed(e);
1894       }
1895     });
1896     hideAllSelection.setText(MessageManager
1897             .getString("label.selected_region"));
1898     hideAllSelection.addActionListener(new ActionListener()
1899     {
1900       @Override
1901       public void actionPerformed(ActionEvent e)
1902       {
1903         hideAllSelection_actionPerformed(e);
1904       }
1905     });
1906     // TODO: should be hidden if no selection exists.
1907     hideAllButSelection.setText(MessageManager
1908             .getString("label.all_but_selected_region"));
1909     hideAllButSelection.addActionListener(new ActionListener()
1910     {
1911       @Override
1912       public void actionPerformed(ActionEvent e)
1913       {
1914         hideAllButSelection_actionPerformed(e);
1915       }
1916     });
1917     showAllhidden.setText(MessageManager
1918             .getString("label.all_sequences_columns"));
1919     showAllhidden.setToolTipText(MessageManager
1920             .getString("label.toggles_visibility_hidden_selected_regions"));
1921     showAllhidden.addActionListener(new ActionListener()
1922     {
1923       @Override
1924       public void actionPerformed(ActionEvent e)
1925       {
1926         showAllhidden_actionPerformed(e);
1927       }
1928     });
1929     showAnnotations.setText(MessageManager.getString("label.annotations"));
1930     showAnnotations.addMouseListener(new MouseAdapter()
1931     {
1932       @Override
1933       public void mouseEntered(MouseEvent e)
1934       {
1935         buildShowHideAnnotationMenus();
1936       }
1937     });
1938     hideAnnotations.setText(MessageManager.getString("label.annotations"));
1939     hideAnnotations.addMouseListener(new MouseAdapter()
1940     {
1941       @Override
1942       public void mouseEntered(MouseEvent e)
1943       {
1944         buildShowHideAnnotationMenus();
1945       }
1946     });
1947
1948     hiddenMarkers.setText(MessageManager
1949             .getString("action.show_hidden_markers"));
1950     hiddenMarkers.addActionListener(new ActionListener()
1951     {
1952       @Override
1953       public void actionPerformed(ActionEvent e)
1954       {
1955         hiddenMarkers_actionPerformed(e);
1956       }
1957     });
1958     invertColSel.setText(MessageManager
1959             .getString("action.invert_column_selection"));
1960     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1961             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1962                     .getMenuShortcutKeyMask()
1963                     | java.awt.event.KeyEvent.ALT_MASK, false));
1964     invertColSel.addActionListener(new ActionListener()
1965     {
1966       @Override
1967       public void actionPerformed(ActionEvent e)
1968       {
1969         invertColSel_actionPerformed(e);
1970       }
1971     });
1972     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1973     {
1974       @Override
1975       public void stateChanged(ChangeEvent evt)
1976       {
1977         JTabbedPane pane = (JTabbedPane) evt.getSource();
1978         int sel = pane.getSelectedIndex();
1979         tabSelectionChanged(sel);
1980       }
1981     });
1982     tabbedPane.addMouseListener(new MouseAdapter()
1983     {
1984       @Override
1985       public void mousePressed(MouseEvent e)
1986       {
1987         tabbedPane_mousePressed(e);
1988       }
1989     });
1990     tabbedPane.addFocusListener(new FocusAdapter()
1991     {
1992       @Override
1993       public void focusGained(FocusEvent e)
1994       {
1995         tabbedPane_focusGained(e);
1996       }
1997     });
1998     save.setText(MessageManager.getString("action.save"));
1999     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2000             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
2001                     .getMenuShortcutKeyMask(), false));
2002     save.addActionListener(new ActionListener()
2003     {
2004       @Override
2005       public void actionPerformed(ActionEvent e)
2006       {
2007         save_actionPerformed(e);
2008       }
2009     });
2010     reload.setEnabled(false);
2011     reload.setText(MessageManager.getString("action.reload"));
2012     reload.addActionListener(new ActionListener()
2013     {
2014       @Override
2015       public void actionPerformed(ActionEvent e)
2016       {
2017         reload_actionPerformed(e);
2018       }
2019     });
2020     newView.setText(MessageManager.getString("action.new_view"));
2021     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2022             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
2023                     .getMenuShortcutKeyMask(), false));
2024     newView.addActionListener(new ActionListener()
2025     {
2026       @Override
2027       public void actionPerformed(ActionEvent e)
2028       {
2029         newView_actionPerformed(e);
2030       }
2031     });
2032     tabbedPane.setToolTipText("<html><i>"
2033             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2034             + "</i></html>");
2035     textColour.setText(MessageManager.getString("label.colour_text")
2036             + "...");
2037     textColour.addActionListener(new ActionListener()
2038     {
2039       @Override
2040       public void actionPerformed(ActionEvent e)
2041       {
2042         textColour_actionPerformed(e);
2043       }
2044     });
2045     formatMenu.setText(MessageManager.getString("action.format"));
2046     selectMenu.setText(MessageManager.getString("action.select"));
2047     idRightAlign.setText(MessageManager
2048             .getString("label.right_align_sequence_id"));
2049     idRightAlign.addActionListener(new ActionListener()
2050     {
2051       @Override
2052       public void actionPerformed(ActionEvent e)
2053       {
2054         idRightAlign_actionPerformed(e);
2055       }
2056     });
2057     gatherViews.setEnabled(false);
2058     gatherViews.setText(MessageManager.getString("action.gather_views"));
2059     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2060             java.awt.event.KeyEvent.VK_G, 0, false));
2061     gatherViews.addActionListener(new ActionListener()
2062     {
2063       @Override
2064       public void actionPerformed(ActionEvent e)
2065       {
2066         gatherViews_actionPerformed(e);
2067       }
2068     });
2069     expandViews.setEnabled(false);
2070     expandViews.setText(MessageManager.getString("action.expand_views"));
2071     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2072             java.awt.event.KeyEvent.VK_X, 0, false));
2073     expandViews.addActionListener(new ActionListener()
2074     {
2075       @Override
2076       public void actionPerformed(ActionEvent e)
2077       {
2078         expandViews_actionPerformed(e);
2079       }
2080     });
2081     pageSetup
2082             .setText(MessageManager.getString("action.page_setup") + "...");
2083     pageSetup.addActionListener(new ActionListener()
2084     {
2085       @Override
2086       public void actionPerformed(ActionEvent e)
2087       {
2088         pageSetup_actionPerformed(e);
2089       }
2090     });
2091     alignmentProperties.setText(MessageManager
2092             .getString("label.alignment_props") + "...");
2093     alignmentProperties.addActionListener(new ActionListener()
2094     {
2095       @Override
2096       public void actionPerformed(ActionEvent actionEvent)
2097       {
2098         alignmentProperties();
2099       }
2100     });
2101     tooltipSettingsMenu.setText(MessageManager
2102             .getString("label.sequence_id_tooltip"));
2103     autoAnnMenu.setText(MessageManager
2104             .getString("label.autocalculated_annotation"));
2105     alignFrameMenuBar.add(fileMenu);
2106     alignFrameMenuBar.add(editMenu);
2107     alignFrameMenuBar.add(selectMenu);
2108     alignFrameMenuBar.add(viewMenu);
2109     alignFrameMenuBar.add(formatMenu);
2110     alignFrameMenuBar.add(colourMenu);
2111     alignFrameMenuBar.add(calculateMenu);
2112     alignFrameMenuBar.add(webService);
2113     fileMenu.add(fetchSequence);
2114     fileMenu.add(addSequenceMenu);
2115     fileMenu.add(reload);
2116     fileMenu.addSeparator();
2117     fileMenu.add(vamsasStore);
2118     fileMenu.add(save);
2119     fileMenu.add(saveAs);
2120     fileMenu.add(outputTextboxMenu);
2121     fileMenu.add(pageSetup);
2122     fileMenu.add(printMenuItem);
2123     fileMenu.addSeparator();
2124     fileMenu.add(jMenu2);
2125     fileMenu.add(exportFeatures);
2126     fileMenu.add(exportAnnotations);
2127     fileMenu.add(LoadtreeMenuItem);
2128     fileMenu.add(associatedData);
2129     fileMenu.addSeparator();
2130     fileMenu.add(closeMenuItem);
2131     editMenu.add(undoMenuItem);
2132     editMenu.add(redoMenuItem);
2133     editMenu.add(cut);
2134     editMenu.add(copy);
2135     editMenu.add(pasteMenu);
2136     editMenu.add(delete);
2137     editMenu.addSeparator();
2138     editMenu.add(remove2LeftMenuItem);
2139     editMenu.add(remove2RightMenuItem);
2140     editMenu.add(removeGappedColumnMenuItem);
2141     editMenu.add(removeAllGapsMenuItem);
2142     editMenu.add(removeRedundancyMenuItem);
2143     editMenu.addSeparator();
2144     // dont add these yet in the CVS build - they cannot be undone!
2145     // Excluded from Jalview 2.5 release - undo needs to be implemented.
2146     // editMenu.add(justifyLeftMenuItem);
2147     // editMenu.add(justifyRightMenuItem);
2148     // editMenu.addSeparator();
2149     editMenu.add(padGapsMenuitem);
2150     viewMenu.add(newView);
2151     viewMenu.add(expandViews);
2152     viewMenu.add(gatherViews);
2153     viewMenu.addSeparator();
2154     viewMenu.add(jMenu3);
2155     viewMenu.add(hideMenu);
2156     viewMenu.addSeparator();
2157     viewMenu.add(followHighlightMenuItem);
2158     viewMenu.add(annotationPanelMenuItem);
2159     autoAnnMenu.add(applyAutoAnnotationSettings);
2160     autoAnnMenu.add(showConsensusHistogram);
2161     autoAnnMenu.add(showSequenceLogo);
2162     autoAnnMenu.add(normaliseSequenceLogo);
2163     autoAnnMenu.addSeparator();
2164     autoAnnMenu.add(showGroupConservation);
2165     autoAnnMenu.add(showGroupConsensus);
2166     viewMenu.add(autoAnnMenu);
2167     viewMenu.addSeparator();
2168     viewMenu.add(showSeqFeatures);
2169     viewMenu.add(chooseAnnotations);
2170     // viewMenu.add(showSeqFeaturesHeight);
2171
2172     viewMenu.add(openFeatureSettings);
2173     tooltipSettingsMenu.add(showDbRefsMenuitem);
2174     tooltipSettingsMenu.add(showNpFeatsMenuitem);
2175     viewMenu.add(tooltipSettingsMenu);
2176     viewMenu.addSeparator();
2177     viewMenu.add(alignmentProperties);
2178     viewMenu.addSeparator();
2179     viewMenu.add(overviewMenuItem);
2180     colourMenu.add(applyToAllGroups);
2181     colourMenu.add(textColour);
2182     colourMenu.addSeparator();
2183     colourMenu.add(noColourmenuItem);
2184     colourMenu.add(clustalColour);
2185     colourMenu.add(BLOSUM62Colour);
2186     colourMenu.add(PIDColour);
2187     colourMenu.add(zappoColour);
2188     colourMenu.add(taylorColour);
2189     colourMenu.add(hydrophobicityColour);
2190     colourMenu.add(helixColour);
2191     colourMenu.add(strandColour);
2192     colourMenu.add(turnColour);
2193     colourMenu.add(buriedColour);
2194     colourMenu.add(nucleotideColour);
2195     colourMenu.add(purinePyrimidineColour);
2196     colourMenu.add(RNAInteractionColour);
2197     // colourMenu.add(covariationColour);
2198     colourMenu.add(tcoffeeColour);
2199     colourMenu.add(userDefinedColour);
2200     colourMenu.addSeparator();
2201     colourMenu.add(conservationMenuItem);
2202     colourMenu.add(modifyConservation);
2203     colourMenu.add(abovePIDThreshold);
2204     colourMenu.add(modifyPID);
2205     colourMenu.add(annotationColour);
2206     colourMenu.add(rnahelicesColour);
2207     calculateMenu.add(sort);
2208     calculateMenu.add(calculateTree);
2209     calculateMenu.addSeparator();
2210     calculateMenu.add(pairwiseAlignmentMenuItem);
2211     calculateMenu.add(PCAMenuItem);
2212     calculateMenu.addSeparator();
2213     calculateMenu.add(showTranslation);
2214     calculateMenu.add(showProducts);
2215     calculateMenu.add(autoCalculate);
2216     calculateMenu.add(sortByTree);
2217     calculateMenu.addSeparator();
2218     calculateMenu.add(extractScores);
2219     webServiceNoServices = new JMenuItem(
2220             MessageManager.getString("label.no_services"));
2221     webService.add(webServiceNoServices);
2222     pasteMenu.add(pasteNew);
2223     pasteMenu.add(pasteThis);
2224     sort.add(sortIDMenuItem);
2225     sort.add(sortLengthMenuItem);
2226     sort.add(sortGroupMenuItem);
2227     sort.add(sortPairwiseMenuItem);
2228     sort.add(sortByTreeMenu);
2229     jMenu2.add(htmlMenuItem);
2230     jMenu2.add(epsFile);
2231     jMenu2.add(createPNG);
2232     addSequenceMenu.add(addFromFile);
2233     addSequenceMenu.add(addFromText);
2234     addSequenceMenu.add(addFromURL);
2235     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2236     statusPanel.add(statusBar, null);
2237     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2238     jMenu3.add(showAllColumns);
2239     jMenu3.add(showAllSeqs);
2240     jMenu3.add(showAllhidden);
2241     jMenu3.add(showAnnotations);
2242     hideMenu.add(hideSelColumns);
2243     hideMenu.add(hideSelSequences);
2244     hideMenu.add(hideAllSelection);
2245     hideMenu.add(hideAllButSelection);
2246     hideMenu.add(hideAnnotations);
2247
2248     formatMenu.add(font);
2249     formatMenu.addSeparator();
2250     formatMenu.add(wrapMenuItem);
2251     formatMenu.add(scaleAbove);
2252     formatMenu.add(scaleLeft);
2253     formatMenu.add(scaleRight);
2254     formatMenu.add(seqLimits);
2255     formatMenu.add(idRightAlign);
2256     formatMenu.add(hiddenMarkers);
2257     formatMenu.add(viewBoxesMenuItem);
2258     formatMenu.add(viewTextMenuItem);
2259     formatMenu.add(colourTextMenuItem);
2260     formatMenu.add(renderGapsMenuItem);
2261     formatMenu.add(centreColumnLabelsMenuItem);
2262     formatMenu.add(showNonconservedMenuItem);
2263     selectMenu.add(findMenuItem);
2264     selectMenu.addSeparator();
2265     selectMenu.add(selectAllSequenceMenuItem);
2266     selectMenu.add(deselectAllSequenceMenuItem);
2267     selectMenu.add(invertSequenceMenuItem);
2268     selectMenu.add(invertColSel);
2269     selectMenu.add(createGroup);
2270     selectMenu.add(unGroup);
2271     selectMenu.add(grpsFromSelection);
2272     selectMenu.add(deleteGroups);
2273     calculateMenu.add(expandAlignment);
2274     // TODO - determine if the listenToViewSelections button is needed : see bug
2275     // JAL-574
2276     // selectMenu.addSeparator();
2277     // selectMenu.add(listenToViewSelections);
2278   }
2279
2280   /**
2281    * Dynamically build list of annotation types to show or hide.
2282    */
2283   protected void buildShowHideAnnotationMenus()
2284   {
2285   }
2286
2287   protected void showHideAnnotation_actionPerformed(String type, boolean b)
2288   {
2289   }
2290
2291   /**
2292    * Action on menu item "Show/hide sequence annotations..."
2293    */
2294   protected void chooseAnnotations_actionPerformed()
2295   {
2296
2297   }
2298
2299   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2300   {
2301     // TODO Auto-generated method stub
2302
2303   }
2304
2305   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2306   {
2307     // TODO Auto-generated method stub
2308
2309   }
2310
2311   protected void showAllhidden_actionPerformed(ActionEvent e)
2312   {
2313     // TODO Auto-generated method stub
2314
2315   }
2316
2317   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2318   {
2319     // TODO Auto-generated method stub
2320
2321   }
2322
2323   protected void hideAllSelection_actionPerformed(ActionEvent e)
2324   {
2325     // TODO Auto-generated method stub
2326
2327   }
2328
2329   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2330   {
2331     // TODO Auto-generated method stub
2332
2333   }
2334
2335   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2336   {
2337     // TODO Auto-generated method stub
2338
2339   }
2340
2341   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2342   {
2343     // TODO Auto-generated method stub
2344
2345   }
2346
2347   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2348   {
2349     // TODO Auto-generated method stub
2350
2351   }
2352
2353   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2354   {
2355     // TODO Auto-generated method stub
2356
2357   }
2358
2359   protected void showGroupConservation_actionPerformed(ActionEvent e)
2360   {
2361     // TODO Auto-generated method stub
2362
2363   }
2364
2365   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2366   {
2367     // TODO Auto-generated method stub
2368
2369   }
2370
2371   protected void showSeqFeaturesHeight_actionPerformed(
2372           ActionEvent actionEvent)
2373   {
2374     // TODO Auto-generated method stub
2375
2376   }
2377
2378   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2379   {
2380     // TODO Auto-generated method stub
2381
2382   }
2383
2384   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2385   {
2386     // TODO Auto-generated method stub
2387
2388   }
2389
2390   protected void followHighlight_actionPerformed()
2391   {
2392     // TODO Auto-generated method stub
2393
2394   }
2395
2396   protected void showNpFeats_actionPerformed(ActionEvent e)
2397   {
2398     // TODO Auto-generated method stub
2399
2400   }
2401
2402   protected void showDbRefs_actionPerformed(ActionEvent e)
2403   {
2404     // TODO Auto-generated method stub
2405
2406   }
2407
2408   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2409   {
2410   }
2411
2412   protected void showProducts_actionPerformed(ActionEvent e)
2413   {
2414   }
2415
2416   protected void buildSortByAnnotationScoresMenu()
2417   {
2418   }
2419
2420   protected void extractScores_actionPerformed(ActionEvent e)
2421   {
2422   }
2423
2424   protected void outputText_actionPerformed(ActionEvent e)
2425   {
2426   }
2427
2428   public void addFromFile_actionPerformed(ActionEvent e)
2429   {
2430
2431   }
2432
2433   public void addFromText_actionPerformed(ActionEvent e)
2434   {
2435
2436   }
2437
2438   public void addFromURL_actionPerformed(ActionEvent e)
2439   {
2440
2441   }
2442
2443   public void exportFeatures_actionPerformed(ActionEvent e)
2444   {
2445
2446   }
2447
2448   public void exportAnnotations_actionPerformed(ActionEvent e)
2449   {
2450
2451   }
2452
2453   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2454   {
2455   }
2456
2457   protected void closeMenuItem_actionPerformed(boolean b)
2458   {
2459   }
2460
2461   protected void redoMenuItem_actionPerformed(ActionEvent e)
2462   {
2463   }
2464
2465   protected void undoMenuItem_actionPerformed(ActionEvent e)
2466   {
2467   }
2468
2469   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2470   {
2471   }
2472
2473   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2474   {
2475   }
2476
2477   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2478   {
2479   }
2480
2481   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2482   {
2483   }
2484
2485   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2486   {
2487   }
2488
2489   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2490   {
2491   }
2492
2493   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2494   {
2495   }
2496
2497   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2498   {
2499   }
2500
2501   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2502   {
2503   }
2504
2505   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2506   {
2507   }
2508
2509   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2510   {
2511   }
2512
2513   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2514   {
2515   }
2516
2517   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2518   {
2519   }
2520
2521   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2522   {
2523   }
2524
2525   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2526   {
2527   }
2528
2529   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2530   {
2531   }
2532
2533   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2534   {
2535   }
2536
2537   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2538   {
2539   }
2540
2541   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2542   {
2543   }
2544
2545   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2546   {
2547   }
2548
2549   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2550   {
2551   }
2552
2553   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2554   {
2555   }
2556
2557   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2558   {
2559   }
2560
2561   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2562   {
2563   }
2564
2565   protected void clustalColour_actionPerformed(ActionEvent e)
2566   {
2567   }
2568
2569   protected void zappoColour_actionPerformed(ActionEvent e)
2570   {
2571   }
2572
2573   protected void taylorColour_actionPerformed(ActionEvent e)
2574   {
2575   }
2576
2577   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2578   {
2579   }
2580
2581   protected void helixColour_actionPerformed(ActionEvent e)
2582   {
2583   }
2584
2585   protected void strandColour_actionPerformed(ActionEvent e)
2586   {
2587   }
2588
2589   protected void turnColour_actionPerformed(ActionEvent e)
2590   {
2591   }
2592
2593   protected void buriedColour_actionPerformed(ActionEvent e)
2594   {
2595   }
2596
2597   protected void userDefinedColour_actionPerformed(ActionEvent e)
2598   {
2599   }
2600
2601   protected void PIDColour_actionPerformed(ActionEvent e)
2602   {
2603   }
2604
2605   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2606   {
2607   }
2608
2609   protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2610   {
2611   }
2612
2613   protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2614   {
2615   }
2616
2617   /*
2618    * protected void covariationColour_actionPerformed(ActionEvent e) { }
2619    */
2620
2621   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2622   {
2623   }
2624
2625   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2626   {
2627   }
2628
2629   protected void printMenuItem_actionPerformed(ActionEvent e)
2630   {
2631   }
2632
2633   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2634   {
2635   }
2636
2637   protected void findMenuItem_actionPerformed(ActionEvent e)
2638   {
2639   }
2640
2641   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2642   {
2643   }
2644
2645   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2646   {
2647   }
2648
2649   protected void nucleotideColour_actionPerformed(ActionEvent e)
2650   {
2651   }
2652
2653   protected void deleteGroups_actionPerformed(ActionEvent e)
2654   {
2655   }
2656
2657   protected void createGroup_actionPerformed(ActionEvent e)
2658   {
2659   }
2660
2661   protected void unGroup_actionPerformed(ActionEvent e)
2662   {
2663   }
2664
2665   protected void copy_actionPerformed(ActionEvent e)
2666   {
2667   }
2668
2669   protected void cut_actionPerformed(ActionEvent e)
2670   {
2671   }
2672
2673   protected void delete_actionPerformed(ActionEvent e)
2674   {
2675   }
2676
2677   protected void pasteNew_actionPerformed(ActionEvent e)
2678   {
2679   }
2680
2681   protected void pasteThis_actionPerformed(ActionEvent e)
2682   {
2683   }
2684
2685   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2686   {
2687   }
2688
2689   public void createPNG(java.io.File f)
2690   {
2691   }
2692
2693   protected void font_actionPerformed(ActionEvent e)
2694   {
2695   }
2696
2697   protected void seqLimit_actionPerformed(ActionEvent e)
2698   {
2699   }
2700
2701   public void seqDBRef_actionPerformed(ActionEvent e)
2702   {
2703
2704   }
2705
2706   public void createEPS(java.io.File f)
2707   {
2708   }
2709
2710   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2711   {
2712
2713   }
2714
2715   /**
2716    * Template method to handle the 'load T-Coffee scores' menu event.
2717    * <p>
2718    * Subclasses override this method to provide a custom action.
2719    *
2720    * @param event
2721    *          The raised event
2722    */
2723   protected void loadScores_actionPerformed(ActionEvent event)
2724   {
2725
2726   }
2727
2728   /**
2729    * Template method to handle the 'Color T-Coffee scores' menu event.
2730    * <p>
2731    * Subclasses override this method to provide a custom action.
2732    *
2733    * @param event
2734    *          The raised event
2735    */
2736   protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2737   {
2738
2739   }
2740
2741   protected void jpred_actionPerformed(ActionEvent e)
2742   {
2743   }
2744
2745   protected void scaleAbove_actionPerformed(ActionEvent e)
2746   {
2747   }
2748
2749   protected void scaleLeft_actionPerformed(ActionEvent e)
2750   {
2751   }
2752
2753   protected void scaleRight_actionPerformed(ActionEvent e)
2754   {
2755   }
2756
2757   protected void modifyPID_actionPerformed(ActionEvent e)
2758   {
2759   }
2760
2761   protected void modifyConservation_actionPerformed(ActionEvent e)
2762   {
2763   }
2764
2765   protected void saveAs_actionPerformed(ActionEvent e)
2766   {
2767   }
2768
2769   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2770   {
2771   }
2772
2773   public void vamsasStore_actionPerformed(ActionEvent e)
2774   {
2775
2776   }
2777
2778   public void vamsasLoad_actionPerformed(ActionEvent e)
2779   {
2780
2781   }
2782
2783   public void showTranslation_actionPerformed(ActionEvent e)
2784   {
2785
2786   }
2787
2788   public void featureSettings_actionPerformed(ActionEvent e)
2789   {
2790
2791   }
2792
2793   public void fetchSequence_actionPerformed(ActionEvent e)
2794   {
2795
2796   }
2797
2798   public void smoothFont_actionPerformed(ActionEvent e)
2799   {
2800
2801   }
2802
2803   public void annotationColour_actionPerformed(ActionEvent e)
2804   {
2805
2806   }
2807
2808   public void rnahelicesColour_actionPerformed(ActionEvent e)
2809   {
2810
2811   }
2812
2813   public void associatedData_actionPerformed(ActionEvent e)
2814   {
2815
2816   }
2817
2818   public void autoCalculate_actionPerformed(ActionEvent e)
2819   {
2820
2821   }
2822
2823   public void sortByTreeOption_actionPerformed(ActionEvent e)
2824   {
2825
2826   }
2827
2828   public void showAllSeqs_actionPerformed(ActionEvent e)
2829   {
2830
2831   }
2832
2833   public void showAllColumns_actionPerformed(ActionEvent e)
2834   {
2835
2836   }
2837
2838   public void hideSelSequences_actionPerformed(ActionEvent e)
2839   {
2840
2841   }
2842
2843   public void hideSelColumns_actionPerformed(ActionEvent e)
2844   {
2845
2846   }
2847
2848   public void hiddenMarkers_actionPerformed(ActionEvent e)
2849   {
2850
2851   }
2852
2853   public void findPdbId_actionPerformed(ActionEvent e)
2854   {
2855
2856   }
2857
2858   public void enterPdbId_actionPerformed(ActionEvent e)
2859   {
2860
2861   }
2862
2863   public void pdbFile_actionPerformed(ActionEvent e)
2864   {
2865
2866   }
2867
2868   public void invertColSel_actionPerformed(ActionEvent e)
2869   {
2870
2871   }
2872
2873   public void tabSelectionChanged(int sel)
2874   {
2875
2876   }
2877
2878   public void tabbedPane_mousePressed(MouseEvent e)
2879   {
2880
2881   }
2882
2883   public void tabbedPane_focusGained(FocusEvent e)
2884   {
2885     requestFocus();
2886   }
2887
2888   public void save_actionPerformed(ActionEvent e)
2889   {
2890
2891   }
2892
2893   public void reload_actionPerformed(ActionEvent e)
2894   {
2895
2896   }
2897
2898   public void newView_actionPerformed(ActionEvent e)
2899   {
2900
2901   }
2902
2903   public void textColour_actionPerformed(ActionEvent e)
2904   {
2905
2906   }
2907
2908   public void idRightAlign_actionPerformed(ActionEvent e)
2909   {
2910
2911   }
2912
2913   public void expandViews_actionPerformed(ActionEvent e)
2914   {
2915
2916   }
2917
2918   public void gatherViews_actionPerformed(ActionEvent e)
2919   {
2920
2921   }
2922
2923   public void buildTreeMenu()
2924   {
2925
2926   }
2927
2928   public void pageSetup_actionPerformed(ActionEvent e)
2929   {
2930
2931   }
2932
2933   public void alignmentProperties()
2934   {
2935
2936   }
2937
2938   protected void expand_newalign(ActionEvent e)
2939   {
2940     // TODO Auto-generated method stub
2941
2942   }
2943 }