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.bin.Cache;
  24 import jalview.gui.JvSwingUtils;
  25 import jalview.schemes.ColourSchemeProperty;
  26 import jalview.util.MessageManager;
  27
  28 import java.awt.BorderLayout;
  29 import java.awt.Color;
  30 import java.awt.GridLayout;
  31 import java.awt.Toolkit;
  32 import java.awt.event.ActionEvent;
  33 import java.awt.event.ActionListener;
  34 import java.awt.event.FocusAdapter;
  35 import java.awt.event.FocusEvent;
  36 import java.awt.event.MouseAdapter;
  37 import java.awt.event.MouseEvent;
  38
  39 import javax.swing.BorderFactory;
  40 import javax.swing.ButtonGroup;
  41 import javax.swing.JCheckBoxMenuItem;
  42 import javax.swing.JInternalFrame;
  43 import javax.swing.JLabel;
  44 import javax.swing.JMenu;
  45 import javax.swing.JMenuBar;
  46 import javax.swing.JMenuItem;
  47 import javax.swing.JOptionPane;
  48 import javax.swing.JPanel;
  49 import javax.swing.JRadioButtonMenuItem;
  50 import javax.swing.JTabbedPane;
  51 import javax.swing.SwingUtilities;
  52 import javax.swing.event.ChangeEvent;
  53 import javax.swing.event.MenuEvent;
  54 import javax.swing.event.MenuListener;
  55
  56 public class GAlignFrame extends JInternalFrame
  57 {
  58   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  59
  60   protected JMenu fileMenu = new JMenu();
  61
  62   protected JMenuItem closeMenuItem = new JMenuItem();
  63
  64   protected JMenu editMenu = new JMenu();
  65
  66   protected JMenu viewMenu = new JMenu();
  67
  68   protected JMenu annotationsMenu = new JMenu();
  69
  70   protected JMenu colourMenu = new JMenu();
  71
  72   protected JMenu calculateMenu = new JMenu();
  73
  74   protected JMenu webService = new JMenu();
  75
  76   protected JMenuItem webServiceNoServices;
  77
  78   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  79
  80   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  81
  82   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  83
  84   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  85
  86   protected JMenuItem remove2RightMenuItem = new JMenuItem();
  87
  88   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  89
  90   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  91
  92   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  93
  94   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  95
  96   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  97
  98   protected JMenuItem sortIDMenuItem = new JMenuItem();
  99
 100   protected JMenuItem sortLengthMenuItem = new JMenuItem();
 101
 102   protected JMenuItem sortGroupMenuItem = new JMenuItem();
 103
 104   protected JMenu sortByAnnotScore = new JMenu();
 105
 106   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
 107
 108   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
 109
 110   protected JMenuItem PCAMenuItem = new JMenuItem();
 111
 112   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
 113
 114   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
 115
 116   BorderLayout borderLayout1 = new BorderLayout();
 117
 118   public JLabel statusBar = new JLabel();
 119
 120   protected JMenuItem saveAs = new JMenuItem();
 121
 122   protected JMenu outputTextboxMenu = new JMenu();
 123
 124   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
 125
 126   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
 127
 128   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
 129
 130   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
 131
 132   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
 133
 134   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
 135
 136   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
 137
 138   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 139
 140   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
 141
 142   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
 143
 144   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 145
 146   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
 147
 148   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
 149
 150   protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
 151
 152   // protected JRadioButtonMenuItem covariationColour = new
 153   // JRadioButtonMenuItem();
 154
 155   protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
 156
 157   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 158
 159   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
 160
 161   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 162
 163   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 164
 165   public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
 166
 167   JMenuItem htmlMenuItem = new JMenuItem();
 168
 169   JMenuItem overviewMenuItem = new JMenuItem();
 170
 171   protected JMenuItem undoMenuItem = new JMenuItem();
 172
 173   protected JMenuItem redoMenuItem = new JMenuItem();
 174
 175   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 176
 177   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 178
 179   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 180
 181   JMenuItem printMenuItem = new JMenuItem();
 182
 183   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 184
 185   JMenuItem findMenuItem = new JMenuItem();
 186
 187   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 188
 189   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 190
 191   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 192
 193   JMenuItem deleteGroups = new JMenuItem();
 194
 195   JMenuItem createGroup = new JMenuItem();
 196
 197   JMenuItem unGroup = new JMenuItem();
 198
 199   JMenuItem delete = new JMenuItem();
 200
 201   JMenuItem copy = new JMenuItem();
 202
 203   JMenuItem cut = new JMenuItem();
 204
 205   JMenu pasteMenu = new JMenu();
 206
 207   JMenuItem pasteNew = new JMenuItem();
 208
 209   JMenuItem pasteThis = new JMenuItem();
 210
 211   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
 212
 213   JMenuItem createPNG = new JMenuItem();
 214
 215   protected JMenuItem font = new JMenuItem();
 216
 217   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 218
 219   JMenuItem epsFile = new JMenuItem();
 220
 221   JMenuItem LoadtreeMenuItem = new JMenuItem();
 222
 223   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 224
 225   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 226
 227   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 228
 229   protected JMenuItem modifyPID = new JMenuItem();
 230
 231   protected JMenuItem modifyConservation = new JMenuItem();
 232
 233   protected JMenu sortByTreeMenu = new JMenu();
 234
 235   protected JMenu sort = new JMenu();
 236
 237   protected JMenu calculateTree = new JMenu();
 238
 239   JMenu jMenu2 = new JMenu();
 240
 241   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 242
 243   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 244
 245   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 246
 247   protected ButtonGroup colours = new ButtonGroup();
 248
 249   JMenuItem vamsasStore = new JMenuItem();
 250
 251   protected JMenuItem showTranslation = new JMenuItem();
 252
 253   protected JMenuItem extractScores = new JMenuItem();
 254
 255   protected JMenuItem expandAlignment = new JMenuItem();
 256
 257   protected JMenu showProducts = new JMenu();
 258
 259   public JMenuItem openFeatureSettings = new JMenuItem();
 260
 261   JMenuItem fetchSequence = new JMenuItem();
 262
 263   JMenuItem annotationColour = new JMenuItem();
 264
 265   protected JMenuItem rnahelicesColour = new JMenuItem();
 266
 267   JMenuItem associatedData = new JMenuItem();
 268
 269   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 270
 271   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 272
 273   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 274
 275   JMenu addSequenceMenu = new JMenu();
 276
 277   JMenuItem addFromFile = new JMenuItem();
 278
 279   JMenuItem addFromText = new JMenuItem();
 280
 281   JMenuItem addFromURL = new JMenuItem();
 282
 283   JMenuItem exportAnnotations = new JMenuItem();
 284
 285   JMenuItem exportFeatures = new JMenuItem();
 286
 287   protected JPanel statusPanel = new JPanel();
 288
 289   GridLayout gridLayout1 = new GridLayout();
 290
 291   JMenu jMenu3 = new JMenu();
 292
 293   JMenuItem showAllSeqs = new JMenuItem();
 294
 295   JMenuItem showAllColumns = new JMenuItem();
 296
 297   JMenu hideMenu = new JMenu();
 298
 299   JMenuItem hideSelSequences = new JMenuItem();
 300
 301   JMenuItem hideSelColumns = new JMenuItem();
 302
 303   JMenuItem hideAllButSelection = new JMenuItem();
 304
 305   JMenuItem hideAllSelection = new JMenuItem();
 306
 307   JMenuItem showAllhidden = new JMenuItem();
 308
 309   protected JMenuItem showAllAnnotations = new JMenuItem();
 310
 311   protected JMenuItem hideAllAnnotations = new JMenuItem();
 312
 313   protected JMenuItem sortAnnBySequence = new JMenuItem();
 314
 315   protected JMenuItem sortAnnByType = new JMenuItem();
 316
 317   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 318
 319   JMenuItem invertColSel = new JMenuItem();
 320
 321   protected JTabbedPane tabbedPane = new JTabbedPane();
 322
 323   JMenuItem save = new JMenuItem();
 324
 325   protected JMenuItem reload = new JMenuItem();
 326
 327   JMenuItem newView = new JMenuItem();
 328
 329   JMenuItem textColour = new JMenuItem();
 330
 331   JMenu formatMenu = new JMenu();
 332
 333   JMenu selectMenu = new JMenu();
 334
 335   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 336
 337   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 338
 339   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 340
 341   protected JMenuItem gatherViews = new JMenuItem();
 342
 343   protected JMenuItem expandViews = new JMenuItem();
 344
 345   JMenuItem pageSetup = new JMenuItem();
 346
 347   JMenuItem alignmentProperties = new JMenuItem();
 348
 349   JMenu tooltipSettingsMenu = new JMenu();
 350
 351   private JMenuItem justifyLeftMenuItem = new JMenuItem();
 352
 353   private JMenuItem justifyRightMenuItem = new JMenuItem();
 354
 355   JMenu autoAnnMenu = new JMenu();
 356
 357   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 358
 359   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 360
 361   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 362
 363   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 364
 365   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 366
 367   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 368
 369   private JMenuItem grpsFromSelection = new JMenuItem();
 370
 371   public GAlignFrame()
 372   {
 373     try
 374     {
 375       jbInit();
 376       setJMenuBar(alignFrameMenuBar);
 377
 378       // dynamically fill save as menu with available formats
 379       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 380       {
 381         JMenuItem item = new JMenuItem(
 382                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 383
 384         item.addActionListener(new java.awt.event.ActionListener()
 385         {
 386           @Override
 387           public void actionPerformed(ActionEvent e)
 388           {
 389             outputText_actionPerformed(e);
 390           }
 391         });
 392
 393         outputTextboxMenu.add(item);
 394       }
 395     } catch (Exception e)
 396     {
 397       System.err.println(e.toString());
 398     }
 399
 400     if (!new jalview.util.Platform().isAMac())
 401     {
 402       closeMenuItem.setMnemonic('C');
 403       outputTextboxMenu.setMnemonic('T');
 404       undoMenuItem.setMnemonic('Z');
 405       redoMenuItem.setMnemonic('0');
 406       copy.setMnemonic('C');
 407       cut.setMnemonic('U');
 408       pasteMenu.setMnemonic('P');
 409       reload.setMnemonic('R');
 410     }
 411
 412     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 413     {
 414       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 415               .getUserColourSchemes().keys();
 416
 417       while (userColours.hasMoreElements())
 418       {
 419         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 420                 userColours.nextElement().toString());
 421         radioItem.setName("USER_DEFINED");
 422         radioItem.addMouseListener(new MouseAdapter()
 423         {
 424           @Override
 425           public void mousePressed(MouseEvent evt)
 426           {
 427             if (evt.isControlDown()
 428                     || SwingUtilities.isRightMouseButton(evt))
 429             {
 430               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 431
 432               int option = JOptionPane.showInternalConfirmDialog(
 433                       jalview.gui.Desktop.desktop,
 434                       MessageManager
 435                               .getString("label.remove_from_default_list"),
 436                       MessageManager
 437                               .getString("label.remove_user_defined_colour"),
 438                       JOptionPane.YES_NO_OPTION);
 439               if (option == JOptionPane.YES_OPTION)
 440               {
 441                 jalview.gui.UserDefinedColours
 442                         .removeColourFromDefaults(radioItem.getText());
 443                 colourMenu.remove(radioItem);
 444               }
 445               else
 446               {
 447                 radioItem.addActionListener(new ActionListener()
 448                 {
 449                   @Override
 450                   public void actionPerformed(ActionEvent evt)
 451                   {
 452                     userDefinedColour_actionPerformed(evt);
 453                   }
 454                 });
 455               }
 456             }
 457           }
 458         });
 459         radioItem.addActionListener(new ActionListener()
 460         {
 461           @Override
 462           public void actionPerformed(ActionEvent evt)
 463           {
 464             userDefinedColour_actionPerformed(evt);
 465           }
 466         });
 467         colourMenu.insert(radioItem, 15);
 468         colours.add(radioItem);
 469       }
 470     }
 471     colours.add(noColourmenuItem);
 472     colours.add(clustalColour);
 473     colours.add(zappoColour);
 474     colours.add(taylorColour);
 475     colours.add(hydrophobicityColour);
 476     colours.add(helixColour);
 477     colours.add(strandColour);
 478     colours.add(turnColour);
 479     colours.add(buriedColour);
 480     colours.add(userDefinedColour);
 481     colours.add(PIDColour);
 482     colours.add(BLOSUM62Colour);
 483     colours.add(nucleotideColour);
 484     colours.add(purinePyrimidineColour);
 485     // colours.add(covariationColour);
 486     colours.add(tcoffeeColour);
 487     colours.add(RNAInteractionColour);
 488     setColourSelected(jalview.bin.Cache
 489             .getDefault("DEFAULT_COLOUR", "None"));
 490
 491   }
 492
 493   public void setColourSelected(String defaultColour)
 494   {
 495
 496     if (defaultColour != null)
 497     {
 498       int index = ColourSchemeProperty
 499               .getColourIndexFromName(defaultColour);
 500
 501       switch (index)
 502       {
 503       case ColourSchemeProperty.CLUSTAL:
 504         clustalColour.setSelected(true);
 505
 506         break;
 507
 508       case ColourSchemeProperty.BLOSUM:
 509         BLOSUM62Colour.setSelected(true);
 510
 511         break;
 512
 513       case ColourSchemeProperty.PID:
 514         PIDColour.setSelected(true);
 515
 516         break;
 517
 518       case ColourSchemeProperty.ZAPPO:
 519         zappoColour.setSelected(true);
 520
 521         break;
 522
 523       case ColourSchemeProperty.TAYLOR:
 524         taylorColour.setSelected(true);
 525         break;
 526
 527       case ColourSchemeProperty.HYDROPHOBIC:
 528         hydrophobicityColour.setSelected(true);
 529
 530         break;
 531
 532       case ColourSchemeProperty.HELIX:
 533         helixColour.setSelected(true);
 534
 535         break;
 536
 537       case ColourSchemeProperty.STRAND:
 538         strandColour.setSelected(true);
 539
 540         break;
 541
 542       case ColourSchemeProperty.TURN:
 543         turnColour.setSelected(true);
 544
 545         break;
 546
 547       case ColourSchemeProperty.BURIED:
 548         buriedColour.setSelected(true);
 549
 550         break;
 551
 552       case ColourSchemeProperty.NUCLEOTIDE:
 553         nucleotideColour.setSelected(true);
 554
 555         break;
 556
 557       case ColourSchemeProperty.TCOFFEE:
 558         tcoffeeColour.setSelected(true);
 559         break;
 560
 561       case ColourSchemeProperty.PURINEPYRIMIDINE:
 562         purinePyrimidineColour.setSelected(true);
 563
 564         break;
 565
 566       case ColourSchemeProperty.RNAINTERACTION:
 567         RNAInteractionColour.setSelected(true);
 568
 569         break;
 570       /*
 571        * case ColourSchemeProperty.COVARIATION:
 572        * covariationColour.setSelected(true);
 573        *
 574        * break;
 575        */
 576       case ColourSchemeProperty.USER_DEFINED:
 577         userDefinedColour.setSelected(true);
 578
 579         break;
 580       case ColourSchemeProperty.NONE:
 581       default:
 582         noColourmenuItem.setSelected(true);
 583         break;
 584
 585       }
 586     }
 587
 588   }
 589
 590   private void jbInit() throws Exception
 591   {
 592     fileMenu.setText(MessageManager.getString("action.file"));
 593     saveAs.setText(MessageManager.getString("action.save_as") + "...");
 594     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 595             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
 596                     .getMenuShortcutKeyMask()
 597                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 598     saveAs.addActionListener(new ActionListener()
 599     {
 600       @Override
 601       public void actionPerformed(ActionEvent e)
 602       {
 603         saveAs_actionPerformed(e);
 604       }
 605     });
 606     closeMenuItem.setText(MessageManager.getString("action.close"));
 607     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 608             java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
 609                     .getMenuShortcutKeyMask(), false));
 610     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 611     {
 612       @Override
 613       public void actionPerformed(ActionEvent e)
 614       {
 615         closeMenuItem_actionPerformed(false);
 616       }
 617     });
 618     editMenu.setText(MessageManager.getString("action.edit"));
 619     viewMenu.setText(MessageManager.getString("action.view"));
 620     annotationsMenu.setText(MessageManager.getString("action.annotations"));
 621     colourMenu.setText(MessageManager.getString("action.colour"));
 622     calculateMenu.setText(MessageManager.getString("action.calculate"));
 623     webService.setText(MessageManager.getString("action.web_service"));
 624     selectAllSequenceMenuItem.setText(MessageManager
 625             .getString("action.select_all"));
 626     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 627             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
 628                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 629     selectAllSequenceMenuItem
 630             .addActionListener(new java.awt.event.ActionListener()
 631             {
 632               @Override
 633               public void actionPerformed(ActionEvent e)
 634               {
 635                 selectAllSequenceMenuItem_actionPerformed(e);
 636               }
 637             });
 638     deselectAllSequenceMenuItem.setText(MessageManager
 639             .getString("action.deselect_all"));
 640     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 641             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 642     deselectAllSequenceMenuItem
 643             .addActionListener(new java.awt.event.ActionListener()
 644             {
 645               @Override
 646               public void actionPerformed(ActionEvent e)
 647               {
 648                 deselectAllSequenceMenuItem_actionPerformed(e);
 649               }
 650             });
 651     invertSequenceMenuItem.setText(MessageManager
 652             .getString("action.invert_sequence_selection"));
 653     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 654             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
 655                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 656     invertSequenceMenuItem
 657             .addActionListener(new java.awt.event.ActionListener()
 658             {
 659               @Override
 660               public void actionPerformed(ActionEvent e)
 661               {
 662                 invertSequenceMenuItem_actionPerformed(e);
 663               }
 664             });
 665     grpsFromSelection.setText(MessageManager
 666             .getString("action.make_groups_selection"));
 667     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
 668     {
 669       @Override
 670       public void actionPerformed(ActionEvent e)
 671       {
 672         makeGrpsFromSelection_actionPerformed(e);
 673       }
 674     });
 675     expandAlignment.setText(MessageManager
 676             .getString("action.view_flanking_regions"));
 677     expandAlignment.setToolTipText(MessageManager
 678             .getString("label.view_flanking_regions"));
 679     expandAlignment.addActionListener(new java.awt.event.ActionListener()
 680     {
 681       @Override
 682       public void actionPerformed(ActionEvent e)
 683       {
 684         expand_newalign(e);
 685       }
 686     });
 687     remove2LeftMenuItem.setText(MessageManager
 688             .getString("action.remove_left"));
 689     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 690             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
 691                     .getMenuShortcutKeyMask(), false));
 692     remove2LeftMenuItem
 693             .addActionListener(new java.awt.event.ActionListener()
 694             {
 695               @Override
 696               public void actionPerformed(ActionEvent e)
 697               {
 698                 remove2LeftMenuItem_actionPerformed(e);
 699               }
 700             });
 701     remove2RightMenuItem.setText(MessageManager
 702             .getString("action.remove_right"));
 703     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 704             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
 705                     .getMenuShortcutKeyMask(), false));
 706     remove2RightMenuItem
 707             .addActionListener(new java.awt.event.ActionListener()
 708             {
 709               @Override
 710               public void actionPerformed(ActionEvent e)
 711               {
 712                 remove2RightMenuItem_actionPerformed(e);
 713               }
 714             });
 715     removeGappedColumnMenuItem.setText(MessageManager
 716             .getString("action.remove_empty_columns"));
 717     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
 718             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 719                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 720     removeGappedColumnMenuItem
 721             .addActionListener(new java.awt.event.ActionListener()
 722             {
 723               @Override
 724               public void actionPerformed(ActionEvent e)
 725               {
 726                 removeGappedColumnMenuItem_actionPerformed(e);
 727               }
 728             });
 729     removeAllGapsMenuItem.setText(MessageManager
 730             .getString("action.remove_all_gaps"));
 731     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
 732             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 733                     .getDefaultToolkit().getMenuShortcutKeyMask()
 734                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 735     removeAllGapsMenuItem
 736             .addActionListener(new java.awt.event.ActionListener()
 737             {
 738               @Override
 739               public void actionPerformed(ActionEvent e)
 740               {
 741                 removeAllGapsMenuItem_actionPerformed(e);
 742               }
 743             });
 744     justifyLeftMenuItem.setText(MessageManager
 745             .getString("action.left_justify_alignment"));
 746     justifyLeftMenuItem
 747             .addActionListener(new java.awt.event.ActionListener()
 748             {
 749               @Override
 750               public void actionPerformed(ActionEvent e)
 751               {
 752                 justifyLeftMenuItem_actionPerformed(e);
 753               }
 754             });
 755     justifyRightMenuItem.setText(MessageManager
 756             .getString("action.right_justify_alignment"));
 757     justifyRightMenuItem
 758             .addActionListener(new java.awt.event.ActionListener()
 759             {
 760               @Override
 761               public void actionPerformed(ActionEvent e)
 762               {
 763                 justifyRightMenuItem_actionPerformed(e);
 764               }
 765             });
 766     viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
 767     viewBoxesMenuItem.setState(true);
 768     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 769     {
 770       @Override
 771       public void actionPerformed(ActionEvent e)
 772       {
 773         viewBoxesMenuItem_actionPerformed(e);
 774       }
 775     });
 776     viewTextMenuItem.setText(MessageManager.getString("action.text"));
 777     viewTextMenuItem.setState(true);
 778     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 779     {
 780       @Override
 781       public void actionPerformed(ActionEvent e)
 782       {
 783         viewTextMenuItem_actionPerformed(e);
 784       }
 785     });
 786     showNonconservedMenuItem.setText(MessageManager
 787             .getString("label.show_non_conversed"));
 788     showNonconservedMenuItem.setState(false);
 789     showNonconservedMenuItem
 790             .addActionListener(new java.awt.event.ActionListener()
 791             {
 792               @Override
 793               public void actionPerformed(ActionEvent e)
 794               {
 795                 showUnconservedMenuItem_actionPerformed(e);
 796               }
 797             });
 798     sortPairwiseMenuItem.setText(MessageManager
 799             .getString("action.by_pairwise_id"));
 800     sortPairwiseMenuItem
 801             .addActionListener(new java.awt.event.ActionListener()
 802             {
 803               @Override
 804               public void actionPerformed(ActionEvent e)
 805               {
 806                 sortPairwiseMenuItem_actionPerformed(e);
 807               }
 808             });
 809     sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
 810     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 811     {
 812       @Override
 813       public void actionPerformed(ActionEvent e)
 814       {
 815         sortIDMenuItem_actionPerformed(e);
 816       }
 817     });
 818     sortLengthMenuItem
 819             .setText(MessageManager.getString("action.by_length"));
 820     sortLengthMenuItem
 821             .addActionListener(new java.awt.event.ActionListener()
 822             {
 823               @Override
 824               public void actionPerformed(ActionEvent e)
 825               {
 826                 sortLengthMenuItem_actionPerformed(e);
 827               }
 828             });
 829     sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
 830     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 831     {
 832       @Override
 833       public void actionPerformed(ActionEvent e)
 834       {
 835         sortGroupMenuItem_actionPerformed(e);
 836       }
 837     });
 838     removeRedundancyMenuItem.setText(MessageManager
 839             .getString("action.remove_redundancy").concat("..."));
 840     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
 841             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
 842                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 843     removeRedundancyMenuItem
 844             .addActionListener(new java.awt.event.ActionListener()
 845             {
 846               @Override
 847               public void actionPerformed(ActionEvent e)
 848               {
 849                 removeRedundancyMenuItem_actionPerformed(e);
 850               }
 851             });
 852     pairwiseAlignmentMenuItem.setText(MessageManager
 853             .getString("action.pairwise_alignment"));
 854     pairwiseAlignmentMenuItem
 855             .addActionListener(new java.awt.event.ActionListener()
 856             {
 857               @Override
 858               public void actionPerformed(ActionEvent e)
 859               {
 860                 pairwiseAlignmentMenuItem_actionPerformed(e);
 861               }
 862             });
 863     PCAMenuItem.setText(MessageManager
 864             .getString("label.principal_component_analysis"));
 865     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 866     {
 867       @Override
 868       public void actionPerformed(ActionEvent e)
 869       {
 870         PCAMenuItem_actionPerformed(e);
 871       }
 872     });
 873     averageDistanceTreeMenuItem.setText(MessageManager
 874             .getString("label.average_distance_identity"));
 875     averageDistanceTreeMenuItem
 876             .addActionListener(new java.awt.event.ActionListener()
 877             {
 878               @Override
 879               public void actionPerformed(ActionEvent e)
 880               {
 881                 averageDistanceTreeMenuItem_actionPerformed(e);
 882               }
 883             });
 884     neighbourTreeMenuItem.setText(MessageManager
 885             .getString("label.neighbour_joining_identity"));
 886     neighbourTreeMenuItem
 887             .addActionListener(new java.awt.event.ActionListener()
 888             {
 889               @Override
 890               public void actionPerformed(ActionEvent e)
 891               {
 892                 neighbourTreeMenuItem_actionPerformed(e);
 893               }
 894             });
 895     this.getContentPane().setLayout(borderLayout1);
 896     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 897     statusBar.setBackground(Color.white);
 898     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 899     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 900     statusBar.setText(MessageManager.getString("label.status_bar"));
 901     outputTextboxMenu.setText(MessageManager
 902             .getString("label.out_to_textbox"));
 903     clustalColour.setText(MessageManager.getString("label.clustalx"));
 904
 905     clustalColour.addActionListener(new java.awt.event.ActionListener()
 906     {
 907       @Override
 908       public void actionPerformed(ActionEvent e)
 909       {
 910         clustalColour_actionPerformed(e);
 911       }
 912     });
 913     zappoColour.setText(MessageManager.getString("label.zappo"));
 914     zappoColour.addActionListener(new java.awt.event.ActionListener()
 915     {
 916       @Override
 917       public void actionPerformed(ActionEvent e)
 918       {
 919         zappoColour_actionPerformed(e);
 920       }
 921     });
 922     taylorColour.setText(MessageManager.getString("label.taylor"));
 923     taylorColour.addActionListener(new java.awt.event.ActionListener()
 924     {
 925       @Override
 926       public void actionPerformed(ActionEvent e)
 927       {
 928         taylorColour_actionPerformed(e);
 929       }
 930     });
 931     hydrophobicityColour.setText(MessageManager
 932             .getString("label.hydrophobicity"));
 933     hydrophobicityColour
 934             .addActionListener(new java.awt.event.ActionListener()
 935             {
 936               @Override
 937               public void actionPerformed(ActionEvent e)
 938               {
 939                 hydrophobicityColour_actionPerformed(e);
 940               }
 941             });
 942     helixColour.setText(MessageManager.getString("label.helix_propensity"));
 943     helixColour.addActionListener(new java.awt.event.ActionListener()
 944     {
 945       @Override
 946       public void actionPerformed(ActionEvent e)
 947       {
 948         helixColour_actionPerformed(e);
 949       }
 950     });
 951     strandColour.setText(MessageManager
 952             .getString("label.strand_propensity"));
 953     strandColour.addActionListener(new java.awt.event.ActionListener()
 954     {
 955       @Override
 956       public void actionPerformed(ActionEvent e)
 957       {
 958         strandColour_actionPerformed(e);
 959       }
 960     });
 961     turnColour.setText(MessageManager.getString("label.turn_propensity"));
 962     turnColour.addActionListener(new java.awt.event.ActionListener()
 963     {
 964       @Override
 965       public void actionPerformed(ActionEvent e)
 966       {
 967         turnColour_actionPerformed(e);
 968       }
 969     });
 970     buriedColour.setText(MessageManager.getString("label.buried_index"));
 971     buriedColour.addActionListener(new java.awt.event.ActionListener()
 972     {
 973       @Override
 974       public void actionPerformed(ActionEvent e)
 975       {
 976         buriedColour_actionPerformed(e);
 977       }
 978     });
 979     userDefinedColour.setText(MessageManager
 980             .getString("action.user_defined"));
 981     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 982     {
 983       @Override
 984       public void actionPerformed(ActionEvent e)
 985       {
 986         userDefinedColour_actionPerformed(e);
 987       }
 988     });
 989     PIDColour
 990             .setText(MessageManager.getString("label.percentage_identity"));
 991     PIDColour.addActionListener(new java.awt.event.ActionListener()
 992     {
 993       @Override
 994       public void actionPerformed(ActionEvent e)
 995       {
 996         PIDColour_actionPerformed(e);
 997       }
 998     });
 999     BLOSUM62Colour
1000             .setText(MessageManager.getString("label.blosum62_score"));
1001     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1002     {
1003       @Override
1004       public void actionPerformed(ActionEvent e)
1005       {
1006         BLOSUM62Colour_actionPerformed(e);
1007       }
1008     });
1009     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1010     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1011     {
1012       @Override
1013       public void actionPerformed(ActionEvent e)
1014       {
1015         nucleotideColour_actionPerformed(e);
1016       }
1017     });
1018
1019     purinePyrimidineColour.setText(MessageManager
1020             .getString("label.purine_pyrimidine"));
1021     purinePyrimidineColour
1022             .addActionListener(new java.awt.event.ActionListener()
1023             {
1024               @Override
1025               public void actionPerformed(ActionEvent e)
1026               {
1027                 purinePyrimidineColour_actionPerformed(e);
1028               }
1029             });
1030
1031     RNAInteractionColour.setText("RNA Interaction type");
1032     RNAInteractionColour
1033             .addActionListener(new java.awt.event.ActionListener()
1034             {
1035               @Override
1036               public void actionPerformed(ActionEvent e)
1037               {
1038                 RNAInteractionColour_actionPerformed(e);
1039               }
1040             });
1041     /*
1042      * covariationColour.setText("Covariation");
1043      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1044      * public void actionPerformed(ActionEvent e) {
1045      * covariationColour_actionPerformed(e); } });
1046      */
1047
1048     avDistanceTreeBlosumMenuItem.setText(MessageManager
1049             .getString("label.average_distance_bloslum62"));
1050     avDistanceTreeBlosumMenuItem
1051             .addActionListener(new java.awt.event.ActionListener()
1052             {
1053               @Override
1054               public void actionPerformed(ActionEvent e)
1055               {
1056                 avTreeBlosumMenuItem_actionPerformed(e);
1057               }
1058             });
1059     njTreeBlosumMenuItem.setText(MessageManager
1060             .getString("label.neighbour_blosum62"));
1061     njTreeBlosumMenuItem
1062             .addActionListener(new java.awt.event.ActionListener()
1063             {
1064               @Override
1065               public void actionPerformed(ActionEvent e)
1066               {
1067                 njTreeBlosumMenuItem_actionPerformed(e);
1068               }
1069             });
1070     annotationPanelMenuItem.setActionCommand("");
1071     annotationPanelMenuItem.setText(MessageManager
1072             .getString("label.show_annotations"));
1073     annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
1074             true));
1075     annotationPanelMenuItem.addActionListener(new ActionListener()
1076     {
1077       @Override
1078       public void actionPerformed(ActionEvent e)
1079       {
1080         annotationPanelMenuItem_actionPerformed(e);
1081       }
1082     });
1083     /*
1084      * Show/hide all annotations only enabled if annotation panel is shown
1085      */
1086     showAllAnnotations.setText(MessageManager
1087             .getString("label.show_all_annotations"));
1088     showAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
1089     showAllAnnotations.addActionListener(new ActionListener()
1090     {
1091       @Override
1092       public void actionPerformed(ActionEvent e)
1093       {
1094         showAllAnnotations_actionPerformed();
1095       }
1096     });
1097     hideAllAnnotations.setText(MessageManager
1098             .getString("label.hide_all_annotations"));
1099     hideAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
1100     hideAllAnnotations.addActionListener(new ActionListener()
1101     {
1102       @Override
1103       public void actionPerformed(ActionEvent e)
1104       {
1105         hideAllAnnotations_actionPerformed();
1106       }
1107     });
1108     sortAnnBySequence.setText(MessageManager
1109             .getString("label.sort_annotations_by_sequence"));
1110     sortAnnBySequence.addActionListener(new ActionListener()
1111     {
1112       @Override
1113       public void actionPerformed(ActionEvent e)
1114       {
1115         sortAnnotationsBySequence_actionPerformed();
1116       }
1117     });
1118     sortAnnByType.setText(MessageManager
1119             .getString("label.sort_annotations_by_type"));
1120     sortAnnByType.addActionListener(new ActionListener()
1121     {
1122       @Override
1123       public void actionPerformed(ActionEvent e)
1124       {
1125         sortAnnotationsByType_actionPerformed();
1126       }
1127     });
1128     colourTextMenuItem.setText(MessageManager
1129             .getString("label.colour_text"));
1130     colourTextMenuItem
1131             .addActionListener(new java.awt.event.ActionListener()
1132             {
1133               @Override
1134               public void actionPerformed(ActionEvent e)
1135               {
1136                 colourTextMenuItem_actionPerformed(e);
1137               }
1138             });
1139     htmlMenuItem.setText(MessageManager.getString("label.html"));
1140     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
1141     {
1142       @Override
1143       public void actionPerformed(ActionEvent e)
1144       {
1145         htmlMenuItem_actionPerformed(e);
1146       }
1147     });
1148     overviewMenuItem.setText(MessageManager
1149             .getString("label.overview_window"));
1150     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
1151     {
1152       @Override
1153       public void actionPerformed(ActionEvent e)
1154       {
1155         overviewMenuItem_actionPerformed(e);
1156       }
1157     });
1158     undoMenuItem.setEnabled(false);
1159     undoMenuItem.setText(MessageManager.getString("action.undo"));
1160     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1161             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1162                     .getMenuShortcutKeyMask(), false));
1163     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1164     {
1165       @Override
1166       public void actionPerformed(ActionEvent e)
1167       {
1168         undoMenuItem_actionPerformed(e);
1169       }
1170     });
1171     redoMenuItem.setEnabled(false);
1172     redoMenuItem.setText(MessageManager.getString("action.redo"));
1173     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1174             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1175                     .getMenuShortcutKeyMask(), false));
1176     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1177     {
1178       @Override
1179       public void actionPerformed(ActionEvent e)
1180       {
1181         redoMenuItem_actionPerformed(e);
1182       }
1183     });
1184     conservationMenuItem.setText(MessageManager
1185             .getString("action.by_conservation"));
1186     conservationMenuItem
1187             .addActionListener(new java.awt.event.ActionListener()
1188             {
1189               @Override
1190               public void actionPerformed(ActionEvent e)
1191               {
1192                 conservationMenuItem_actionPerformed(e);
1193               }
1194             });
1195     noColourmenuItem.setText(MessageManager.getString("label.none"));
1196     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1197     {
1198       @Override
1199       public void actionPerformed(ActionEvent e)
1200       {
1201         noColourmenuItem_actionPerformed(e);
1202       }
1203     });
1204     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1205     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1206     {
1207       @Override
1208       public void actionPerformed(ActionEvent e)
1209       {
1210         wrapMenuItem_actionPerformed(e);
1211       }
1212     });
1213     printMenuItem.setText(MessageManager.getString("action.print") + "...");
1214     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1215             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1216                     .getMenuShortcutKeyMask(), false));
1217     printMenuItem.addActionListener(new java.awt.event.ActionListener()
1218     {
1219       @Override
1220       public void actionPerformed(ActionEvent e)
1221       {
1222         printMenuItem_actionPerformed(e);
1223       }
1224     });
1225     renderGapsMenuItem
1226             .setText(MessageManager.getString("action.show_gaps"));
1227     renderGapsMenuItem.setState(true);
1228     renderGapsMenuItem
1229             .addActionListener(new java.awt.event.ActionListener()
1230             {
1231               @Override
1232               public void actionPerformed(ActionEvent e)
1233               {
1234                 renderGapsMenuItem_actionPerformed(e);
1235               }
1236             });
1237     findMenuItem.setText(MessageManager.getString("action.find"));
1238     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1239             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1240                     .getMenuShortcutKeyMask(), false));
1241     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
1242             MessageManager.getString("label.find_tip")));
1243     findMenuItem.addActionListener(new java.awt.event.ActionListener()
1244     {
1245       @Override
1246       public void actionPerformed(ActionEvent e)
1247       {
1248         findMenuItem_actionPerformed(e);
1249       }
1250     });
1251     abovePIDThreshold.setText(MessageManager
1252             .getString("label.above_identity_threshold"));
1253     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1254     {
1255       @Override
1256       public void actionPerformed(ActionEvent e)
1257       {
1258         abovePIDThreshold_actionPerformed(e);
1259       }
1260     });
1261     showSeqFeatures.setText(MessageManager
1262             .getString("label.show_sequence_features"));
1263     showSeqFeatures.addActionListener(new ActionListener()
1264     {
1265       @Override
1266       public void actionPerformed(ActionEvent actionEvent)
1267       {
1268         showSeqFeatures_actionPerformed(actionEvent);
1269       }
1270     });
1271     /*
1272      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1273      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1274      * void actionPerformed(ActionEvent actionEvent) {
1275      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1276      */
1277     showDbRefsMenuitem.setText(MessageManager
1278             .getString("label.show_database_refs"));
1279     showDbRefsMenuitem.addActionListener(new ActionListener()
1280     {
1281
1282       @Override
1283       public void actionPerformed(ActionEvent e)
1284       {
1285         showDbRefs_actionPerformed(e);
1286       }
1287
1288     });
1289     showNpFeatsMenuitem.setText(MessageManager
1290             .getString("label.show_non_positional_features"));
1291     showNpFeatsMenuitem.addActionListener(new ActionListener()
1292     {
1293
1294       @Override
1295       public void actionPerformed(ActionEvent e)
1296       {
1297         showNpFeats_actionPerformed(e);
1298       }
1299
1300     });
1301     showGroupConservation.setText(MessageManager
1302             .getString("label.group_conservation"));
1303     showGroupConservation.addActionListener(new ActionListener()
1304     {
1305
1306       @Override
1307       public void actionPerformed(ActionEvent e)
1308       {
1309         showGroupConservation_actionPerformed(e);
1310       }
1311
1312     });
1313
1314     showGroupConsensus.setText(MessageManager
1315             .getString("label.group_consensus"));
1316     showGroupConsensus.addActionListener(new ActionListener()
1317     {
1318
1319       @Override
1320       public void actionPerformed(ActionEvent e)
1321       {
1322         showGroupConsensus_actionPerformed(e);
1323       }
1324
1325     });
1326     showConsensusHistogram.setText(MessageManager
1327             .getString("label.show_consensus_histogram"));
1328     showConsensusHistogram.addActionListener(new ActionListener()
1329     {
1330
1331       @Override
1332       public void actionPerformed(ActionEvent e)
1333       {
1334         showConsensusHistogram_actionPerformed(e);
1335       }
1336
1337     });
1338     showSequenceLogo.setText(MessageManager
1339             .getString("label.show_consensus_logo"));
1340     showSequenceLogo.addActionListener(new ActionListener()
1341     {
1342
1343       @Override
1344       public void actionPerformed(ActionEvent e)
1345       {
1346         showSequenceLogo_actionPerformed(e);
1347       }
1348
1349     });
1350     normaliseSequenceLogo.setText(MessageManager
1351             .getString("label.norm_consensus_logo"));
1352     normaliseSequenceLogo.addActionListener(new ActionListener()
1353     {
1354
1355       @Override
1356       public void actionPerformed(ActionEvent e)
1357       {
1358         normaliseSequenceLogo_actionPerformed(e);
1359       }
1360
1361     });
1362     applyAutoAnnotationSettings.setText(MessageManager
1363             .getString("label.apply_all_groups"));
1364     applyAutoAnnotationSettings.setState(false);
1365     applyAutoAnnotationSettings.setVisible(true);
1366     applyAutoAnnotationSettings.addActionListener(new ActionListener()
1367     {
1368
1369       @Override
1370       public void actionPerformed(ActionEvent e)
1371       {
1372         applyAutoAnnotationSettings_actionPerformed(e);
1373       }
1374
1375     });
1376
1377     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1378     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1379     {
1380       @Override
1381       public void actionPerformed(ActionEvent e)
1382       {
1383         nucleotideColour_actionPerformed(e);
1384       }
1385     });
1386
1387     tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1388     tcoffeeColour.setEnabled(false);
1389     tcoffeeColour.addActionListener(new ActionListener()
1390     {
1391
1392       @Override
1393       public void actionPerformed(ActionEvent e)
1394       {
1395         tcoffeeColorScheme_actionPerformed(e);
1396       }
1397     });
1398
1399     deleteGroups
1400             .setText(MessageManager.getString("action.undefine_groups"));
1401     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1402             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1403                     .getMenuShortcutKeyMask(), false));
1404     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1405     {
1406       @Override
1407       public void actionPerformed(ActionEvent e)
1408       {
1409         deleteGroups_actionPerformed(e);
1410       }
1411     });
1412     createGroup.setText(MessageManager.getString("action.create_groups"));
1413     createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1414             java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1415                     .getMenuShortcutKeyMask(), false));
1416     createGroup.addActionListener(new java.awt.event.ActionListener()
1417     {
1418       @Override
1419       public void actionPerformed(ActionEvent e)
1420       {
1421         createGroup_actionPerformed(e);
1422       }
1423     });
1424     unGroup.setText(MessageManager.getString("action.remove_group"));
1425     unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1426             java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1427                     .getMenuShortcutKeyMask()
1428                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1429     unGroup.addActionListener(new java.awt.event.ActionListener()
1430     {
1431       @Override
1432       public void actionPerformed(ActionEvent e)
1433       {
1434         unGroup_actionPerformed(e);
1435       }
1436     });
1437     copy.setText(MessageManager.getString("action.copy"));
1438     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1439             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1440                     .getMenuShortcutKeyMask(), false));
1441
1442     copy.addActionListener(new java.awt.event.ActionListener()
1443     {
1444       @Override
1445       public void actionPerformed(ActionEvent e)
1446       {
1447         copy_actionPerformed(e);
1448       }
1449     });
1450     cut.setText(MessageManager.getString("action.cut"));
1451     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1452             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1453                     .getMenuShortcutKeyMask(), false));
1454     cut.addActionListener(new java.awt.event.ActionListener()
1455     {
1456       @Override
1457       public void actionPerformed(ActionEvent e)
1458       {
1459         cut_actionPerformed(e);
1460       }
1461     });
1462     delete.setText(MessageManager.getString("action.delete"));
1463     delete.addActionListener(new java.awt.event.ActionListener()
1464     {
1465       @Override
1466       public void actionPerformed(ActionEvent e)
1467       {
1468         delete_actionPerformed(e);
1469       }
1470     });
1471     pasteMenu.setText(MessageManager.getString("action.paste"));
1472     pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1473     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1474             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1475                     .getMenuShortcutKeyMask()
1476                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1477     pasteNew.addActionListener(new java.awt.event.ActionListener()
1478     {
1479       @Override
1480       public void actionPerformed(ActionEvent e)
1481       {
1482         pasteNew_actionPerformed(e);
1483       }
1484     });
1485     pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1486     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1487             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1488                     .getMenuShortcutKeyMask(), false));
1489     pasteThis.addActionListener(new java.awt.event.ActionListener()
1490     {
1491       @Override
1492       public void actionPerformed(ActionEvent e)
1493       {
1494         pasteThis_actionPerformed(e);
1495       }
1496     });
1497     applyToAllGroups.setText(MessageManager
1498             .getString("label.apply_colour_to_all_groups"));
1499     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1500     {
1501       @Override
1502       public void actionPerformed(ActionEvent e)
1503       {
1504         applyToAllGroups_actionPerformed(e);
1505       }
1506     });
1507     createPNG.addActionListener(new java.awt.event.ActionListener()
1508     {
1509       @Override
1510       public void actionPerformed(ActionEvent e)
1511       {
1512         createPNG(null);
1513       }
1514     });
1515     createPNG.setActionCommand(MessageManager
1516             .getString("label.save_png_image"));
1517     createPNG.setText("PNG");
1518     font.setText(MessageManager.getString("action.font"));
1519     font.addActionListener(new java.awt.event.ActionListener()
1520     {
1521       @Override
1522       public void actionPerformed(ActionEvent e)
1523       {
1524         font_actionPerformed(e);
1525       }
1526     });
1527
1528     seqLimits.setText(MessageManager
1529             .getString("label.show_sequence_limits"));
1530     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1531     seqLimits.addActionListener(new java.awt.event.ActionListener()
1532     {
1533       @Override
1534       public void actionPerformed(ActionEvent e)
1535       {
1536         seqLimit_actionPerformed(e);
1537       }
1538     });
1539     epsFile.setText("EPS");
1540     epsFile.addActionListener(new java.awt.event.ActionListener()
1541     {
1542       @Override
1543       public void actionPerformed(ActionEvent e)
1544       {
1545         createEPS(null);
1546       }
1547     });
1548     LoadtreeMenuItem.setActionCommand(MessageManager
1549             .getString("label.load_tree_for_sequence_set"));
1550     LoadtreeMenuItem.setText(MessageManager
1551             .getString("label.load_associated_tree"));
1552     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1553     {
1554       @Override
1555       public void actionPerformed(ActionEvent e)
1556       {
1557         LoadtreeMenuItem_actionPerformed(e);
1558       }
1559     });
1560
1561     scaleAbove.setVisible(false);
1562     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1563     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1564     {
1565       @Override
1566       public void actionPerformed(ActionEvent e)
1567       {
1568         scaleAbove_actionPerformed(e);
1569       }
1570     });
1571     scaleLeft.setVisible(false);
1572     scaleLeft.setSelected(true);
1573     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1574     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1575     {
1576       @Override
1577       public void actionPerformed(ActionEvent e)
1578       {
1579         scaleLeft_actionPerformed(e);
1580       }
1581     });
1582     scaleRight.setVisible(false);
1583     scaleRight.setSelected(true);
1584     scaleRight.setText(MessageManager.getString("action.scale_right"));
1585     scaleRight.addActionListener(new java.awt.event.ActionListener()
1586     {
1587       @Override
1588       public void actionPerformed(ActionEvent e)
1589       {
1590         scaleRight_actionPerformed(e);
1591       }
1592     });
1593     centreColumnLabelsMenuItem.setVisible(true);
1594     centreColumnLabelsMenuItem.setState(false);
1595     centreColumnLabelsMenuItem.setText(MessageManager
1596             .getString("label.centre_column_labels"));
1597     centreColumnLabelsMenuItem
1598             .addActionListener(new java.awt.event.ActionListener()
1599             {
1600               @Override
1601               public void actionPerformed(ActionEvent e)
1602               {
1603                 centreColumnLabels_actionPerformed(e);
1604               }
1605             });
1606     followHighlightMenuItem.setVisible(true);
1607     followHighlightMenuItem.setState(true);
1608     followHighlightMenuItem.setText(MessageManager
1609             .getString("label.automatic_scrolling"));
1610     followHighlightMenuItem.addActionListener(new ActionListener()
1611     {
1612
1613       @Override
1614       public void actionPerformed(ActionEvent e)
1615       {
1616         followHighlight_actionPerformed();
1617       }
1618
1619     });
1620
1621     modifyPID.setText(MessageManager
1622             .getString("label.modify_identity_thereshold"));
1623     modifyPID.addActionListener(new java.awt.event.ActionListener()
1624     {
1625       @Override
1626       public void actionPerformed(ActionEvent e)
1627       {
1628         modifyPID_actionPerformed(e);
1629       }
1630     });
1631     modifyConservation.setText(MessageManager
1632             .getString("label.modify_conservation_thereshold"));
1633     modifyConservation
1634             .addActionListener(new java.awt.event.ActionListener()
1635             {
1636               @Override
1637               public void actionPerformed(ActionEvent e)
1638               {
1639                 modifyConservation_actionPerformed(e);
1640               }
1641             });
1642     sortByTreeMenu
1643             .setText(MessageManager.getString("action.by_tree_order"));
1644     sort.setText(MessageManager.getString("action.sort"));
1645     sort.addMenuListener(new MenuListener()
1646     {
1647       @Override
1648       public void menuSelected(MenuEvent e)
1649       {
1650         buildTreeMenu();
1651       }
1652
1653       @Override
1654       public void menuDeselected(MenuEvent e)
1655       {
1656       }
1657
1658       @Override
1659       public void menuCanceled(MenuEvent e)
1660       {
1661       }
1662     });
1663     sortByAnnotScore.setText(MessageManager
1664             .getString("label.sort_by_score"));
1665     sort.add(sortByAnnotScore);
1666     sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1667     {
1668
1669       @Override
1670       public void menuCanceled(MenuEvent e)
1671       {
1672       }
1673
1674       @Override
1675       public void menuDeselected(MenuEvent e)
1676       {
1677       }
1678
1679       @Override
1680       public void menuSelected(MenuEvent e)
1681       {
1682         buildSortByAnnotationScoresMenu();
1683       }
1684     });
1685     sortByAnnotScore.setVisible(false);
1686
1687     calculateTree
1688             .setText(MessageManager.getString("action.calculate_tree"));
1689
1690     jMenu2.setText(MessageManager.getString("label.export_image"));
1691     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1692     padGapsMenuitem.setState(jalview.bin.Cache
1693             .getDefault("PAD_GAPS", false));
1694     padGapsMenuitem.addActionListener(new ActionListener()
1695     {
1696       @Override
1697       public void actionPerformed(ActionEvent e)
1698       {
1699         padGapsMenuitem_actionPerformed(e);
1700       }
1701     });
1702     vamsasStore.setVisible(false);
1703     vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1704     vamsasStore.addActionListener(new ActionListener()
1705     {
1706       @Override
1707       public void actionPerformed(ActionEvent e)
1708       {
1709         vamsasStore_actionPerformed(e);
1710       }
1711     });
1712     showTranslation.setText(MessageManager
1713             .getString("label.translate_cDNA"));
1714     showTranslation.addActionListener(new ActionListener()
1715     {
1716       @Override
1717       public void actionPerformed(ActionEvent e)
1718       {
1719         showTranslation_actionPerformed(e);
1720       }
1721     });
1722     extractScores.setText(MessageManager.getString("label.extract_scores")
1723             + "...");
1724     extractScores.addActionListener(new ActionListener()
1725     {
1726       @Override
1727       public void actionPerformed(ActionEvent e)
1728       {
1729         extractScores_actionPerformed(e);
1730       }
1731     });
1732     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1733     // score extraction
1734     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1735     /*
1736      * showProducts.addActionListener(new ActionListener() {
1737      *
1738      * public void actionPerformed(ActionEvent e) {
1739      * showProducts_actionPerformed(e); } });
1740      */
1741     openFeatureSettings.setText(MessageManager
1742             .getString("label.feature_settings"));
1743     openFeatureSettings.addActionListener(new ActionListener()
1744     {
1745       @Override
1746       public void actionPerformed(ActionEvent e)
1747       {
1748         featureSettings_actionPerformed(e);
1749       }
1750     });
1751     fetchSequence
1752             .setText(MessageManager.getString("label.fetch_sequences"));
1753     fetchSequence.addActionListener(new ActionListener()
1754     {
1755       @Override
1756       public void actionPerformed(ActionEvent e)
1757       {
1758         fetchSequence_actionPerformed(e);
1759       }
1760     });
1761
1762     annotationColour.setText(MessageManager
1763             .getString("action.by_annotation"));
1764     annotationColour.addActionListener(new ActionListener()
1765     {
1766       @Override
1767       public void actionPerformed(ActionEvent e)
1768       {
1769         annotationColour_actionPerformed(e);
1770       }
1771     });
1772
1773     rnahelicesColour.setText(MessageManager
1774             .getString("action.by_rna_helixes"));
1775     rnahelicesColour.addActionListener(new ActionListener()
1776     {
1777       @Override
1778       public void actionPerformed(ActionEvent e)
1779       {
1780         rnahelicesColour_actionPerformed(e);
1781       }
1782     });
1783
1784     associatedData.setText(MessageManager
1785             .getString("label.load_features_annotations"));
1786     associatedData.addActionListener(new ActionListener()
1787     {
1788       @Override
1789       public void actionPerformed(ActionEvent e)
1790       {
1791         associatedData_actionPerformed(e);
1792       }
1793     });
1794     autoCalculate.setText(MessageManager
1795             .getString("label.autocalculate_consensus"));
1796     autoCalculate.setState(jalview.bin.Cache.getDefault(
1797             "AUTO_CALC_CONSENSUS", true));
1798     autoCalculate.addActionListener(new ActionListener()
1799     {
1800       @Override
1801       public void actionPerformed(ActionEvent e)
1802       {
1803         autoCalculate_actionPerformed(e);
1804       }
1805     });
1806     sortByTree.setText(MessageManager
1807             .getString("label.sort_alignment_new_tree"));
1808     sortByTree
1809             .setToolTipText("<html>"
1810                     + MessageManager
1811                             .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1812     sortByTree
1813             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1814     sortByTree.addActionListener(new ActionListener()
1815     {
1816       @Override
1817       public void actionPerformed(ActionEvent e)
1818       {
1819         sortByTreeOption_actionPerformed(e);
1820       }
1821     });
1822
1823     listenToViewSelections.setText(MessageManager
1824             .getString("label.listen_for_selections"));
1825     listenToViewSelections
1826             .setToolTipText("<html>"
1827                     + MessageManager
1828                             .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1829     listenToViewSelections.setState(false);
1830     listenToViewSelections.addActionListener(new ActionListener()
1831     {
1832       @Override
1833       public void actionPerformed(ActionEvent e)
1834       {
1835         listenToViewSelections_actionPerformed(e);
1836       }
1837     });
1838
1839     addSequenceMenu
1840             .setText(MessageManager.getString("label.add_sequences"));
1841     addFromFile.setText(MessageManager.getString("label.from_file"));
1842     addFromFile.addActionListener(new ActionListener()
1843     {
1844       @Override
1845       public void actionPerformed(ActionEvent e)
1846       {
1847         addFromFile_actionPerformed(e);
1848       }
1849     });
1850     addFromText.setText(MessageManager.getString("label.from_textbox"));
1851     addFromText.addActionListener(new ActionListener()
1852     {
1853       @Override
1854       public void actionPerformed(ActionEvent e)
1855       {
1856         addFromText_actionPerformed(e);
1857       }
1858     });
1859     addFromURL.setText(MessageManager.getString("label.from_url"));
1860     addFromURL.addActionListener(new ActionListener()
1861     {
1862       @Override
1863       public void actionPerformed(ActionEvent e)
1864       {
1865         addFromURL_actionPerformed(e);
1866       }
1867     });
1868     exportFeatures.setText(MessageManager
1869             .getString("label.export_features"));
1870     exportFeatures.addActionListener(new ActionListener()
1871     {
1872       @Override
1873       public void actionPerformed(ActionEvent e)
1874       {
1875         exportFeatures_actionPerformed(e);
1876       }
1877     });
1878     exportAnnotations.setText(MessageManager
1879             .getString("label.export_annotations"));
1880     exportAnnotations.addActionListener(new ActionListener()
1881     {
1882       @Override
1883       public void actionPerformed(ActionEvent e)
1884       {
1885         exportAnnotations_actionPerformed(e);
1886       }
1887     });
1888     statusPanel.setLayout(gridLayout1);
1889     jMenu3.setText(MessageManager.getString("action.show"));
1890     showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
1891     showAllSeqs.setToolTipText(MessageManager
1892             .getString("label.toggle_sequence_visibility"));
1893     showAllSeqs.addActionListener(new ActionListener()
1894     {
1895       @Override
1896       public void actionPerformed(ActionEvent e)
1897       {
1898         showAllSeqs_actionPerformed(e);
1899       }
1900     });
1901     showAllColumns.setText(MessageManager.getString("label.all_columns"));
1902     showAllColumns.setToolTipText(MessageManager
1903             .getString("label.toggle_columns_visibility"));
1904     showAllColumns.addActionListener(new ActionListener()
1905     {
1906       @Override
1907       public void actionPerformed(ActionEvent e)
1908       {
1909         showAllColumns_actionPerformed(e);
1910       }
1911     });
1912     hideMenu.setText(MessageManager.getString("action.hide"));
1913     hideSelSequences.setText(MessageManager
1914             .getString("label.selected_sequences"));
1915     hideSelSequences.setToolTipText(MessageManager
1916             .getString("label.toggle_sequence_visibility"));
1917     hideSelSequences.addActionListener(new ActionListener()
1918     {
1919       @Override
1920       public void actionPerformed(ActionEvent e)
1921       {
1922         hideSelSequences_actionPerformed(e);
1923       }
1924     });
1925     hideSelColumns.setText(MessageManager
1926             .getString("label.selected_columns"));
1927     hideSelColumns.setToolTipText(MessageManager
1928             .getString("label.toggle_columns_visibility"));
1929     hideSelColumns.addActionListener(new ActionListener()
1930     {
1931       @Override
1932       public void actionPerformed(ActionEvent e)
1933       {
1934         hideSelColumns_actionPerformed(e);
1935       }
1936     });
1937     hideAllSelection.setText(MessageManager
1938             .getString("label.selected_region"));
1939     hideAllSelection.addActionListener(new ActionListener()
1940     {
1941       @Override
1942       public void actionPerformed(ActionEvent e)
1943       {
1944         hideAllSelection_actionPerformed(e);
1945       }
1946     });
1947     // TODO: should be hidden if no selection exists.
1948     hideAllButSelection.setText(MessageManager
1949             .getString("label.all_but_selected_region"));
1950     hideAllButSelection.addActionListener(new ActionListener()
1951     {
1952       @Override
1953       public void actionPerformed(ActionEvent e)
1954       {
1955         hideAllButSelection_actionPerformed(e);
1956       }
1957     });
1958     showAllhidden.setText(MessageManager
1959             .getString("label.all_sequences_columns"));
1960     showAllhidden.setToolTipText(MessageManager
1961             .getString("label.toggles_visibility_hidden_selected_regions"));
1962     showAllhidden.addActionListener(new ActionListener()
1963     {
1964       @Override
1965       public void actionPerformed(ActionEvent e)
1966       {
1967         showAllhidden_actionPerformed(e);
1968       }
1969     });
1970     hiddenMarkers.setText(MessageManager
1971             .getString("action.show_hidden_markers"));
1972     hiddenMarkers.addActionListener(new ActionListener()
1973     {
1974       @Override
1975       public void actionPerformed(ActionEvent e)
1976       {
1977         hiddenMarkers_actionPerformed(e);
1978       }
1979     });
1980     invertColSel.setText(MessageManager
1981             .getString("action.invert_column_selection"));
1982     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1983             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1984                     .getMenuShortcutKeyMask()
1985                     | java.awt.event.KeyEvent.ALT_MASK, false));
1986     invertColSel.addActionListener(new ActionListener()
1987     {
1988       @Override
1989       public void actionPerformed(ActionEvent e)
1990       {
1991         invertColSel_actionPerformed(e);
1992       }
1993     });
1994     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1995     {
1996       @Override
1997       public void stateChanged(ChangeEvent evt)
1998       {
1999         JTabbedPane pane = (JTabbedPane) evt.getSource();
2000         int sel = pane.getSelectedIndex();
2001         tabSelectionChanged(sel);
2002       }
2003     });
2004     tabbedPane.addMouseListener(new MouseAdapter()
2005     {
2006       @Override
2007       public void mousePressed(MouseEvent e)
2008       {
2009         tabbedPane_mousePressed(e);
2010       }
2011     });
2012     tabbedPane.addFocusListener(new FocusAdapter()
2013     {
2014       @Override
2015       public void focusGained(FocusEvent e)
2016       {
2017         tabbedPane_focusGained(e);
2018       }
2019     });
2020     save.setText(MessageManager.getString("action.save"));
2021     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2022             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
2023                     .getMenuShortcutKeyMask(), false));
2024     save.addActionListener(new ActionListener()
2025     {
2026       @Override
2027       public void actionPerformed(ActionEvent e)
2028       {
2029         save_actionPerformed(e);
2030       }
2031     });
2032     reload.setEnabled(false);
2033     reload.setText(MessageManager.getString("action.reload"));
2034     reload.addActionListener(new ActionListener()
2035     {
2036       @Override
2037       public void actionPerformed(ActionEvent e)
2038       {
2039         reload_actionPerformed(e);
2040       }
2041     });
2042     newView.setText(MessageManager.getString("action.new_view"));
2043     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2044             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
2045                     .getMenuShortcutKeyMask(), false));
2046     newView.addActionListener(new ActionListener()
2047     {
2048       @Override
2049       public void actionPerformed(ActionEvent e)
2050       {
2051         newView_actionPerformed(e);
2052       }
2053     });
2054     tabbedPane.setToolTipText("<html><i>"
2055             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2056             + "</i></html>");
2057     textColour.setText(MessageManager.getString("label.colour_text")
2058             + "...");
2059     textColour.addActionListener(new ActionListener()
2060     {
2061       @Override
2062       public void actionPerformed(ActionEvent e)
2063       {
2064         textColour_actionPerformed(e);
2065       }
2066     });
2067     formatMenu.setText(MessageManager.getString("action.format"));
2068     selectMenu.setText(MessageManager.getString("action.select"));
2069     idRightAlign.setText(MessageManager
2070             .getString("label.right_align_sequence_id"));
2071     idRightAlign.addActionListener(new ActionListener()
2072     {
2073       @Override
2074       public void actionPerformed(ActionEvent e)
2075       {
2076         idRightAlign_actionPerformed(e);
2077       }
2078     });
2079     gatherViews.setEnabled(false);
2080     gatherViews.setText(MessageManager.getString("action.gather_views"));
2081     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2082             java.awt.event.KeyEvent.VK_G, 0, false));
2083     gatherViews.addActionListener(new ActionListener()
2084     {
2085       @Override
2086       public void actionPerformed(ActionEvent e)
2087       {
2088         gatherViews_actionPerformed(e);
2089       }
2090     });
2091     expandViews.setEnabled(false);
2092     expandViews.setText(MessageManager.getString("action.expand_views"));
2093     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2094             java.awt.event.KeyEvent.VK_X, 0, false));
2095     expandViews.addActionListener(new ActionListener()
2096     {
2097       @Override
2098       public void actionPerformed(ActionEvent e)
2099       {
2100         expandViews_actionPerformed(e);
2101       }
2102     });
2103     pageSetup
2104             .setText(MessageManager.getString("action.page_setup") + "...");
2105     pageSetup.addActionListener(new ActionListener()
2106     {
2107       @Override
2108       public void actionPerformed(ActionEvent e)
2109       {
2110         pageSetup_actionPerformed(e);
2111       }
2112     });
2113     alignmentProperties.setText(MessageManager
2114             .getString("label.alignment_props") + "...");
2115     alignmentProperties.addActionListener(new ActionListener()
2116     {
2117       @Override
2118       public void actionPerformed(ActionEvent actionEvent)
2119       {
2120         alignmentProperties();
2121       }
2122     });
2123     tooltipSettingsMenu.setText(MessageManager
2124             .getString("label.sequence_id_tooltip"));
2125     autoAnnMenu.setText(MessageManager
2126             .getString("label.autocalculated_annotation"));
2127     alignFrameMenuBar.add(fileMenu);
2128     alignFrameMenuBar.add(editMenu);
2129     alignFrameMenuBar.add(selectMenu);
2130     alignFrameMenuBar.add(viewMenu);
2131     alignFrameMenuBar.add(annotationsMenu);
2132     alignFrameMenuBar.add(formatMenu);
2133     alignFrameMenuBar.add(colourMenu);
2134     alignFrameMenuBar.add(calculateMenu);
2135     alignFrameMenuBar.add(webService);
2136     fileMenu.add(fetchSequence);
2137     fileMenu.add(addSequenceMenu);
2138     fileMenu.add(reload);
2139     fileMenu.addSeparator();
2140     fileMenu.add(vamsasStore);
2141     fileMenu.add(save);
2142     fileMenu.add(saveAs);
2143     fileMenu.add(outputTextboxMenu);
2144     fileMenu.add(pageSetup);
2145     fileMenu.add(printMenuItem);
2146     fileMenu.addSeparator();
2147     fileMenu.add(jMenu2);
2148     fileMenu.add(exportFeatures);
2149     fileMenu.add(exportAnnotations);
2150     fileMenu.add(LoadtreeMenuItem);
2151     fileMenu.add(associatedData);
2152     fileMenu.addSeparator();
2153     fileMenu.add(closeMenuItem);
2154     editMenu.add(undoMenuItem);
2155     editMenu.add(redoMenuItem);
2156     editMenu.add(cut);
2157     editMenu.add(copy);
2158     editMenu.add(pasteMenu);
2159     editMenu.add(delete);
2160     editMenu.addSeparator();
2161     editMenu.add(remove2LeftMenuItem);
2162     editMenu.add(remove2RightMenuItem);
2163     editMenu.add(removeGappedColumnMenuItem);
2164     editMenu.add(removeAllGapsMenuItem);
2165     editMenu.add(removeRedundancyMenuItem);
2166     editMenu.addSeparator();
2167     // dont add these yet in the CVS build - they cannot be undone!
2168     // Excluded from Jalview 2.5 release - undo needs to be implemented.
2169     // editMenu.add(justifyLeftMenuItem);
2170     // editMenu.add(justifyRightMenuItem);
2171     // editMenu.addSeparator();
2172     editMenu.add(padGapsMenuitem);
2173     viewMenu.add(newView);
2174     viewMenu.add(expandViews);
2175     viewMenu.add(gatherViews);
2176     viewMenu.addSeparator();
2177     viewMenu.add(jMenu3);
2178     viewMenu.add(hideMenu);
2179     viewMenu.addSeparator();
2180     viewMenu.add(followHighlightMenuItem);
2181     annotationsMenu.add(annotationPanelMenuItem);
2182     annotationsMenu.add(showAllAnnotations);
2183     annotationsMenu.add(hideAllAnnotations);
2184     annotationsMenu.add(sortAnnBySequence);
2185     annotationsMenu.add(sortAnnByType);
2186     autoAnnMenu.add(applyAutoAnnotationSettings);
2187     autoAnnMenu.add(showConsensusHistogram);
2188     autoAnnMenu.add(showSequenceLogo);
2189     autoAnnMenu.add(normaliseSequenceLogo);
2190     autoAnnMenu.addSeparator();
2191     autoAnnMenu.add(showGroupConservation);
2192     autoAnnMenu.add(showGroupConsensus);
2193     annotationsMenu.add(autoAnnMenu);
2194     viewMenu.addSeparator();
2195     viewMenu.add(showSeqFeatures);
2196     // viewMenu.add(showSeqFeaturesHeight);
2197
2198     viewMenu.add(openFeatureSettings);
2199     tooltipSettingsMenu.add(showDbRefsMenuitem);
2200     tooltipSettingsMenu.add(showNpFeatsMenuitem);
2201     viewMenu.add(tooltipSettingsMenu);
2202     viewMenu.addSeparator();
2203     viewMenu.add(alignmentProperties);
2204     viewMenu.addSeparator();
2205     viewMenu.add(overviewMenuItem);
2206     colourMenu.add(applyToAllGroups);
2207     colourMenu.add(textColour);
2208     colourMenu.addSeparator();
2209     colourMenu.add(noColourmenuItem);
2210     colourMenu.add(clustalColour);
2211     colourMenu.add(BLOSUM62Colour);
2212     colourMenu.add(PIDColour);
2213     colourMenu.add(zappoColour);
2214     colourMenu.add(taylorColour);
2215     colourMenu.add(hydrophobicityColour);
2216     colourMenu.add(helixColour);
2217     colourMenu.add(strandColour);
2218     colourMenu.add(turnColour);
2219     colourMenu.add(buriedColour);
2220     colourMenu.add(nucleotideColour);
2221     colourMenu.add(purinePyrimidineColour);
2222     colourMenu.add(RNAInteractionColour);
2223     // colourMenu.add(covariationColour);
2224     colourMenu.add(tcoffeeColour);
2225     colourMenu.add(userDefinedColour);
2226     colourMenu.addSeparator();
2227     colourMenu.add(conservationMenuItem);
2228     colourMenu.add(modifyConservation);
2229     colourMenu.add(abovePIDThreshold);
2230     colourMenu.add(modifyPID);
2231     colourMenu.add(annotationColour);
2232     colourMenu.add(rnahelicesColour);
2233     calculateMenu.add(sort);
2234     calculateMenu.add(calculateTree);
2235     calculateMenu.addSeparator();
2236     calculateMenu.add(pairwiseAlignmentMenuItem);
2237     calculateMenu.add(PCAMenuItem);
2238     calculateMenu.addSeparator();
2239     calculateMenu.add(showTranslation);
2240     calculateMenu.add(showProducts);
2241     calculateMenu.add(autoCalculate);
2242     calculateMenu.add(sortByTree);
2243     calculateMenu.addSeparator();
2244     calculateMenu.add(extractScores);
2245     webServiceNoServices = new JMenuItem(
2246             MessageManager.getString("label.no_services"));
2247     webService.add(webServiceNoServices);
2248     pasteMenu.add(pasteNew);
2249     pasteMenu.add(pasteThis);
2250     sort.add(sortIDMenuItem);
2251     sort.add(sortLengthMenuItem);
2252     sort.add(sortGroupMenuItem);
2253     sort.add(sortPairwiseMenuItem);
2254     sort.add(sortByTreeMenu);
2255     jMenu2.add(htmlMenuItem);
2256     jMenu2.add(epsFile);
2257     jMenu2.add(createPNG);
2258     addSequenceMenu.add(addFromFile);
2259     addSequenceMenu.add(addFromText);
2260     addSequenceMenu.add(addFromURL);
2261     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2262     statusPanel.add(statusBar, null);
2263     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2264     jMenu3.add(showAllColumns);
2265     jMenu3.add(showAllSeqs);
2266     jMenu3.add(showAllhidden);
2267     hideMenu.add(hideSelColumns);
2268     hideMenu.add(hideSelSequences);
2269     hideMenu.add(hideAllSelection);
2270     hideMenu.add(hideAllButSelection);
2271
2272     formatMenu.add(font);
2273     formatMenu.addSeparator();
2274     formatMenu.add(wrapMenuItem);
2275     formatMenu.add(scaleAbove);
2276     formatMenu.add(scaleLeft);
2277     formatMenu.add(scaleRight);
2278     formatMenu.add(seqLimits);
2279     formatMenu.add(idRightAlign);
2280     formatMenu.add(hiddenMarkers);
2281     formatMenu.add(viewBoxesMenuItem);
2282     formatMenu.add(viewTextMenuItem);
2283     formatMenu.add(colourTextMenuItem);
2284     formatMenu.add(renderGapsMenuItem);
2285     formatMenu.add(centreColumnLabelsMenuItem);
2286     formatMenu.add(showNonconservedMenuItem);
2287     selectMenu.add(findMenuItem);
2288     selectMenu.addSeparator();
2289     selectMenu.add(selectAllSequenceMenuItem);
2290     selectMenu.add(deselectAllSequenceMenuItem);
2291     selectMenu.add(invertSequenceMenuItem);
2292     selectMenu.add(invertColSel);
2293     selectMenu.add(createGroup);
2294     selectMenu.add(unGroup);
2295     selectMenu.add(grpsFromSelection);
2296     selectMenu.add(deleteGroups);
2297     calculateMenu.add(expandAlignment);
2298     // TODO - determine if the listenToViewSelections button is needed : see bug
2299     // JAL-574
2300     // selectMenu.addSeparator();
2301     // selectMenu.add(listenToViewSelections);
2302   }
2303
2304   /**
2305    * Action on clicking sort annotations by type.
2306    */
2307   protected void sortAnnotationsByType_actionPerformed()
2308   {
2309   }
2310
2311   /**
2312    * Action on clicking sort annotations by sequence
2313    */
2314   protected void sortAnnotationsBySequence_actionPerformed()
2315   {
2316   }
2317
2318   /**
2319    * Action on clicking Show all annotations.
2320    */
2321   protected void showAllAnnotations_actionPerformed()
2322   {
2323     setAllAnnotationsVisibility(true);
2324   }
2325
2326   /**
2327    * Action on clicking Hide all annotations.
2328    */
2329   protected void hideAllAnnotations_actionPerformed()
2330   {
2331     setAllAnnotationsVisibility(false);
2332   }
2333
2334   /**
2335    * Set the visibility of all annotations to true or false.
2336    *
2337    * @param visible
2338    */
2339   protected void setAllAnnotationsVisibility(boolean visible)
2340   {
2341
2342   }
2343
2344   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2345   {
2346     // TODO Auto-generated method stub
2347
2348   }
2349
2350   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2351   {
2352     // TODO Auto-generated method stub
2353
2354   }
2355
2356   protected void showAllhidden_actionPerformed(ActionEvent e)
2357   {
2358     // TODO Auto-generated method stub
2359
2360   }
2361
2362   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2363   {
2364     // TODO Auto-generated method stub
2365
2366   }
2367
2368   protected void hideAllSelection_actionPerformed(ActionEvent e)
2369   {
2370     // TODO Auto-generated method stub
2371
2372   }
2373
2374   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2375   {
2376     // TODO Auto-generated method stub
2377
2378   }
2379
2380   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2381   {
2382     // TODO Auto-generated method stub
2383
2384   }
2385
2386   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2387   {
2388     // TODO Auto-generated method stub
2389
2390   }
2391
2392   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2393   {
2394     // TODO Auto-generated method stub
2395
2396   }
2397
2398   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2399   {
2400     // TODO Auto-generated method stub
2401
2402   }
2403
2404   protected void showGroupConservation_actionPerformed(ActionEvent e)
2405   {
2406     // TODO Auto-generated method stub
2407
2408   }
2409
2410   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2411   {
2412     // TODO Auto-generated method stub
2413
2414   }
2415
2416   protected void showSeqFeaturesHeight_actionPerformed(
2417           ActionEvent actionEvent)
2418   {
2419     // TODO Auto-generated method stub
2420
2421   }
2422
2423   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2424   {
2425     // TODO Auto-generated method stub
2426
2427   }
2428
2429   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2430   {
2431     // TODO Auto-generated method stub
2432
2433   }
2434
2435   protected void followHighlight_actionPerformed()
2436   {
2437     // TODO Auto-generated method stub
2438
2439   }
2440
2441   protected void showNpFeats_actionPerformed(ActionEvent e)
2442   {
2443     // TODO Auto-generated method stub
2444
2445   }
2446
2447   protected void showDbRefs_actionPerformed(ActionEvent e)
2448   {
2449     // TODO Auto-generated method stub
2450
2451   }
2452
2453   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2454   {
2455   }
2456
2457   protected void showProducts_actionPerformed(ActionEvent e)
2458   {
2459   }
2460
2461   protected void buildSortByAnnotationScoresMenu()
2462   {
2463   }
2464
2465   protected void extractScores_actionPerformed(ActionEvent e)
2466   {
2467   }
2468
2469   protected void outputText_actionPerformed(ActionEvent e)
2470   {
2471   }
2472
2473   public void addFromFile_actionPerformed(ActionEvent e)
2474   {
2475
2476   }
2477
2478   public void addFromText_actionPerformed(ActionEvent e)
2479   {
2480
2481   }
2482
2483   public void addFromURL_actionPerformed(ActionEvent e)
2484   {
2485
2486   }
2487
2488   public void exportFeatures_actionPerformed(ActionEvent e)
2489   {
2490
2491   }
2492
2493   public void exportAnnotations_actionPerformed(ActionEvent e)
2494   {
2495
2496   }
2497
2498   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2499   {
2500   }
2501
2502   protected void closeMenuItem_actionPerformed(boolean b)
2503   {
2504   }
2505
2506   protected void redoMenuItem_actionPerformed(ActionEvent e)
2507   {
2508   }
2509
2510   protected void undoMenuItem_actionPerformed(ActionEvent e)
2511   {
2512   }
2513
2514   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2515   {
2516   }
2517
2518   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2519   {
2520   }
2521
2522   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2523   {
2524   }
2525
2526   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2527   {
2528   }
2529
2530   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2531   {
2532   }
2533
2534   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2535   {
2536   }
2537
2538   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2539   {
2540   }
2541
2542   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2543   {
2544   }
2545
2546   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2547   {
2548   }
2549
2550   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2551   {
2552   }
2553
2554   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2555   {
2556   }
2557
2558   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2559   {
2560   }
2561
2562   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2563   {
2564   }
2565
2566   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2567   {
2568   }
2569
2570   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2571   {
2572   }
2573
2574   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2575   {
2576   }
2577
2578   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2579   {
2580   }
2581
2582   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2583   {
2584   }
2585
2586   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2587   {
2588   }
2589
2590   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2591   {
2592   }
2593
2594   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2595   {
2596   }
2597
2598   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2599   {
2600   }
2601
2602   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2603   {
2604   }
2605
2606   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2607   {
2608   }
2609
2610   protected void clustalColour_actionPerformed(ActionEvent e)
2611   {
2612   }
2613
2614   protected void zappoColour_actionPerformed(ActionEvent e)
2615   {
2616   }
2617
2618   protected void taylorColour_actionPerformed(ActionEvent e)
2619   {
2620   }
2621
2622   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2623   {
2624   }
2625
2626   protected void helixColour_actionPerformed(ActionEvent e)
2627   {
2628   }
2629
2630   protected void strandColour_actionPerformed(ActionEvent e)
2631   {
2632   }
2633
2634   protected void turnColour_actionPerformed(ActionEvent e)
2635   {
2636   }
2637
2638   protected void buriedColour_actionPerformed(ActionEvent e)
2639   {
2640   }
2641
2642   protected void userDefinedColour_actionPerformed(ActionEvent e)
2643   {
2644   }
2645
2646   protected void PIDColour_actionPerformed(ActionEvent e)
2647   {
2648   }
2649
2650   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2651   {
2652   }
2653
2654   protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2655   {
2656   }
2657
2658   protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2659   {
2660   }
2661
2662   /*
2663    * protected void covariationColour_actionPerformed(ActionEvent e) { }
2664    */
2665
2666   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2667   {
2668   }
2669
2670   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2671   {
2672   }
2673
2674   protected void printMenuItem_actionPerformed(ActionEvent e)
2675   {
2676   }
2677
2678   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2679   {
2680   }
2681
2682   protected void findMenuItem_actionPerformed(ActionEvent e)
2683   {
2684   }
2685
2686   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2687   {
2688   }
2689
2690   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2691   {
2692   }
2693
2694   protected void nucleotideColour_actionPerformed(ActionEvent e)
2695   {
2696   }
2697
2698   protected void deleteGroups_actionPerformed(ActionEvent e)
2699   {
2700   }
2701
2702   protected void createGroup_actionPerformed(ActionEvent e)
2703   {
2704   }
2705
2706   protected void unGroup_actionPerformed(ActionEvent e)
2707   {
2708   }
2709
2710   protected void copy_actionPerformed(ActionEvent e)
2711   {
2712   }
2713
2714   protected void cut_actionPerformed(ActionEvent e)
2715   {
2716   }
2717
2718   protected void delete_actionPerformed(ActionEvent e)
2719   {
2720   }
2721
2722   protected void pasteNew_actionPerformed(ActionEvent e)
2723   {
2724   }
2725
2726   protected void pasteThis_actionPerformed(ActionEvent e)
2727   {
2728   }
2729
2730   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2731   {
2732   }
2733
2734   public void createPNG(java.io.File f)
2735   {
2736   }
2737
2738   protected void font_actionPerformed(ActionEvent e)
2739   {
2740   }
2741
2742   protected void seqLimit_actionPerformed(ActionEvent e)
2743   {
2744   }
2745
2746   public void seqDBRef_actionPerformed(ActionEvent e)
2747   {
2748
2749   }
2750
2751   public void createEPS(java.io.File f)
2752   {
2753   }
2754
2755   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2756   {
2757
2758   }
2759
2760   /**
2761    * Template method to handle the 'load T-Coffee scores' menu event.
2762    * <p>
2763    * Subclasses override this method to provide a custom action.
2764    *
2765    * @param event
2766    *          The raised event
2767    */
2768   protected void loadScores_actionPerformed(ActionEvent event)
2769   {
2770
2771   }
2772
2773   /**
2774    * Template method to handle the 'Color T-Coffee scores' menu event.
2775    * <p>
2776    * Subclasses override this method to provide a custom action.
2777    *
2778    * @param event
2779    *          The raised event
2780    */
2781   protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2782   {
2783
2784   }
2785
2786   protected void jpred_actionPerformed(ActionEvent e)
2787   {
2788   }
2789
2790   protected void scaleAbove_actionPerformed(ActionEvent e)
2791   {
2792   }
2793
2794   protected void scaleLeft_actionPerformed(ActionEvent e)
2795   {
2796   }
2797
2798   protected void scaleRight_actionPerformed(ActionEvent e)
2799   {
2800   }
2801
2802   protected void modifyPID_actionPerformed(ActionEvent e)
2803   {
2804   }
2805
2806   protected void modifyConservation_actionPerformed(ActionEvent e)
2807   {
2808   }
2809
2810   protected void saveAs_actionPerformed(ActionEvent e)
2811   {
2812   }
2813
2814   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2815   {
2816   }
2817
2818   public void vamsasStore_actionPerformed(ActionEvent e)
2819   {
2820
2821   }
2822
2823   public void vamsasLoad_actionPerformed(ActionEvent e)
2824   {
2825
2826   }
2827
2828   public void showTranslation_actionPerformed(ActionEvent e)
2829   {
2830
2831   }
2832
2833   public void featureSettings_actionPerformed(ActionEvent e)
2834   {
2835
2836   }
2837
2838   public void fetchSequence_actionPerformed(ActionEvent e)
2839   {
2840
2841   }
2842
2843   public void smoothFont_actionPerformed(ActionEvent e)
2844   {
2845
2846   }
2847
2848   public void annotationColour_actionPerformed(ActionEvent e)
2849   {
2850
2851   }
2852
2853   public void rnahelicesColour_actionPerformed(ActionEvent e)
2854   {
2855
2856   }
2857
2858   public void associatedData_actionPerformed(ActionEvent e)
2859   {
2860
2861   }
2862
2863   public void autoCalculate_actionPerformed(ActionEvent e)
2864   {
2865
2866   }
2867
2868   public void sortByTreeOption_actionPerformed(ActionEvent e)
2869   {
2870
2871   }
2872
2873   public void showAllSeqs_actionPerformed(ActionEvent e)
2874   {
2875
2876   }
2877
2878   public void showAllColumns_actionPerformed(ActionEvent e)
2879   {
2880
2881   }
2882
2883   public void hideSelSequences_actionPerformed(ActionEvent e)
2884   {
2885
2886   }
2887
2888   public void hideSelColumns_actionPerformed(ActionEvent e)
2889   {
2890
2891   }
2892
2893   public void hiddenMarkers_actionPerformed(ActionEvent e)
2894   {
2895
2896   }
2897
2898   public void findPdbId_actionPerformed(ActionEvent e)
2899   {
2900
2901   }
2902
2903   public void enterPdbId_actionPerformed(ActionEvent e)
2904   {
2905
2906   }
2907
2908   public void pdbFile_actionPerformed(ActionEvent e)
2909   {
2910
2911   }
2912
2913   public void invertColSel_actionPerformed(ActionEvent e)
2914   {
2915
2916   }
2917
2918   public void tabSelectionChanged(int sel)
2919   {
2920
2921   }
2922
2923   public void tabbedPane_mousePressed(MouseEvent e)
2924   {
2925
2926   }
2927
2928   public void tabbedPane_focusGained(FocusEvent e)
2929   {
2930     requestFocus();
2931   }
2932
2933   public void save_actionPerformed(ActionEvent e)
2934   {
2935
2936   }
2937
2938   public void reload_actionPerformed(ActionEvent e)
2939   {
2940
2941   }
2942
2943   public void newView_actionPerformed(ActionEvent e)
2944   {
2945
2946   }
2947
2948   public void textColour_actionPerformed(ActionEvent e)
2949   {
2950
2951   }
2952
2953   public void idRightAlign_actionPerformed(ActionEvent e)
2954   {
2955
2956   }
2957
2958   public void expandViews_actionPerformed(ActionEvent e)
2959   {
2960
2961   }
2962
2963   public void gatherViews_actionPerformed(ActionEvent e)
2964   {
2965
2966   }
2967
2968   public void buildTreeMenu()
2969   {
2970
2971   }
2972
2973   public void pageSetup_actionPerformed(ActionEvent e)
2974   {
2975
2976   }
2977
2978   public void alignmentProperties()
2979   {
2980
2981   }
2982
2983   protected void expand_newalign(ActionEvent e)
2984   {
2985     // TODO Auto-generated method stub
2986
2987   }
2988 }