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.analysis.AnnotationSorter.SortOrder;
  24 import jalview.bin.Cache;
  25 import jalview.gui.JvSwingUtils;
  26 import jalview.schemes.ColourSchemeProperty;
  27 import jalview.util.MessageManager;
  28
  29 import java.awt.BorderLayout;
  30 import java.awt.Color;
  31 import java.awt.GridLayout;
  32 import java.awt.Toolkit;
  33 import java.awt.event.ActionEvent;
  34 import java.awt.event.ActionListener;
  35 import java.awt.event.FocusAdapter;
  36 import java.awt.event.FocusEvent;
  37 import java.awt.event.MouseAdapter;
  38 import java.awt.event.MouseEvent;
  39
  40 import javax.swing.BorderFactory;
  41 import javax.swing.ButtonGroup;
  42 import javax.swing.JCheckBoxMenuItem;
  43 import javax.swing.JInternalFrame;
  44 import javax.swing.JLabel;
  45 import javax.swing.JMenu;
  46 import javax.swing.JMenuBar;
  47 import javax.swing.JMenuItem;
  48 import javax.swing.JOptionPane;
  49 import javax.swing.JPanel;
  50 import javax.swing.JRadioButtonMenuItem;
  51 import javax.swing.JTabbedPane;
  52 import javax.swing.SwingUtilities;
  53 import javax.swing.event.ChangeEvent;
  54 import javax.swing.event.MenuEvent;
  55 import javax.swing.event.MenuListener;
  56
  57 public class GAlignFrame extends JInternalFrame
  58 {
  59   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  60
  61   protected JMenu fileMenu = new JMenu();
  62
  63   protected JMenuItem closeMenuItem = new JMenuItem();
  64
  65   protected JMenu editMenu = new JMenu();
  66
  67   protected JMenu viewMenu = new JMenu();
  68
  69   protected JMenu annotationsMenu = new JMenu();
  70
  71   protected JMenu colourMenu = new JMenu();
  72
  73   protected JMenu calculateMenu = new JMenu();
  74
  75   protected JMenu webService = new JMenu();
  76
  77   protected JMenuItem webServiceNoServices;
  78
  79   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  80
  81   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  82
  83   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  84
  85   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  86
  87   protected JMenuItem remove2RightMenuItem = new JMenuItem();
  88
  89   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  90
  91   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  92
  93   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  94
  95   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  96
  97   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  98
  99   protected JMenuItem sortIDMenuItem = new JMenuItem();
 100
 101   protected JMenuItem sortLengthMenuItem = new JMenuItem();
 102
 103   protected JMenuItem sortGroupMenuItem = new JMenuItem();
 104
 105   protected JMenu sortByAnnotScore = new JMenu();
 106
 107   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
 108
 109   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
 110
 111   protected JMenuItem PCAMenuItem = new JMenuItem();
 112
 113   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
 114
 115   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
 116
 117   BorderLayout borderLayout1 = new BorderLayout();
 118
 119   public JLabel statusBar = new JLabel();
 120
 121   protected JMenuItem saveAs = new JMenuItem();
 122
 123   protected JMenu outputTextboxMenu = new JMenu();
 124
 125   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
 126
 127   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
 128
 129   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
 130
 131   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
 132
 133   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
 134
 135   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
 136
 137   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
 138
 139   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 140
 141   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
 142
 143   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
 144
 145   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 146
 147   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
 148
 149   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
 150
 151   protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
 152
 153   // protected JRadioButtonMenuItem covariationColour = new
 154   // JRadioButtonMenuItem();
 155
 156   protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
 157
 158   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 159
 160   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
 161
 162   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 163
 164   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 165
 166   public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
 167
 168   JMenuItem htmlMenuItem = new JMenuItem();
 169
 170   JMenuItem overviewMenuItem = new JMenuItem();
 171
 172   protected JMenuItem undoMenuItem = new JMenuItem();
 173
 174   protected JMenuItem redoMenuItem = new JMenuItem();
 175
 176   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 177
 178   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 179
 180   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 181
 182   JMenuItem printMenuItem = new JMenuItem();
 183
 184   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 185
 186   JMenuItem findMenuItem = new JMenuItem();
 187
 188   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 189
 190   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 191
 192   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 193
 194   JMenuItem deleteGroups = new JMenuItem();
 195
 196   JMenuItem createGroup = new JMenuItem();
 197
 198   JMenuItem unGroup = new JMenuItem();
 199
 200   JMenuItem delete = new JMenuItem();
 201
 202   JMenuItem copy = new JMenuItem();
 203
 204   JMenuItem cut = new JMenuItem();
 205
 206   JMenu pasteMenu = new JMenu();
 207
 208   JMenuItem pasteNew = new JMenuItem();
 209
 210   JMenuItem pasteThis = new JMenuItem();
 211
 212   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
 213
 214   JMenuItem createPNG = new JMenuItem();
 215
 216   protected JMenuItem font = new JMenuItem();
 217
 218   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 219
 220   JMenuItem epsFile = new JMenuItem();
 221
 222   JMenuItem LoadtreeMenuItem = new JMenuItem();
 223
 224   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 225
 226   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 227
 228   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 229
 230   protected JMenuItem modifyPID = new JMenuItem();
 231
 232   protected JMenuItem modifyConservation = new JMenuItem();
 233
 234   protected JMenu sortByTreeMenu = new JMenu();
 235
 236   protected JMenu sort = new JMenu();
 237
 238   protected JMenu calculateTree = new JMenu();
 239
 240   JMenu jMenu2 = new JMenu();
 241
 242   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 243
 244   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 245
 246   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 247
 248   protected ButtonGroup colours = new ButtonGroup();
 249
 250   JMenuItem vamsasStore = new JMenuItem();
 251
 252   protected JMenuItem showTranslation = new JMenuItem();
 253
 254   protected JMenuItem extractScores = new JMenuItem();
 255
 256   protected JMenuItem expandAlignment = new JMenuItem();
 257
 258   protected JMenu showProducts = new JMenu();
 259
 260   public JMenuItem openFeatureSettings = new JMenuItem();
 261
 262   JMenuItem fetchSequence = new JMenuItem();
 263
 264   JMenuItem annotationColour = new JMenuItem();
 265
 266   protected JMenuItem rnahelicesColour = new JMenuItem();
 267
 268   JMenuItem associatedData = new JMenuItem();
 269
 270   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 271
 272   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 273
 274   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 275
 276   JMenu addSequenceMenu = new JMenu();
 277
 278   JMenuItem addFromFile = new JMenuItem();
 279
 280   JMenuItem addFromText = new JMenuItem();
 281
 282   JMenuItem addFromURL = new JMenuItem();
 283
 284   JMenuItem exportAnnotations = new JMenuItem();
 285
 286   JMenuItem exportFeatures = new JMenuItem();
 287
 288   protected JPanel statusPanel = new JPanel();
 289
 290   GridLayout gridLayout1 = new GridLayout();
 291
 292   JMenu jMenu3 = new JMenu();
 293
 294   JMenuItem showAllSeqs = new JMenuItem();
 295
 296   JMenuItem showAllColumns = new JMenuItem();
 297
 298   JMenu hideMenu = new JMenu();
 299
 300   JMenuItem hideSelSequences = new JMenuItem();
 301
 302   JMenuItem hideSelColumns = new JMenuItem();
 303
 304   JMenuItem hideAllButSelection = new JMenuItem();
 305
 306   JMenuItem hideAllSelection = new JMenuItem();
 307
 308   JMenuItem showAllhidden = new JMenuItem();
 309
 310   protected JMenuItem showAllAnnotations = new JMenuItem();
 311
 312   protected JMenuItem hideAllAnnotations = new JMenuItem();
 313
 314   protected JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem();
 315
 316   protected JCheckBoxMenuItem sortAnnByType = new JCheckBoxMenuItem();
 317
 318   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 319
 320   JMenuItem invertColSel = new JMenuItem();
 321
 322   protected JTabbedPane tabbedPane = new JTabbedPane();
 323
 324   JMenuItem save = new JMenuItem();
 325
 326   protected JMenuItem reload = new JMenuItem();
 327
 328   JMenuItem newView = new JMenuItem();
 329
 330   JMenuItem textColour = new JMenuItem();
 331
 332   JMenu formatMenu = new JMenu();
 333
 334   JMenu selectMenu = new JMenu();
 335
 336   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 337
 338   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 339
 340   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 341
 342   protected JMenuItem gatherViews = new JMenuItem();
 343
 344   protected JMenuItem expandViews = new JMenuItem();
 345
 346   JMenuItem pageSetup = new JMenuItem();
 347
 348   JMenuItem alignmentProperties = new JMenuItem();
 349
 350   JMenu tooltipSettingsMenu = new JMenu();
 351
 352   private JMenuItem justifyLeftMenuItem = new JMenuItem();
 353
 354   private JMenuItem justifyRightMenuItem = new JMenuItem();
 355
 356   JMenu autoAnnMenu = new JMenu();
 357
 358   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 359
 360   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 361
 362   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 363
 364   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 365
 366   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 367
 368   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 369
 370   private JMenuItem grpsFromSelection = new JMenuItem();
 371
 372   public GAlignFrame()
 373   {
 374     try
 375     {
 376       jbInit();
 377       setJMenuBar(alignFrameMenuBar);
 378
 379       // dynamically fill save as menu with available formats
 380       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 381       {
 382         JMenuItem item = new JMenuItem(
 383                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 384
 385         item.addActionListener(new java.awt.event.ActionListener()
 386         {
 387           @Override
 388           public void actionPerformed(ActionEvent e)
 389           {
 390             outputText_actionPerformed(e);
 391           }
 392         });
 393
 394         outputTextboxMenu.add(item);
 395       }
 396     } catch (Exception e)
 397     {
 398       System.err.println(e.toString());
 399     }
 400
 401     if (!new jalview.util.Platform().isAMac())
 402     {
 403       closeMenuItem.setMnemonic('C');
 404       outputTextboxMenu.setMnemonic('T');
 405       undoMenuItem.setMnemonic('Z');
 406       redoMenuItem.setMnemonic('0');
 407       copy.setMnemonic('C');
 408       cut.setMnemonic('U');
 409       pasteMenu.setMnemonic('P');
 410       reload.setMnemonic('R');
 411     }
 412
 413     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 414     {
 415       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 416               .getUserColourSchemes().keys();
 417
 418       while (userColours.hasMoreElements())
 419       {
 420         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 421                 userColours.nextElement().toString());
 422         radioItem.setName("USER_DEFINED");
 423         radioItem.addMouseListener(new MouseAdapter()
 424         {
 425           @Override
 426           public void mousePressed(MouseEvent evt)
 427           {
 428             if (evt.isControlDown()
 429                     || SwingUtilities.isRightMouseButton(evt))
 430             {
 431               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 432
 433               int option = JOptionPane.showInternalConfirmDialog(
 434                       jalview.gui.Desktop.desktop,
 435                       MessageManager
 436                               .getString("label.remove_from_default_list"),
 437                       MessageManager
 438                               .getString("label.remove_user_defined_colour"),
 439                       JOptionPane.YES_NO_OPTION);
 440               if (option == JOptionPane.YES_OPTION)
 441               {
 442                 jalview.gui.UserDefinedColours
 443                         .removeColourFromDefaults(radioItem.getText());
 444                 colourMenu.remove(radioItem);
 445               }
 446               else
 447               {
 448                 radioItem.addActionListener(new ActionListener()
 449                 {
 450                   @Override
 451                   public void actionPerformed(ActionEvent evt)
 452                   {
 453                     userDefinedColour_actionPerformed(evt);
 454                   }
 455                 });
 456               }
 457             }
 458           }
 459         });
 460         radioItem.addActionListener(new ActionListener()
 461         {
 462           @Override
 463           public void actionPerformed(ActionEvent evt)
 464           {
 465             userDefinedColour_actionPerformed(evt);
 466           }
 467         });
 468         colourMenu.insert(radioItem, 15);
 469         colours.add(radioItem);
 470       }
 471     }
 472     colours.add(noColourmenuItem);
 473     colours.add(clustalColour);
 474     colours.add(zappoColour);
 475     colours.add(taylorColour);
 476     colours.add(hydrophobicityColour);
 477     colours.add(helixColour);
 478     colours.add(strandColour);
 479     colours.add(turnColour);
 480     colours.add(buriedColour);
 481     colours.add(userDefinedColour);
 482     colours.add(PIDColour);
 483     colours.add(BLOSUM62Colour);
 484     colours.add(nucleotideColour);
 485     colours.add(purinePyrimidineColour);
 486     // colours.add(covariationColour);
 487     colours.add(tcoffeeColour);
 488     colours.add(RNAInteractionColour);
 489     setColourSelected(jalview.bin.Cache
 490             .getDefault("DEFAULT_COLOUR", "None"));
 491
 492   }
 493
 494   public void setColourSelected(String defaultColour)
 495   {
 496
 497     if (defaultColour != null)
 498     {
 499       int index = ColourSchemeProperty
 500               .getColourIndexFromName(defaultColour);
 501
 502       switch (index)
 503       {
 504       case ColourSchemeProperty.CLUSTAL:
 505         clustalColour.setSelected(true);
 506
 507         break;
 508
 509       case ColourSchemeProperty.BLOSUM:
 510         BLOSUM62Colour.setSelected(true);
 511
 512         break;
 513
 514       case ColourSchemeProperty.PID:
 515         PIDColour.setSelected(true);
 516
 517         break;
 518
 519       case ColourSchemeProperty.ZAPPO:
 520         zappoColour.setSelected(true);
 521
 522         break;
 523
 524       case ColourSchemeProperty.TAYLOR:
 525         taylorColour.setSelected(true);
 526         break;
 527
 528       case ColourSchemeProperty.HYDROPHOBIC:
 529         hydrophobicityColour.setSelected(true);
 530
 531         break;
 532
 533       case ColourSchemeProperty.HELIX:
 534         helixColour.setSelected(true);
 535
 536         break;
 537
 538       case ColourSchemeProperty.STRAND:
 539         strandColour.setSelected(true);
 540
 541         break;
 542
 543       case ColourSchemeProperty.TURN:
 544         turnColour.setSelected(true);
 545
 546         break;
 547
 548       case ColourSchemeProperty.BURIED:
 549         buriedColour.setSelected(true);
 550
 551         break;
 552
 553       case ColourSchemeProperty.NUCLEOTIDE:
 554         nucleotideColour.setSelected(true);
 555
 556         break;
 557
 558       case ColourSchemeProperty.TCOFFEE:
 559         tcoffeeColour.setSelected(true);
 560         break;
 561
 562       case ColourSchemeProperty.PURINEPYRIMIDINE:
 563         purinePyrimidineColour.setSelected(true);
 564
 565         break;
 566
 567       case ColourSchemeProperty.RNAINTERACTION:
 568         RNAInteractionColour.setSelected(true);
 569
 570         break;
 571       /*
 572        * case ColourSchemeProperty.COVARIATION:
 573        * covariationColour.setSelected(true);
 574        *
 575        * break;
 576        */
 577       case ColourSchemeProperty.USER_DEFINED:
 578         userDefinedColour.setSelected(true);
 579
 580         break;
 581       case ColourSchemeProperty.NONE:
 582       default:
 583         noColourmenuItem.setSelected(true);
 584         break;
 585
 586       }
 587     }
 588
 589   }
 590
 591   private void jbInit() throws Exception
 592   {
 593     fileMenu.setText(MessageManager.getString("action.file"));
 594     saveAs.setText(MessageManager.getString("action.save_as") + "...");
 595     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 596             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
 597                     .getMenuShortcutKeyMask()
 598                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 599     saveAs.addActionListener(new ActionListener()
 600     {
 601       @Override
 602       public void actionPerformed(ActionEvent e)
 603       {
 604         saveAs_actionPerformed(e);
 605       }
 606     });
 607     closeMenuItem.setText(MessageManager.getString("action.close"));
 608     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 609             java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
 610                     .getMenuShortcutKeyMask(), false));
 611     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 612     {
 613       @Override
 614       public void actionPerformed(ActionEvent e)
 615       {
 616         closeMenuItem_actionPerformed(false);
 617       }
 618     });
 619     editMenu.setText(MessageManager.getString("action.edit"));
 620     viewMenu.setText(MessageManager.getString("action.view"));
 621     annotationsMenu.setText(MessageManager.getString("action.annotations"));
 622     colourMenu.setText(MessageManager.getString("action.colour"));
 623     calculateMenu.setText(MessageManager.getString("action.calculate"));
 624     webService.setText(MessageManager.getString("action.web_service"));
 625     selectAllSequenceMenuItem.setText(MessageManager
 626             .getString("action.select_all"));
 627     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 628             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
 629                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 630     selectAllSequenceMenuItem
 631             .addActionListener(new java.awt.event.ActionListener()
 632             {
 633               @Override
 634               public void actionPerformed(ActionEvent e)
 635               {
 636                 selectAllSequenceMenuItem_actionPerformed(e);
 637               }
 638             });
 639     deselectAllSequenceMenuItem.setText(MessageManager
 640             .getString("action.deselect_all"));
 641     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 642             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 643     deselectAllSequenceMenuItem
 644             .addActionListener(new java.awt.event.ActionListener()
 645             {
 646               @Override
 647               public void actionPerformed(ActionEvent e)
 648               {
 649                 deselectAllSequenceMenuItem_actionPerformed(e);
 650               }
 651             });
 652     invertSequenceMenuItem.setText(MessageManager
 653             .getString("action.invert_sequence_selection"));
 654     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 655             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
 656                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 657     invertSequenceMenuItem
 658             .addActionListener(new java.awt.event.ActionListener()
 659             {
 660               @Override
 661               public void actionPerformed(ActionEvent e)
 662               {
 663                 invertSequenceMenuItem_actionPerformed(e);
 664               }
 665             });
 666     grpsFromSelection.setText(MessageManager
 667             .getString("action.make_groups_selection"));
 668     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
 669     {
 670       @Override
 671       public void actionPerformed(ActionEvent e)
 672       {
 673         makeGrpsFromSelection_actionPerformed(e);
 674       }
 675     });
 676     expandAlignment.setText(MessageManager
 677             .getString("action.view_flanking_regions"));
 678     expandAlignment.setToolTipText(MessageManager
 679             .getString("label.view_flanking_regions"));
 680     expandAlignment.addActionListener(new java.awt.event.ActionListener()
 681     {
 682       @Override
 683       public void actionPerformed(ActionEvent e)
 684       {
 685         expand_newalign(e);
 686       }
 687     });
 688     remove2LeftMenuItem.setText(MessageManager
 689             .getString("action.remove_left"));
 690     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 691             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
 692                     .getMenuShortcutKeyMask(), false));
 693     remove2LeftMenuItem
 694             .addActionListener(new java.awt.event.ActionListener()
 695             {
 696               @Override
 697               public void actionPerformed(ActionEvent e)
 698               {
 699                 remove2LeftMenuItem_actionPerformed(e);
 700               }
 701             });
 702     remove2RightMenuItem.setText(MessageManager
 703             .getString("action.remove_right"));
 704     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 705             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
 706                     .getMenuShortcutKeyMask(), false));
 707     remove2RightMenuItem
 708             .addActionListener(new java.awt.event.ActionListener()
 709             {
 710               @Override
 711               public void actionPerformed(ActionEvent e)
 712               {
 713                 remove2RightMenuItem_actionPerformed(e);
 714               }
 715             });
 716     removeGappedColumnMenuItem.setText(MessageManager
 717             .getString("action.remove_empty_columns"));
 718     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
 719             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 720                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 721     removeGappedColumnMenuItem
 722             .addActionListener(new java.awt.event.ActionListener()
 723             {
 724               @Override
 725               public void actionPerformed(ActionEvent e)
 726               {
 727                 removeGappedColumnMenuItem_actionPerformed(e);
 728               }
 729             });
 730     removeAllGapsMenuItem.setText(MessageManager
 731             .getString("action.remove_all_gaps"));
 732     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
 733             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 734                     .getDefaultToolkit().getMenuShortcutKeyMask()
 735                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 736     removeAllGapsMenuItem
 737             .addActionListener(new java.awt.event.ActionListener()
 738             {
 739               @Override
 740               public void actionPerformed(ActionEvent e)
 741               {
 742                 removeAllGapsMenuItem_actionPerformed(e);
 743               }
 744             });
 745     justifyLeftMenuItem.setText(MessageManager
 746             .getString("action.left_justify_alignment"));
 747     justifyLeftMenuItem
 748             .addActionListener(new java.awt.event.ActionListener()
 749             {
 750               @Override
 751               public void actionPerformed(ActionEvent e)
 752               {
 753                 justifyLeftMenuItem_actionPerformed(e);
 754               }
 755             });
 756     justifyRightMenuItem.setText(MessageManager
 757             .getString("action.right_justify_alignment"));
 758     justifyRightMenuItem
 759             .addActionListener(new java.awt.event.ActionListener()
 760             {
 761               @Override
 762               public void actionPerformed(ActionEvent e)
 763               {
 764                 justifyRightMenuItem_actionPerformed(e);
 765               }
 766             });
 767     viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
 768     viewBoxesMenuItem.setState(true);
 769     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 770     {
 771       @Override
 772       public void actionPerformed(ActionEvent e)
 773       {
 774         viewBoxesMenuItem_actionPerformed(e);
 775       }
 776     });
 777     viewTextMenuItem.setText(MessageManager.getString("action.text"));
 778     viewTextMenuItem.setState(true);
 779     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 780     {
 781       @Override
 782       public void actionPerformed(ActionEvent e)
 783       {
 784         viewTextMenuItem_actionPerformed(e);
 785       }
 786     });
 787     showNonconservedMenuItem.setText(MessageManager
 788             .getString("label.show_non_conversed"));
 789     showNonconservedMenuItem.setState(false);
 790     showNonconservedMenuItem
 791             .addActionListener(new java.awt.event.ActionListener()
 792             {
 793               @Override
 794               public void actionPerformed(ActionEvent e)
 795               {
 796                 showUnconservedMenuItem_actionPerformed(e);
 797               }
 798             });
 799     sortPairwiseMenuItem.setText(MessageManager
 800             .getString("action.by_pairwise_id"));
 801     sortPairwiseMenuItem
 802             .addActionListener(new java.awt.event.ActionListener()
 803             {
 804               @Override
 805               public void actionPerformed(ActionEvent e)
 806               {
 807                 sortPairwiseMenuItem_actionPerformed(e);
 808               }
 809             });
 810     sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
 811     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 812     {
 813       @Override
 814       public void actionPerformed(ActionEvent e)
 815       {
 816         sortIDMenuItem_actionPerformed(e);
 817       }
 818     });
 819     sortLengthMenuItem
 820             .setText(MessageManager.getString("action.by_length"));
 821     sortLengthMenuItem
 822             .addActionListener(new java.awt.event.ActionListener()
 823             {
 824               @Override
 825               public void actionPerformed(ActionEvent e)
 826               {
 827                 sortLengthMenuItem_actionPerformed(e);
 828               }
 829             });
 830     sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
 831     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 832     {
 833       @Override
 834       public void actionPerformed(ActionEvent e)
 835       {
 836         sortGroupMenuItem_actionPerformed(e);
 837       }
 838     });
 839     removeRedundancyMenuItem.setText(MessageManager
 840             .getString("action.remove_redundancy").concat("..."));
 841     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
 842             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
 843                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 844     removeRedundancyMenuItem
 845             .addActionListener(new java.awt.event.ActionListener()
 846             {
 847               @Override
 848               public void actionPerformed(ActionEvent e)
 849               {
 850                 removeRedundancyMenuItem_actionPerformed(e);
 851               }
 852             });
 853     pairwiseAlignmentMenuItem.setText(MessageManager
 854             .getString("action.pairwise_alignment"));
 855     pairwiseAlignmentMenuItem
 856             .addActionListener(new java.awt.event.ActionListener()
 857             {
 858               @Override
 859               public void actionPerformed(ActionEvent e)
 860               {
 861                 pairwiseAlignmentMenuItem_actionPerformed(e);
 862               }
 863             });
 864     PCAMenuItem.setText(MessageManager
 865             .getString("label.principal_component_analysis"));
 866     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 867     {
 868       @Override
 869       public void actionPerformed(ActionEvent e)
 870       {
 871         PCAMenuItem_actionPerformed(e);
 872       }
 873     });
 874     averageDistanceTreeMenuItem.setText(MessageManager
 875             .getString("label.average_distance_identity"));
 876     averageDistanceTreeMenuItem
 877             .addActionListener(new java.awt.event.ActionListener()
 878             {
 879               @Override
 880               public void actionPerformed(ActionEvent e)
 881               {
 882                 averageDistanceTreeMenuItem_actionPerformed(e);
 883               }
 884             });
 885     neighbourTreeMenuItem.setText(MessageManager
 886             .getString("label.neighbour_joining_identity"));
 887     neighbourTreeMenuItem
 888             .addActionListener(new java.awt.event.ActionListener()
 889             {
 890               @Override
 891               public void actionPerformed(ActionEvent e)
 892               {
 893                 neighbourTreeMenuItem_actionPerformed(e);
 894               }
 895             });
 896     this.getContentPane().setLayout(borderLayout1);
 897     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 898     statusBar.setBackground(Color.white);
 899     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 900     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 901     statusBar.setText(MessageManager.getString("label.status_bar"));
 902     outputTextboxMenu.setText(MessageManager
 903             .getString("label.out_to_textbox"));
 904     clustalColour.setText(MessageManager.getString("label.clustalx"));
 905
 906     clustalColour.addActionListener(new java.awt.event.ActionListener()
 907     {
 908       @Override
 909       public void actionPerformed(ActionEvent e)
 910       {
 911         clustalColour_actionPerformed(e);
 912       }
 913     });
 914     zappoColour.setText(MessageManager.getString("label.zappo"));
 915     zappoColour.addActionListener(new java.awt.event.ActionListener()
 916     {
 917       @Override
 918       public void actionPerformed(ActionEvent e)
 919       {
 920         zappoColour_actionPerformed(e);
 921       }
 922     });
 923     taylorColour.setText(MessageManager.getString("label.taylor"));
 924     taylorColour.addActionListener(new java.awt.event.ActionListener()
 925     {
 926       @Override
 927       public void actionPerformed(ActionEvent e)
 928       {
 929         taylorColour_actionPerformed(e);
 930       }
 931     });
 932     hydrophobicityColour.setText(MessageManager
 933             .getString("label.hydrophobicity"));
 934     hydrophobicityColour
 935             .addActionListener(new java.awt.event.ActionListener()
 936             {
 937               @Override
 938               public void actionPerformed(ActionEvent e)
 939               {
 940                 hydrophobicityColour_actionPerformed(e);
 941               }
 942             });
 943     helixColour.setText(MessageManager.getString("label.helix_propensity"));
 944     helixColour.addActionListener(new java.awt.event.ActionListener()
 945     {
 946       @Override
 947       public void actionPerformed(ActionEvent e)
 948       {
 949         helixColour_actionPerformed(e);
 950       }
 951     });
 952     strandColour.setText(MessageManager
 953             .getString("label.strand_propensity"));
 954     strandColour.addActionListener(new java.awt.event.ActionListener()
 955     {
 956       @Override
 957       public void actionPerformed(ActionEvent e)
 958       {
 959         strandColour_actionPerformed(e);
 960       }
 961     });
 962     turnColour.setText(MessageManager.getString("label.turn_propensity"));
 963     turnColour.addActionListener(new java.awt.event.ActionListener()
 964     {
 965       @Override
 966       public void actionPerformed(ActionEvent e)
 967       {
 968         turnColour_actionPerformed(e);
 969       }
 970     });
 971     buriedColour.setText(MessageManager.getString("label.buried_index"));
 972     buriedColour.addActionListener(new java.awt.event.ActionListener()
 973     {
 974       @Override
 975       public void actionPerformed(ActionEvent e)
 976       {
 977         buriedColour_actionPerformed(e);
 978       }
 979     });
 980     userDefinedColour.setText(MessageManager
 981             .getString("action.user_defined"));
 982     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 983     {
 984       @Override
 985       public void actionPerformed(ActionEvent e)
 986       {
 987         userDefinedColour_actionPerformed(e);
 988       }
 989     });
 990     PIDColour
 991             .setText(MessageManager.getString("label.percentage_identity"));
 992     PIDColour.addActionListener(new java.awt.event.ActionListener()
 993     {
 994       @Override
 995       public void actionPerformed(ActionEvent e)
 996       {
 997         PIDColour_actionPerformed(e);
 998       }
 999     });
1000     BLOSUM62Colour
1001             .setText(MessageManager.getString("label.blosum62_score"));
1002     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1003     {
1004       @Override
1005       public void actionPerformed(ActionEvent e)
1006       {
1007         BLOSUM62Colour_actionPerformed(e);
1008       }
1009     });
1010     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1011     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1012     {
1013       @Override
1014       public void actionPerformed(ActionEvent e)
1015       {
1016         nucleotideColour_actionPerformed(e);
1017       }
1018     });
1019
1020     purinePyrimidineColour.setText(MessageManager
1021             .getString("label.purine_pyrimidine"));
1022     purinePyrimidineColour
1023             .addActionListener(new java.awt.event.ActionListener()
1024             {
1025               @Override
1026               public void actionPerformed(ActionEvent e)
1027               {
1028                 purinePyrimidineColour_actionPerformed(e);
1029               }
1030             });
1031
1032     RNAInteractionColour.setText("RNA Interaction type");
1033     RNAInteractionColour
1034             .addActionListener(new java.awt.event.ActionListener()
1035             {
1036               @Override
1037               public void actionPerformed(ActionEvent e)
1038               {
1039                 RNAInteractionColour_actionPerformed(e);
1040               }
1041             });
1042     /*
1043      * covariationColour.setText("Covariation");
1044      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1045      * public void actionPerformed(ActionEvent e) {
1046      * covariationColour_actionPerformed(e); } });
1047      */
1048
1049     avDistanceTreeBlosumMenuItem.setText(MessageManager
1050             .getString("label.average_distance_bloslum62"));
1051     avDistanceTreeBlosumMenuItem
1052             .addActionListener(new java.awt.event.ActionListener()
1053             {
1054               @Override
1055               public void actionPerformed(ActionEvent e)
1056               {
1057                 avTreeBlosumMenuItem_actionPerformed(e);
1058               }
1059             });
1060     njTreeBlosumMenuItem.setText(MessageManager
1061             .getString("label.neighbour_blosum62"));
1062     njTreeBlosumMenuItem
1063             .addActionListener(new java.awt.event.ActionListener()
1064             {
1065               @Override
1066               public void actionPerformed(ActionEvent e)
1067               {
1068                 njTreeBlosumMenuItem_actionPerformed(e);
1069               }
1070             });
1071     annotationPanelMenuItem.setActionCommand("");
1072     annotationPanelMenuItem.setText(MessageManager
1073             .getString("label.show_annotations"));
1074     annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
1075             true));
1076     annotationPanelMenuItem.addActionListener(new ActionListener()
1077     {
1078       @Override
1079       public void actionPerformed(ActionEvent e)
1080       {
1081         annotationPanelMenuItem_actionPerformed(e);
1082       }
1083     });
1084     /*
1085      * Show/hide all annotations only enabled if annotation panel is shown
1086      */
1087     showAllAnnotations.setText(MessageManager
1088             .getString("label.show_all_annotations"));
1089     showAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
1090     showAllAnnotations.addActionListener(new ActionListener()
1091     {
1092       @Override
1093       public void actionPerformed(ActionEvent e)
1094       {
1095         showAllAnnotations_actionPerformed();
1096       }
1097     });
1098     hideAllAnnotations.setText(MessageManager
1099             .getString("label.hide_all_annotations"));
1100     hideAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
1101     hideAllAnnotations.addActionListener(new ActionListener()
1102     {
1103       @Override
1104       public void actionPerformed(ActionEvent e)
1105       {
1106         hideAllAnnotations_actionPerformed();
1107       }
1108     });
1109     sortAnnBySequence.setText(MessageManager
1110             .getString("label.sort_annotations_by_sequence"));
1111     sortAnnBySequence.addActionListener(new ActionListener()
1112     {
1113       @Override
1114       public void actionPerformed(ActionEvent e)
1115       {
1116         sortAnnBySequence.setEnabled(false);
1117         sortAnnBySequence.setState(true);
1118         sortAnnByType.setEnabled(true);
1119         sortAnnByType.setState(false);
1120         sortAnnotations_actionPerformed(SortOrder.SEQUENCE_AND_TYPE);
1121       }
1122     });
1123     sortAnnByType.setText(MessageManager
1124             .getString("label.sort_annotations_by_type"));
1125     sortAnnByType.addActionListener(new ActionListener()
1126     {
1127       @Override
1128       public void actionPerformed(ActionEvent e)
1129       {
1130         sortAnnByType.setEnabled(false);
1131         sortAnnByType.setState(true);
1132         sortAnnBySequence.setEnabled(true);
1133         sortAnnBySequence.setState(false);
1134         sortAnnotations_actionPerformed(SortOrder.TYPE_AND_SEQUENCE);
1135       }
1136     });
1137     colourTextMenuItem.setText(MessageManager
1138             .getString("label.colour_text"));
1139     colourTextMenuItem
1140             .addActionListener(new java.awt.event.ActionListener()
1141             {
1142               @Override
1143               public void actionPerformed(ActionEvent e)
1144               {
1145                 colourTextMenuItem_actionPerformed(e);
1146               }
1147             });
1148     htmlMenuItem.setText(MessageManager.getString("label.html"));
1149     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
1150     {
1151       @Override
1152       public void actionPerformed(ActionEvent e)
1153       {
1154         htmlMenuItem_actionPerformed(e);
1155       }
1156     });
1157     overviewMenuItem.setText(MessageManager
1158             .getString("label.overview_window"));
1159     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
1160     {
1161       @Override
1162       public void actionPerformed(ActionEvent e)
1163       {
1164         overviewMenuItem_actionPerformed(e);
1165       }
1166     });
1167     undoMenuItem.setEnabled(false);
1168     undoMenuItem.setText(MessageManager.getString("action.undo"));
1169     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1170             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1171                     .getMenuShortcutKeyMask(), false));
1172     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1173     {
1174       @Override
1175       public void actionPerformed(ActionEvent e)
1176       {
1177         undoMenuItem_actionPerformed(e);
1178       }
1179     });
1180     redoMenuItem.setEnabled(false);
1181     redoMenuItem.setText(MessageManager.getString("action.redo"));
1182     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1183             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1184                     .getMenuShortcutKeyMask(), false));
1185     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1186     {
1187       @Override
1188       public void actionPerformed(ActionEvent e)
1189       {
1190         redoMenuItem_actionPerformed(e);
1191       }
1192     });
1193     conservationMenuItem.setText(MessageManager
1194             .getString("action.by_conservation"));
1195     conservationMenuItem
1196             .addActionListener(new java.awt.event.ActionListener()
1197             {
1198               @Override
1199               public void actionPerformed(ActionEvent e)
1200               {
1201                 conservationMenuItem_actionPerformed(e);
1202               }
1203             });
1204     noColourmenuItem.setText(MessageManager.getString("label.none"));
1205     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1206     {
1207       @Override
1208       public void actionPerformed(ActionEvent e)
1209       {
1210         noColourmenuItem_actionPerformed(e);
1211       }
1212     });
1213     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1214     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1215     {
1216       @Override
1217       public void actionPerformed(ActionEvent e)
1218       {
1219         wrapMenuItem_actionPerformed(e);
1220       }
1221     });
1222     printMenuItem.setText(MessageManager.getString("action.print") + "...");
1223     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1224             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1225                     .getMenuShortcutKeyMask(), false));
1226     printMenuItem.addActionListener(new java.awt.event.ActionListener()
1227     {
1228       @Override
1229       public void actionPerformed(ActionEvent e)
1230       {
1231         printMenuItem_actionPerformed(e);
1232       }
1233     });
1234     renderGapsMenuItem
1235             .setText(MessageManager.getString("action.show_gaps"));
1236     renderGapsMenuItem.setState(true);
1237     renderGapsMenuItem
1238             .addActionListener(new java.awt.event.ActionListener()
1239             {
1240               @Override
1241               public void actionPerformed(ActionEvent e)
1242               {
1243                 renderGapsMenuItem_actionPerformed(e);
1244               }
1245             });
1246     findMenuItem.setText(MessageManager.getString("action.find"));
1247     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1248             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1249                     .getMenuShortcutKeyMask(), false));
1250     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
1251             MessageManager.getString("label.find_tip")));
1252     findMenuItem.addActionListener(new java.awt.event.ActionListener()
1253     {
1254       @Override
1255       public void actionPerformed(ActionEvent e)
1256       {
1257         findMenuItem_actionPerformed(e);
1258       }
1259     });
1260     abovePIDThreshold.setText(MessageManager
1261             .getString("label.above_identity_threshold"));
1262     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1263     {
1264       @Override
1265       public void actionPerformed(ActionEvent e)
1266       {
1267         abovePIDThreshold_actionPerformed(e);
1268       }
1269     });
1270     showSeqFeatures.setText(MessageManager
1271             .getString("label.show_sequence_features"));
1272     showSeqFeatures.addActionListener(new ActionListener()
1273     {
1274       @Override
1275       public void actionPerformed(ActionEvent actionEvent)
1276       {
1277         showSeqFeatures_actionPerformed(actionEvent);
1278       }
1279     });
1280     /*
1281      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1282      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1283      * void actionPerformed(ActionEvent actionEvent) {
1284      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1285      */
1286     showDbRefsMenuitem.setText(MessageManager
1287             .getString("label.show_database_refs"));
1288     showDbRefsMenuitem.addActionListener(new ActionListener()
1289     {
1290
1291       @Override
1292       public void actionPerformed(ActionEvent e)
1293       {
1294         showDbRefs_actionPerformed(e);
1295       }
1296
1297     });
1298     showNpFeatsMenuitem.setText(MessageManager
1299             .getString("label.show_non_positional_features"));
1300     showNpFeatsMenuitem.addActionListener(new ActionListener()
1301     {
1302
1303       @Override
1304       public void actionPerformed(ActionEvent e)
1305       {
1306         showNpFeats_actionPerformed(e);
1307       }
1308
1309     });
1310     showGroupConservation.setText(MessageManager
1311             .getString("label.group_conservation"));
1312     showGroupConservation.addActionListener(new ActionListener()
1313     {
1314
1315       @Override
1316       public void actionPerformed(ActionEvent e)
1317       {
1318         showGroupConservation_actionPerformed(e);
1319       }
1320
1321     });
1322
1323     showGroupConsensus.setText(MessageManager
1324             .getString("label.group_consensus"));
1325     showGroupConsensus.addActionListener(new ActionListener()
1326     {
1327
1328       @Override
1329       public void actionPerformed(ActionEvent e)
1330       {
1331         showGroupConsensus_actionPerformed(e);
1332       }
1333
1334     });
1335     showConsensusHistogram.setText(MessageManager
1336             .getString("label.show_consensus_histogram"));
1337     showConsensusHistogram.addActionListener(new ActionListener()
1338     {
1339
1340       @Override
1341       public void actionPerformed(ActionEvent e)
1342       {
1343         showConsensusHistogram_actionPerformed(e);
1344       }
1345
1346     });
1347     showSequenceLogo.setText(MessageManager
1348             .getString("label.show_consensus_logo"));
1349     showSequenceLogo.addActionListener(new ActionListener()
1350     {
1351
1352       @Override
1353       public void actionPerformed(ActionEvent e)
1354       {
1355         showSequenceLogo_actionPerformed(e);
1356       }
1357
1358     });
1359     normaliseSequenceLogo.setText(MessageManager
1360             .getString("label.norm_consensus_logo"));
1361     normaliseSequenceLogo.addActionListener(new ActionListener()
1362     {
1363
1364       @Override
1365       public void actionPerformed(ActionEvent e)
1366       {
1367         normaliseSequenceLogo_actionPerformed(e);
1368       }
1369
1370     });
1371     applyAutoAnnotationSettings.setText(MessageManager
1372             .getString("label.apply_all_groups"));
1373     applyAutoAnnotationSettings.setState(false);
1374     applyAutoAnnotationSettings.setVisible(true);
1375     applyAutoAnnotationSettings.addActionListener(new ActionListener()
1376     {
1377
1378       @Override
1379       public void actionPerformed(ActionEvent e)
1380       {
1381         applyAutoAnnotationSettings_actionPerformed(e);
1382       }
1383
1384     });
1385
1386     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1387     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1388     {
1389       @Override
1390       public void actionPerformed(ActionEvent e)
1391       {
1392         nucleotideColour_actionPerformed(e);
1393       }
1394     });
1395
1396     tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1397     tcoffeeColour.setEnabled(false);
1398     tcoffeeColour.addActionListener(new ActionListener()
1399     {
1400
1401       @Override
1402       public void actionPerformed(ActionEvent e)
1403       {
1404         tcoffeeColorScheme_actionPerformed(e);
1405       }
1406     });
1407
1408     deleteGroups
1409             .setText(MessageManager.getString("action.undefine_groups"));
1410     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1411             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1412                     .getMenuShortcutKeyMask(), false));
1413     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1414     {
1415       @Override
1416       public void actionPerformed(ActionEvent e)
1417       {
1418         deleteGroups_actionPerformed(e);
1419       }
1420     });
1421     createGroup.setText(MessageManager.getString("action.create_groups"));
1422     createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1423             java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1424                     .getMenuShortcutKeyMask(), false));
1425     createGroup.addActionListener(new java.awt.event.ActionListener()
1426     {
1427       @Override
1428       public void actionPerformed(ActionEvent e)
1429       {
1430         createGroup_actionPerformed(e);
1431       }
1432     });
1433     unGroup.setText(MessageManager.getString("action.remove_group"));
1434     unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1435             java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1436                     .getMenuShortcutKeyMask()
1437                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1438     unGroup.addActionListener(new java.awt.event.ActionListener()
1439     {
1440       @Override
1441       public void actionPerformed(ActionEvent e)
1442       {
1443         unGroup_actionPerformed(e);
1444       }
1445     });
1446     copy.setText(MessageManager.getString("action.copy"));
1447     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1448             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1449                     .getMenuShortcutKeyMask(), false));
1450
1451     copy.addActionListener(new java.awt.event.ActionListener()
1452     {
1453       @Override
1454       public void actionPerformed(ActionEvent e)
1455       {
1456         copy_actionPerformed(e);
1457       }
1458     });
1459     cut.setText(MessageManager.getString("action.cut"));
1460     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1461             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1462                     .getMenuShortcutKeyMask(), false));
1463     cut.addActionListener(new java.awt.event.ActionListener()
1464     {
1465       @Override
1466       public void actionPerformed(ActionEvent e)
1467       {
1468         cut_actionPerformed(e);
1469       }
1470     });
1471     delete.setText(MessageManager.getString("action.delete"));
1472     delete.addActionListener(new java.awt.event.ActionListener()
1473     {
1474       @Override
1475       public void actionPerformed(ActionEvent e)
1476       {
1477         delete_actionPerformed(e);
1478       }
1479     });
1480     pasteMenu.setText(MessageManager.getString("action.paste"));
1481     pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1482     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1483             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1484                     .getMenuShortcutKeyMask()
1485                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1486     pasteNew.addActionListener(new java.awt.event.ActionListener()
1487     {
1488       @Override
1489       public void actionPerformed(ActionEvent e)
1490       {
1491         pasteNew_actionPerformed(e);
1492       }
1493     });
1494     pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1495     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1496             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1497                     .getMenuShortcutKeyMask(), false));
1498     pasteThis.addActionListener(new java.awt.event.ActionListener()
1499     {
1500       @Override
1501       public void actionPerformed(ActionEvent e)
1502       {
1503         pasteThis_actionPerformed(e);
1504       }
1505     });
1506     applyToAllGroups.setText(MessageManager
1507             .getString("label.apply_colour_to_all_groups"));
1508     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1509     {
1510       @Override
1511       public void actionPerformed(ActionEvent e)
1512       {
1513         applyToAllGroups_actionPerformed(e);
1514       }
1515     });
1516     createPNG.addActionListener(new java.awt.event.ActionListener()
1517     {
1518       @Override
1519       public void actionPerformed(ActionEvent e)
1520       {
1521         createPNG(null);
1522       }
1523     });
1524     createPNG.setActionCommand(MessageManager
1525             .getString("label.save_png_image"));
1526     createPNG.setText("PNG");
1527     font.setText(MessageManager.getString("action.font"));
1528     font.addActionListener(new java.awt.event.ActionListener()
1529     {
1530       @Override
1531       public void actionPerformed(ActionEvent e)
1532       {
1533         font_actionPerformed(e);
1534       }
1535     });
1536
1537     seqLimits.setText(MessageManager
1538             .getString("label.show_sequence_limits"));
1539     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1540     seqLimits.addActionListener(new java.awt.event.ActionListener()
1541     {
1542       @Override
1543       public void actionPerformed(ActionEvent e)
1544       {
1545         seqLimit_actionPerformed(e);
1546       }
1547     });
1548     epsFile.setText("EPS");
1549     epsFile.addActionListener(new java.awt.event.ActionListener()
1550     {
1551       @Override
1552       public void actionPerformed(ActionEvent e)
1553       {
1554         createEPS(null);
1555       }
1556     });
1557     LoadtreeMenuItem.setActionCommand(MessageManager
1558             .getString("label.load_tree_for_sequence_set"));
1559     LoadtreeMenuItem.setText(MessageManager
1560             .getString("label.load_associated_tree"));
1561     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1562     {
1563       @Override
1564       public void actionPerformed(ActionEvent e)
1565       {
1566         LoadtreeMenuItem_actionPerformed(e);
1567       }
1568     });
1569
1570     scaleAbove.setVisible(false);
1571     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1572     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1573     {
1574       @Override
1575       public void actionPerformed(ActionEvent e)
1576       {
1577         scaleAbove_actionPerformed(e);
1578       }
1579     });
1580     scaleLeft.setVisible(false);
1581     scaleLeft.setSelected(true);
1582     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1583     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1584     {
1585       @Override
1586       public void actionPerformed(ActionEvent e)
1587       {
1588         scaleLeft_actionPerformed(e);
1589       }
1590     });
1591     scaleRight.setVisible(false);
1592     scaleRight.setSelected(true);
1593     scaleRight.setText(MessageManager.getString("action.scale_right"));
1594     scaleRight.addActionListener(new java.awt.event.ActionListener()
1595     {
1596       @Override
1597       public void actionPerformed(ActionEvent e)
1598       {
1599         scaleRight_actionPerformed(e);
1600       }
1601     });
1602     centreColumnLabelsMenuItem.setVisible(true);
1603     centreColumnLabelsMenuItem.setState(false);
1604     centreColumnLabelsMenuItem.setText(MessageManager
1605             .getString("label.centre_column_labels"));
1606     centreColumnLabelsMenuItem
1607             .addActionListener(new java.awt.event.ActionListener()
1608             {
1609               @Override
1610               public void actionPerformed(ActionEvent e)
1611               {
1612                 centreColumnLabels_actionPerformed(e);
1613               }
1614             });
1615     followHighlightMenuItem.setVisible(true);
1616     followHighlightMenuItem.setState(true);
1617     followHighlightMenuItem.setText(MessageManager
1618             .getString("label.automatic_scrolling"));
1619     followHighlightMenuItem.addActionListener(new ActionListener()
1620     {
1621
1622       @Override
1623       public void actionPerformed(ActionEvent e)
1624       {
1625         followHighlight_actionPerformed();
1626       }
1627
1628     });
1629
1630     modifyPID.setText(MessageManager
1631             .getString("label.modify_identity_thereshold"));
1632     modifyPID.addActionListener(new java.awt.event.ActionListener()
1633     {
1634       @Override
1635       public void actionPerformed(ActionEvent e)
1636       {
1637         modifyPID_actionPerformed(e);
1638       }
1639     });
1640     modifyConservation.setText(MessageManager
1641             .getString("label.modify_conservation_thereshold"));
1642     modifyConservation
1643             .addActionListener(new java.awt.event.ActionListener()
1644             {
1645               @Override
1646               public void actionPerformed(ActionEvent e)
1647               {
1648                 modifyConservation_actionPerformed(e);
1649               }
1650             });
1651     sortByTreeMenu
1652             .setText(MessageManager.getString("action.by_tree_order"));
1653     sort.setText(MessageManager.getString("action.sort"));
1654     sort.addMenuListener(new MenuListener()
1655     {
1656       @Override
1657       public void menuSelected(MenuEvent e)
1658       {
1659         buildTreeMenu();
1660       }
1661
1662       @Override
1663       public void menuDeselected(MenuEvent e)
1664       {
1665       }
1666
1667       @Override
1668       public void menuCanceled(MenuEvent e)
1669       {
1670       }
1671     });
1672     sortByAnnotScore.setText(MessageManager
1673             .getString("label.sort_by_score"));
1674     sort.add(sortByAnnotScore);
1675     sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1676     {
1677
1678       @Override
1679       public void menuCanceled(MenuEvent e)
1680       {
1681       }
1682
1683       @Override
1684       public void menuDeselected(MenuEvent e)
1685       {
1686       }
1687
1688       @Override
1689       public void menuSelected(MenuEvent e)
1690       {
1691         buildSortByAnnotationScoresMenu();
1692       }
1693     });
1694     sortByAnnotScore.setVisible(false);
1695
1696     calculateTree
1697             .setText(MessageManager.getString("action.calculate_tree"));
1698
1699     jMenu2.setText(MessageManager.getString("label.export_image"));
1700     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1701     padGapsMenuitem.setState(jalview.bin.Cache
1702             .getDefault("PAD_GAPS", false));
1703     padGapsMenuitem.addActionListener(new ActionListener()
1704     {
1705       @Override
1706       public void actionPerformed(ActionEvent e)
1707       {
1708         padGapsMenuitem_actionPerformed(e);
1709       }
1710     });
1711     vamsasStore.setVisible(false);
1712     vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1713     vamsasStore.addActionListener(new ActionListener()
1714     {
1715       @Override
1716       public void actionPerformed(ActionEvent e)
1717       {
1718         vamsasStore_actionPerformed(e);
1719       }
1720     });
1721     showTranslation.setText(MessageManager
1722             .getString("label.translate_cDNA"));
1723     showTranslation.addActionListener(new ActionListener()
1724     {
1725       @Override
1726       public void actionPerformed(ActionEvent e)
1727       {
1728         showTranslation_actionPerformed(e);
1729       }
1730     });
1731     extractScores.setText(MessageManager.getString("label.extract_scores")
1732             + "...");
1733     extractScores.addActionListener(new ActionListener()
1734     {
1735       @Override
1736       public void actionPerformed(ActionEvent e)
1737       {
1738         extractScores_actionPerformed(e);
1739       }
1740     });
1741     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1742     // score extraction
1743     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1744     /*
1745      * showProducts.addActionListener(new ActionListener() {
1746      *
1747      * public void actionPerformed(ActionEvent e) {
1748      * showProducts_actionPerformed(e); } });
1749      */
1750     openFeatureSettings.setText(MessageManager
1751             .getString("label.feature_settings"));
1752     openFeatureSettings.addActionListener(new ActionListener()
1753     {
1754       @Override
1755       public void actionPerformed(ActionEvent e)
1756       {
1757         featureSettings_actionPerformed(e);
1758       }
1759     });
1760     fetchSequence
1761             .setText(MessageManager.getString("label.fetch_sequences"));
1762     fetchSequence.addActionListener(new ActionListener()
1763     {
1764       @Override
1765       public void actionPerformed(ActionEvent e)
1766       {
1767         fetchSequence_actionPerformed(e);
1768       }
1769     });
1770
1771     annotationColour.setText(MessageManager
1772             .getString("action.by_annotation"));
1773     annotationColour.addActionListener(new ActionListener()
1774     {
1775       @Override
1776       public void actionPerformed(ActionEvent e)
1777       {
1778         annotationColour_actionPerformed(e);
1779       }
1780     });
1781
1782     rnahelicesColour.setText(MessageManager
1783             .getString("action.by_rna_helixes"));
1784     rnahelicesColour.addActionListener(new ActionListener()
1785     {
1786       @Override
1787       public void actionPerformed(ActionEvent e)
1788       {
1789         rnahelicesColour_actionPerformed(e);
1790       }
1791     });
1792
1793     associatedData.setText(MessageManager
1794             .getString("label.load_features_annotations"));
1795     associatedData.addActionListener(new ActionListener()
1796     {
1797       @Override
1798       public void actionPerformed(ActionEvent e)
1799       {
1800         associatedData_actionPerformed(e);
1801       }
1802     });
1803     autoCalculate.setText(MessageManager
1804             .getString("label.autocalculate_consensus"));
1805     autoCalculate.setState(jalview.bin.Cache.getDefault(
1806             "AUTO_CALC_CONSENSUS", true));
1807     autoCalculate.addActionListener(new ActionListener()
1808     {
1809       @Override
1810       public void actionPerformed(ActionEvent e)
1811       {
1812         autoCalculate_actionPerformed(e);
1813       }
1814     });
1815     sortByTree.setText(MessageManager
1816             .getString("label.sort_alignment_new_tree"));
1817     sortByTree
1818             .setToolTipText("<html>"
1819                     + MessageManager
1820                             .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1821     sortByTree
1822             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1823     sortByTree.addActionListener(new ActionListener()
1824     {
1825       @Override
1826       public void actionPerformed(ActionEvent e)
1827       {
1828         sortByTreeOption_actionPerformed(e);
1829       }
1830     });
1831
1832     listenToViewSelections.setText(MessageManager
1833             .getString("label.listen_for_selections"));
1834     listenToViewSelections
1835             .setToolTipText("<html>"
1836                     + MessageManager
1837                             .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1838     listenToViewSelections.setState(false);
1839     listenToViewSelections.addActionListener(new ActionListener()
1840     {
1841       @Override
1842       public void actionPerformed(ActionEvent e)
1843       {
1844         listenToViewSelections_actionPerformed(e);
1845       }
1846     });
1847
1848     addSequenceMenu
1849             .setText(MessageManager.getString("label.add_sequences"));
1850     addFromFile.setText(MessageManager.getString("label.from_file"));
1851     addFromFile.addActionListener(new ActionListener()
1852     {
1853       @Override
1854       public void actionPerformed(ActionEvent e)
1855       {
1856         addFromFile_actionPerformed(e);
1857       }
1858     });
1859     addFromText.setText(MessageManager.getString("label.from_textbox"));
1860     addFromText.addActionListener(new ActionListener()
1861     {
1862       @Override
1863       public void actionPerformed(ActionEvent e)
1864       {
1865         addFromText_actionPerformed(e);
1866       }
1867     });
1868     addFromURL.setText(MessageManager.getString("label.from_url"));
1869     addFromURL.addActionListener(new ActionListener()
1870     {
1871       @Override
1872       public void actionPerformed(ActionEvent e)
1873       {
1874         addFromURL_actionPerformed(e);
1875       }
1876     });
1877     exportFeatures.setText(MessageManager
1878             .getString("label.export_features"));
1879     exportFeatures.addActionListener(new ActionListener()
1880     {
1881       @Override
1882       public void actionPerformed(ActionEvent e)
1883       {
1884         exportFeatures_actionPerformed(e);
1885       }
1886     });
1887     exportAnnotations.setText(MessageManager
1888             .getString("label.export_annotations"));
1889     exportAnnotations.addActionListener(new ActionListener()
1890     {
1891       @Override
1892       public void actionPerformed(ActionEvent e)
1893       {
1894         exportAnnotations_actionPerformed(e);
1895       }
1896     });
1897     statusPanel.setLayout(gridLayout1);
1898     jMenu3.setText(MessageManager.getString("action.show"));
1899     showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
1900     showAllSeqs.setToolTipText(MessageManager
1901             .getString("label.toggle_sequence_visibility"));
1902     showAllSeqs.addActionListener(new ActionListener()
1903     {
1904       @Override
1905       public void actionPerformed(ActionEvent e)
1906       {
1907         showAllSeqs_actionPerformed(e);
1908       }
1909     });
1910     showAllColumns.setText(MessageManager.getString("label.all_columns"));
1911     showAllColumns.setToolTipText(MessageManager
1912             .getString("label.toggle_columns_visibility"));
1913     showAllColumns.addActionListener(new ActionListener()
1914     {
1915       @Override
1916       public void actionPerformed(ActionEvent e)
1917       {
1918         showAllColumns_actionPerformed(e);
1919       }
1920     });
1921     hideMenu.setText(MessageManager.getString("action.hide"));
1922     hideSelSequences.setText(MessageManager
1923             .getString("label.selected_sequences"));
1924     hideSelSequences.setToolTipText(MessageManager
1925             .getString("label.toggle_sequence_visibility"));
1926     hideSelSequences.addActionListener(new ActionListener()
1927     {
1928       @Override
1929       public void actionPerformed(ActionEvent e)
1930       {
1931         hideSelSequences_actionPerformed(e);
1932       }
1933     });
1934     hideSelColumns.setText(MessageManager
1935             .getString("label.selected_columns"));
1936     hideSelColumns.setToolTipText(MessageManager
1937             .getString("label.toggle_columns_visibility"));
1938     hideSelColumns.addActionListener(new ActionListener()
1939     {
1940       @Override
1941       public void actionPerformed(ActionEvent e)
1942       {
1943         hideSelColumns_actionPerformed(e);
1944       }
1945     });
1946     hideAllSelection.setText(MessageManager
1947             .getString("label.selected_region"));
1948     hideAllSelection.addActionListener(new ActionListener()
1949     {
1950       @Override
1951       public void actionPerformed(ActionEvent e)
1952       {
1953         hideAllSelection_actionPerformed(e);
1954       }
1955     });
1956     // TODO: should be hidden if no selection exists.
1957     hideAllButSelection.setText(MessageManager
1958             .getString("label.all_but_selected_region"));
1959     hideAllButSelection.addActionListener(new ActionListener()
1960     {
1961       @Override
1962       public void actionPerformed(ActionEvent e)
1963       {
1964         hideAllButSelection_actionPerformed(e);
1965       }
1966     });
1967     showAllhidden.setText(MessageManager
1968             .getString("label.all_sequences_columns"));
1969     showAllhidden.setToolTipText(MessageManager
1970             .getString("label.toggles_visibility_hidden_selected_regions"));
1971     showAllhidden.addActionListener(new ActionListener()
1972     {
1973       @Override
1974       public void actionPerformed(ActionEvent e)
1975       {
1976         showAllhidden_actionPerformed(e);
1977       }
1978     });
1979     hiddenMarkers.setText(MessageManager
1980             .getString("action.show_hidden_markers"));
1981     hiddenMarkers.addActionListener(new ActionListener()
1982     {
1983       @Override
1984       public void actionPerformed(ActionEvent e)
1985       {
1986         hiddenMarkers_actionPerformed(e);
1987       }
1988     });
1989     invertColSel.setText(MessageManager
1990             .getString("action.invert_column_selection"));
1991     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1992             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1993                     .getMenuShortcutKeyMask()
1994                     | java.awt.event.KeyEvent.ALT_MASK, false));
1995     invertColSel.addActionListener(new ActionListener()
1996     {
1997       @Override
1998       public void actionPerformed(ActionEvent e)
1999       {
2000         invertColSel_actionPerformed(e);
2001       }
2002     });
2003     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
2004     {
2005       @Override
2006       public void stateChanged(ChangeEvent evt)
2007       {
2008         JTabbedPane pane = (JTabbedPane) evt.getSource();
2009         int sel = pane.getSelectedIndex();
2010         tabSelectionChanged(sel);
2011       }
2012     });
2013     tabbedPane.addMouseListener(new MouseAdapter()
2014     {
2015       @Override
2016       public void mousePressed(MouseEvent e)
2017       {
2018         tabbedPane_mousePressed(e);
2019       }
2020     });
2021     tabbedPane.addFocusListener(new FocusAdapter()
2022     {
2023       @Override
2024       public void focusGained(FocusEvent e)
2025       {
2026         tabbedPane_focusGained(e);
2027       }
2028     });
2029     save.setText(MessageManager.getString("action.save"));
2030     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2031             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
2032                     .getMenuShortcutKeyMask(), false));
2033     save.addActionListener(new ActionListener()
2034     {
2035       @Override
2036       public void actionPerformed(ActionEvent e)
2037       {
2038         save_actionPerformed(e);
2039       }
2040     });
2041     reload.setEnabled(false);
2042     reload.setText(MessageManager.getString("action.reload"));
2043     reload.addActionListener(new ActionListener()
2044     {
2045       @Override
2046       public void actionPerformed(ActionEvent e)
2047       {
2048         reload_actionPerformed(e);
2049       }
2050     });
2051     newView.setText(MessageManager.getString("action.new_view"));
2052     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2053             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
2054                     .getMenuShortcutKeyMask(), false));
2055     newView.addActionListener(new ActionListener()
2056     {
2057       @Override
2058       public void actionPerformed(ActionEvent e)
2059       {
2060         newView_actionPerformed(e);
2061       }
2062     });
2063     tabbedPane.setToolTipText("<html><i>"
2064             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2065             + "</i></html>");
2066     textColour.setText(MessageManager.getString("label.colour_text")
2067             + "...");
2068     textColour.addActionListener(new ActionListener()
2069     {
2070       @Override
2071       public void actionPerformed(ActionEvent e)
2072       {
2073         textColour_actionPerformed(e);
2074       }
2075     });
2076     formatMenu.setText(MessageManager.getString("action.format"));
2077     selectMenu.setText(MessageManager.getString("action.select"));
2078     idRightAlign.setText(MessageManager
2079             .getString("label.right_align_sequence_id"));
2080     idRightAlign.addActionListener(new ActionListener()
2081     {
2082       @Override
2083       public void actionPerformed(ActionEvent e)
2084       {
2085         idRightAlign_actionPerformed(e);
2086       }
2087     });
2088     gatherViews.setEnabled(false);
2089     gatherViews.setText(MessageManager.getString("action.gather_views"));
2090     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2091             java.awt.event.KeyEvent.VK_G, 0, false));
2092     gatherViews.addActionListener(new ActionListener()
2093     {
2094       @Override
2095       public void actionPerformed(ActionEvent e)
2096       {
2097         gatherViews_actionPerformed(e);
2098       }
2099     });
2100     expandViews.setEnabled(false);
2101     expandViews.setText(MessageManager.getString("action.expand_views"));
2102     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2103             java.awt.event.KeyEvent.VK_X, 0, false));
2104     expandViews.addActionListener(new ActionListener()
2105     {
2106       @Override
2107       public void actionPerformed(ActionEvent e)
2108       {
2109         expandViews_actionPerformed(e);
2110       }
2111     });
2112     pageSetup
2113             .setText(MessageManager.getString("action.page_setup") + "...");
2114     pageSetup.addActionListener(new ActionListener()
2115     {
2116       @Override
2117       public void actionPerformed(ActionEvent e)
2118       {
2119         pageSetup_actionPerformed(e);
2120       }
2121     });
2122     alignmentProperties.setText(MessageManager
2123             .getString("label.alignment_props") + "...");
2124     alignmentProperties.addActionListener(new ActionListener()
2125     {
2126       @Override
2127       public void actionPerformed(ActionEvent actionEvent)
2128       {
2129         alignmentProperties();
2130       }
2131     });
2132     tooltipSettingsMenu.setText(MessageManager
2133             .getString("label.sequence_id_tooltip"));
2134     autoAnnMenu.setText(MessageManager
2135             .getString("label.autocalculated_annotation"));
2136     alignFrameMenuBar.add(fileMenu);
2137     alignFrameMenuBar.add(editMenu);
2138     alignFrameMenuBar.add(selectMenu);
2139     alignFrameMenuBar.add(viewMenu);
2140     alignFrameMenuBar.add(annotationsMenu);
2141     alignFrameMenuBar.add(formatMenu);
2142     alignFrameMenuBar.add(colourMenu);
2143     alignFrameMenuBar.add(calculateMenu);
2144     alignFrameMenuBar.add(webService);
2145     fileMenu.add(fetchSequence);
2146     fileMenu.add(addSequenceMenu);
2147     fileMenu.add(reload);
2148     fileMenu.addSeparator();
2149     fileMenu.add(vamsasStore);
2150     fileMenu.add(save);
2151     fileMenu.add(saveAs);
2152     fileMenu.add(outputTextboxMenu);
2153     fileMenu.add(pageSetup);
2154     fileMenu.add(printMenuItem);
2155     fileMenu.addSeparator();
2156     fileMenu.add(jMenu2);
2157     fileMenu.add(exportFeatures);
2158     fileMenu.add(exportAnnotations);
2159     fileMenu.add(LoadtreeMenuItem);
2160     fileMenu.add(associatedData);
2161     fileMenu.addSeparator();
2162     fileMenu.add(closeMenuItem);
2163     editMenu.add(undoMenuItem);
2164     editMenu.add(redoMenuItem);
2165     editMenu.add(cut);
2166     editMenu.add(copy);
2167     editMenu.add(pasteMenu);
2168     editMenu.add(delete);
2169     editMenu.addSeparator();
2170     editMenu.add(remove2LeftMenuItem);
2171     editMenu.add(remove2RightMenuItem);
2172     editMenu.add(removeGappedColumnMenuItem);
2173     editMenu.add(removeAllGapsMenuItem);
2174     editMenu.add(removeRedundancyMenuItem);
2175     editMenu.addSeparator();
2176     // dont add these yet in the CVS build - they cannot be undone!
2177     // Excluded from Jalview 2.5 release - undo needs to be implemented.
2178     // editMenu.add(justifyLeftMenuItem);
2179     // editMenu.add(justifyRightMenuItem);
2180     // editMenu.addSeparator();
2181     editMenu.add(padGapsMenuitem);
2182     viewMenu.add(newView);
2183     viewMenu.add(expandViews);
2184     viewMenu.add(gatherViews);
2185     viewMenu.addSeparator();
2186     viewMenu.add(jMenu3);
2187     viewMenu.add(hideMenu);
2188     viewMenu.addSeparator();
2189     viewMenu.add(followHighlightMenuItem);
2190     annotationsMenu.add(annotationPanelMenuItem);
2191     annotationsMenu.add(showAllAnnotations);
2192     annotationsMenu.add(hideAllAnnotations);
2193     annotationsMenu.add(sortAnnBySequence);
2194     annotationsMenu.add(sortAnnByType);
2195     autoAnnMenu.add(applyAutoAnnotationSettings);
2196     autoAnnMenu.add(showConsensusHistogram);
2197     autoAnnMenu.add(showSequenceLogo);
2198     autoAnnMenu.add(normaliseSequenceLogo);
2199     autoAnnMenu.addSeparator();
2200     autoAnnMenu.add(showGroupConservation);
2201     autoAnnMenu.add(showGroupConsensus);
2202     annotationsMenu.add(autoAnnMenu);
2203     viewMenu.addSeparator();
2204     viewMenu.add(showSeqFeatures);
2205     // viewMenu.add(showSeqFeaturesHeight);
2206
2207     viewMenu.add(openFeatureSettings);
2208     tooltipSettingsMenu.add(showDbRefsMenuitem);
2209     tooltipSettingsMenu.add(showNpFeatsMenuitem);
2210     viewMenu.add(tooltipSettingsMenu);
2211     viewMenu.addSeparator();
2212     viewMenu.add(alignmentProperties);
2213     viewMenu.addSeparator();
2214     viewMenu.add(overviewMenuItem);
2215     colourMenu.add(applyToAllGroups);
2216     colourMenu.add(textColour);
2217     colourMenu.addSeparator();
2218     colourMenu.add(noColourmenuItem);
2219     colourMenu.add(clustalColour);
2220     colourMenu.add(BLOSUM62Colour);
2221     colourMenu.add(PIDColour);
2222     colourMenu.add(zappoColour);
2223     colourMenu.add(taylorColour);
2224     colourMenu.add(hydrophobicityColour);
2225     colourMenu.add(helixColour);
2226     colourMenu.add(strandColour);
2227     colourMenu.add(turnColour);
2228     colourMenu.add(buriedColour);
2229     colourMenu.add(nucleotideColour);
2230     colourMenu.add(purinePyrimidineColour);
2231     colourMenu.add(RNAInteractionColour);
2232     // colourMenu.add(covariationColour);
2233     colourMenu.add(tcoffeeColour);
2234     colourMenu.add(userDefinedColour);
2235     colourMenu.addSeparator();
2236     colourMenu.add(conservationMenuItem);
2237     colourMenu.add(modifyConservation);
2238     colourMenu.add(abovePIDThreshold);
2239     colourMenu.add(modifyPID);
2240     colourMenu.add(annotationColour);
2241     colourMenu.add(rnahelicesColour);
2242     calculateMenu.add(sort);
2243     calculateMenu.add(calculateTree);
2244     calculateMenu.addSeparator();
2245     calculateMenu.add(pairwiseAlignmentMenuItem);
2246     calculateMenu.add(PCAMenuItem);
2247     calculateMenu.addSeparator();
2248     calculateMenu.add(showTranslation);
2249     calculateMenu.add(showProducts);
2250     calculateMenu.add(autoCalculate);
2251     calculateMenu.add(sortByTree);
2252     calculateMenu.addSeparator();
2253     calculateMenu.add(extractScores);
2254     webServiceNoServices = new JMenuItem(
2255             MessageManager.getString("label.no_services"));
2256     webService.add(webServiceNoServices);
2257     pasteMenu.add(pasteNew);
2258     pasteMenu.add(pasteThis);
2259     sort.add(sortIDMenuItem);
2260     sort.add(sortLengthMenuItem);
2261     sort.add(sortGroupMenuItem);
2262     sort.add(sortPairwiseMenuItem);
2263     sort.add(sortByTreeMenu);
2264     jMenu2.add(htmlMenuItem);
2265     jMenu2.add(epsFile);
2266     jMenu2.add(createPNG);
2267     addSequenceMenu.add(addFromFile);
2268     addSequenceMenu.add(addFromText);
2269     addSequenceMenu.add(addFromURL);
2270     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2271     statusPanel.add(statusBar, null);
2272     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2273     jMenu3.add(showAllColumns);
2274     jMenu3.add(showAllSeqs);
2275     jMenu3.add(showAllhidden);
2276     hideMenu.add(hideSelColumns);
2277     hideMenu.add(hideSelSequences);
2278     hideMenu.add(hideAllSelection);
2279     hideMenu.add(hideAllButSelection);
2280
2281     formatMenu.add(font);
2282     formatMenu.addSeparator();
2283     formatMenu.add(wrapMenuItem);
2284     formatMenu.add(scaleAbove);
2285     formatMenu.add(scaleLeft);
2286     formatMenu.add(scaleRight);
2287     formatMenu.add(seqLimits);
2288     formatMenu.add(idRightAlign);
2289     formatMenu.add(hiddenMarkers);
2290     formatMenu.add(viewBoxesMenuItem);
2291     formatMenu.add(viewTextMenuItem);
2292     formatMenu.add(colourTextMenuItem);
2293     formatMenu.add(renderGapsMenuItem);
2294     formatMenu.add(centreColumnLabelsMenuItem);
2295     formatMenu.add(showNonconservedMenuItem);
2296     selectMenu.add(findMenuItem);
2297     selectMenu.addSeparator();
2298     selectMenu.add(selectAllSequenceMenuItem);
2299     selectMenu.add(deselectAllSequenceMenuItem);
2300     selectMenu.add(invertSequenceMenuItem);
2301     selectMenu.add(invertColSel);
2302     selectMenu.add(createGroup);
2303     selectMenu.add(unGroup);
2304     selectMenu.add(grpsFromSelection);
2305     selectMenu.add(deleteGroups);
2306     calculateMenu.add(expandAlignment);
2307     // TODO - determine if the listenToViewSelections button is needed : see bug
2308     // JAL-574
2309     // selectMenu.addSeparator();
2310     // selectMenu.add(listenToViewSelections);
2311   }
2312
2313   /**
2314    * Action on clicking sort annotations by type.
2315    *
2316    * @param sortOrder
2317    */
2318   protected void sortAnnotations_actionPerformed(SortOrder sortOrder)
2319   {
2320   }
2321
2322   /**
2323    * Action on clicking Show all annotations.
2324    */
2325   protected void showAllAnnotations_actionPerformed()
2326   {
2327     setAllAnnotationsVisibility(true);
2328   }
2329
2330   /**
2331    * Action on clicking Hide all annotations.
2332    */
2333   protected void hideAllAnnotations_actionPerformed()
2334   {
2335     setAllAnnotationsVisibility(false);
2336   }
2337
2338   /**
2339    * Set the visibility of all annotations to true or false.
2340    *
2341    * @param visible
2342    */
2343   protected void setAllAnnotationsVisibility(boolean visible)
2344   {
2345
2346   }
2347
2348   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2349   {
2350     // TODO Auto-generated method stub
2351
2352   }
2353
2354   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2355   {
2356     // TODO Auto-generated method stub
2357
2358   }
2359
2360   protected void showAllhidden_actionPerformed(ActionEvent e)
2361   {
2362     // TODO Auto-generated method stub
2363
2364   }
2365
2366   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2367   {
2368     // TODO Auto-generated method stub
2369
2370   }
2371
2372   protected void hideAllSelection_actionPerformed(ActionEvent e)
2373   {
2374     // TODO Auto-generated method stub
2375
2376   }
2377
2378   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2379   {
2380     // TODO Auto-generated method stub
2381
2382   }
2383
2384   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2385   {
2386     // TODO Auto-generated method stub
2387
2388   }
2389
2390   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2391   {
2392     // TODO Auto-generated method stub
2393
2394   }
2395
2396   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2397   {
2398     // TODO Auto-generated method stub
2399
2400   }
2401
2402   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2403   {
2404     // TODO Auto-generated method stub
2405
2406   }
2407
2408   protected void showGroupConservation_actionPerformed(ActionEvent e)
2409   {
2410     // TODO Auto-generated method stub
2411
2412   }
2413
2414   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2415   {
2416     // TODO Auto-generated method stub
2417
2418   }
2419
2420   protected void showSeqFeaturesHeight_actionPerformed(
2421           ActionEvent actionEvent)
2422   {
2423     // TODO Auto-generated method stub
2424
2425   }
2426
2427   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2428   {
2429     // TODO Auto-generated method stub
2430
2431   }
2432
2433   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2434   {
2435     // TODO Auto-generated method stub
2436
2437   }
2438
2439   protected void followHighlight_actionPerformed()
2440   {
2441     // TODO Auto-generated method stub
2442
2443   }
2444
2445   protected void showNpFeats_actionPerformed(ActionEvent e)
2446   {
2447     // TODO Auto-generated method stub
2448
2449   }
2450
2451   protected void showDbRefs_actionPerformed(ActionEvent e)
2452   {
2453     // TODO Auto-generated method stub
2454
2455   }
2456
2457   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2458   {
2459   }
2460
2461   protected void showProducts_actionPerformed(ActionEvent e)
2462   {
2463   }
2464
2465   protected void buildSortByAnnotationScoresMenu()
2466   {
2467   }
2468
2469   protected void extractScores_actionPerformed(ActionEvent e)
2470   {
2471   }
2472
2473   protected void outputText_actionPerformed(ActionEvent e)
2474   {
2475   }
2476
2477   public void addFromFile_actionPerformed(ActionEvent e)
2478   {
2479
2480   }
2481
2482   public void addFromText_actionPerformed(ActionEvent e)
2483   {
2484
2485   }
2486
2487   public void addFromURL_actionPerformed(ActionEvent e)
2488   {
2489
2490   }
2491
2492   public void exportFeatures_actionPerformed(ActionEvent e)
2493   {
2494
2495   }
2496
2497   public void exportAnnotations_actionPerformed(ActionEvent e)
2498   {
2499
2500   }
2501
2502   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2503   {
2504   }
2505
2506   protected void closeMenuItem_actionPerformed(boolean b)
2507   {
2508   }
2509
2510   protected void redoMenuItem_actionPerformed(ActionEvent e)
2511   {
2512   }
2513
2514   protected void undoMenuItem_actionPerformed(ActionEvent e)
2515   {
2516   }
2517
2518   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2519   {
2520   }
2521
2522   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2523   {
2524   }
2525
2526   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2527   {
2528   }
2529
2530   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2531   {
2532   }
2533
2534   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2535   {
2536   }
2537
2538   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2539   {
2540   }
2541
2542   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2543   {
2544   }
2545
2546   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2547   {
2548   }
2549
2550   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2551   {
2552   }
2553
2554   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2555   {
2556   }
2557
2558   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2559   {
2560   }
2561
2562   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2563   {
2564   }
2565
2566   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2567   {
2568   }
2569
2570   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2571   {
2572   }
2573
2574   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2575   {
2576   }
2577
2578   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2579   {
2580   }
2581
2582   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2583   {
2584   }
2585
2586   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2587   {
2588   }
2589
2590   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2591   {
2592   }
2593
2594   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2595   {
2596   }
2597
2598   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2599   {
2600   }
2601
2602   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2603   {
2604   }
2605
2606   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2607   {
2608   }
2609
2610   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2611   {
2612   }
2613
2614   protected void clustalColour_actionPerformed(ActionEvent e)
2615   {
2616   }
2617
2618   protected void zappoColour_actionPerformed(ActionEvent e)
2619   {
2620   }
2621
2622   protected void taylorColour_actionPerformed(ActionEvent e)
2623   {
2624   }
2625
2626   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2627   {
2628   }
2629
2630   protected void helixColour_actionPerformed(ActionEvent e)
2631   {
2632   }
2633
2634   protected void strandColour_actionPerformed(ActionEvent e)
2635   {
2636   }
2637
2638   protected void turnColour_actionPerformed(ActionEvent e)
2639   {
2640   }
2641
2642   protected void buriedColour_actionPerformed(ActionEvent e)
2643   {
2644   }
2645
2646   protected void userDefinedColour_actionPerformed(ActionEvent e)
2647   {
2648   }
2649
2650   protected void PIDColour_actionPerformed(ActionEvent e)
2651   {
2652   }
2653
2654   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2655   {
2656   }
2657
2658   protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2659   {
2660   }
2661
2662   protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2663   {
2664   }
2665
2666   /*
2667    * protected void covariationColour_actionPerformed(ActionEvent e) { }
2668    */
2669
2670   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2671   {
2672   }
2673
2674   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2675   {
2676   }
2677
2678   protected void printMenuItem_actionPerformed(ActionEvent e)
2679   {
2680   }
2681
2682   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2683   {
2684   }
2685
2686   protected void findMenuItem_actionPerformed(ActionEvent e)
2687   {
2688   }
2689
2690   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2691   {
2692   }
2693
2694   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2695   {
2696   }
2697
2698   protected void nucleotideColour_actionPerformed(ActionEvent e)
2699   {
2700   }
2701
2702   protected void deleteGroups_actionPerformed(ActionEvent e)
2703   {
2704   }
2705
2706   protected void createGroup_actionPerformed(ActionEvent e)
2707   {
2708   }
2709
2710   protected void unGroup_actionPerformed(ActionEvent e)
2711   {
2712   }
2713
2714   protected void copy_actionPerformed(ActionEvent e)
2715   {
2716   }
2717
2718   protected void cut_actionPerformed(ActionEvent e)
2719   {
2720   }
2721
2722   protected void delete_actionPerformed(ActionEvent e)
2723   {
2724   }
2725
2726   protected void pasteNew_actionPerformed(ActionEvent e)
2727   {
2728   }
2729
2730   protected void pasteThis_actionPerformed(ActionEvent e)
2731   {
2732   }
2733
2734   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2735   {
2736   }
2737
2738   public void createPNG(java.io.File f)
2739   {
2740   }
2741
2742   protected void font_actionPerformed(ActionEvent e)
2743   {
2744   }
2745
2746   protected void seqLimit_actionPerformed(ActionEvent e)
2747   {
2748   }
2749
2750   public void seqDBRef_actionPerformed(ActionEvent e)
2751   {
2752
2753   }
2754
2755   public void createEPS(java.io.File f)
2756   {
2757   }
2758
2759   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2760   {
2761
2762   }
2763
2764   /**
2765    * Template method to handle the 'load T-Coffee scores' menu event.
2766    * <p>
2767    * Subclasses override this method to provide a custom action.
2768    *
2769    * @param event
2770    *          The raised event
2771    */
2772   protected void loadScores_actionPerformed(ActionEvent event)
2773   {
2774
2775   }
2776
2777   /**
2778    * Template method to handle the 'Color T-Coffee scores' menu event.
2779    * <p>
2780    * Subclasses override this method to provide a custom action.
2781    *
2782    * @param event
2783    *          The raised event
2784    */
2785   protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2786   {
2787
2788   }
2789
2790   protected void jpred_actionPerformed(ActionEvent e)
2791   {
2792   }
2793
2794   protected void scaleAbove_actionPerformed(ActionEvent e)
2795   {
2796   }
2797
2798   protected void scaleLeft_actionPerformed(ActionEvent e)
2799   {
2800   }
2801
2802   protected void scaleRight_actionPerformed(ActionEvent e)
2803   {
2804   }
2805
2806   protected void modifyPID_actionPerformed(ActionEvent e)
2807   {
2808   }
2809
2810   protected void modifyConservation_actionPerformed(ActionEvent e)
2811   {
2812   }
2813
2814   protected void saveAs_actionPerformed(ActionEvent e)
2815   {
2816   }
2817
2818   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2819   {
2820   }
2821
2822   public void vamsasStore_actionPerformed(ActionEvent e)
2823   {
2824
2825   }
2826
2827   public void vamsasLoad_actionPerformed(ActionEvent e)
2828   {
2829
2830   }
2831
2832   public void showTranslation_actionPerformed(ActionEvent e)
2833   {
2834
2835   }
2836
2837   public void featureSettings_actionPerformed(ActionEvent e)
2838   {
2839
2840   }
2841
2842   public void fetchSequence_actionPerformed(ActionEvent e)
2843   {
2844
2845   }
2846
2847   public void smoothFont_actionPerformed(ActionEvent e)
2848   {
2849
2850   }
2851
2852   public void annotationColour_actionPerformed(ActionEvent e)
2853   {
2854
2855   }
2856
2857   public void rnahelicesColour_actionPerformed(ActionEvent e)
2858   {
2859
2860   }
2861
2862   public void associatedData_actionPerformed(ActionEvent e)
2863   {
2864
2865   }
2866
2867   public void autoCalculate_actionPerformed(ActionEvent e)
2868   {
2869
2870   }
2871
2872   public void sortByTreeOption_actionPerformed(ActionEvent e)
2873   {
2874
2875   }
2876
2877   public void showAllSeqs_actionPerformed(ActionEvent e)
2878   {
2879
2880   }
2881
2882   public void showAllColumns_actionPerformed(ActionEvent e)
2883   {
2884
2885   }
2886
2887   public void hideSelSequences_actionPerformed(ActionEvent e)
2888   {
2889
2890   }
2891
2892   public void hideSelColumns_actionPerformed(ActionEvent e)
2893   {
2894
2895   }
2896
2897   public void hiddenMarkers_actionPerformed(ActionEvent e)
2898   {
2899
2900   }
2901
2902   public void findPdbId_actionPerformed(ActionEvent e)
2903   {
2904
2905   }
2906
2907   public void enterPdbId_actionPerformed(ActionEvent e)
2908   {
2909
2910   }
2911
2912   public void pdbFile_actionPerformed(ActionEvent e)
2913   {
2914
2915   }
2916
2917   public void invertColSel_actionPerformed(ActionEvent e)
2918   {
2919
2920   }
2921
2922   public void tabSelectionChanged(int sel)
2923   {
2924
2925   }
2926
2927   public void tabbedPane_mousePressed(MouseEvent e)
2928   {
2929
2930   }
2931
2932   public void tabbedPane_focusGained(FocusEvent e)
2933   {
2934     requestFocus();
2935   }
2936
2937   public void save_actionPerformed(ActionEvent e)
2938   {
2939
2940   }
2941
2942   public void reload_actionPerformed(ActionEvent e)
2943   {
2944
2945   }
2946
2947   public void newView_actionPerformed(ActionEvent e)
2948   {
2949
2950   }
2951
2952   public void textColour_actionPerformed(ActionEvent e)
2953   {
2954
2955   }
2956
2957   public void idRightAlign_actionPerformed(ActionEvent e)
2958   {
2959
2960   }
2961
2962   public void expandViews_actionPerformed(ActionEvent e)
2963   {
2964
2965   }
2966
2967   public void gatherViews_actionPerformed(ActionEvent e)
2968   {
2969
2970   }
2971
2972   public void buildTreeMenu()
2973   {
2974
2975   }
2976
2977   public void pageSetup_actionPerformed(ActionEvent e)
2978   {
2979
2980   }
2981
2982   public void alignmentProperties()
2983   {
2984
2985   }
2986
2987   protected void expand_newalign(ActionEvent e)
2988   {
2989     // TODO Auto-generated method stub
2990
2991   }
2992 }