src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.jbgui;
  22
  23 import jalview.bin.Cache;
  24 import jalview.schemes.ColourSchemeProperty;
  25 import jalview.util.MessageManager;
  26
  27 import java.awt.BorderLayout;
  28 import java.awt.Color;
  29 import java.awt.GridLayout;
  30 import java.awt.Toolkit;
  31 import java.awt.event.ActionEvent;
  32 import java.awt.event.ActionListener;
  33 import java.awt.event.FocusAdapter;
  34 import java.awt.event.FocusEvent;
  35 import java.awt.event.MouseAdapter;
  36 import java.awt.event.MouseEvent;
  37
  38 import javax.swing.BorderFactory;
  39 import javax.swing.ButtonGroup;
  40 import javax.swing.JCheckBoxMenuItem;
  41 import javax.swing.JInternalFrame;
  42 import javax.swing.JLabel;
  43 import javax.swing.JMenu;
  44 import javax.swing.JMenuBar;
  45 import javax.swing.JMenuItem;
  46 import javax.swing.JOptionPane;
  47 import javax.swing.JPanel;
  48 import javax.swing.JRadioButtonMenuItem;
  49 import javax.swing.JTabbedPane;
  50 import javax.swing.SwingUtilities;
  51 import javax.swing.event.ChangeEvent;
  52 import javax.swing.event.MenuEvent;
  53 import javax.swing.event.MenuListener;
  54
  55 public class GAlignFrame extends JInternalFrame
  56 {
  57   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  58
  59   protected JMenu fileMenu = new JMenu();
  60
  61   protected JMenuItem closeMenuItem = new JMenuItem();
  62
  63   protected JMenu editMenu = new JMenu();
  64
  65   protected JMenu viewMenu = new JMenu();
  66
  67   protected JMenu colourMenu = new JMenu();
  68
  69   protected JMenu calculateMenu = new JMenu();
  70
  71   protected JMenu webService = new JMenu();
  72
  73   protected JMenuItem webServiceNoServices;
  74
  75   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  76
  77   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  78
  79   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  80
  81   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  82
  83   protected JMenuItem remove2RightMenuItem = new JMenuItem();
  84
  85   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  86
  87   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  88
  89   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  90
  91   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  92
  93   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  94
  95   protected JMenuItem sortIDMenuItem = new JMenuItem();
  96
  97   protected JMenuItem sortLengthMenuItem = new JMenuItem();
  98
  99   protected JMenuItem sortGroupMenuItem = new JMenuItem();
 100
 101   protected JMenu sortByAnnotScore = new JMenu();
 102
 103   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
 104
 105   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
 106
 107   protected JMenuItem PCAMenuItem = new JMenuItem();
 108
 109   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
 110
 111   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
 112
 113   BorderLayout borderLayout1 = new BorderLayout();
 114
 115   public JLabel statusBar = new JLabel();
 116
 117   protected JMenuItem saveAs = new JMenuItem();
 118
 119   protected JMenu outputTextboxMenu = new JMenu();
 120
 121   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
 122
 123   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
 124
 125   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
 126
 127   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
 128
 129   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
 130
 131   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
 132
 133   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
 134
 135   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 136
 137   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
 138
 139   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
 140
 141   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 142
 143   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
 144
 145   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
 146
 147   protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
 148
 149   // protected JRadioButtonMenuItem covariationColour = new
 150   // JRadioButtonMenuItem();
 151
 152   protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
 153
 154   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 155
 156   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
 157
 158   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 159
 160   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 161
 162   public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
 163
 164   JMenuItem htmlMenuItem = new JMenuItem();
 165
 166   JMenuItem overviewMenuItem = new JMenuItem();
 167
 168   protected JMenuItem undoMenuItem = new JMenuItem();
 169
 170   protected JMenuItem redoMenuItem = new JMenuItem();
 171
 172   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 173
 174   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 175
 176   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 177
 178   JMenuItem printMenuItem = new JMenuItem();
 179
 180   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 181
 182   JMenuItem findMenuItem = new JMenuItem();
 183
 184   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 185
 186   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 187
 188   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 189
 190   JMenuItem deleteGroups = new JMenuItem();
 191
 192   JMenuItem createGroup = new JMenuItem();
 193
 194   JMenuItem unGroup = new JMenuItem();
 195
 196   JMenuItem delete = new JMenuItem();
 197
 198   JMenuItem copy = new JMenuItem();
 199
 200   JMenuItem cut = new JMenuItem();
 201
 202   JMenu pasteMenu = new JMenu();
 203
 204   JMenuItem pasteNew = new JMenuItem();
 205
 206   JMenuItem pasteThis = new JMenuItem();
 207
 208   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
 209
 210   JMenuItem createPNG = new JMenuItem();
 211
 212   protected JMenuItem font = new JMenuItem();
 213
 214   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 215
 216   JMenuItem epsFile = new JMenuItem();
 217
 218   JMenuItem LoadtreeMenuItem = new JMenuItem();
 219
 220   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 221
 222   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 223
 224   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 225
 226   protected JMenuItem modifyPID = new JMenuItem();
 227
 228   protected JMenuItem modifyConservation = new JMenuItem();
 229
 230   protected JMenu sortByTreeMenu = new JMenu();
 231
 232   protected JMenu sort = new JMenu();
 233
 234   protected JMenu calculateTree = new JMenu();
 235
 236   JMenu jMenu2 = new JMenu();
 237
 238   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 239
 240   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 241
 242   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 243
 244   protected ButtonGroup colours = new ButtonGroup();
 245
 246   JMenuItem vamsasStore = new JMenuItem();
 247
 248   protected JMenuItem showTranslation = new JMenuItem();
 249
 250   protected JMenuItem extractScores = new JMenuItem();
 251
 252   protected JMenuItem expandAlignment = new JMenuItem();
 253
 254   protected JMenu showProducts = new JMenu();
 255
 256   public JMenuItem openFeatureSettings = new JMenuItem();
 257
 258   JMenuItem fetchSequence = new JMenuItem();
 259
 260   JMenuItem annotationColour = new JMenuItem();
 261
 262   protected JMenuItem rnahelicesColour = new JMenuItem();
 263
 264   JMenuItem associatedData = new JMenuItem();
 265
 266   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 267
 268   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 269
 270   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 271
 272   JMenu addSequenceMenu = new JMenu();
 273
 274   JMenuItem addFromFile = new JMenuItem();
 275
 276   JMenuItem addFromText = new JMenuItem();
 277
 278   JMenuItem addFromURL = new JMenuItem();
 279
 280   JMenuItem exportAnnotations = new JMenuItem();
 281
 282   JMenuItem exportFeatures = new JMenuItem();
 283
 284   protected JPanel statusPanel = new JPanel();
 285
 286   GridLayout gridLayout1 = new GridLayout();
 287
 288   JMenu jMenu3 = new JMenu();
 289
 290   JMenuItem showAllSeqs = new JMenuItem();
 291
 292   JMenuItem showAllColumns = new JMenuItem();
 293
 294   JMenu hideMenu = new JMenu();
 295
 296   JMenuItem hideSelSequences = new JMenuItem();
 297
 298   JMenuItem hideSelColumns = new JMenuItem();
 299
 300   JMenuItem hideAllButSelection = new JMenuItem();
 301
 302   JMenuItem hideAllSelection = new JMenuItem();
 303
 304   JMenuItem showAllhidden = new JMenuItem();
 305
 306   protected JMenuItem showAllAnnotations = new JMenuItem();
 307
 308   protected JMenuItem hideAllAnnotations = new JMenuItem();
 309
 310   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 311
 312   JMenuItem invertColSel = new JMenuItem();
 313
 314   protected JTabbedPane tabbedPane = new JTabbedPane();
 315
 316   JMenuItem save = new JMenuItem();
 317
 318   protected JMenuItem reload = new JMenuItem();
 319
 320   JMenuItem newView = new JMenuItem();
 321
 322   JMenuItem textColour = new JMenuItem();
 323
 324   JMenu formatMenu = new JMenu();
 325
 326   JMenu selectMenu = new JMenu();
 327
 328   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 329
 330   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 331
 332   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 333
 334   protected JMenuItem gatherViews = new JMenuItem();
 335
 336   protected JMenuItem expandViews = new JMenuItem();
 337
 338   JMenuItem pageSetup = new JMenuItem();
 339
 340   JMenuItem alignmentProperties = new JMenuItem();
 341
 342   JMenu tooltipSettingsMenu = new JMenu();
 343
 344   private JMenuItem justifyLeftMenuItem = new JMenuItem();
 345
 346   private JMenuItem justifyRightMenuItem = new JMenuItem();
 347
 348   JMenu autoAnnMenu = new JMenu();
 349
 350   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 351
 352   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 353
 354   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 355
 356   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 357
 358   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 359
 360   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 361
 362   private JMenuItem grpsFromSelection = new JMenuItem();
 363
 364   public GAlignFrame()
 365   {
 366     try
 367     {
 368       jbInit();
 369       setJMenuBar(alignFrameMenuBar);
 370
 371       // dynamically fill save as menu with available formats
 372       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 373       {
 374         JMenuItem item = new JMenuItem(
 375                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 376
 377         item.addActionListener(new java.awt.event.ActionListener()
 378         {
 379           @Override
 380           public void actionPerformed(ActionEvent e)
 381           {
 382             outputText_actionPerformed(e);
 383           }
 384         });
 385
 386         outputTextboxMenu.add(item);
 387       }
 388     } catch (Exception e)
 389     {
 390       System.err.println(e.toString());
 391     }
 392
 393     if (!new jalview.util.Platform().isAMac())
 394     {
 395       closeMenuItem.setMnemonic('C');
 396       outputTextboxMenu.setMnemonic('T');
 397       undoMenuItem.setMnemonic('Z');
 398       redoMenuItem.setMnemonic('0');
 399       copy.setMnemonic('C');
 400       cut.setMnemonic('U');
 401       pasteMenu.setMnemonic('P');
 402       reload.setMnemonic('R');
 403     }
 404
 405     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 406     {
 407       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 408               .getUserColourSchemes().keys();
 409
 410       while (userColours.hasMoreElements())
 411       {
 412         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 413                 userColours.nextElement().toString());
 414         radioItem.setName("USER_DEFINED");
 415         radioItem.addMouseListener(new MouseAdapter()
 416         {
 417           @Override
 418           public void mousePressed(MouseEvent evt)
 419           {
 420             if (evt.isControlDown()
 421                     || SwingUtilities.isRightMouseButton(evt))
 422             {
 423               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 424
 425               int option = JOptionPane.showInternalConfirmDialog(
 426                       jalview.gui.Desktop.desktop,
 427                       MessageManager
 428                               .getString("label.remove_from_default_list"),
 429                       MessageManager
 430                               .getString("label.remove_user_defined_colour"),
 431                       JOptionPane.YES_NO_OPTION);
 432               if (option == JOptionPane.YES_OPTION)
 433               {
 434                 jalview.gui.UserDefinedColours
 435                         .removeColourFromDefaults(radioItem.getText());
 436                 colourMenu.remove(radioItem);
 437               }
 438               else
 439               {
 440                 radioItem.addActionListener(new ActionListener()
 441                 {
 442                   @Override
 443                   public void actionPerformed(ActionEvent evt)
 444                   {
 445                     userDefinedColour_actionPerformed(evt);
 446                   }
 447                 });
 448               }
 449             }
 450           }
 451         });
 452         radioItem.addActionListener(new ActionListener()
 453         {
 454           @Override
 455           public void actionPerformed(ActionEvent evt)
 456           {
 457             userDefinedColour_actionPerformed(evt);
 458           }
 459         });
 460         colourMenu.insert(radioItem, 15);
 461         colours.add(radioItem);
 462       }
 463     }
 464     colours.add(noColourmenuItem);
 465     colours.add(clustalColour);
 466     colours.add(zappoColour);
 467     colours.add(taylorColour);
 468     colours.add(hydrophobicityColour);
 469     colours.add(helixColour);
 470     colours.add(strandColour);
 471     colours.add(turnColour);
 472     colours.add(buriedColour);
 473     colours.add(userDefinedColour);
 474     colours.add(PIDColour);
 475     colours.add(BLOSUM62Colour);
 476     colours.add(nucleotideColour);
 477     colours.add(purinePyrimidineColour);
 478     // colours.add(covariationColour);
 479     colours.add(tcoffeeColour);
 480     colours.add(RNAInteractionColour);
 481     setColourSelected(jalview.bin.Cache
 482             .getDefault("DEFAULT_COLOUR", "None"));
 483
 484   }
 485
 486   public void setColourSelected(String defaultColour)
 487   {
 488
 489     if (defaultColour != null)
 490     {
 491       int index = ColourSchemeProperty
 492               .getColourIndexFromName(defaultColour);
 493
 494       switch (index)
 495       {
 496       case ColourSchemeProperty.CLUSTAL:
 497         clustalColour.setSelected(true);
 498
 499         break;
 500
 501       case ColourSchemeProperty.BLOSUM:
 502         BLOSUM62Colour.setSelected(true);
 503
 504         break;
 505
 506       case ColourSchemeProperty.PID:
 507         PIDColour.setSelected(true);
 508
 509         break;
 510
 511       case ColourSchemeProperty.ZAPPO:
 512         zappoColour.setSelected(true);
 513
 514         break;
 515
 516       case ColourSchemeProperty.TAYLOR:
 517         taylorColour.setSelected(true);
 518         break;
 519
 520       case ColourSchemeProperty.HYDROPHOBIC:
 521         hydrophobicityColour.setSelected(true);
 522
 523         break;
 524
 525       case ColourSchemeProperty.HELIX:
 526         helixColour.setSelected(true);
 527
 528         break;
 529
 530       case ColourSchemeProperty.STRAND:
 531         strandColour.setSelected(true);
 532
 533         break;
 534
 535       case ColourSchemeProperty.TURN:
 536         turnColour.setSelected(true);
 537
 538         break;
 539
 540       case ColourSchemeProperty.BURIED:
 541         buriedColour.setSelected(true);
 542
 543         break;
 544
 545       case ColourSchemeProperty.NUCLEOTIDE:
 546         nucleotideColour.setSelected(true);
 547
 548         break;
 549
 550       case ColourSchemeProperty.TCOFFEE:
 551         tcoffeeColour.setSelected(true);
 552         break;
 553
 554       case ColourSchemeProperty.PURINEPYRIMIDINE:
 555         purinePyrimidineColour.setSelected(true);
 556
 557         break;
 558
 559       case ColourSchemeProperty.RNAINTERACTION:
 560         RNAInteractionColour.setSelected(true);
 561
 562         break;
 563       /*
 564        * case ColourSchemeProperty.COVARIATION:
 565        * covariationColour.setSelected(true);
 566        *
 567        * break;
 568        */
 569       case ColourSchemeProperty.USER_DEFINED:
 570         userDefinedColour.setSelected(true);
 571
 572         break;
 573       case ColourSchemeProperty.NONE:
 574       default:
 575         noColourmenuItem.setSelected(true);
 576         break;
 577
 578       }
 579     }
 580
 581   }
 582
 583   private void jbInit() throws Exception
 584   {
 585     fileMenu.setText(MessageManager.getString("action.file"));
 586     saveAs.setText(MessageManager.getString("action.save_as") + "...");
 587     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 588             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
 589                     .getMenuShortcutKeyMask()
 590                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 591     saveAs.addActionListener(new ActionListener()
 592     {
 593       @Override
 594       public void actionPerformed(ActionEvent e)
 595       {
 596         saveAs_actionPerformed(e);
 597       }
 598     });
 599     closeMenuItem.setText(MessageManager.getString("action.close"));
 600     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 601             java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
 602                     .getMenuShortcutKeyMask(), false));
 603     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 604     {
 605       @Override
 606       public void actionPerformed(ActionEvent e)
 607       {
 608         closeMenuItem_actionPerformed(false);
 609       }
 610     });
 611     editMenu.setText(MessageManager.getString("action.edit"));
 612     viewMenu.setText(MessageManager.getString("action.view"));
 613     colourMenu.setText(MessageManager.getString("action.colour"));
 614     calculateMenu.setText(MessageManager.getString("action.calculate"));
 615     webService.setText(MessageManager.getString("action.web_service"));
 616     selectAllSequenceMenuItem.setText(MessageManager
 617             .getString("action.select_all"));
 618     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 619             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
 620                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 621     selectAllSequenceMenuItem
 622             .addActionListener(new java.awt.event.ActionListener()
 623             {
 624               @Override
 625               public void actionPerformed(ActionEvent e)
 626               {
 627                 selectAllSequenceMenuItem_actionPerformed(e);
 628               }
 629             });
 630     deselectAllSequenceMenuItem.setText(MessageManager
 631             .getString("action.deselect_all"));
 632     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 633             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 634     deselectAllSequenceMenuItem
 635             .addActionListener(new java.awt.event.ActionListener()
 636             {
 637               @Override
 638               public void actionPerformed(ActionEvent e)
 639               {
 640                 deselectAllSequenceMenuItem_actionPerformed(e);
 641               }
 642             });
 643     invertSequenceMenuItem.setText(MessageManager
 644             .getString("action.invert_sequence_selection"));
 645     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 646             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
 647                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 648     invertSequenceMenuItem
 649             .addActionListener(new java.awt.event.ActionListener()
 650             {
 651               @Override
 652               public void actionPerformed(ActionEvent e)
 653               {
 654                 invertSequenceMenuItem_actionPerformed(e);
 655               }
 656             });
 657     grpsFromSelection.setText(MessageManager
 658             .getString("action.make_groups_selection"));
 659     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
 660     {
 661       @Override
 662       public void actionPerformed(ActionEvent e)
 663       {
 664         makeGrpsFromSelection_actionPerformed(e);
 665       }
 666     });
 667     expandAlignment.setText(MessageManager
 668             .getString("action.view_flanking_regions"));
 669     expandAlignment.setToolTipText(MessageManager
 670             .getString("label.view_flanking_regions"));
 671     expandAlignment.addActionListener(new java.awt.event.ActionListener()
 672     {
 673       @Override
 674       public void actionPerformed(ActionEvent e)
 675       {
 676         expand_newalign(e);
 677       }
 678     });
 679     remove2LeftMenuItem.setText(MessageManager
 680             .getString("action.remove_left"));
 681     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 682             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
 683                     .getMenuShortcutKeyMask(), false));
 684     remove2LeftMenuItem
 685             .addActionListener(new java.awt.event.ActionListener()
 686             {
 687               @Override
 688               public void actionPerformed(ActionEvent e)
 689               {
 690                 remove2LeftMenuItem_actionPerformed(e);
 691               }
 692             });
 693     remove2RightMenuItem.setText(MessageManager
 694             .getString("action.remove_right"));
 695     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 696             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
 697                     .getMenuShortcutKeyMask(), false));
 698     remove2RightMenuItem
 699             .addActionListener(new java.awt.event.ActionListener()
 700             {
 701               @Override
 702               public void actionPerformed(ActionEvent e)
 703               {
 704                 remove2RightMenuItem_actionPerformed(e);
 705               }
 706             });
 707     removeGappedColumnMenuItem.setText(MessageManager
 708             .getString("action.remove_empty_columns"));
 709     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
 710             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 711                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 712     removeGappedColumnMenuItem
 713             .addActionListener(new java.awt.event.ActionListener()
 714             {
 715               @Override
 716               public void actionPerformed(ActionEvent e)
 717               {
 718                 removeGappedColumnMenuItem_actionPerformed(e);
 719               }
 720             });
 721     removeAllGapsMenuItem.setText(MessageManager
 722             .getString("action.remove_all_gaps"));
 723     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
 724             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 725                     .getDefaultToolkit().getMenuShortcutKeyMask()
 726                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 727     removeAllGapsMenuItem
 728             .addActionListener(new java.awt.event.ActionListener()
 729             {
 730               @Override
 731               public void actionPerformed(ActionEvent e)
 732               {
 733                 removeAllGapsMenuItem_actionPerformed(e);
 734               }
 735             });
 736     justifyLeftMenuItem.setText(MessageManager
 737             .getString("action.left_justify_alignment"));
 738     justifyLeftMenuItem
 739             .addActionListener(new java.awt.event.ActionListener()
 740             {
 741               @Override
 742               public void actionPerformed(ActionEvent e)
 743               {
 744                 justifyLeftMenuItem_actionPerformed(e);
 745               }
 746             });
 747     justifyRightMenuItem.setText(MessageManager
 748             .getString("action.right_justify_alignment"));
 749     justifyRightMenuItem
 750             .addActionListener(new java.awt.event.ActionListener()
 751             {
 752               @Override
 753               public void actionPerformed(ActionEvent e)
 754               {
 755                 justifyRightMenuItem_actionPerformed(e);
 756               }
 757             });
 758     viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
 759     viewBoxesMenuItem.setState(true);
 760     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 761     {
 762       @Override
 763       public void actionPerformed(ActionEvent e)
 764       {
 765         viewBoxesMenuItem_actionPerformed(e);
 766       }
 767     });
 768     viewTextMenuItem.setText(MessageManager.getString("action.text"));
 769     viewTextMenuItem.setState(true);
 770     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 771     {
 772       @Override
 773       public void actionPerformed(ActionEvent e)
 774       {
 775         viewTextMenuItem_actionPerformed(e);
 776       }
 777     });
 778     showNonconservedMenuItem.setText(MessageManager
 779             .getString("label.show_non_conversed"));
 780     showNonconservedMenuItem.setState(false);
 781     showNonconservedMenuItem
 782             .addActionListener(new java.awt.event.ActionListener()
 783             {
 784               @Override
 785               public void actionPerformed(ActionEvent e)
 786               {
 787                 showUnconservedMenuItem_actionPerformed(e);
 788               }
 789             });
 790     sortPairwiseMenuItem.setText(MessageManager
 791             .getString("action.by_pairwise_id"));
 792     sortPairwiseMenuItem
 793             .addActionListener(new java.awt.event.ActionListener()
 794             {
 795               @Override
 796               public void actionPerformed(ActionEvent e)
 797               {
 798                 sortPairwiseMenuItem_actionPerformed(e);
 799               }
 800             });
 801     sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
 802     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 803     {
 804       @Override
 805       public void actionPerformed(ActionEvent e)
 806       {
 807         sortIDMenuItem_actionPerformed(e);
 808       }
 809     });
 810     sortLengthMenuItem
 811             .setText(MessageManager.getString("action.by_length"));
 812     sortLengthMenuItem
 813             .addActionListener(new java.awt.event.ActionListener()
 814             {
 815               @Override
 816               public void actionPerformed(ActionEvent e)
 817               {
 818                 sortLengthMenuItem_actionPerformed(e);
 819               }
 820             });
 821     sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
 822     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 823     {
 824       @Override
 825       public void actionPerformed(ActionEvent e)
 826       {
 827         sortGroupMenuItem_actionPerformed(e);
 828       }
 829     });
 830     removeRedundancyMenuItem.setText(MessageManager
 831             .getString("action.remove_redundancy"));
 832     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
 833             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
 834                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 835     removeRedundancyMenuItem
 836             .addActionListener(new java.awt.event.ActionListener()
 837             {
 838               @Override
 839               public void actionPerformed(ActionEvent e)
 840               {
 841                 removeRedundancyMenuItem_actionPerformed(e);
 842               }
 843             });
 844     pairwiseAlignmentMenuItem.setText(MessageManager
 845             .getString("action.pairwise_alignment"));
 846     pairwiseAlignmentMenuItem
 847             .addActionListener(new java.awt.event.ActionListener()
 848             {
 849               @Override
 850               public void actionPerformed(ActionEvent e)
 851               {
 852                 pairwiseAlignmentMenuItem_actionPerformed(e);
 853               }
 854             });
 855     PCAMenuItem.setText(MessageManager
 856             .getString("label.principal_component_analysis"));
 857     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 858     {
 859       @Override
 860       public void actionPerformed(ActionEvent e)
 861       {
 862         PCAMenuItem_actionPerformed(e);
 863       }
 864     });
 865     averageDistanceTreeMenuItem.setText(MessageManager
 866             .getString("label.average_distance_identity"));
 867     averageDistanceTreeMenuItem
 868             .addActionListener(new java.awt.event.ActionListener()
 869             {
 870               @Override
 871               public void actionPerformed(ActionEvent e)
 872               {
 873                 averageDistanceTreeMenuItem_actionPerformed(e);
 874               }
 875             });
 876     neighbourTreeMenuItem.setText(MessageManager
 877             .getString("label.neighbour_joining_identity"));
 878     neighbourTreeMenuItem
 879             .addActionListener(new java.awt.event.ActionListener()
 880             {
 881               @Override
 882               public void actionPerformed(ActionEvent e)
 883               {
 884                 neighbourTreeMenuItem_actionPerformed(e);
 885               }
 886             });
 887     this.getContentPane().setLayout(borderLayout1);
 888     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 889     statusBar.setBackground(Color.white);
 890     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 891     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 892     statusBar.setText(MessageManager.getString("label.status_bar"));
 893     outputTextboxMenu.setText(MessageManager
 894             .getString("label.out_to_textbox"));
 895     clustalColour.setText(MessageManager.getString("label.clustalx"));
 896
 897     clustalColour.addActionListener(new java.awt.event.ActionListener()
 898     {
 899       @Override
 900       public void actionPerformed(ActionEvent e)
 901       {
 902         clustalColour_actionPerformed(e);
 903       }
 904     });
 905     zappoColour.setText(MessageManager.getString("label.zappo"));
 906     zappoColour.addActionListener(new java.awt.event.ActionListener()
 907     {
 908       @Override
 909       public void actionPerformed(ActionEvent e)
 910       {
 911         zappoColour_actionPerformed(e);
 912       }
 913     });
 914     taylorColour.setText(MessageManager.getString("label.taylor"));
 915     taylorColour.addActionListener(new java.awt.event.ActionListener()
 916     {
 917       @Override
 918       public void actionPerformed(ActionEvent e)
 919       {
 920         taylorColour_actionPerformed(e);
 921       }
 922     });
 923     hydrophobicityColour.setText(MessageManager
 924             .getString("label.hydrophobicity"));
 925     hydrophobicityColour
 926             .addActionListener(new java.awt.event.ActionListener()
 927             {
 928               @Override
 929               public void actionPerformed(ActionEvent e)
 930               {
 931                 hydrophobicityColour_actionPerformed(e);
 932               }
 933             });
 934     helixColour.setText(MessageManager.getString("label.helix_propensity"));
 935     helixColour.addActionListener(new java.awt.event.ActionListener()
 936     {
 937       @Override
 938       public void actionPerformed(ActionEvent e)
 939       {
 940         helixColour_actionPerformed(e);
 941       }
 942     });
 943     strandColour.setText(MessageManager
 944             .getString("label.strand_propensity"));
 945     strandColour.addActionListener(new java.awt.event.ActionListener()
 946     {
 947       @Override
 948       public void actionPerformed(ActionEvent e)
 949       {
 950         strandColour_actionPerformed(e);
 951       }
 952     });
 953     turnColour.setText(MessageManager.getString("label.turn_propensity"));
 954     turnColour.addActionListener(new java.awt.event.ActionListener()
 955     {
 956       @Override
 957       public void actionPerformed(ActionEvent e)
 958       {
 959         turnColour_actionPerformed(e);
 960       }
 961     });
 962     buriedColour.setText(MessageManager.getString("label.buried_index"));
 963     buriedColour.addActionListener(new java.awt.event.ActionListener()
 964     {
 965       @Override
 966       public void actionPerformed(ActionEvent e)
 967       {
 968         buriedColour_actionPerformed(e);
 969       }
 970     });
 971     userDefinedColour.setText(MessageManager
 972             .getString("action.user_defined"));
 973     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 974     {
 975       @Override
 976       public void actionPerformed(ActionEvent e)
 977       {
 978         userDefinedColour_actionPerformed(e);
 979       }
 980     });
 981     PIDColour
 982             .setText(MessageManager.getString("label.percentage_identity"));
 983     PIDColour.addActionListener(new java.awt.event.ActionListener()
 984     {
 985       @Override
 986       public void actionPerformed(ActionEvent e)
 987       {
 988         PIDColour_actionPerformed(e);
 989       }
 990     });
 991     BLOSUM62Colour
 992             .setText(MessageManager.getString("label.blosum62_score"));
 993     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 994     {
 995       @Override
 996       public void actionPerformed(ActionEvent e)
 997       {
 998         BLOSUM62Colour_actionPerformed(e);
 999       }
1000     });
1001     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1002     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1003     {
1004       @Override
1005       public void actionPerformed(ActionEvent e)
1006       {
1007         nucleotideColour_actionPerformed(e);
1008       }
1009     });
1010
1011     purinePyrimidineColour.setText(MessageManager
1012             .getString("label.purine_pyrimidine"));
1013     purinePyrimidineColour
1014             .addActionListener(new java.awt.event.ActionListener()
1015             {
1016               @Override
1017               public void actionPerformed(ActionEvent e)
1018               {
1019                 purinePyrimidineColour_actionPerformed(e);
1020               }
1021             });
1022
1023     RNAInteractionColour.setText("RNA Interaction type");
1024     RNAInteractionColour
1025             .addActionListener(new java.awt.event.ActionListener()
1026             {
1027               @Override
1028               public void actionPerformed(ActionEvent e)
1029               {
1030                 RNAInteractionColour_actionPerformed(e);
1031               }
1032             });
1033     /*
1034      * covariationColour.setText("Covariation");
1035      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1036      * public void actionPerformed(ActionEvent e) {
1037      * covariationColour_actionPerformed(e); } });
1038      */
1039
1040     avDistanceTreeBlosumMenuItem.setText(MessageManager
1041             .getString("label.average_distance_bloslum62"));
1042     avDistanceTreeBlosumMenuItem
1043             .addActionListener(new java.awt.event.ActionListener()
1044             {
1045               @Override
1046               public void actionPerformed(ActionEvent e)
1047               {
1048                 avTreeBlosumMenuItem_actionPerformed(e);
1049               }
1050             });
1051     njTreeBlosumMenuItem.setText(MessageManager
1052             .getString("label.neighbour_blosum62"));
1053     njTreeBlosumMenuItem
1054             .addActionListener(new java.awt.event.ActionListener()
1055             {
1056               @Override
1057               public void actionPerformed(ActionEvent e)
1058               {
1059                 njTreeBlosumMenuItem_actionPerformed(e);
1060               }
1061             });
1062     annotationPanelMenuItem.setActionCommand("");
1063     annotationPanelMenuItem.setText(MessageManager
1064             .getString("label.show_annotations"));
1065     annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
1066             true));
1067     annotationPanelMenuItem.addActionListener(new ActionListener()
1068     {
1069       @Override
1070       public void actionPerformed(ActionEvent e)
1071       {
1072         annotationPanelMenuItem_actionPerformed(e);
1073       }
1074     });
1075     /*
1076      * Show/hide all annotations only enabled if annotation panel is shown
1077      */
1078     showAllAnnotations.setText(MessageManager
1079             .getString("label.show_all_annotations"));
1080     showAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
1081     showAllAnnotations.addActionListener(new ActionListener()
1082     {
1083       @Override
1084       public void actionPerformed(ActionEvent e)
1085       {
1086         showAllAnnotations_actionPerformed();
1087       }
1088     });
1089     hideAllAnnotations.setText(MessageManager
1090             .getString("label.hide_all_annotations"));
1091     hideAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
1092     hideAllAnnotations.addActionListener(new ActionListener()
1093     {
1094       @Override
1095       public void actionPerformed(ActionEvent e)
1096       {
1097         hideAllAnnotations_actionPerformed();
1098       }
1099     });
1100     colourTextMenuItem.setText(MessageManager
1101             .getString("label.colour_text"));
1102     colourTextMenuItem
1103             .addActionListener(new java.awt.event.ActionListener()
1104             {
1105               @Override
1106               public void actionPerformed(ActionEvent e)
1107               {
1108                 colourTextMenuItem_actionPerformed(e);
1109               }
1110             });
1111     htmlMenuItem.setText(MessageManager.getString("label.html"));
1112     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
1113     {
1114       @Override
1115       public void actionPerformed(ActionEvent e)
1116       {
1117         htmlMenuItem_actionPerformed(e);
1118       }
1119     });
1120     overviewMenuItem.setText(MessageManager
1121             .getString("label.overview_window"));
1122     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
1123     {
1124       @Override
1125       public void actionPerformed(ActionEvent e)
1126       {
1127         overviewMenuItem_actionPerformed(e);
1128       }
1129     });
1130     undoMenuItem.setEnabled(false);
1131     undoMenuItem.setText(MessageManager.getString("action.undo"));
1132     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1133             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1134                     .getMenuShortcutKeyMask(), false));
1135     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1136     {
1137       @Override
1138       public void actionPerformed(ActionEvent e)
1139       {
1140         undoMenuItem_actionPerformed(e);
1141       }
1142     });
1143     redoMenuItem.setEnabled(false);
1144     redoMenuItem.setText(MessageManager.getString("action.redo"));
1145     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1146             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1147                     .getMenuShortcutKeyMask(), false));
1148     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1149     {
1150       @Override
1151       public void actionPerformed(ActionEvent e)
1152       {
1153         redoMenuItem_actionPerformed(e);
1154       }
1155     });
1156     conservationMenuItem.setText(MessageManager
1157             .getString("action.by_conservation"));
1158     conservationMenuItem
1159             .addActionListener(new java.awt.event.ActionListener()
1160             {
1161               @Override
1162               public void actionPerformed(ActionEvent e)
1163               {
1164                 conservationMenuItem_actionPerformed(e);
1165               }
1166             });
1167     noColourmenuItem.setText(MessageManager.getString("label.none"));
1168     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1169     {
1170       @Override
1171       public void actionPerformed(ActionEvent e)
1172       {
1173         noColourmenuItem_actionPerformed(e);
1174       }
1175     });
1176     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1177     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1178     {
1179       @Override
1180       public void actionPerformed(ActionEvent e)
1181       {
1182         wrapMenuItem_actionPerformed(e);
1183       }
1184     });
1185     printMenuItem.setText(MessageManager.getString("action.print") + "...");
1186     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1187             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1188                     .getMenuShortcutKeyMask(), false));
1189     printMenuItem.addActionListener(new java.awt.event.ActionListener()
1190     {
1191       @Override
1192       public void actionPerformed(ActionEvent e)
1193       {
1194         printMenuItem_actionPerformed(e);
1195       }
1196     });
1197     renderGapsMenuItem
1198             .setText(MessageManager.getString("action.show_gaps"));
1199     renderGapsMenuItem.setState(true);
1200     renderGapsMenuItem
1201             .addActionListener(new java.awt.event.ActionListener()
1202             {
1203               @Override
1204               public void actionPerformed(ActionEvent e)
1205               {
1206                 renderGapsMenuItem_actionPerformed(e);
1207               }
1208             });
1209     findMenuItem.setText(MessageManager.getString("action.find"));
1210     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1211             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1212                     .getMenuShortcutKeyMask(), false));
1213     findMenuItem.setToolTipText(MessageManager.getString("label.find_tip"));
1214     findMenuItem.addActionListener(new java.awt.event.ActionListener()
1215     {
1216       @Override
1217       public void actionPerformed(ActionEvent e)
1218       {
1219         findMenuItem_actionPerformed(e);
1220       }
1221     });
1222     abovePIDThreshold.setText(MessageManager
1223             .getString("label.above_identity_threshold"));
1224     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1225     {
1226       @Override
1227       public void actionPerformed(ActionEvent e)
1228       {
1229         abovePIDThreshold_actionPerformed(e);
1230       }
1231     });
1232     showSeqFeatures.setText(MessageManager
1233             .getString("label.show_sequence_features"));
1234     showSeqFeatures.addActionListener(new ActionListener()
1235     {
1236       @Override
1237       public void actionPerformed(ActionEvent actionEvent)
1238       {
1239         showSeqFeatures_actionPerformed(actionEvent);
1240       }
1241     });
1242     /*
1243      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1244      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1245      * void actionPerformed(ActionEvent actionEvent) {
1246      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1247      */
1248     showDbRefsMenuitem.setText(MessageManager
1249             .getString("label.show_database_refs"));
1250     showDbRefsMenuitem.addActionListener(new ActionListener()
1251     {
1252
1253       @Override
1254       public void actionPerformed(ActionEvent e)
1255       {
1256         showDbRefs_actionPerformed(e);
1257       }
1258
1259     });
1260     showNpFeatsMenuitem.setText(MessageManager
1261             .getString("label.show_non_positional_features"));
1262     showNpFeatsMenuitem.addActionListener(new ActionListener()
1263     {
1264
1265       @Override
1266       public void actionPerformed(ActionEvent e)
1267       {
1268         showNpFeats_actionPerformed(e);
1269       }
1270
1271     });
1272     showGroupConservation.setText(MessageManager
1273             .getString("label.group_conservation"));
1274     showGroupConservation.addActionListener(new ActionListener()
1275     {
1276
1277       @Override
1278       public void actionPerformed(ActionEvent e)
1279       {
1280         showGroupConservation_actionPerformed(e);
1281       }
1282
1283     });
1284
1285     showGroupConsensus.setText(MessageManager
1286             .getString("label.group_consensus"));
1287     showGroupConsensus.addActionListener(new ActionListener()
1288     {
1289
1290       @Override
1291       public void actionPerformed(ActionEvent e)
1292       {
1293         showGroupConsensus_actionPerformed(e);
1294       }
1295
1296     });
1297     showConsensusHistogram.setText(MessageManager
1298             .getString("label.show_consensus_histogram"));
1299     showConsensusHistogram.addActionListener(new ActionListener()
1300     {
1301
1302       @Override
1303       public void actionPerformed(ActionEvent e)
1304       {
1305         showConsensusHistogram_actionPerformed(e);
1306       }
1307
1308     });
1309     showSequenceLogo.setText(MessageManager
1310             .getString("label.show_consensus_logo"));
1311     showSequenceLogo.addActionListener(new ActionListener()
1312     {
1313
1314       @Override
1315       public void actionPerformed(ActionEvent e)
1316       {
1317         showSequenceLogo_actionPerformed(e);
1318       }
1319
1320     });
1321     normaliseSequenceLogo.setText(MessageManager
1322             .getString("label.norm_consensus_logo"));
1323     normaliseSequenceLogo.addActionListener(new ActionListener()
1324     {
1325
1326       @Override
1327       public void actionPerformed(ActionEvent e)
1328       {
1329         normaliseSequenceLogo_actionPerformed(e);
1330       }
1331
1332     });
1333     applyAutoAnnotationSettings.setText(MessageManager
1334             .getString("label.apply_all_groups"));
1335     applyAutoAnnotationSettings.setState(false);
1336     applyAutoAnnotationSettings.setVisible(true);
1337     applyAutoAnnotationSettings.addActionListener(new ActionListener()
1338     {
1339
1340       @Override
1341       public void actionPerformed(ActionEvent e)
1342       {
1343         applyAutoAnnotationSettings_actionPerformed(e);
1344       }
1345
1346     });
1347
1348     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1349     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1350     {
1351       @Override
1352       public void actionPerformed(ActionEvent e)
1353       {
1354         nucleotideColour_actionPerformed(e);
1355       }
1356     });
1357
1358     tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1359     tcoffeeColour.setEnabled(false);
1360     tcoffeeColour.addActionListener(new ActionListener()
1361     {
1362
1363       @Override
1364       public void actionPerformed(ActionEvent e)
1365       {
1366         tcoffeeColorScheme_actionPerformed(e);
1367       }
1368     });
1369
1370     deleteGroups
1371             .setText(MessageManager.getString("action.undefine_groups"));
1372     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1373             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1374                     .getMenuShortcutKeyMask(), false));
1375     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1376     {
1377       @Override
1378       public void actionPerformed(ActionEvent e)
1379       {
1380         deleteGroups_actionPerformed(e);
1381       }
1382     });
1383     createGroup.setText(MessageManager.getString("action.create_groups"));
1384     createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1385             java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1386                     .getMenuShortcutKeyMask(), false));
1387     createGroup.addActionListener(new java.awt.event.ActionListener()
1388     {
1389       @Override
1390       public void actionPerformed(ActionEvent e)
1391       {
1392         createGroup_actionPerformed(e);
1393       }
1394     });
1395     unGroup.setText(MessageManager.getString("action.remove_group"));
1396     unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1397             java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1398                     .getMenuShortcutKeyMask()
1399                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1400     unGroup.addActionListener(new java.awt.event.ActionListener()
1401     {
1402       @Override
1403       public void actionPerformed(ActionEvent e)
1404       {
1405         unGroup_actionPerformed(e);
1406       }
1407     });
1408     copy.setText(MessageManager.getString("action.copy"));
1409     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1410             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1411                     .getMenuShortcutKeyMask(), false));
1412
1413     copy.addActionListener(new java.awt.event.ActionListener()
1414     {
1415       @Override
1416       public void actionPerformed(ActionEvent e)
1417       {
1418         copy_actionPerformed(e);
1419       }
1420     });
1421     cut.setText(MessageManager.getString("action.cut"));
1422     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1423             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1424                     .getMenuShortcutKeyMask(), false));
1425     cut.addActionListener(new java.awt.event.ActionListener()
1426     {
1427       @Override
1428       public void actionPerformed(ActionEvent e)
1429       {
1430         cut_actionPerformed(e);
1431       }
1432     });
1433     delete.setText(MessageManager.getString("action.delete"));
1434     delete.addActionListener(new java.awt.event.ActionListener()
1435     {
1436       @Override
1437       public void actionPerformed(ActionEvent e)
1438       {
1439         delete_actionPerformed(e);
1440       }
1441     });
1442     pasteMenu.setText(MessageManager.getString("action.paste"));
1443     pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1444     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1445             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1446                     .getMenuShortcutKeyMask()
1447                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1448     pasteNew.addActionListener(new java.awt.event.ActionListener()
1449     {
1450       @Override
1451       public void actionPerformed(ActionEvent e)
1452       {
1453         pasteNew_actionPerformed(e);
1454       }
1455     });
1456     pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1457     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1458             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1459                     .getMenuShortcutKeyMask(), false));
1460     pasteThis.addActionListener(new java.awt.event.ActionListener()
1461     {
1462       @Override
1463       public void actionPerformed(ActionEvent e)
1464       {
1465         pasteThis_actionPerformed(e);
1466       }
1467     });
1468     applyToAllGroups.setText(MessageManager
1469             .getString("label.apply_colour_to_all_groups"));
1470     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1471     {
1472       @Override
1473       public void actionPerformed(ActionEvent e)
1474       {
1475         applyToAllGroups_actionPerformed(e);
1476       }
1477     });
1478     createPNG.addActionListener(new java.awt.event.ActionListener()
1479     {
1480       @Override
1481       public void actionPerformed(ActionEvent e)
1482       {
1483         createPNG(null);
1484       }
1485     });
1486     createPNG.setActionCommand(MessageManager
1487             .getString("label.save_png_image"));
1488     createPNG.setText("PNG");
1489     font.setText(MessageManager.getString("action.font"));
1490     font.addActionListener(new java.awt.event.ActionListener()
1491     {
1492       @Override
1493       public void actionPerformed(ActionEvent e)
1494       {
1495         font_actionPerformed(e);
1496       }
1497     });
1498
1499     seqLimits.setText(MessageManager
1500             .getString("label.show_sequence_limits"));
1501     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1502     seqLimits.addActionListener(new java.awt.event.ActionListener()
1503     {
1504       @Override
1505       public void actionPerformed(ActionEvent e)
1506       {
1507         seqLimit_actionPerformed(e);
1508       }
1509     });
1510     epsFile.setText("EPS");
1511     epsFile.addActionListener(new java.awt.event.ActionListener()
1512     {
1513       @Override
1514       public void actionPerformed(ActionEvent e)
1515       {
1516         createEPS(null);
1517       }
1518     });
1519     LoadtreeMenuItem.setActionCommand(MessageManager
1520             .getString("label.load_tree_for_sequence_set"));
1521     LoadtreeMenuItem.setText(MessageManager
1522             .getString("label.load_associated_tree"));
1523     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1524     {
1525       @Override
1526       public void actionPerformed(ActionEvent e)
1527       {
1528         LoadtreeMenuItem_actionPerformed(e);
1529       }
1530     });
1531
1532     scaleAbove.setVisible(false);
1533     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1534     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1535     {
1536       @Override
1537       public void actionPerformed(ActionEvent e)
1538       {
1539         scaleAbove_actionPerformed(e);
1540       }
1541     });
1542     scaleLeft.setVisible(false);
1543     scaleLeft.setSelected(true);
1544     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1545     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1546     {
1547       @Override
1548       public void actionPerformed(ActionEvent e)
1549       {
1550         scaleLeft_actionPerformed(e);
1551       }
1552     });
1553     scaleRight.setVisible(false);
1554     scaleRight.setSelected(true);
1555     scaleRight.setText(MessageManager.getString("action.scale_right"));
1556     scaleRight.addActionListener(new java.awt.event.ActionListener()
1557     {
1558       @Override
1559       public void actionPerformed(ActionEvent e)
1560       {
1561         scaleRight_actionPerformed(e);
1562       }
1563     });
1564     centreColumnLabelsMenuItem.setVisible(true);
1565     centreColumnLabelsMenuItem.setState(false);
1566     centreColumnLabelsMenuItem.setText(MessageManager
1567             .getString("label.centre_column_labels"));
1568     centreColumnLabelsMenuItem
1569             .addActionListener(new java.awt.event.ActionListener()
1570             {
1571               @Override
1572               public void actionPerformed(ActionEvent e)
1573               {
1574                 centreColumnLabels_actionPerformed(e);
1575               }
1576             });
1577     followHighlightMenuItem.setVisible(true);
1578     followHighlightMenuItem.setState(true);
1579     followHighlightMenuItem.setText(MessageManager
1580             .getString("label.automatic_scrolling"));
1581     followHighlightMenuItem.addActionListener(new ActionListener()
1582     {
1583
1584       @Override
1585       public void actionPerformed(ActionEvent e)
1586       {
1587         followHighlight_actionPerformed();
1588       }
1589
1590     });
1591
1592     modifyPID.setText(MessageManager
1593             .getString("label.modify_identity_thereshold"));
1594     modifyPID.addActionListener(new java.awt.event.ActionListener()
1595     {
1596       @Override
1597       public void actionPerformed(ActionEvent e)
1598       {
1599         modifyPID_actionPerformed(e);
1600       }
1601     });
1602     modifyConservation.setText(MessageManager
1603             .getString("label.modify_conservation_thereshold"));
1604     modifyConservation
1605             .addActionListener(new java.awt.event.ActionListener()
1606             {
1607               @Override
1608               public void actionPerformed(ActionEvent e)
1609               {
1610                 modifyConservation_actionPerformed(e);
1611               }
1612             });
1613     sortByTreeMenu
1614             .setText(MessageManager.getString("action.by_tree_order"));
1615     sort.setText(MessageManager.getString("action.sort"));
1616     sort.addMenuListener(new MenuListener()
1617     {
1618       @Override
1619       public void menuSelected(MenuEvent e)
1620       {
1621         buildTreeMenu();
1622       }
1623
1624       @Override
1625       public void menuDeselected(MenuEvent e)
1626       {
1627       }
1628
1629       @Override
1630       public void menuCanceled(MenuEvent e)
1631       {
1632       }
1633     });
1634     sortByAnnotScore.setText(MessageManager
1635             .getString("label.sort_by_score"));
1636     sort.add(sortByAnnotScore);
1637     sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1638     {
1639
1640       @Override
1641       public void menuCanceled(MenuEvent e)
1642       {
1643       }
1644
1645       @Override
1646       public void menuDeselected(MenuEvent e)
1647       {
1648       }
1649
1650       @Override
1651       public void menuSelected(MenuEvent e)
1652       {
1653         buildSortByAnnotationScoresMenu();
1654       }
1655     });
1656     sortByAnnotScore.setVisible(false);
1657
1658     calculateTree
1659             .setText(MessageManager.getString("action.calculate_tree"));
1660
1661     jMenu2.setText(MessageManager.getString("label.export_image"));
1662     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1663     padGapsMenuitem.setState(jalview.bin.Cache
1664             .getDefault("PAD_GAPS", false));
1665     padGapsMenuitem.addActionListener(new ActionListener()
1666     {
1667       @Override
1668       public void actionPerformed(ActionEvent e)
1669       {
1670         padGapsMenuitem_actionPerformed(e);
1671       }
1672     });
1673     vamsasStore.setVisible(false);
1674     vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1675     vamsasStore.addActionListener(new ActionListener()
1676     {
1677       @Override
1678       public void actionPerformed(ActionEvent e)
1679       {
1680         vamsasStore_actionPerformed(e);
1681       }
1682     });
1683     showTranslation.setText(MessageManager
1684             .getString("label.translate_cDNA"));
1685     showTranslation.addActionListener(new ActionListener()
1686     {
1687       @Override
1688       public void actionPerformed(ActionEvent e)
1689       {
1690         showTranslation_actionPerformed(e);
1691       }
1692     });
1693     extractScores.setText(MessageManager.getString("label.extract_scores")
1694             + "...");
1695     extractScores.addActionListener(new ActionListener()
1696     {
1697       @Override
1698       public void actionPerformed(ActionEvent e)
1699       {
1700         extractScores_actionPerformed(e);
1701       }
1702     });
1703     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1704     // score extraction
1705     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1706     /*
1707      * showProducts.addActionListener(new ActionListener() {
1708      *
1709      * public void actionPerformed(ActionEvent e) {
1710      * showProducts_actionPerformed(e); } });
1711      */
1712     openFeatureSettings.setText(MessageManager
1713             .getString("label.feature_settings"));
1714     openFeatureSettings.addActionListener(new ActionListener()
1715     {
1716       @Override
1717       public void actionPerformed(ActionEvent e)
1718       {
1719         featureSettings_actionPerformed(e);
1720       }
1721     });
1722     fetchSequence
1723             .setText(MessageManager.getString("label.fetch_sequences"));
1724     fetchSequence.addActionListener(new ActionListener()
1725     {
1726       @Override
1727       public void actionPerformed(ActionEvent e)
1728       {
1729         fetchSequence_actionPerformed(e);
1730       }
1731     });
1732
1733     annotationColour.setText(MessageManager
1734             .getString("action.by_annotation"));
1735     annotationColour.addActionListener(new ActionListener()
1736     {
1737       @Override
1738       public void actionPerformed(ActionEvent e)
1739       {
1740         annotationColour_actionPerformed(e);
1741       }
1742     });
1743
1744     rnahelicesColour.setText(MessageManager
1745             .getString("action.by_rna_helixes"));
1746     rnahelicesColour.addActionListener(new ActionListener()
1747     {
1748       @Override
1749       public void actionPerformed(ActionEvent e)
1750       {
1751         rnahelicesColour_actionPerformed(e);
1752       }
1753     });
1754
1755     associatedData.setText(MessageManager
1756             .getString("label.load_features_annotations"));
1757     associatedData.addActionListener(new ActionListener()
1758     {
1759       @Override
1760       public void actionPerformed(ActionEvent e)
1761       {
1762         associatedData_actionPerformed(e);
1763       }
1764     });
1765     autoCalculate.setText(MessageManager
1766             .getString("label.autocalculate_consensus"));
1767     autoCalculate.setState(jalview.bin.Cache.getDefault(
1768             "AUTO_CALC_CONSENSUS", true));
1769     autoCalculate.addActionListener(new ActionListener()
1770     {
1771       @Override
1772       public void actionPerformed(ActionEvent e)
1773       {
1774         autoCalculate_actionPerformed(e);
1775       }
1776     });
1777     sortByTree.setText(MessageManager
1778             .getString("label.sort_alignment_new_tree"));
1779     sortByTree
1780             .setToolTipText("<html>"
1781                     + MessageManager
1782                             .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1783     sortByTree
1784             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1785     sortByTree.addActionListener(new ActionListener()
1786     {
1787       @Override
1788       public void actionPerformed(ActionEvent e)
1789       {
1790         sortByTreeOption_actionPerformed(e);
1791       }
1792     });
1793
1794     listenToViewSelections.setText(MessageManager
1795             .getString("label.listen_for_selections"));
1796     listenToViewSelections
1797             .setToolTipText("<html>"
1798                     + MessageManager
1799                             .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1800     listenToViewSelections.setState(false);
1801     listenToViewSelections.addActionListener(new ActionListener()
1802     {
1803       @Override
1804       public void actionPerformed(ActionEvent e)
1805       {
1806         listenToViewSelections_actionPerformed(e);
1807       }
1808     });
1809
1810     addSequenceMenu
1811             .setText(MessageManager.getString("label.add_sequences"));
1812     addFromFile.setText(MessageManager.getString("label.from_file"));
1813     addFromFile.addActionListener(new ActionListener()
1814     {
1815       @Override
1816       public void actionPerformed(ActionEvent e)
1817       {
1818         addFromFile_actionPerformed(e);
1819       }
1820     });
1821     addFromText.setText(MessageManager.getString("label.from_textbox"));
1822     addFromText.addActionListener(new ActionListener()
1823     {
1824       @Override
1825       public void actionPerformed(ActionEvent e)
1826       {
1827         addFromText_actionPerformed(e);
1828       }
1829     });
1830     addFromURL.setText(MessageManager.getString("label.from_url"));
1831     addFromURL.addActionListener(new ActionListener()
1832     {
1833       @Override
1834       public void actionPerformed(ActionEvent e)
1835       {
1836         addFromURL_actionPerformed(e);
1837       }
1838     });
1839     exportFeatures.setText(MessageManager
1840             .getString("label.export_features"));
1841     exportFeatures.addActionListener(new ActionListener()
1842     {
1843       @Override
1844       public void actionPerformed(ActionEvent e)
1845       {
1846         exportFeatures_actionPerformed(e);
1847       }
1848     });
1849     exportAnnotations.setText(MessageManager
1850             .getString("label.export_annotations"));
1851     exportAnnotations.addActionListener(new ActionListener()
1852     {
1853       @Override
1854       public void actionPerformed(ActionEvent e)
1855       {
1856         exportAnnotations_actionPerformed(e);
1857       }
1858     });
1859     statusPanel.setLayout(gridLayout1);
1860     jMenu3.setText(MessageManager.getString("action.show"));
1861     showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
1862     showAllSeqs.setToolTipText(MessageManager
1863             .getString("label.toggle_sequence_visibility"));
1864     showAllSeqs.addActionListener(new ActionListener()
1865     {
1866       @Override
1867       public void actionPerformed(ActionEvent e)
1868       {
1869         showAllSeqs_actionPerformed(e);
1870       }
1871     });
1872     showAllColumns.setText(MessageManager.getString("label.all_columns"));
1873     showAllColumns.setToolTipText(MessageManager
1874             .getString("label.toggle_columns_visibility"));
1875     showAllColumns.addActionListener(new ActionListener()
1876     {
1877       @Override
1878       public void actionPerformed(ActionEvent e)
1879       {
1880         showAllColumns_actionPerformed(e);
1881       }
1882     });
1883     hideMenu.setText(MessageManager.getString("action.hide"));
1884     hideSelSequences.setText(MessageManager
1885             .getString("label.selected_sequences"));
1886     hideSelSequences.setToolTipText(MessageManager
1887             .getString("label.toggle_sequence_visibility"));
1888     hideSelSequences.addActionListener(new ActionListener()
1889     {
1890       @Override
1891       public void actionPerformed(ActionEvent e)
1892       {
1893         hideSelSequences_actionPerformed(e);
1894       }
1895     });
1896     hideSelColumns.setText(MessageManager
1897             .getString("label.selected_columns"));
1898     hideSelColumns.setToolTipText(MessageManager
1899             .getString("label.toggle_columns_visibility"));
1900     hideSelColumns.addActionListener(new ActionListener()
1901     {
1902       @Override
1903       public void actionPerformed(ActionEvent e)
1904       {
1905         hideSelColumns_actionPerformed(e);
1906       }
1907     });
1908     hideAllSelection.setText(MessageManager
1909             .getString("label.selected_region"));
1910     hideAllSelection.addActionListener(new ActionListener()
1911     {
1912       @Override
1913       public void actionPerformed(ActionEvent e)
1914       {
1915         hideAllSelection_actionPerformed(e);
1916       }
1917     });
1918     // TODO: should be hidden if no selection exists.
1919     hideAllButSelection.setText(MessageManager
1920             .getString("label.all_but_selected_region"));
1921     hideAllButSelection.addActionListener(new ActionListener()
1922     {
1923       @Override
1924       public void actionPerformed(ActionEvent e)
1925       {
1926         hideAllButSelection_actionPerformed(e);
1927       }
1928     });
1929     showAllhidden.setText(MessageManager
1930             .getString("label.all_sequences_columns"));
1931     showAllhidden.setToolTipText(MessageManager
1932             .getString("label.toggles_visibility_hidden_selected_regions"));
1933     showAllhidden.addActionListener(new ActionListener()
1934     {
1935       @Override
1936       public void actionPerformed(ActionEvent e)
1937       {
1938         showAllhidden_actionPerformed(e);
1939       }
1940     });
1941     hiddenMarkers.setText(MessageManager
1942             .getString("action.show_hidden_markers"));
1943     hiddenMarkers.addActionListener(new ActionListener()
1944     {
1945       @Override
1946       public void actionPerformed(ActionEvent e)
1947       {
1948         hiddenMarkers_actionPerformed(e);
1949       }
1950     });
1951     invertColSel.setText(MessageManager
1952             .getString("action.invert_column_selection"));
1953     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1954             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1955                     .getMenuShortcutKeyMask()
1956                     | java.awt.event.KeyEvent.ALT_MASK, false));
1957     invertColSel.addActionListener(new ActionListener()
1958     {
1959       @Override
1960       public void actionPerformed(ActionEvent e)
1961       {
1962         invertColSel_actionPerformed(e);
1963       }
1964     });
1965     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1966     {
1967       @Override
1968       public void stateChanged(ChangeEvent evt)
1969       {
1970         JTabbedPane pane = (JTabbedPane) evt.getSource();
1971         int sel = pane.getSelectedIndex();
1972         tabSelectionChanged(sel);
1973       }
1974     });
1975     tabbedPane.addMouseListener(new MouseAdapter()
1976     {
1977       @Override
1978       public void mousePressed(MouseEvent e)
1979       {
1980         tabbedPane_mousePressed(e);
1981       }
1982     });
1983     tabbedPane.addFocusListener(new FocusAdapter()
1984     {
1985       @Override
1986       public void focusGained(FocusEvent e)
1987       {
1988         tabbedPane_focusGained(e);
1989       }
1990     });
1991     save.setText(MessageManager.getString("action.save"));
1992     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1993             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1994                     .getMenuShortcutKeyMask(), false));
1995     save.addActionListener(new ActionListener()
1996     {
1997       @Override
1998       public void actionPerformed(ActionEvent e)
1999       {
2000         save_actionPerformed(e);
2001       }
2002     });
2003     reload.setEnabled(false);
2004     reload.setText(MessageManager.getString("action.reload"));
2005     reload.addActionListener(new ActionListener()
2006     {
2007       @Override
2008       public void actionPerformed(ActionEvent e)
2009       {
2010         reload_actionPerformed(e);
2011       }
2012     });
2013     newView.setText(MessageManager.getString("action.new_view"));
2014     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2015             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
2016                     .getMenuShortcutKeyMask(), false));
2017     newView.addActionListener(new ActionListener()
2018     {
2019       @Override
2020       public void actionPerformed(ActionEvent e)
2021       {
2022         newView_actionPerformed(e);
2023       }
2024     });
2025     tabbedPane.setToolTipText("<html><i>"
2026             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2027             + "</i></html>");
2028     textColour.setText(MessageManager.getString("label.colour_text")
2029             + "...");
2030     textColour.addActionListener(new ActionListener()
2031     {
2032       @Override
2033       public void actionPerformed(ActionEvent e)
2034       {
2035         textColour_actionPerformed(e);
2036       }
2037     });
2038     formatMenu.setText(MessageManager.getString("action.format"));
2039     selectMenu.setText(MessageManager.getString("action.select"));
2040     idRightAlign.setText(MessageManager
2041             .getString("label.right_align_sequence_id"));
2042     idRightAlign.addActionListener(new ActionListener()
2043     {
2044       @Override
2045       public void actionPerformed(ActionEvent e)
2046       {
2047         idRightAlign_actionPerformed(e);
2048       }
2049     });
2050     gatherViews.setEnabled(false);
2051     gatherViews.setText(MessageManager.getString("action.gather_views"));
2052     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2053             java.awt.event.KeyEvent.VK_G, 0, false));
2054     gatherViews.addActionListener(new ActionListener()
2055     {
2056       @Override
2057       public void actionPerformed(ActionEvent e)
2058       {
2059         gatherViews_actionPerformed(e);
2060       }
2061     });
2062     expandViews.setEnabled(false);
2063     expandViews.setText(MessageManager.getString("action.expand_views"));
2064     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2065             java.awt.event.KeyEvent.VK_X, 0, false));
2066     expandViews.addActionListener(new ActionListener()
2067     {
2068       @Override
2069       public void actionPerformed(ActionEvent e)
2070       {
2071         expandViews_actionPerformed(e);
2072       }
2073     });
2074     pageSetup
2075             .setText(MessageManager.getString("action.page_setup") + "...");
2076     pageSetup.addActionListener(new ActionListener()
2077     {
2078       @Override
2079       public void actionPerformed(ActionEvent e)
2080       {
2081         pageSetup_actionPerformed(e);
2082       }
2083     });
2084     alignmentProperties.setText(MessageManager
2085             .getString("label.alignment_props") + "...");
2086     alignmentProperties.addActionListener(new ActionListener()
2087     {
2088       @Override
2089       public void actionPerformed(ActionEvent actionEvent)
2090       {
2091         alignmentProperties();
2092       }
2093     });
2094     tooltipSettingsMenu.setText(MessageManager
2095             .getString("label.sequence_id_tooltip"));
2096     autoAnnMenu.setText(MessageManager
2097             .getString("label.autocalculated_annotation"));
2098     alignFrameMenuBar.add(fileMenu);
2099     alignFrameMenuBar.add(editMenu);
2100     alignFrameMenuBar.add(selectMenu);
2101     alignFrameMenuBar.add(viewMenu);
2102     alignFrameMenuBar.add(formatMenu);
2103     alignFrameMenuBar.add(colourMenu);
2104     alignFrameMenuBar.add(calculateMenu);
2105     alignFrameMenuBar.add(webService);
2106     fileMenu.add(fetchSequence);
2107     fileMenu.add(addSequenceMenu);
2108     fileMenu.add(reload);
2109     fileMenu.addSeparator();
2110     fileMenu.add(vamsasStore);
2111     fileMenu.add(save);
2112     fileMenu.add(saveAs);
2113     fileMenu.add(outputTextboxMenu);
2114     fileMenu.add(pageSetup);
2115     fileMenu.add(printMenuItem);
2116     fileMenu.addSeparator();
2117     fileMenu.add(jMenu2);
2118     fileMenu.add(exportFeatures);
2119     fileMenu.add(exportAnnotations);
2120     fileMenu.add(LoadtreeMenuItem);
2121     fileMenu.add(associatedData);
2122     fileMenu.addSeparator();
2123     fileMenu.add(closeMenuItem);
2124     editMenu.add(undoMenuItem);
2125     editMenu.add(redoMenuItem);
2126     editMenu.add(cut);
2127     editMenu.add(copy);
2128     editMenu.add(pasteMenu);
2129     editMenu.add(delete);
2130     editMenu.addSeparator();
2131     editMenu.add(remove2LeftMenuItem);
2132     editMenu.add(remove2RightMenuItem);
2133     editMenu.add(removeGappedColumnMenuItem);
2134     editMenu.add(removeAllGapsMenuItem);
2135     editMenu.add(removeRedundancyMenuItem);
2136     editMenu.addSeparator();
2137     // dont add these yet in the CVS build - they cannot be undone!
2138     // Excluded from Jalview 2.5 release - undo needs to be implemented.
2139     // editMenu.add(justifyLeftMenuItem);
2140     // editMenu.add(justifyRightMenuItem);
2141     // editMenu.addSeparator();
2142     editMenu.add(padGapsMenuitem);
2143     viewMenu.add(newView);
2144     viewMenu.add(expandViews);
2145     viewMenu.add(gatherViews);
2146     viewMenu.addSeparator();
2147     viewMenu.add(jMenu3);
2148     viewMenu.add(hideMenu);
2149     viewMenu.addSeparator();
2150     viewMenu.add(followHighlightMenuItem);
2151     viewMenu.add(annotationPanelMenuItem);
2152     viewMenu.add(showAllAnnotations);
2153     viewMenu.add(hideAllAnnotations);
2154     autoAnnMenu.add(applyAutoAnnotationSettings);
2155     autoAnnMenu.add(showConsensusHistogram);
2156     autoAnnMenu.add(showSequenceLogo);
2157     autoAnnMenu.add(normaliseSequenceLogo);
2158     autoAnnMenu.addSeparator();
2159     autoAnnMenu.add(showGroupConservation);
2160     autoAnnMenu.add(showGroupConsensus);
2161     viewMenu.add(autoAnnMenu);
2162     viewMenu.addSeparator();
2163     viewMenu.add(showSeqFeatures);
2164     // viewMenu.add(showSeqFeaturesHeight);
2165
2166     viewMenu.add(openFeatureSettings);
2167     tooltipSettingsMenu.add(showDbRefsMenuitem);
2168     tooltipSettingsMenu.add(showNpFeatsMenuitem);
2169     viewMenu.add(tooltipSettingsMenu);
2170     viewMenu.addSeparator();
2171     viewMenu.add(alignmentProperties);
2172     viewMenu.addSeparator();
2173     viewMenu.add(overviewMenuItem);
2174     colourMenu.add(applyToAllGroups);
2175     colourMenu.add(textColour);
2176     colourMenu.addSeparator();
2177     colourMenu.add(noColourmenuItem);
2178     colourMenu.add(clustalColour);
2179     colourMenu.add(BLOSUM62Colour);
2180     colourMenu.add(PIDColour);
2181     colourMenu.add(zappoColour);
2182     colourMenu.add(taylorColour);
2183     colourMenu.add(hydrophobicityColour);
2184     colourMenu.add(helixColour);
2185     colourMenu.add(strandColour);
2186     colourMenu.add(turnColour);
2187     colourMenu.add(buriedColour);
2188     colourMenu.add(nucleotideColour);
2189     colourMenu.add(purinePyrimidineColour);
2190     colourMenu.add(RNAInteractionColour);
2191     // colourMenu.add(covariationColour);
2192     colourMenu.add(tcoffeeColour);
2193     colourMenu.add(userDefinedColour);
2194     colourMenu.addSeparator();
2195     colourMenu.add(conservationMenuItem);
2196     colourMenu.add(modifyConservation);
2197     colourMenu.add(abovePIDThreshold);
2198     colourMenu.add(modifyPID);
2199     colourMenu.add(annotationColour);
2200     colourMenu.add(rnahelicesColour);
2201     calculateMenu.add(sort);
2202     calculateMenu.add(calculateTree);
2203     calculateMenu.addSeparator();
2204     calculateMenu.add(pairwiseAlignmentMenuItem);
2205     calculateMenu.add(PCAMenuItem);
2206     calculateMenu.addSeparator();
2207     calculateMenu.add(showTranslation);
2208     calculateMenu.add(showProducts);
2209     calculateMenu.add(autoCalculate);
2210     calculateMenu.add(sortByTree);
2211     calculateMenu.addSeparator();
2212     calculateMenu.add(extractScores);
2213     webServiceNoServices = new JMenuItem(
2214             MessageManager.getString("label.no_services"));
2215     webService.add(webServiceNoServices);
2216     pasteMenu.add(pasteNew);
2217     pasteMenu.add(pasteThis);
2218     sort.add(sortIDMenuItem);
2219     sort.add(sortLengthMenuItem);
2220     sort.add(sortGroupMenuItem);
2221     sort.add(sortPairwiseMenuItem);
2222     sort.add(sortByTreeMenu);
2223     jMenu2.add(htmlMenuItem);
2224     jMenu2.add(epsFile);
2225     jMenu2.add(createPNG);
2226     addSequenceMenu.add(addFromFile);
2227     addSequenceMenu.add(addFromText);
2228     addSequenceMenu.add(addFromURL);
2229     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2230     statusPanel.add(statusBar, null);
2231     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2232     jMenu3.add(showAllColumns);
2233     jMenu3.add(showAllSeqs);
2234     jMenu3.add(showAllhidden);
2235     hideMenu.add(hideSelColumns);
2236     hideMenu.add(hideSelSequences);
2237     hideMenu.add(hideAllSelection);
2238     hideMenu.add(hideAllButSelection);
2239
2240     formatMenu.add(font);
2241     formatMenu.addSeparator();
2242     formatMenu.add(wrapMenuItem);
2243     formatMenu.add(scaleAbove);
2244     formatMenu.add(scaleLeft);
2245     formatMenu.add(scaleRight);
2246     formatMenu.add(seqLimits);
2247     formatMenu.add(idRightAlign);
2248     formatMenu.add(hiddenMarkers);
2249     formatMenu.add(viewBoxesMenuItem);
2250     formatMenu.add(viewTextMenuItem);
2251     formatMenu.add(colourTextMenuItem);
2252     formatMenu.add(renderGapsMenuItem);
2253     formatMenu.add(centreColumnLabelsMenuItem);
2254     formatMenu.add(showNonconservedMenuItem);
2255     selectMenu.add(findMenuItem);
2256     selectMenu.addSeparator();
2257     selectMenu.add(selectAllSequenceMenuItem);
2258     selectMenu.add(deselectAllSequenceMenuItem);
2259     selectMenu.add(invertSequenceMenuItem);
2260     selectMenu.add(invertColSel);
2261     selectMenu.add(createGroup);
2262     selectMenu.add(unGroup);
2263     selectMenu.add(grpsFromSelection);
2264     selectMenu.add(deleteGroups);
2265     calculateMenu.add(expandAlignment);
2266     // TODO - determine if the listenToViewSelections button is needed : see bug
2267     // JAL-574
2268     // selectMenu.addSeparator();
2269     // selectMenu.add(listenToViewSelections);
2270   }
2271
2272   /**
2273    * Action on clicking Show all annotations.
2274    */
2275   protected void showAllAnnotations_actionPerformed()
2276   {
2277     setAllAnnotationsVisibility(true);
2278   }
2279
2280   /**
2281    * Action on clicking Hide all annotations.
2282    */
2283   protected void hideAllAnnotations_actionPerformed()
2284   {
2285     setAllAnnotationsVisibility(false);
2286   }
2287
2288   /**
2289    * Set the visibility of all annotations to true or false.
2290    *
2291    * @param visible
2292    */
2293   protected void setAllAnnotationsVisibility(boolean visible)
2294   {
2295
2296   }
2297
2298   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2299   {
2300     // TODO Auto-generated method stub
2301
2302   }
2303
2304   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2305   {
2306     // TODO Auto-generated method stub
2307
2308   }
2309
2310   protected void showAllhidden_actionPerformed(ActionEvent e)
2311   {
2312     // TODO Auto-generated method stub
2313
2314   }
2315
2316   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2317   {
2318     // TODO Auto-generated method stub
2319
2320   }
2321
2322   protected void hideAllSelection_actionPerformed(ActionEvent e)
2323   {
2324     // TODO Auto-generated method stub
2325
2326   }
2327
2328   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2329   {
2330     // TODO Auto-generated method stub
2331
2332   }
2333
2334   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2335   {
2336     // TODO Auto-generated method stub
2337
2338   }
2339
2340   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2341   {
2342     // TODO Auto-generated method stub
2343
2344   }
2345
2346   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2347   {
2348     // TODO Auto-generated method stub
2349
2350   }
2351
2352   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2353   {
2354     // TODO Auto-generated method stub
2355
2356   }
2357
2358   protected void showGroupConservation_actionPerformed(ActionEvent e)
2359   {
2360     // TODO Auto-generated method stub
2361
2362   }
2363
2364   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2365   {
2366     // TODO Auto-generated method stub
2367
2368   }
2369
2370   protected void showSeqFeaturesHeight_actionPerformed(
2371           ActionEvent actionEvent)
2372   {
2373     // TODO Auto-generated method stub
2374
2375   }
2376
2377   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2378   {
2379     // TODO Auto-generated method stub
2380
2381   }
2382
2383   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2384   {
2385     // TODO Auto-generated method stub
2386
2387   }
2388
2389   protected void followHighlight_actionPerformed()
2390   {
2391     // TODO Auto-generated method stub
2392
2393   }
2394
2395   protected void showNpFeats_actionPerformed(ActionEvent e)
2396   {
2397     // TODO Auto-generated method stub
2398
2399   }
2400
2401   protected void showDbRefs_actionPerformed(ActionEvent e)
2402   {
2403     // TODO Auto-generated method stub
2404
2405   }
2406
2407   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2408   {
2409   }
2410
2411   protected void showProducts_actionPerformed(ActionEvent e)
2412   {
2413   }
2414
2415   protected void buildSortByAnnotationScoresMenu()
2416   {
2417   }
2418
2419   protected void extractScores_actionPerformed(ActionEvent e)
2420   {
2421   }
2422
2423   protected void outputText_actionPerformed(ActionEvent e)
2424   {
2425   }
2426
2427   public void addFromFile_actionPerformed(ActionEvent e)
2428   {
2429
2430   }
2431
2432   public void addFromText_actionPerformed(ActionEvent e)
2433   {
2434
2435   }
2436
2437   public void addFromURL_actionPerformed(ActionEvent e)
2438   {
2439
2440   }
2441
2442   public void exportFeatures_actionPerformed(ActionEvent e)
2443   {
2444
2445   }
2446
2447   public void exportAnnotations_actionPerformed(ActionEvent e)
2448   {
2449
2450   }
2451
2452   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2453   {
2454   }
2455
2456   protected void closeMenuItem_actionPerformed(boolean b)
2457   {
2458   }
2459
2460   protected void redoMenuItem_actionPerformed(ActionEvent e)
2461   {
2462   }
2463
2464   protected void undoMenuItem_actionPerformed(ActionEvent e)
2465   {
2466   }
2467
2468   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2469   {
2470   }
2471
2472   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2473   {
2474   }
2475
2476   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2477   {
2478   }
2479
2480   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2481   {
2482   }
2483
2484   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2485   {
2486   }
2487
2488   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2489   {
2490   }
2491
2492   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2493   {
2494   }
2495
2496   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2497   {
2498   }
2499
2500   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2501   {
2502   }
2503
2504   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2505   {
2506   }
2507
2508   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2509   {
2510   }
2511
2512   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2513   {
2514   }
2515
2516   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2517   {
2518   }
2519
2520   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2521   {
2522   }
2523
2524   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2525   {
2526   }
2527
2528   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2529   {
2530   }
2531
2532   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2533   {
2534   }
2535
2536   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2537   {
2538   }
2539
2540   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2541   {
2542   }
2543
2544   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2545   {
2546   }
2547
2548   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2549   {
2550   }
2551
2552   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2553   {
2554   }
2555
2556   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2557   {
2558   }
2559
2560   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2561   {
2562   }
2563
2564   protected void clustalColour_actionPerformed(ActionEvent e)
2565   {
2566   }
2567
2568   protected void zappoColour_actionPerformed(ActionEvent e)
2569   {
2570   }
2571
2572   protected void taylorColour_actionPerformed(ActionEvent e)
2573   {
2574   }
2575
2576   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2577   {
2578   }
2579
2580   protected void helixColour_actionPerformed(ActionEvent e)
2581   {
2582   }
2583
2584   protected void strandColour_actionPerformed(ActionEvent e)
2585   {
2586   }
2587
2588   protected void turnColour_actionPerformed(ActionEvent e)
2589   {
2590   }
2591
2592   protected void buriedColour_actionPerformed(ActionEvent e)
2593   {
2594   }
2595
2596   protected void userDefinedColour_actionPerformed(ActionEvent e)
2597   {
2598   }
2599
2600   protected void PIDColour_actionPerformed(ActionEvent e)
2601   {
2602   }
2603
2604   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2605   {
2606   }
2607
2608   protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2609   {
2610   }
2611
2612   protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2613   {
2614   }
2615
2616   /*
2617    * protected void covariationColour_actionPerformed(ActionEvent e) { }
2618    */
2619
2620   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2621   {
2622   }
2623
2624   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2625   {
2626   }
2627
2628   protected void printMenuItem_actionPerformed(ActionEvent e)
2629   {
2630   }
2631
2632   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2633   {
2634   }
2635
2636   protected void findMenuItem_actionPerformed(ActionEvent e)
2637   {
2638   }
2639
2640   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2641   {
2642   }
2643
2644   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2645   {
2646   }
2647
2648   protected void nucleotideColour_actionPerformed(ActionEvent e)
2649   {
2650   }
2651
2652   protected void deleteGroups_actionPerformed(ActionEvent e)
2653   {
2654   }
2655
2656   protected void createGroup_actionPerformed(ActionEvent e)
2657   {
2658   }
2659
2660   protected void unGroup_actionPerformed(ActionEvent e)
2661   {
2662   }
2663
2664   protected void copy_actionPerformed(ActionEvent e)
2665   {
2666   }
2667
2668   protected void cut_actionPerformed(ActionEvent e)
2669   {
2670   }
2671
2672   protected void delete_actionPerformed(ActionEvent e)
2673   {
2674   }
2675
2676   protected void pasteNew_actionPerformed(ActionEvent e)
2677   {
2678   }
2679
2680   protected void pasteThis_actionPerformed(ActionEvent e)
2681   {
2682   }
2683
2684   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2685   {
2686   }
2687
2688   public void createPNG(java.io.File f)
2689   {
2690   }
2691
2692   protected void font_actionPerformed(ActionEvent e)
2693   {
2694   }
2695
2696   protected void seqLimit_actionPerformed(ActionEvent e)
2697   {
2698   }
2699
2700   public void seqDBRef_actionPerformed(ActionEvent e)
2701   {
2702
2703   }
2704
2705   public void createEPS(java.io.File f)
2706   {
2707   }
2708
2709   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2710   {
2711
2712   }
2713
2714   /**
2715    * Template method to handle the 'load T-Coffee scores' menu event.
2716    * <p>
2717    * Subclasses override this method to provide a custom action.
2718    *
2719    * @param event
2720    *          The raised event
2721    */
2722   protected void loadScores_actionPerformed(ActionEvent event)
2723   {
2724
2725   }
2726
2727   /**
2728    * Template method to handle the 'Color T-Coffee scores' menu event.
2729    * <p>
2730    * Subclasses override this method to provide a custom action.
2731    *
2732    * @param event
2733    *          The raised event
2734    */
2735   protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2736   {
2737
2738   }
2739
2740   protected void jpred_actionPerformed(ActionEvent e)
2741   {
2742   }
2743
2744   protected void scaleAbove_actionPerformed(ActionEvent e)
2745   {
2746   }
2747
2748   protected void scaleLeft_actionPerformed(ActionEvent e)
2749   {
2750   }
2751
2752   protected void scaleRight_actionPerformed(ActionEvent e)
2753   {
2754   }
2755
2756   protected void modifyPID_actionPerformed(ActionEvent e)
2757   {
2758   }
2759
2760   protected void modifyConservation_actionPerformed(ActionEvent e)
2761   {
2762   }
2763
2764   protected void saveAs_actionPerformed(ActionEvent e)
2765   {
2766   }
2767
2768   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2769   {
2770   }
2771
2772   public void vamsasStore_actionPerformed(ActionEvent e)
2773   {
2774
2775   }
2776
2777   public void vamsasLoad_actionPerformed(ActionEvent e)
2778   {
2779
2780   }
2781
2782   public void showTranslation_actionPerformed(ActionEvent e)
2783   {
2784
2785   }
2786
2787   public void featureSettings_actionPerformed(ActionEvent e)
2788   {
2789
2790   }
2791
2792   public void fetchSequence_actionPerformed(ActionEvent e)
2793   {
2794
2795   }
2796
2797   public void smoothFont_actionPerformed(ActionEvent e)
2798   {
2799
2800   }
2801
2802   public void annotationColour_actionPerformed(ActionEvent e)
2803   {
2804
2805   }
2806
2807   public void rnahelicesColour_actionPerformed(ActionEvent e)
2808   {
2809
2810   }
2811
2812   public void associatedData_actionPerformed(ActionEvent e)
2813   {
2814
2815   }
2816
2817   public void autoCalculate_actionPerformed(ActionEvent e)
2818   {
2819
2820   }
2821
2822   public void sortByTreeOption_actionPerformed(ActionEvent e)
2823   {
2824
2825   }
2826
2827   public void showAllSeqs_actionPerformed(ActionEvent e)
2828   {
2829
2830   }
2831
2832   public void showAllColumns_actionPerformed(ActionEvent e)
2833   {
2834
2835   }
2836
2837   public void hideSelSequences_actionPerformed(ActionEvent e)
2838   {
2839
2840   }
2841
2842   public void hideSelColumns_actionPerformed(ActionEvent e)
2843   {
2844
2845   }
2846
2847   public void hiddenMarkers_actionPerformed(ActionEvent e)
2848   {
2849
2850   }
2851
2852   public void findPdbId_actionPerformed(ActionEvent e)
2853   {
2854
2855   }
2856
2857   public void enterPdbId_actionPerformed(ActionEvent e)
2858   {
2859
2860   }
2861
2862   public void pdbFile_actionPerformed(ActionEvent e)
2863   {
2864
2865   }
2866
2867   public void invertColSel_actionPerformed(ActionEvent e)
2868   {
2869
2870   }
2871
2872   public void tabSelectionChanged(int sel)
2873   {
2874
2875   }
2876
2877   public void tabbedPane_mousePressed(MouseEvent e)
2878   {
2879
2880   }
2881
2882   public void tabbedPane_focusGained(FocusEvent e)
2883   {
2884     requestFocus();
2885   }
2886
2887   public void save_actionPerformed(ActionEvent e)
2888   {
2889
2890   }
2891
2892   public void reload_actionPerformed(ActionEvent e)
2893   {
2894
2895   }
2896
2897   public void newView_actionPerformed(ActionEvent e)
2898   {
2899
2900   }
2901
2902   public void textColour_actionPerformed(ActionEvent e)
2903   {
2904
2905   }
2906
2907   public void idRightAlign_actionPerformed(ActionEvent e)
2908   {
2909
2910   }
2911
2912   public void expandViews_actionPerformed(ActionEvent e)
2913   {
2914
2915   }
2916
2917   public void gatherViews_actionPerformed(ActionEvent e)
2918   {
2919
2920   }
2921
2922   public void buildTreeMenu()
2923   {
2924
2925   }
2926
2927   public void pageSetup_actionPerformed(ActionEvent e)
2928   {
2929
2930   }
2931
2932   public void alignmentProperties()
2933   {
2934
2935   }
2936
2937   protected void expand_newalign(ActionEvent e)
2938   {
2939     // TODO Auto-generated method stub
2940
2941   }
2942 }