src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.jbgui;
  22
  23 import jalview.bin.Cache;
  24 import jalview.gui.JvSwingUtils;
  25 import jalview.schemes.ColourSchemeProperty;
  26 import jalview.util.MessageManager;
  27
  28 import java.awt.BorderLayout;
  29 import java.awt.Color;
  30 import java.awt.GridLayout;
  31 import java.awt.Toolkit;
  32 import java.awt.event.ActionEvent;
  33 import java.awt.event.ActionListener;
  34 import java.awt.event.FocusAdapter;
  35 import java.awt.event.FocusEvent;
  36 import java.awt.event.MouseAdapter;
  37 import java.awt.event.MouseEvent;
  38
  39 import javax.swing.BorderFactory;
  40 import javax.swing.ButtonGroup;
  41 import javax.swing.JCheckBoxMenuItem;
  42 import javax.swing.JInternalFrame;
  43 import javax.swing.JLabel;
  44 import javax.swing.JMenu;
  45 import javax.swing.JMenuBar;
  46 import javax.swing.JMenuItem;
  47 import javax.swing.JOptionPane;
  48 import javax.swing.JPanel;
  49 import javax.swing.JRadioButtonMenuItem;
  50 import javax.swing.JTabbedPane;
  51 import javax.swing.SwingUtilities;
  52 import javax.swing.event.ChangeEvent;
  53 import javax.swing.event.MenuEvent;
  54 import javax.swing.event.MenuListener;
  55
  56 public class GAlignFrame extends JInternalFrame
  57 {
  58   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  59
  60   protected JMenu fileMenu = new JMenu();
  61
  62   protected JMenuItem closeMenuItem = new JMenuItem();
  63
  64   protected JMenu editMenu = new JMenu();
  65
  66   protected JMenu viewMenu = new JMenu();
  67
  68   protected JMenu colourMenu = new JMenu();
  69
  70   protected JMenu calculateMenu = new JMenu();
  71
  72   protected JMenu webService = new JMenu();
  73
  74   protected JMenuItem webServiceNoServices;
  75
  76   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  77
  78   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  79
  80   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  81
  82   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  83
  84   protected JMenuItem remove2RightMenuItem = new JMenuItem();
  85
  86   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  87
  88   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  89
  90   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  91
  92   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  93
  94   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  95
  96   protected JMenuItem sortIDMenuItem = new JMenuItem();
  97
  98   protected JMenuItem sortLengthMenuItem = new JMenuItem();
  99
 100   protected JMenuItem sortGroupMenuItem = new JMenuItem();
 101
 102   protected JMenu sortByAnnotScore = new JMenu();
 103
 104   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
 105
 106   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
 107
 108   protected JMenuItem PCAMenuItem = new JMenuItem();
 109
 110   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
 111
 112   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
 113
 114   BorderLayout borderLayout1 = new BorderLayout();
 115
 116   public JLabel statusBar = new JLabel();
 117
 118   protected JMenuItem saveAs = new JMenuItem();
 119
 120   protected JMenu outputTextboxMenu = new JMenu();
 121
 122   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
 123
 124   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
 125
 126   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
 127
 128   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
 129
 130   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
 131
 132   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
 133
 134   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
 135
 136   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 137
 138   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
 139
 140   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
 141
 142   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 143
 144   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
 145
 146   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
 147
 148   protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
 149
 150   // protected JRadioButtonMenuItem covariationColour = new
 151   // JRadioButtonMenuItem();
 152
 153   protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
 154
 155   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 156
 157   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
 158
 159   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 160
 161   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 162
 163   public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
 164
 165   JMenuItem htmlMenuItem = new JMenuItem();
 166
 167   JMenuItem overviewMenuItem = new JMenuItem();
 168
 169   protected JMenuItem undoMenuItem = new JMenuItem();
 170
 171   protected JMenuItem redoMenuItem = new JMenuItem();
 172
 173   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 174
 175   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 176
 177   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 178
 179   JMenuItem printMenuItem = new JMenuItem();
 180
 181   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 182
 183   JMenuItem findMenuItem = new JMenuItem();
 184
 185   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 186
 187   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 188
 189   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 190
 191   JMenuItem deleteGroups = new JMenuItem();
 192
 193   JMenuItem createGroup = new JMenuItem();
 194
 195   JMenuItem unGroup = new JMenuItem();
 196
 197   JMenuItem delete = new JMenuItem();
 198
 199   JMenuItem copy = new JMenuItem();
 200
 201   JMenuItem cut = new JMenuItem();
 202
 203   JMenu pasteMenu = new JMenu();
 204
 205   JMenuItem pasteNew = new JMenuItem();
 206
 207   JMenuItem pasteThis = new JMenuItem();
 208
 209   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
 210
 211   JMenuItem createPNG = new JMenuItem();
 212
 213   protected JMenuItem font = new JMenuItem();
 214
 215   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 216
 217   JMenuItem epsFile = new JMenuItem();
 218
 219   JMenuItem LoadtreeMenuItem = new JMenuItem();
 220
 221   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 222
 223   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 224
 225   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 226
 227   protected JMenuItem modifyPID = new JMenuItem();
 228
 229   protected JMenuItem modifyConservation = new JMenuItem();
 230
 231   protected JMenu sortByTreeMenu = new JMenu();
 232
 233   protected JMenu sort = new JMenu();
 234
 235   protected JMenu calculateTree = new JMenu();
 236
 237   JMenu jMenu2 = new JMenu();
 238
 239   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 240
 241   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 242
 243   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 244
 245   protected ButtonGroup colours = new ButtonGroup();
 246
 247   JMenuItem vamsasStore = new JMenuItem();
 248
 249   protected JMenuItem showTranslation = new JMenuItem();
 250
 251   protected JMenuItem extractScores = new JMenuItem();
 252
 253   protected JMenuItem expandAlignment = new JMenuItem();
 254
 255   protected JMenu showProducts = new JMenu();
 256
 257   public JMenuItem openFeatureSettings = new JMenuItem();
 258
 259   JMenuItem fetchSequence = new JMenuItem();
 260
 261   JMenuItem annotationColour = new JMenuItem();
 262
 263   protected JMenuItem rnahelicesColour = new JMenuItem();
 264
 265   JMenuItem associatedData = new JMenuItem();
 266
 267   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 268
 269   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 270
 271   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 272
 273   JMenu addSequenceMenu = new JMenu();
 274
 275   JMenuItem addFromFile = new JMenuItem();
 276
 277   JMenuItem addFromText = new JMenuItem();
 278
 279   JMenuItem addFromURL = new JMenuItem();
 280
 281   JMenuItem exportAnnotations = new JMenuItem();
 282
 283   JMenuItem exportFeatures = new JMenuItem();
 284
 285   protected JPanel statusPanel = new JPanel();
 286
 287   GridLayout gridLayout1 = new GridLayout();
 288
 289   JMenu jMenu3 = new JMenu();
 290
 291   JMenuItem showAllSeqs = new JMenuItem();
 292
 293   JMenuItem showAllColumns = new JMenuItem();
 294
 295   JMenu hideMenu = new JMenu();
 296
 297   JMenuItem hideSelSequences = new JMenuItem();
 298
 299   JMenuItem hideSelColumns = new JMenuItem();
 300
 301   JMenuItem hideAllButSelection = new JMenuItem();
 302
 303   JMenuItem hideAllSelection = new JMenuItem();
 304
 305   JMenuItem showAllhidden = new JMenuItem();
 306
 307   protected JMenuItem showAllAnnotations = new JMenuItem();
 308
 309   protected JMenuItem hideAllAnnotations = new JMenuItem();
 310
 311   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 312
 313   JMenuItem invertColSel = new JMenuItem();
 314
 315   protected JTabbedPane tabbedPane = new JTabbedPane();
 316
 317   JMenuItem save = new JMenuItem();
 318
 319   protected JMenuItem reload = new JMenuItem();
 320
 321   JMenuItem newView = new JMenuItem();
 322
 323   JMenuItem textColour = new JMenuItem();
 324
 325   JMenu formatMenu = new JMenu();
 326
 327   JMenu selectMenu = new JMenu();
 328
 329   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 330
 331   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 332
 333   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 334
 335   protected JMenuItem gatherViews = new JMenuItem();
 336
 337   protected JMenuItem expandViews = new JMenuItem();
 338
 339   JMenuItem pageSetup = new JMenuItem();
 340
 341   JMenuItem alignmentProperties = new JMenuItem();
 342
 343   JMenu tooltipSettingsMenu = new JMenu();
 344
 345   private JMenuItem justifyLeftMenuItem = new JMenuItem();
 346
 347   private JMenuItem justifyRightMenuItem = new JMenuItem();
 348
 349   JMenu autoAnnMenu = new JMenu();
 350
 351   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 352
 353   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 354
 355   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 356
 357   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 358
 359   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 360
 361   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 362
 363   private JMenuItem grpsFromSelection = new JMenuItem();
 364
 365   public GAlignFrame()
 366   {
 367     try
 368     {
 369       jbInit();
 370       setJMenuBar(alignFrameMenuBar);
 371
 372       // dynamically fill save as menu with available formats
 373       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 374       {
 375         JMenuItem item = new JMenuItem(
 376                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 377
 378         item.addActionListener(new java.awt.event.ActionListener()
 379         {
 380           @Override
 381           public void actionPerformed(ActionEvent e)
 382           {
 383             outputText_actionPerformed(e);
 384           }
 385         });
 386
 387         outputTextboxMenu.add(item);
 388       }
 389     } catch (Exception e)
 390     {
 391       System.err.println(e.toString());
 392     }
 393
 394     if (!new jalview.util.Platform().isAMac())
 395     {
 396       closeMenuItem.setMnemonic('C');
 397       outputTextboxMenu.setMnemonic('T');
 398       undoMenuItem.setMnemonic('Z');
 399       redoMenuItem.setMnemonic('0');
 400       copy.setMnemonic('C');
 401       cut.setMnemonic('U');
 402       pasteMenu.setMnemonic('P');
 403       reload.setMnemonic('R');
 404     }
 405
 406     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 407     {
 408       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 409               .getUserColourSchemes().keys();
 410
 411       while (userColours.hasMoreElements())
 412       {
 413         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 414                 userColours.nextElement().toString());
 415         radioItem.setName("USER_DEFINED");
 416         radioItem.addMouseListener(new MouseAdapter()
 417         {
 418           @Override
 419           public void mousePressed(MouseEvent evt)
 420           {
 421             if (evt.isControlDown()
 422                     || SwingUtilities.isRightMouseButton(evt))
 423             {
 424               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 425
 426               int option = JOptionPane.showInternalConfirmDialog(
 427                       jalview.gui.Desktop.desktop,
 428                       MessageManager
 429                               .getString("label.remove_from_default_list"),
 430                       MessageManager
 431                               .getString("label.remove_user_defined_colour"),
 432                       JOptionPane.YES_NO_OPTION);
 433               if (option == JOptionPane.YES_OPTION)
 434               {
 435                 jalview.gui.UserDefinedColours
 436                         .removeColourFromDefaults(radioItem.getText());
 437                 colourMenu.remove(radioItem);
 438               }
 439               else
 440               {
 441                 radioItem.addActionListener(new ActionListener()
 442                 {
 443                   @Override
 444                   public void actionPerformed(ActionEvent evt)
 445                   {
 446                     userDefinedColour_actionPerformed(evt);
 447                   }
 448                 });
 449               }
 450             }
 451           }
 452         });
 453         radioItem.addActionListener(new ActionListener()
 454         {
 455           @Override
 456           public void actionPerformed(ActionEvent evt)
 457           {
 458             userDefinedColour_actionPerformed(evt);
 459           }
 460         });
 461         colourMenu.insert(radioItem, 15);
 462         colours.add(radioItem);
 463       }
 464     }
 465     colours.add(noColourmenuItem);
 466     colours.add(clustalColour);
 467     colours.add(zappoColour);
 468     colours.add(taylorColour);
 469     colours.add(hydrophobicityColour);
 470     colours.add(helixColour);
 471     colours.add(strandColour);
 472     colours.add(turnColour);
 473     colours.add(buriedColour);
 474     colours.add(userDefinedColour);
 475     colours.add(PIDColour);
 476     colours.add(BLOSUM62Colour);
 477     colours.add(nucleotideColour);
 478     colours.add(purinePyrimidineColour);
 479     // colours.add(covariationColour);
 480     colours.add(tcoffeeColour);
 481     colours.add(RNAInteractionColour);
 482     setColourSelected(jalview.bin.Cache
 483             .getDefault("DEFAULT_COLOUR", "None"));
 484
 485   }
 486
 487   public void setColourSelected(String defaultColour)
 488   {
 489
 490     if (defaultColour != null)
 491     {
 492       int index = ColourSchemeProperty
 493               .getColourIndexFromName(defaultColour);
 494
 495       switch (index)
 496       {
 497       case ColourSchemeProperty.CLUSTAL:
 498         clustalColour.setSelected(true);
 499
 500         break;
 501
 502       case ColourSchemeProperty.BLOSUM:
 503         BLOSUM62Colour.setSelected(true);
 504
 505         break;
 506
 507       case ColourSchemeProperty.PID:
 508         PIDColour.setSelected(true);
 509
 510         break;
 511
 512       case ColourSchemeProperty.ZAPPO:
 513         zappoColour.setSelected(true);
 514
 515         break;
 516
 517       case ColourSchemeProperty.TAYLOR:
 518         taylorColour.setSelected(true);
 519         break;
 520
 521       case ColourSchemeProperty.HYDROPHOBIC:
 522         hydrophobicityColour.setSelected(true);
 523
 524         break;
 525
 526       case ColourSchemeProperty.HELIX:
 527         helixColour.setSelected(true);
 528
 529         break;
 530
 531       case ColourSchemeProperty.STRAND:
 532         strandColour.setSelected(true);
 533
 534         break;
 535
 536       case ColourSchemeProperty.TURN:
 537         turnColour.setSelected(true);
 538
 539         break;
 540
 541       case ColourSchemeProperty.BURIED:
 542         buriedColour.setSelected(true);
 543
 544         break;
 545
 546       case ColourSchemeProperty.NUCLEOTIDE:
 547         nucleotideColour.setSelected(true);
 548
 549         break;
 550
 551       case ColourSchemeProperty.TCOFFEE:
 552         tcoffeeColour.setSelected(true);
 553         break;
 554
 555       case ColourSchemeProperty.PURINEPYRIMIDINE:
 556         purinePyrimidineColour.setSelected(true);
 557
 558         break;
 559
 560       case ColourSchemeProperty.RNAINTERACTION:
 561         RNAInteractionColour.setSelected(true);
 562
 563         break;
 564       /*
 565        * case ColourSchemeProperty.COVARIATION:
 566        * covariationColour.setSelected(true);
 567        *
 568        * break;
 569        */
 570       case ColourSchemeProperty.USER_DEFINED:
 571         userDefinedColour.setSelected(true);
 572
 573         break;
 574       case ColourSchemeProperty.NONE:
 575       default:
 576         noColourmenuItem.setSelected(true);
 577         break;
 578
 579       }
 580     }
 581
 582   }
 583
 584   private void jbInit() throws Exception
 585   {
 586     fileMenu.setText(MessageManager.getString("action.file"));
 587     saveAs.setText(MessageManager.getString("action.save_as") + "...");
 588     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 589             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
 590                     .getMenuShortcutKeyMask()
 591                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 592     saveAs.addActionListener(new ActionListener()
 593     {
 594       @Override
 595       public void actionPerformed(ActionEvent e)
 596       {
 597         saveAs_actionPerformed(e);
 598       }
 599     });
 600     closeMenuItem.setText(MessageManager.getString("action.close"));
 601     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 602             java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
 603                     .getMenuShortcutKeyMask(), false));
 604     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 605     {
 606       @Override
 607       public void actionPerformed(ActionEvent e)
 608       {
 609         closeMenuItem_actionPerformed(false);
 610       }
 611     });
 612     editMenu.setText(MessageManager.getString("action.edit"));
 613     viewMenu.setText(MessageManager.getString("action.view"));
 614     colourMenu.setText(MessageManager.getString("action.colour"));
 615     calculateMenu.setText(MessageManager.getString("action.calculate"));
 616     webService.setText(MessageManager.getString("action.web_service"));
 617     selectAllSequenceMenuItem.setText(MessageManager
 618             .getString("action.select_all"));
 619     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 620             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
 621                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 622     selectAllSequenceMenuItem
 623             .addActionListener(new java.awt.event.ActionListener()
 624             {
 625               @Override
 626               public void actionPerformed(ActionEvent e)
 627               {
 628                 selectAllSequenceMenuItem_actionPerformed(e);
 629               }
 630             });
 631     deselectAllSequenceMenuItem.setText(MessageManager
 632             .getString("action.deselect_all"));
 633     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 634             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 635     deselectAllSequenceMenuItem
 636             .addActionListener(new java.awt.event.ActionListener()
 637             {
 638               @Override
 639               public void actionPerformed(ActionEvent e)
 640               {
 641                 deselectAllSequenceMenuItem_actionPerformed(e);
 642               }
 643             });
 644     invertSequenceMenuItem.setText(MessageManager
 645             .getString("action.invert_sequence_selection"));
 646     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 647             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
 648                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 649     invertSequenceMenuItem
 650             .addActionListener(new java.awt.event.ActionListener()
 651             {
 652               @Override
 653               public void actionPerformed(ActionEvent e)
 654               {
 655                 invertSequenceMenuItem_actionPerformed(e);
 656               }
 657             });
 658     grpsFromSelection.setText(MessageManager
 659             .getString("action.make_groups_selection"));
 660     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
 661     {
 662       @Override
 663       public void actionPerformed(ActionEvent e)
 664       {
 665         makeGrpsFromSelection_actionPerformed(e);
 666       }
 667     });
 668     expandAlignment.setText(MessageManager
 669             .getString("action.view_flanking_regions"));
 670     expandAlignment.setToolTipText(MessageManager
 671             .getString("label.view_flanking_regions"));
 672     expandAlignment.addActionListener(new java.awt.event.ActionListener()
 673     {
 674       @Override
 675       public void actionPerformed(ActionEvent e)
 676       {
 677         expand_newalign(e);
 678       }
 679     });
 680     remove2LeftMenuItem.setText(MessageManager
 681             .getString("action.remove_left"));
 682     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 683             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
 684                     .getMenuShortcutKeyMask(), false));
 685     remove2LeftMenuItem
 686             .addActionListener(new java.awt.event.ActionListener()
 687             {
 688               @Override
 689               public void actionPerformed(ActionEvent e)
 690               {
 691                 remove2LeftMenuItem_actionPerformed(e);
 692               }
 693             });
 694     remove2RightMenuItem.setText(MessageManager
 695             .getString("action.remove_right"));
 696     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 697             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
 698                     .getMenuShortcutKeyMask(), false));
 699     remove2RightMenuItem
 700             .addActionListener(new java.awt.event.ActionListener()
 701             {
 702               @Override
 703               public void actionPerformed(ActionEvent e)
 704               {
 705                 remove2RightMenuItem_actionPerformed(e);
 706               }
 707             });
 708     removeGappedColumnMenuItem.setText(MessageManager
 709             .getString("action.remove_empty_columns"));
 710     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
 711             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 712                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 713     removeGappedColumnMenuItem
 714             .addActionListener(new java.awt.event.ActionListener()
 715             {
 716               @Override
 717               public void actionPerformed(ActionEvent e)
 718               {
 719                 removeGappedColumnMenuItem_actionPerformed(e);
 720               }
 721             });
 722     removeAllGapsMenuItem.setText(MessageManager
 723             .getString("action.remove_all_gaps"));
 724     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
 725             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 726                     .getDefaultToolkit().getMenuShortcutKeyMask()
 727                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 728     removeAllGapsMenuItem
 729             .addActionListener(new java.awt.event.ActionListener()
 730             {
 731               @Override
 732               public void actionPerformed(ActionEvent e)
 733               {
 734                 removeAllGapsMenuItem_actionPerformed(e);
 735               }
 736             });
 737     justifyLeftMenuItem.setText(MessageManager
 738             .getString("action.left_justify_alignment"));
 739     justifyLeftMenuItem
 740             .addActionListener(new java.awt.event.ActionListener()
 741             {
 742               @Override
 743               public void actionPerformed(ActionEvent e)
 744               {
 745                 justifyLeftMenuItem_actionPerformed(e);
 746               }
 747             });
 748     justifyRightMenuItem.setText(MessageManager
 749             .getString("action.right_justify_alignment"));
 750     justifyRightMenuItem
 751             .addActionListener(new java.awt.event.ActionListener()
 752             {
 753               @Override
 754               public void actionPerformed(ActionEvent e)
 755               {
 756                 justifyRightMenuItem_actionPerformed(e);
 757               }
 758             });
 759     viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
 760     viewBoxesMenuItem.setState(true);
 761     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 762     {
 763       @Override
 764       public void actionPerformed(ActionEvent e)
 765       {
 766         viewBoxesMenuItem_actionPerformed(e);
 767       }
 768     });
 769     viewTextMenuItem.setText(MessageManager.getString("action.text"));
 770     viewTextMenuItem.setState(true);
 771     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 772     {
 773       @Override
 774       public void actionPerformed(ActionEvent e)
 775       {
 776         viewTextMenuItem_actionPerformed(e);
 777       }
 778     });
 779     showNonconservedMenuItem.setText(MessageManager
 780             .getString("label.show_non_conversed"));
 781     showNonconservedMenuItem.setState(false);
 782     showNonconservedMenuItem
 783             .addActionListener(new java.awt.event.ActionListener()
 784             {
 785               @Override
 786               public void actionPerformed(ActionEvent e)
 787               {
 788                 showUnconservedMenuItem_actionPerformed(e);
 789               }
 790             });
 791     sortPairwiseMenuItem.setText(MessageManager
 792             .getString("action.by_pairwise_id"));
 793     sortPairwiseMenuItem
 794             .addActionListener(new java.awt.event.ActionListener()
 795             {
 796               @Override
 797               public void actionPerformed(ActionEvent e)
 798               {
 799                 sortPairwiseMenuItem_actionPerformed(e);
 800               }
 801             });
 802     sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
 803     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 804     {
 805       @Override
 806       public void actionPerformed(ActionEvent e)
 807       {
 808         sortIDMenuItem_actionPerformed(e);
 809       }
 810     });
 811     sortLengthMenuItem
 812             .setText(MessageManager.getString("action.by_length"));
 813     sortLengthMenuItem
 814             .addActionListener(new java.awt.event.ActionListener()
 815             {
 816               @Override
 817               public void actionPerformed(ActionEvent e)
 818               {
 819                 sortLengthMenuItem_actionPerformed(e);
 820               }
 821             });
 822     sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
 823     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 824     {
 825       @Override
 826       public void actionPerformed(ActionEvent e)
 827       {
 828         sortGroupMenuItem_actionPerformed(e);
 829       }
 830     });
 831     removeRedundancyMenuItem.setText(MessageManager
 832             .getString("action.remove_redundancy").concat("..."));
 833     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
 834             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
 835                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 836     removeRedundancyMenuItem
 837             .addActionListener(new java.awt.event.ActionListener()
 838             {
 839               @Override
 840               public void actionPerformed(ActionEvent e)
 841               {
 842                 removeRedundancyMenuItem_actionPerformed(e);
 843               }
 844             });
 845     pairwiseAlignmentMenuItem.setText(MessageManager
 846             .getString("action.pairwise_alignment"));
 847     pairwiseAlignmentMenuItem
 848             .addActionListener(new java.awt.event.ActionListener()
 849             {
 850               @Override
 851               public void actionPerformed(ActionEvent e)
 852               {
 853                 pairwiseAlignmentMenuItem_actionPerformed(e);
 854               }
 855             });
 856     PCAMenuItem.setText(MessageManager
 857             .getString("label.principal_component_analysis"));
 858     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 859     {
 860       @Override
 861       public void actionPerformed(ActionEvent e)
 862       {
 863         PCAMenuItem_actionPerformed(e);
 864       }
 865     });
 866     averageDistanceTreeMenuItem.setText(MessageManager
 867             .getString("label.average_distance_identity"));
 868     averageDistanceTreeMenuItem
 869             .addActionListener(new java.awt.event.ActionListener()
 870             {
 871               @Override
 872               public void actionPerformed(ActionEvent e)
 873               {
 874                 averageDistanceTreeMenuItem_actionPerformed(e);
 875               }
 876             });
 877     neighbourTreeMenuItem.setText(MessageManager
 878             .getString("label.neighbour_joining_identity"));
 879     neighbourTreeMenuItem
 880             .addActionListener(new java.awt.event.ActionListener()
 881             {
 882               @Override
 883               public void actionPerformed(ActionEvent e)
 884               {
 885                 neighbourTreeMenuItem_actionPerformed(e);
 886               }
 887             });
 888     this.getContentPane().setLayout(borderLayout1);
 889     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 890     statusBar.setBackground(Color.white);
 891     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 892     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 893     statusBar.setText(MessageManager.getString("label.status_bar"));
 894     outputTextboxMenu.setText(MessageManager
 895             .getString("label.out_to_textbox"));
 896     clustalColour.setText(MessageManager.getString("label.clustalx"));
 897
 898     clustalColour.addActionListener(new java.awt.event.ActionListener()
 899     {
 900       @Override
 901       public void actionPerformed(ActionEvent e)
 902       {
 903         clustalColour_actionPerformed(e);
 904       }
 905     });
 906     zappoColour.setText(MessageManager.getString("label.zappo"));
 907     zappoColour.addActionListener(new java.awt.event.ActionListener()
 908     {
 909       @Override
 910       public void actionPerformed(ActionEvent e)
 911       {
 912         zappoColour_actionPerformed(e);
 913       }
 914     });
 915     taylorColour.setText(MessageManager.getString("label.taylor"));
 916     taylorColour.addActionListener(new java.awt.event.ActionListener()
 917     {
 918       @Override
 919       public void actionPerformed(ActionEvent e)
 920       {
 921         taylorColour_actionPerformed(e);
 922       }
 923     });
 924     hydrophobicityColour.setText(MessageManager
 925             .getString("label.hydrophobicity"));
 926     hydrophobicityColour
 927             .addActionListener(new java.awt.event.ActionListener()
 928             {
 929               @Override
 930               public void actionPerformed(ActionEvent e)
 931               {
 932                 hydrophobicityColour_actionPerformed(e);
 933               }
 934             });
 935     helixColour.setText(MessageManager.getString("label.helix_propensity"));
 936     helixColour.addActionListener(new java.awt.event.ActionListener()
 937     {
 938       @Override
 939       public void actionPerformed(ActionEvent e)
 940       {
 941         helixColour_actionPerformed(e);
 942       }
 943     });
 944     strandColour.setText(MessageManager
 945             .getString("label.strand_propensity"));
 946     strandColour.addActionListener(new java.awt.event.ActionListener()
 947     {
 948       @Override
 949       public void actionPerformed(ActionEvent e)
 950       {
 951         strandColour_actionPerformed(e);
 952       }
 953     });
 954     turnColour.setText(MessageManager.getString("label.turn_propensity"));
 955     turnColour.addActionListener(new java.awt.event.ActionListener()
 956     {
 957       @Override
 958       public void actionPerformed(ActionEvent e)
 959       {
 960         turnColour_actionPerformed(e);
 961       }
 962     });
 963     buriedColour.setText(MessageManager.getString("label.buried_index"));
 964     buriedColour.addActionListener(new java.awt.event.ActionListener()
 965     {
 966       @Override
 967       public void actionPerformed(ActionEvent e)
 968       {
 969         buriedColour_actionPerformed(e);
 970       }
 971     });
 972     userDefinedColour.setText(MessageManager
 973             .getString("action.user_defined"));
 974     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 975     {
 976       @Override
 977       public void actionPerformed(ActionEvent e)
 978       {
 979         userDefinedColour_actionPerformed(e);
 980       }
 981     });
 982     PIDColour
 983             .setText(MessageManager.getString("label.percentage_identity"));
 984     PIDColour.addActionListener(new java.awt.event.ActionListener()
 985     {
 986       @Override
 987       public void actionPerformed(ActionEvent e)
 988       {
 989         PIDColour_actionPerformed(e);
 990       }
 991     });
 992     BLOSUM62Colour
 993             .setText(MessageManager.getString("label.blosum62_score"));
 994     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 995     {
 996       @Override
 997       public void actionPerformed(ActionEvent e)
 998       {
 999         BLOSUM62Colour_actionPerformed(e);
1000       }
1001     });
1002     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1003     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1004     {
1005       @Override
1006       public void actionPerformed(ActionEvent e)
1007       {
1008         nucleotideColour_actionPerformed(e);
1009       }
1010     });
1011
1012     purinePyrimidineColour.setText(MessageManager
1013             .getString("label.purine_pyrimidine"));
1014     purinePyrimidineColour
1015             .addActionListener(new java.awt.event.ActionListener()
1016             {
1017               @Override
1018               public void actionPerformed(ActionEvent e)
1019               {
1020                 purinePyrimidineColour_actionPerformed(e);
1021               }
1022             });
1023
1024     RNAInteractionColour.setText("RNA Interaction type");
1025     RNAInteractionColour
1026             .addActionListener(new java.awt.event.ActionListener()
1027             {
1028               @Override
1029               public void actionPerformed(ActionEvent e)
1030               {
1031                 RNAInteractionColour_actionPerformed(e);
1032               }
1033             });
1034     /*
1035      * covariationColour.setText("Covariation");
1036      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1037      * public void actionPerformed(ActionEvent e) {
1038      * covariationColour_actionPerformed(e); } });
1039      */
1040
1041     avDistanceTreeBlosumMenuItem.setText(MessageManager
1042             .getString("label.average_distance_bloslum62"));
1043     avDistanceTreeBlosumMenuItem
1044             .addActionListener(new java.awt.event.ActionListener()
1045             {
1046               @Override
1047               public void actionPerformed(ActionEvent e)
1048               {
1049                 avTreeBlosumMenuItem_actionPerformed(e);
1050               }
1051             });
1052     njTreeBlosumMenuItem.setText(MessageManager
1053             .getString("label.neighbour_blosum62"));
1054     njTreeBlosumMenuItem
1055             .addActionListener(new java.awt.event.ActionListener()
1056             {
1057               @Override
1058               public void actionPerformed(ActionEvent e)
1059               {
1060                 njTreeBlosumMenuItem_actionPerformed(e);
1061               }
1062             });
1063     annotationPanelMenuItem.setActionCommand("");
1064     annotationPanelMenuItem.setText(MessageManager
1065             .getString("label.show_annotations"));
1066     annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
1067             true));
1068     annotationPanelMenuItem.addActionListener(new ActionListener()
1069     {
1070       @Override
1071       public void actionPerformed(ActionEvent e)
1072       {
1073         annotationPanelMenuItem_actionPerformed(e);
1074       }
1075     });
1076     /*
1077      * Show/hide all annotations only enabled if annotation panel is shown
1078      */
1079     showAllAnnotations.setText(MessageManager
1080             .getString("label.show_all_annotations"));
1081     showAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
1082     showAllAnnotations.addActionListener(new ActionListener()
1083     {
1084       @Override
1085       public void actionPerformed(ActionEvent e)
1086       {
1087         showAllAnnotations_actionPerformed();
1088       }
1089     });
1090     hideAllAnnotations.setText(MessageManager
1091             .getString("label.hide_all_annotations"));
1092     hideAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
1093     hideAllAnnotations.addActionListener(new ActionListener()
1094     {
1095       @Override
1096       public void actionPerformed(ActionEvent e)
1097       {
1098         hideAllAnnotations_actionPerformed();
1099       }
1100     });
1101     colourTextMenuItem.setText(MessageManager
1102             .getString("label.colour_text"));
1103     colourTextMenuItem
1104             .addActionListener(new java.awt.event.ActionListener()
1105             {
1106               @Override
1107               public void actionPerformed(ActionEvent e)
1108               {
1109                 colourTextMenuItem_actionPerformed(e);
1110               }
1111             });
1112     htmlMenuItem.setText(MessageManager.getString("label.html"));
1113     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
1114     {
1115       @Override
1116       public void actionPerformed(ActionEvent e)
1117       {
1118         htmlMenuItem_actionPerformed(e);
1119       }
1120     });
1121     overviewMenuItem.setText(MessageManager
1122             .getString("label.overview_window"));
1123     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
1124     {
1125       @Override
1126       public void actionPerformed(ActionEvent e)
1127       {
1128         overviewMenuItem_actionPerformed(e);
1129       }
1130     });
1131     undoMenuItem.setEnabled(false);
1132     undoMenuItem.setText(MessageManager.getString("action.undo"));
1133     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1134             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1135                     .getMenuShortcutKeyMask(), false));
1136     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1137     {
1138       @Override
1139       public void actionPerformed(ActionEvent e)
1140       {
1141         undoMenuItem_actionPerformed(e);
1142       }
1143     });
1144     redoMenuItem.setEnabled(false);
1145     redoMenuItem.setText(MessageManager.getString("action.redo"));
1146     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1147             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1148                     .getMenuShortcutKeyMask(), false));
1149     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1150     {
1151       @Override
1152       public void actionPerformed(ActionEvent e)
1153       {
1154         redoMenuItem_actionPerformed(e);
1155       }
1156     });
1157     conservationMenuItem.setText(MessageManager
1158             .getString("action.by_conservation"));
1159     conservationMenuItem
1160             .addActionListener(new java.awt.event.ActionListener()
1161             {
1162               @Override
1163               public void actionPerformed(ActionEvent e)
1164               {
1165                 conservationMenuItem_actionPerformed(e);
1166               }
1167             });
1168     noColourmenuItem.setText(MessageManager.getString("label.none"));
1169     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1170     {
1171       @Override
1172       public void actionPerformed(ActionEvent e)
1173       {
1174         noColourmenuItem_actionPerformed(e);
1175       }
1176     });
1177     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1178     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1179     {
1180       @Override
1181       public void actionPerformed(ActionEvent e)
1182       {
1183         wrapMenuItem_actionPerformed(e);
1184       }
1185     });
1186     printMenuItem.setText(MessageManager.getString("action.print") + "...");
1187     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1188             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1189                     .getMenuShortcutKeyMask(), false));
1190     printMenuItem.addActionListener(new java.awt.event.ActionListener()
1191     {
1192       @Override
1193       public void actionPerformed(ActionEvent e)
1194       {
1195         printMenuItem_actionPerformed(e);
1196       }
1197     });
1198     renderGapsMenuItem
1199             .setText(MessageManager.getString("action.show_gaps"));
1200     renderGapsMenuItem.setState(true);
1201     renderGapsMenuItem
1202             .addActionListener(new java.awt.event.ActionListener()
1203             {
1204               @Override
1205               public void actionPerformed(ActionEvent e)
1206               {
1207                 renderGapsMenuItem_actionPerformed(e);
1208               }
1209             });
1210     findMenuItem.setText(MessageManager.getString("action.find"));
1211     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1212             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1213                     .getMenuShortcutKeyMask(), false));
1214     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
1215             MessageManager.getString("label.find_tip")));
1216     findMenuItem.addActionListener(new java.awt.event.ActionListener()
1217     {
1218       @Override
1219       public void actionPerformed(ActionEvent e)
1220       {
1221         findMenuItem_actionPerformed(e);
1222       }
1223     });
1224     abovePIDThreshold.setText(MessageManager
1225             .getString("label.above_identity_threshold"));
1226     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1227     {
1228       @Override
1229       public void actionPerformed(ActionEvent e)
1230       {
1231         abovePIDThreshold_actionPerformed(e);
1232       }
1233     });
1234     showSeqFeatures.setText(MessageManager
1235             .getString("label.show_sequence_features"));
1236     showSeqFeatures.addActionListener(new ActionListener()
1237     {
1238       @Override
1239       public void actionPerformed(ActionEvent actionEvent)
1240       {
1241         showSeqFeatures_actionPerformed(actionEvent);
1242       }
1243     });
1244     /*
1245      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1246      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1247      * void actionPerformed(ActionEvent actionEvent) {
1248      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1249      */
1250     showDbRefsMenuitem.setText(MessageManager
1251             .getString("label.show_database_refs"));
1252     showDbRefsMenuitem.addActionListener(new ActionListener()
1253     {
1254
1255       @Override
1256       public void actionPerformed(ActionEvent e)
1257       {
1258         showDbRefs_actionPerformed(e);
1259       }
1260
1261     });
1262     showNpFeatsMenuitem.setText(MessageManager
1263             .getString("label.show_non_positional_features"));
1264     showNpFeatsMenuitem.addActionListener(new ActionListener()
1265     {
1266
1267       @Override
1268       public void actionPerformed(ActionEvent e)
1269       {
1270         showNpFeats_actionPerformed(e);
1271       }
1272
1273     });
1274     showGroupConservation.setText(MessageManager
1275             .getString("label.group_conservation"));
1276     showGroupConservation.addActionListener(new ActionListener()
1277     {
1278
1279       @Override
1280       public void actionPerformed(ActionEvent e)
1281       {
1282         showGroupConservation_actionPerformed(e);
1283       }
1284
1285     });
1286
1287     showGroupConsensus.setText(MessageManager
1288             .getString("label.group_consensus"));
1289     showGroupConsensus.addActionListener(new ActionListener()
1290     {
1291
1292       @Override
1293       public void actionPerformed(ActionEvent e)
1294       {
1295         showGroupConsensus_actionPerformed(e);
1296       }
1297
1298     });
1299     showConsensusHistogram.setText(MessageManager
1300             .getString("label.show_consensus_histogram"));
1301     showConsensusHistogram.addActionListener(new ActionListener()
1302     {
1303
1304       @Override
1305       public void actionPerformed(ActionEvent e)
1306       {
1307         showConsensusHistogram_actionPerformed(e);
1308       }
1309
1310     });
1311     showSequenceLogo.setText(MessageManager
1312             .getString("label.show_consensus_logo"));
1313     showSequenceLogo.addActionListener(new ActionListener()
1314     {
1315
1316       @Override
1317       public void actionPerformed(ActionEvent e)
1318       {
1319         showSequenceLogo_actionPerformed(e);
1320       }
1321
1322     });
1323     normaliseSequenceLogo.setText(MessageManager
1324             .getString("label.norm_consensus_logo"));
1325     normaliseSequenceLogo.addActionListener(new ActionListener()
1326     {
1327
1328       @Override
1329       public void actionPerformed(ActionEvent e)
1330       {
1331         normaliseSequenceLogo_actionPerformed(e);
1332       }
1333
1334     });
1335     applyAutoAnnotationSettings.setText(MessageManager
1336             .getString("label.apply_all_groups"));
1337     applyAutoAnnotationSettings.setState(false);
1338     applyAutoAnnotationSettings.setVisible(true);
1339     applyAutoAnnotationSettings.addActionListener(new ActionListener()
1340     {
1341
1342       @Override
1343       public void actionPerformed(ActionEvent e)
1344       {
1345         applyAutoAnnotationSettings_actionPerformed(e);
1346       }
1347
1348     });
1349
1350     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1351     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1352     {
1353       @Override
1354       public void actionPerformed(ActionEvent e)
1355       {
1356         nucleotideColour_actionPerformed(e);
1357       }
1358     });
1359
1360     tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1361     tcoffeeColour.setEnabled(false);
1362     tcoffeeColour.addActionListener(new ActionListener()
1363     {
1364
1365       @Override
1366       public void actionPerformed(ActionEvent e)
1367       {
1368         tcoffeeColorScheme_actionPerformed(e);
1369       }
1370     });
1371
1372     deleteGroups
1373             .setText(MessageManager.getString("action.undefine_groups"));
1374     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1375             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1376                     .getMenuShortcutKeyMask(), false));
1377     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1378     {
1379       @Override
1380       public void actionPerformed(ActionEvent e)
1381       {
1382         deleteGroups_actionPerformed(e);
1383       }
1384     });
1385     createGroup.setText(MessageManager.getString("action.create_groups"));
1386     createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1387             java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1388                     .getMenuShortcutKeyMask(), false));
1389     createGroup.addActionListener(new java.awt.event.ActionListener()
1390     {
1391       @Override
1392       public void actionPerformed(ActionEvent e)
1393       {
1394         createGroup_actionPerformed(e);
1395       }
1396     });
1397     unGroup.setText(MessageManager.getString("action.remove_group"));
1398     unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1399             java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1400                     .getMenuShortcutKeyMask()
1401                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1402     unGroup.addActionListener(new java.awt.event.ActionListener()
1403     {
1404       @Override
1405       public void actionPerformed(ActionEvent e)
1406       {
1407         unGroup_actionPerformed(e);
1408       }
1409     });
1410     copy.setText(MessageManager.getString("action.copy"));
1411     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1412             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1413                     .getMenuShortcutKeyMask(), false));
1414
1415     copy.addActionListener(new java.awt.event.ActionListener()
1416     {
1417       @Override
1418       public void actionPerformed(ActionEvent e)
1419       {
1420         copy_actionPerformed(e);
1421       }
1422     });
1423     cut.setText(MessageManager.getString("action.cut"));
1424     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1425             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1426                     .getMenuShortcutKeyMask(), false));
1427     cut.addActionListener(new java.awt.event.ActionListener()
1428     {
1429       @Override
1430       public void actionPerformed(ActionEvent e)
1431       {
1432         cut_actionPerformed(e);
1433       }
1434     });
1435     delete.setText(MessageManager.getString("action.delete"));
1436     delete.addActionListener(new java.awt.event.ActionListener()
1437     {
1438       @Override
1439       public void actionPerformed(ActionEvent e)
1440       {
1441         delete_actionPerformed(e);
1442       }
1443     });
1444     pasteMenu.setText(MessageManager.getString("action.paste"));
1445     pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1446     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1447             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1448                     .getMenuShortcutKeyMask()
1449                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1450     pasteNew.addActionListener(new java.awt.event.ActionListener()
1451     {
1452       @Override
1453       public void actionPerformed(ActionEvent e)
1454       {
1455         pasteNew_actionPerformed(e);
1456       }
1457     });
1458     pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1459     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1460             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1461                     .getMenuShortcutKeyMask(), false));
1462     pasteThis.addActionListener(new java.awt.event.ActionListener()
1463     {
1464       @Override
1465       public void actionPerformed(ActionEvent e)
1466       {
1467         pasteThis_actionPerformed(e);
1468       }
1469     });
1470     applyToAllGroups.setText(MessageManager
1471             .getString("label.apply_colour_to_all_groups"));
1472     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1473     {
1474       @Override
1475       public void actionPerformed(ActionEvent e)
1476       {
1477         applyToAllGroups_actionPerformed(e);
1478       }
1479     });
1480     createPNG.addActionListener(new java.awt.event.ActionListener()
1481     {
1482       @Override
1483       public void actionPerformed(ActionEvent e)
1484       {
1485         createPNG(null);
1486       }
1487     });
1488     createPNG.setActionCommand(MessageManager
1489             .getString("label.save_png_image"));
1490     createPNG.setText("PNG");
1491     font.setText(MessageManager.getString("action.font"));
1492     font.addActionListener(new java.awt.event.ActionListener()
1493     {
1494       @Override
1495       public void actionPerformed(ActionEvent e)
1496       {
1497         font_actionPerformed(e);
1498       }
1499     });
1500
1501     seqLimits.setText(MessageManager
1502             .getString("label.show_sequence_limits"));
1503     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1504     seqLimits.addActionListener(new java.awt.event.ActionListener()
1505     {
1506       @Override
1507       public void actionPerformed(ActionEvent e)
1508       {
1509         seqLimit_actionPerformed(e);
1510       }
1511     });
1512     epsFile.setText("EPS");
1513     epsFile.addActionListener(new java.awt.event.ActionListener()
1514     {
1515       @Override
1516       public void actionPerformed(ActionEvent e)
1517       {
1518         createEPS(null);
1519       }
1520     });
1521     LoadtreeMenuItem.setActionCommand(MessageManager
1522             .getString("label.load_tree_for_sequence_set"));
1523     LoadtreeMenuItem.setText(MessageManager
1524             .getString("label.load_associated_tree"));
1525     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1526     {
1527       @Override
1528       public void actionPerformed(ActionEvent e)
1529       {
1530         LoadtreeMenuItem_actionPerformed(e);
1531       }
1532     });
1533
1534     scaleAbove.setVisible(false);
1535     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1536     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1537     {
1538       @Override
1539       public void actionPerformed(ActionEvent e)
1540       {
1541         scaleAbove_actionPerformed(e);
1542       }
1543     });
1544     scaleLeft.setVisible(false);
1545     scaleLeft.setSelected(true);
1546     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1547     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1548     {
1549       @Override
1550       public void actionPerformed(ActionEvent e)
1551       {
1552         scaleLeft_actionPerformed(e);
1553       }
1554     });
1555     scaleRight.setVisible(false);
1556     scaleRight.setSelected(true);
1557     scaleRight.setText(MessageManager.getString("action.scale_right"));
1558     scaleRight.addActionListener(new java.awt.event.ActionListener()
1559     {
1560       @Override
1561       public void actionPerformed(ActionEvent e)
1562       {
1563         scaleRight_actionPerformed(e);
1564       }
1565     });
1566     centreColumnLabelsMenuItem.setVisible(true);
1567     centreColumnLabelsMenuItem.setState(false);
1568     centreColumnLabelsMenuItem.setText(MessageManager
1569             .getString("label.centre_column_labels"));
1570     centreColumnLabelsMenuItem
1571             .addActionListener(new java.awt.event.ActionListener()
1572             {
1573               @Override
1574               public void actionPerformed(ActionEvent e)
1575               {
1576                 centreColumnLabels_actionPerformed(e);
1577               }
1578             });
1579     followHighlightMenuItem.setVisible(true);
1580     followHighlightMenuItem.setState(true);
1581     followHighlightMenuItem.setText(MessageManager
1582             .getString("label.automatic_scrolling"));
1583     followHighlightMenuItem.addActionListener(new ActionListener()
1584     {
1585
1586       @Override
1587       public void actionPerformed(ActionEvent e)
1588       {
1589         followHighlight_actionPerformed();
1590       }
1591
1592     });
1593
1594     modifyPID.setText(MessageManager
1595             .getString("label.modify_identity_thereshold"));
1596     modifyPID.addActionListener(new java.awt.event.ActionListener()
1597     {
1598       @Override
1599       public void actionPerformed(ActionEvent e)
1600       {
1601         modifyPID_actionPerformed(e);
1602       }
1603     });
1604     modifyConservation.setText(MessageManager
1605             .getString("label.modify_conservation_thereshold"));
1606     modifyConservation
1607             .addActionListener(new java.awt.event.ActionListener()
1608             {
1609               @Override
1610               public void actionPerformed(ActionEvent e)
1611               {
1612                 modifyConservation_actionPerformed(e);
1613               }
1614             });
1615     sortByTreeMenu
1616             .setText(MessageManager.getString("action.by_tree_order"));
1617     sort.setText(MessageManager.getString("action.sort"));
1618     sort.addMenuListener(new MenuListener()
1619     {
1620       @Override
1621       public void menuSelected(MenuEvent e)
1622       {
1623         buildTreeMenu();
1624       }
1625
1626       @Override
1627       public void menuDeselected(MenuEvent e)
1628       {
1629       }
1630
1631       @Override
1632       public void menuCanceled(MenuEvent e)
1633       {
1634       }
1635     });
1636     sortByAnnotScore.setText(MessageManager
1637             .getString("label.sort_by_score"));
1638     sort.add(sortByAnnotScore);
1639     sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1640     {
1641
1642       @Override
1643       public void menuCanceled(MenuEvent e)
1644       {
1645       }
1646
1647       @Override
1648       public void menuDeselected(MenuEvent e)
1649       {
1650       }
1651
1652       @Override
1653       public void menuSelected(MenuEvent e)
1654       {
1655         buildSortByAnnotationScoresMenu();
1656       }
1657     });
1658     sortByAnnotScore.setVisible(false);
1659
1660     calculateTree
1661             .setText(MessageManager.getString("action.calculate_tree"));
1662
1663     jMenu2.setText(MessageManager.getString("label.export_image"));
1664     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1665     padGapsMenuitem.setState(jalview.bin.Cache
1666             .getDefault("PAD_GAPS", false));
1667     padGapsMenuitem.addActionListener(new ActionListener()
1668     {
1669       @Override
1670       public void actionPerformed(ActionEvent e)
1671       {
1672         padGapsMenuitem_actionPerformed(e);
1673       }
1674     });
1675     vamsasStore.setVisible(false);
1676     vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1677     vamsasStore.addActionListener(new ActionListener()
1678     {
1679       @Override
1680       public void actionPerformed(ActionEvent e)
1681       {
1682         vamsasStore_actionPerformed(e);
1683       }
1684     });
1685     showTranslation.setText(MessageManager
1686             .getString("label.translate_cDNA"));
1687     showTranslation.addActionListener(new ActionListener()
1688     {
1689       @Override
1690       public void actionPerformed(ActionEvent e)
1691       {
1692         showTranslation_actionPerformed(e);
1693       }
1694     });
1695     extractScores.setText(MessageManager.getString("label.extract_scores")
1696             + "...");
1697     extractScores.addActionListener(new ActionListener()
1698     {
1699       @Override
1700       public void actionPerformed(ActionEvent e)
1701       {
1702         extractScores_actionPerformed(e);
1703       }
1704     });
1705     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1706     // score extraction
1707     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1708     /*
1709      * showProducts.addActionListener(new ActionListener() {
1710      *
1711      * public void actionPerformed(ActionEvent e) {
1712      * showProducts_actionPerformed(e); } });
1713      */
1714     openFeatureSettings.setText(MessageManager
1715             .getString("label.feature_settings"));
1716     openFeatureSettings.addActionListener(new ActionListener()
1717     {
1718       @Override
1719       public void actionPerformed(ActionEvent e)
1720       {
1721         featureSettings_actionPerformed(e);
1722       }
1723     });
1724     fetchSequence
1725             .setText(MessageManager.getString("label.fetch_sequences"));
1726     fetchSequence.addActionListener(new ActionListener()
1727     {
1728       @Override
1729       public void actionPerformed(ActionEvent e)
1730       {
1731         fetchSequence_actionPerformed(e);
1732       }
1733     });
1734
1735     annotationColour.setText(MessageManager
1736             .getString("action.by_annotation"));
1737     annotationColour.addActionListener(new ActionListener()
1738     {
1739       @Override
1740       public void actionPerformed(ActionEvent e)
1741       {
1742         annotationColour_actionPerformed(e);
1743       }
1744     });
1745
1746     rnahelicesColour.setText(MessageManager
1747             .getString("action.by_rna_helixes"));
1748     rnahelicesColour.addActionListener(new ActionListener()
1749     {
1750       @Override
1751       public void actionPerformed(ActionEvent e)
1752       {
1753         rnahelicesColour_actionPerformed(e);
1754       }
1755     });
1756
1757     associatedData.setText(MessageManager
1758             .getString("label.load_features_annotations"));
1759     associatedData.addActionListener(new ActionListener()
1760     {
1761       @Override
1762       public void actionPerformed(ActionEvent e)
1763       {
1764         associatedData_actionPerformed(e);
1765       }
1766     });
1767     autoCalculate.setText(MessageManager
1768             .getString("label.autocalculate_consensus"));
1769     autoCalculate.setState(jalview.bin.Cache.getDefault(
1770             "AUTO_CALC_CONSENSUS", true));
1771     autoCalculate.addActionListener(new ActionListener()
1772     {
1773       @Override
1774       public void actionPerformed(ActionEvent e)
1775       {
1776         autoCalculate_actionPerformed(e);
1777       }
1778     });
1779     sortByTree.setText(MessageManager
1780             .getString("label.sort_alignment_new_tree"));
1781     sortByTree
1782             .setToolTipText("<html>"
1783                     + MessageManager
1784                             .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1785     sortByTree
1786             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1787     sortByTree.addActionListener(new ActionListener()
1788     {
1789       @Override
1790       public void actionPerformed(ActionEvent e)
1791       {
1792         sortByTreeOption_actionPerformed(e);
1793       }
1794     });
1795
1796     listenToViewSelections.setText(MessageManager
1797             .getString("label.listen_for_selections"));
1798     listenToViewSelections
1799             .setToolTipText("<html>"
1800                     + MessageManager
1801                             .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1802     listenToViewSelections.setState(false);
1803     listenToViewSelections.addActionListener(new ActionListener()
1804     {
1805       @Override
1806       public void actionPerformed(ActionEvent e)
1807       {
1808         listenToViewSelections_actionPerformed(e);
1809       }
1810     });
1811
1812     addSequenceMenu
1813             .setText(MessageManager.getString("label.add_sequences"));
1814     addFromFile.setText(MessageManager.getString("label.from_file"));
1815     addFromFile.addActionListener(new ActionListener()
1816     {
1817       @Override
1818       public void actionPerformed(ActionEvent e)
1819       {
1820         addFromFile_actionPerformed(e);
1821       }
1822     });
1823     addFromText.setText(MessageManager.getString("label.from_textbox"));
1824     addFromText.addActionListener(new ActionListener()
1825     {
1826       @Override
1827       public void actionPerformed(ActionEvent e)
1828       {
1829         addFromText_actionPerformed(e);
1830       }
1831     });
1832     addFromURL.setText(MessageManager.getString("label.from_url"));
1833     addFromURL.addActionListener(new ActionListener()
1834     {
1835       @Override
1836       public void actionPerformed(ActionEvent e)
1837       {
1838         addFromURL_actionPerformed(e);
1839       }
1840     });
1841     exportFeatures.setText(MessageManager
1842             .getString("label.export_features"));
1843     exportFeatures.addActionListener(new ActionListener()
1844     {
1845       @Override
1846       public void actionPerformed(ActionEvent e)
1847       {
1848         exportFeatures_actionPerformed(e);
1849       }
1850     });
1851     exportAnnotations.setText(MessageManager
1852             .getString("label.export_annotations"));
1853     exportAnnotations.addActionListener(new ActionListener()
1854     {
1855       @Override
1856       public void actionPerformed(ActionEvent e)
1857       {
1858         exportAnnotations_actionPerformed(e);
1859       }
1860     });
1861     statusPanel.setLayout(gridLayout1);
1862     jMenu3.setText(MessageManager.getString("action.show"));
1863     showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
1864     showAllSeqs.setToolTipText(MessageManager
1865             .getString("label.toggle_sequence_visibility"));
1866     showAllSeqs.addActionListener(new ActionListener()
1867     {
1868       @Override
1869       public void actionPerformed(ActionEvent e)
1870       {
1871         showAllSeqs_actionPerformed(e);
1872       }
1873     });
1874     showAllColumns.setText(MessageManager.getString("label.all_columns"));
1875     showAllColumns.setToolTipText(MessageManager
1876             .getString("label.toggle_columns_visibility"));
1877     showAllColumns.addActionListener(new ActionListener()
1878     {
1879       @Override
1880       public void actionPerformed(ActionEvent e)
1881       {
1882         showAllColumns_actionPerformed(e);
1883       }
1884     });
1885     hideMenu.setText(MessageManager.getString("action.hide"));
1886     hideSelSequences.setText(MessageManager
1887             .getString("label.selected_sequences"));
1888     hideSelSequences.setToolTipText(MessageManager
1889             .getString("label.toggle_sequence_visibility"));
1890     hideSelSequences.addActionListener(new ActionListener()
1891     {
1892       @Override
1893       public void actionPerformed(ActionEvent e)
1894       {
1895         hideSelSequences_actionPerformed(e);
1896       }
1897     });
1898     hideSelColumns.setText(MessageManager
1899             .getString("label.selected_columns"));
1900     hideSelColumns.setToolTipText(MessageManager
1901             .getString("label.toggle_columns_visibility"));
1902     hideSelColumns.addActionListener(new ActionListener()
1903     {
1904       @Override
1905       public void actionPerformed(ActionEvent e)
1906       {
1907         hideSelColumns_actionPerformed(e);
1908       }
1909     });
1910     hideAllSelection.setText(MessageManager
1911             .getString("label.selected_region"));
1912     hideAllSelection.addActionListener(new ActionListener()
1913     {
1914       @Override
1915       public void actionPerformed(ActionEvent e)
1916       {
1917         hideAllSelection_actionPerformed(e);
1918       }
1919     });
1920     // TODO: should be hidden if no selection exists.
1921     hideAllButSelection.setText(MessageManager
1922             .getString("label.all_but_selected_region"));
1923     hideAllButSelection.addActionListener(new ActionListener()
1924     {
1925       @Override
1926       public void actionPerformed(ActionEvent e)
1927       {
1928         hideAllButSelection_actionPerformed(e);
1929       }
1930     });
1931     showAllhidden.setText(MessageManager
1932             .getString("label.all_sequences_columns"));
1933     showAllhidden.setToolTipText(MessageManager
1934             .getString("label.toggles_visibility_hidden_selected_regions"));
1935     showAllhidden.addActionListener(new ActionListener()
1936     {
1937       @Override
1938       public void actionPerformed(ActionEvent e)
1939       {
1940         showAllhidden_actionPerformed(e);
1941       }
1942     });
1943     hiddenMarkers.setText(MessageManager
1944             .getString("action.show_hidden_markers"));
1945     hiddenMarkers.addActionListener(new ActionListener()
1946     {
1947       @Override
1948       public void actionPerformed(ActionEvent e)
1949       {
1950         hiddenMarkers_actionPerformed(e);
1951       }
1952     });
1953     invertColSel.setText(MessageManager
1954             .getString("action.invert_column_selection"));
1955     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1956             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1957                     .getMenuShortcutKeyMask()
1958                     | java.awt.event.KeyEvent.ALT_MASK, false));
1959     invertColSel.addActionListener(new ActionListener()
1960     {
1961       @Override
1962       public void actionPerformed(ActionEvent e)
1963       {
1964         invertColSel_actionPerformed(e);
1965       }
1966     });
1967     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1968     {
1969       @Override
1970       public void stateChanged(ChangeEvent evt)
1971       {
1972         JTabbedPane pane = (JTabbedPane) evt.getSource();
1973         int sel = pane.getSelectedIndex();
1974         tabSelectionChanged(sel);
1975       }
1976     });
1977     tabbedPane.addMouseListener(new MouseAdapter()
1978     {
1979       @Override
1980       public void mousePressed(MouseEvent e)
1981       {
1982         tabbedPane_mousePressed(e);
1983       }
1984     });
1985     tabbedPane.addFocusListener(new FocusAdapter()
1986     {
1987       @Override
1988       public void focusGained(FocusEvent e)
1989       {
1990         tabbedPane_focusGained(e);
1991       }
1992     });
1993     save.setText(MessageManager.getString("action.save"));
1994     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1995             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1996                     .getMenuShortcutKeyMask(), false));
1997     save.addActionListener(new ActionListener()
1998     {
1999       @Override
2000       public void actionPerformed(ActionEvent e)
2001       {
2002         save_actionPerformed(e);
2003       }
2004     });
2005     reload.setEnabled(false);
2006     reload.setText(MessageManager.getString("action.reload"));
2007     reload.addActionListener(new ActionListener()
2008     {
2009       @Override
2010       public void actionPerformed(ActionEvent e)
2011       {
2012         reload_actionPerformed(e);
2013       }
2014     });
2015     newView.setText(MessageManager.getString("action.new_view"));
2016     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2017             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
2018                     .getMenuShortcutKeyMask(), false));
2019     newView.addActionListener(new ActionListener()
2020     {
2021       @Override
2022       public void actionPerformed(ActionEvent e)
2023       {
2024         newView_actionPerformed(e);
2025       }
2026     });
2027     tabbedPane.setToolTipText("<html><i>"
2028             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2029             + "</i></html>");
2030     textColour.setText(MessageManager.getString("label.colour_text")
2031             + "...");
2032     textColour.addActionListener(new ActionListener()
2033     {
2034       @Override
2035       public void actionPerformed(ActionEvent e)
2036       {
2037         textColour_actionPerformed(e);
2038       }
2039     });
2040     formatMenu.setText(MessageManager.getString("action.format"));
2041     selectMenu.setText(MessageManager.getString("action.select"));
2042     idRightAlign.setText(MessageManager
2043             .getString("label.right_align_sequence_id"));
2044     idRightAlign.addActionListener(new ActionListener()
2045     {
2046       @Override
2047       public void actionPerformed(ActionEvent e)
2048       {
2049         idRightAlign_actionPerformed(e);
2050       }
2051     });
2052     gatherViews.setEnabled(false);
2053     gatherViews.setText(MessageManager.getString("action.gather_views"));
2054     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2055             java.awt.event.KeyEvent.VK_G, 0, false));
2056     gatherViews.addActionListener(new ActionListener()
2057     {
2058       @Override
2059       public void actionPerformed(ActionEvent e)
2060       {
2061         gatherViews_actionPerformed(e);
2062       }
2063     });
2064     expandViews.setEnabled(false);
2065     expandViews.setText(MessageManager.getString("action.expand_views"));
2066     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2067             java.awt.event.KeyEvent.VK_X, 0, false));
2068     expandViews.addActionListener(new ActionListener()
2069     {
2070       @Override
2071       public void actionPerformed(ActionEvent e)
2072       {
2073         expandViews_actionPerformed(e);
2074       }
2075     });
2076     pageSetup
2077             .setText(MessageManager.getString("action.page_setup") + "...");
2078     pageSetup.addActionListener(new ActionListener()
2079     {
2080       @Override
2081       public void actionPerformed(ActionEvent e)
2082       {
2083         pageSetup_actionPerformed(e);
2084       }
2085     });
2086     alignmentProperties.setText(MessageManager
2087             .getString("label.alignment_props") + "...");
2088     alignmentProperties.addActionListener(new ActionListener()
2089     {
2090       @Override
2091       public void actionPerformed(ActionEvent actionEvent)
2092       {
2093         alignmentProperties();
2094       }
2095     });
2096     tooltipSettingsMenu.setText(MessageManager
2097             .getString("label.sequence_id_tooltip"));
2098     autoAnnMenu.setText(MessageManager
2099             .getString("label.autocalculated_annotation"));
2100     alignFrameMenuBar.add(fileMenu);
2101     alignFrameMenuBar.add(editMenu);
2102     alignFrameMenuBar.add(selectMenu);
2103     alignFrameMenuBar.add(viewMenu);
2104     alignFrameMenuBar.add(formatMenu);
2105     alignFrameMenuBar.add(colourMenu);
2106     alignFrameMenuBar.add(calculateMenu);
2107     alignFrameMenuBar.add(webService);
2108     fileMenu.add(fetchSequence);
2109     fileMenu.add(addSequenceMenu);
2110     fileMenu.add(reload);
2111     fileMenu.addSeparator();
2112     fileMenu.add(vamsasStore);
2113     fileMenu.add(save);
2114     fileMenu.add(saveAs);
2115     fileMenu.add(outputTextboxMenu);
2116     fileMenu.add(pageSetup);
2117     fileMenu.add(printMenuItem);
2118     fileMenu.addSeparator();
2119     fileMenu.add(jMenu2);
2120     fileMenu.add(exportFeatures);
2121     fileMenu.add(exportAnnotations);
2122     fileMenu.add(LoadtreeMenuItem);
2123     fileMenu.add(associatedData);
2124     fileMenu.addSeparator();
2125     fileMenu.add(closeMenuItem);
2126     editMenu.add(undoMenuItem);
2127     editMenu.add(redoMenuItem);
2128     editMenu.add(cut);
2129     editMenu.add(copy);
2130     editMenu.add(pasteMenu);
2131     editMenu.add(delete);
2132     editMenu.addSeparator();
2133     editMenu.add(remove2LeftMenuItem);
2134     editMenu.add(remove2RightMenuItem);
2135     editMenu.add(removeGappedColumnMenuItem);
2136     editMenu.add(removeAllGapsMenuItem);
2137     editMenu.add(removeRedundancyMenuItem);
2138     editMenu.addSeparator();
2139     // dont add these yet in the CVS build - they cannot be undone!
2140     // Excluded from Jalview 2.5 release - undo needs to be implemented.
2141     // editMenu.add(justifyLeftMenuItem);
2142     // editMenu.add(justifyRightMenuItem);
2143     // editMenu.addSeparator();
2144     editMenu.add(padGapsMenuitem);
2145     viewMenu.add(newView);
2146     viewMenu.add(expandViews);
2147     viewMenu.add(gatherViews);
2148     viewMenu.addSeparator();
2149     viewMenu.add(jMenu3);
2150     viewMenu.add(hideMenu);
2151     viewMenu.addSeparator();
2152     viewMenu.add(followHighlightMenuItem);
2153     viewMenu.add(annotationPanelMenuItem);
2154     viewMenu.add(showAllAnnotations);
2155     viewMenu.add(hideAllAnnotations);
2156     autoAnnMenu.add(applyAutoAnnotationSettings);
2157     autoAnnMenu.add(showConsensusHistogram);
2158     autoAnnMenu.add(showSequenceLogo);
2159     autoAnnMenu.add(normaliseSequenceLogo);
2160     autoAnnMenu.addSeparator();
2161     autoAnnMenu.add(showGroupConservation);
2162     autoAnnMenu.add(showGroupConsensus);
2163     viewMenu.add(autoAnnMenu);
2164     viewMenu.addSeparator();
2165     viewMenu.add(showSeqFeatures);
2166     // viewMenu.add(showSeqFeaturesHeight);
2167
2168     viewMenu.add(openFeatureSettings);
2169     tooltipSettingsMenu.add(showDbRefsMenuitem);
2170     tooltipSettingsMenu.add(showNpFeatsMenuitem);
2171     viewMenu.add(tooltipSettingsMenu);
2172     viewMenu.addSeparator();
2173     viewMenu.add(alignmentProperties);
2174     viewMenu.addSeparator();
2175     viewMenu.add(overviewMenuItem);
2176     colourMenu.add(applyToAllGroups);
2177     colourMenu.add(textColour);
2178     colourMenu.addSeparator();
2179     colourMenu.add(noColourmenuItem);
2180     colourMenu.add(clustalColour);
2181     colourMenu.add(BLOSUM62Colour);
2182     colourMenu.add(PIDColour);
2183     colourMenu.add(zappoColour);
2184     colourMenu.add(taylorColour);
2185     colourMenu.add(hydrophobicityColour);
2186     colourMenu.add(helixColour);
2187     colourMenu.add(strandColour);
2188     colourMenu.add(turnColour);
2189     colourMenu.add(buriedColour);
2190     colourMenu.add(nucleotideColour);
2191     colourMenu.add(purinePyrimidineColour);
2192     colourMenu.add(RNAInteractionColour);
2193     // colourMenu.add(covariationColour);
2194     colourMenu.add(tcoffeeColour);
2195     colourMenu.add(userDefinedColour);
2196     colourMenu.addSeparator();
2197     colourMenu.add(conservationMenuItem);
2198     colourMenu.add(modifyConservation);
2199     colourMenu.add(abovePIDThreshold);
2200     colourMenu.add(modifyPID);
2201     colourMenu.add(annotationColour);
2202     colourMenu.add(rnahelicesColour);
2203     calculateMenu.add(sort);
2204     calculateMenu.add(calculateTree);
2205     calculateMenu.addSeparator();
2206     calculateMenu.add(pairwiseAlignmentMenuItem);
2207     calculateMenu.add(PCAMenuItem);
2208     calculateMenu.addSeparator();
2209     calculateMenu.add(showTranslation);
2210     calculateMenu.add(showProducts);
2211     calculateMenu.add(autoCalculate);
2212     calculateMenu.add(sortByTree);
2213     calculateMenu.addSeparator();
2214     calculateMenu.add(extractScores);
2215     webServiceNoServices = new JMenuItem(
2216             MessageManager.getString("label.no_services"));
2217     webService.add(webServiceNoServices);
2218     pasteMenu.add(pasteNew);
2219     pasteMenu.add(pasteThis);
2220     sort.add(sortIDMenuItem);
2221     sort.add(sortLengthMenuItem);
2222     sort.add(sortGroupMenuItem);
2223     sort.add(sortPairwiseMenuItem);
2224     sort.add(sortByTreeMenu);
2225     jMenu2.add(htmlMenuItem);
2226     jMenu2.add(epsFile);
2227     jMenu2.add(createPNG);
2228     addSequenceMenu.add(addFromFile);
2229     addSequenceMenu.add(addFromText);
2230     addSequenceMenu.add(addFromURL);
2231     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2232     statusPanel.add(statusBar, null);
2233     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2234     jMenu3.add(showAllColumns);
2235     jMenu3.add(showAllSeqs);
2236     jMenu3.add(showAllhidden);
2237     hideMenu.add(hideSelColumns);
2238     hideMenu.add(hideSelSequences);
2239     hideMenu.add(hideAllSelection);
2240     hideMenu.add(hideAllButSelection);
2241
2242     formatMenu.add(font);
2243     formatMenu.addSeparator();
2244     formatMenu.add(wrapMenuItem);
2245     formatMenu.add(scaleAbove);
2246     formatMenu.add(scaleLeft);
2247     formatMenu.add(scaleRight);
2248     formatMenu.add(seqLimits);
2249     formatMenu.add(idRightAlign);
2250     formatMenu.add(hiddenMarkers);
2251     formatMenu.add(viewBoxesMenuItem);
2252     formatMenu.add(viewTextMenuItem);
2253     formatMenu.add(colourTextMenuItem);
2254     formatMenu.add(renderGapsMenuItem);
2255     formatMenu.add(centreColumnLabelsMenuItem);
2256     formatMenu.add(showNonconservedMenuItem);
2257     selectMenu.add(findMenuItem);
2258     selectMenu.addSeparator();
2259     selectMenu.add(selectAllSequenceMenuItem);
2260     selectMenu.add(deselectAllSequenceMenuItem);
2261     selectMenu.add(invertSequenceMenuItem);
2262     selectMenu.add(invertColSel);
2263     selectMenu.add(createGroup);
2264     selectMenu.add(unGroup);
2265     selectMenu.add(grpsFromSelection);
2266     selectMenu.add(deleteGroups);
2267     calculateMenu.add(expandAlignment);
2268     // TODO - determine if the listenToViewSelections button is needed : see bug
2269     // JAL-574
2270     // selectMenu.addSeparator();
2271     // selectMenu.add(listenToViewSelections);
2272   }
2273
2274   /**
2275    * Action on clicking Show all annotations.
2276    */
2277   protected void showAllAnnotations_actionPerformed()
2278   {
2279     setAllAnnotationsVisibility(true);
2280   }
2281
2282   /**
2283    * Action on clicking Hide all annotations.
2284    */
2285   protected void hideAllAnnotations_actionPerformed()
2286   {
2287     setAllAnnotationsVisibility(false);
2288   }
2289
2290   /**
2291    * Set the visibility of all annotations to true or false.
2292    *
2293    * @param visible
2294    */
2295   protected void setAllAnnotationsVisibility(boolean visible)
2296   {
2297
2298   }
2299
2300   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2301   {
2302     // TODO Auto-generated method stub
2303
2304   }
2305
2306   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2307   {
2308     // TODO Auto-generated method stub
2309
2310   }
2311
2312   protected void showAllhidden_actionPerformed(ActionEvent e)
2313   {
2314     // TODO Auto-generated method stub
2315
2316   }
2317
2318   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2319   {
2320     // TODO Auto-generated method stub
2321
2322   }
2323
2324   protected void hideAllSelection_actionPerformed(ActionEvent e)
2325   {
2326     // TODO Auto-generated method stub
2327
2328   }
2329
2330   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2331   {
2332     // TODO Auto-generated method stub
2333
2334   }
2335
2336   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2337   {
2338     // TODO Auto-generated method stub
2339
2340   }
2341
2342   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2343   {
2344     // TODO Auto-generated method stub
2345
2346   }
2347
2348   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2349   {
2350     // TODO Auto-generated method stub
2351
2352   }
2353
2354   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2355   {
2356     // TODO Auto-generated method stub
2357
2358   }
2359
2360   protected void showGroupConservation_actionPerformed(ActionEvent e)
2361   {
2362     // TODO Auto-generated method stub
2363
2364   }
2365
2366   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2367   {
2368     // TODO Auto-generated method stub
2369
2370   }
2371
2372   protected void showSeqFeaturesHeight_actionPerformed(
2373           ActionEvent actionEvent)
2374   {
2375     // TODO Auto-generated method stub
2376
2377   }
2378
2379   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2380   {
2381     // TODO Auto-generated method stub
2382
2383   }
2384
2385   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2386   {
2387     // TODO Auto-generated method stub
2388
2389   }
2390
2391   protected void followHighlight_actionPerformed()
2392   {
2393     // TODO Auto-generated method stub
2394
2395   }
2396
2397   protected void showNpFeats_actionPerformed(ActionEvent e)
2398   {
2399     // TODO Auto-generated method stub
2400
2401   }
2402
2403   protected void showDbRefs_actionPerformed(ActionEvent e)
2404   {
2405     // TODO Auto-generated method stub
2406
2407   }
2408
2409   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2410   {
2411   }
2412
2413   protected void showProducts_actionPerformed(ActionEvent e)
2414   {
2415   }
2416
2417   protected void buildSortByAnnotationScoresMenu()
2418   {
2419   }
2420
2421   protected void extractScores_actionPerformed(ActionEvent e)
2422   {
2423   }
2424
2425   protected void outputText_actionPerformed(ActionEvent e)
2426   {
2427   }
2428
2429   public void addFromFile_actionPerformed(ActionEvent e)
2430   {
2431
2432   }
2433
2434   public void addFromText_actionPerformed(ActionEvent e)
2435   {
2436
2437   }
2438
2439   public void addFromURL_actionPerformed(ActionEvent e)
2440   {
2441
2442   }
2443
2444   public void exportFeatures_actionPerformed(ActionEvent e)
2445   {
2446
2447   }
2448
2449   public void exportAnnotations_actionPerformed(ActionEvent e)
2450   {
2451
2452   }
2453
2454   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2455   {
2456   }
2457
2458   protected void closeMenuItem_actionPerformed(boolean b)
2459   {
2460   }
2461
2462   protected void redoMenuItem_actionPerformed(ActionEvent e)
2463   {
2464   }
2465
2466   protected void undoMenuItem_actionPerformed(ActionEvent e)
2467   {
2468   }
2469
2470   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2471   {
2472   }
2473
2474   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2475   {
2476   }
2477
2478   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2479   {
2480   }
2481
2482   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2483   {
2484   }
2485
2486   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2487   {
2488   }
2489
2490   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2491   {
2492   }
2493
2494   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2495   {
2496   }
2497
2498   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2499   {
2500   }
2501
2502   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2503   {
2504   }
2505
2506   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2507   {
2508   }
2509
2510   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2511   {
2512   }
2513
2514   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2515   {
2516   }
2517
2518   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2519   {
2520   }
2521
2522   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2523   {
2524   }
2525
2526   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2527   {
2528   }
2529
2530   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2531   {
2532   }
2533
2534   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2535   {
2536   }
2537
2538   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2539   {
2540   }
2541
2542   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2543   {
2544   }
2545
2546   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2547   {
2548   }
2549
2550   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2551   {
2552   }
2553
2554   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2555   {
2556   }
2557
2558   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2559   {
2560   }
2561
2562   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2563   {
2564   }
2565
2566   protected void clustalColour_actionPerformed(ActionEvent e)
2567   {
2568   }
2569
2570   protected void zappoColour_actionPerformed(ActionEvent e)
2571   {
2572   }
2573
2574   protected void taylorColour_actionPerformed(ActionEvent e)
2575   {
2576   }
2577
2578   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2579   {
2580   }
2581
2582   protected void helixColour_actionPerformed(ActionEvent e)
2583   {
2584   }
2585
2586   protected void strandColour_actionPerformed(ActionEvent e)
2587   {
2588   }
2589
2590   protected void turnColour_actionPerformed(ActionEvent e)
2591   {
2592   }
2593
2594   protected void buriedColour_actionPerformed(ActionEvent e)
2595   {
2596   }
2597
2598   protected void userDefinedColour_actionPerformed(ActionEvent e)
2599   {
2600   }
2601
2602   protected void PIDColour_actionPerformed(ActionEvent e)
2603   {
2604   }
2605
2606   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2607   {
2608   }
2609
2610   protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2611   {
2612   }
2613
2614   protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2615   {
2616   }
2617
2618   /*
2619    * protected void covariationColour_actionPerformed(ActionEvent e) { }
2620    */
2621
2622   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2623   {
2624   }
2625
2626   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2627   {
2628   }
2629
2630   protected void printMenuItem_actionPerformed(ActionEvent e)
2631   {
2632   }
2633
2634   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2635   {
2636   }
2637
2638   protected void findMenuItem_actionPerformed(ActionEvent e)
2639   {
2640   }
2641
2642   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2643   {
2644   }
2645
2646   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2647   {
2648   }
2649
2650   protected void nucleotideColour_actionPerformed(ActionEvent e)
2651   {
2652   }
2653
2654   protected void deleteGroups_actionPerformed(ActionEvent e)
2655   {
2656   }
2657
2658   protected void createGroup_actionPerformed(ActionEvent e)
2659   {
2660   }
2661
2662   protected void unGroup_actionPerformed(ActionEvent e)
2663   {
2664   }
2665
2666   protected void copy_actionPerformed(ActionEvent e)
2667   {
2668   }
2669
2670   protected void cut_actionPerformed(ActionEvent e)
2671   {
2672   }
2673
2674   protected void delete_actionPerformed(ActionEvent e)
2675   {
2676   }
2677
2678   protected void pasteNew_actionPerformed(ActionEvent e)
2679   {
2680   }
2681
2682   protected void pasteThis_actionPerformed(ActionEvent e)
2683   {
2684   }
2685
2686   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2687   {
2688   }
2689
2690   public void createPNG(java.io.File f)
2691   {
2692   }
2693
2694   protected void font_actionPerformed(ActionEvent e)
2695   {
2696   }
2697
2698   protected void seqLimit_actionPerformed(ActionEvent e)
2699   {
2700   }
2701
2702   public void seqDBRef_actionPerformed(ActionEvent e)
2703   {
2704
2705   }
2706
2707   public void createEPS(java.io.File f)
2708   {
2709   }
2710
2711   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2712   {
2713
2714   }
2715
2716   /**
2717    * Template method to handle the 'load T-Coffee scores' menu event.
2718    * <p>
2719    * Subclasses override this method to provide a custom action.
2720    *
2721    * @param event
2722    *          The raised event
2723    */
2724   protected void loadScores_actionPerformed(ActionEvent event)
2725   {
2726
2727   }
2728
2729   /**
2730    * Template method to handle the 'Color T-Coffee scores' menu event.
2731    * <p>
2732    * Subclasses override this method to provide a custom action.
2733    *
2734    * @param event
2735    *          The raised event
2736    */
2737   protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2738   {
2739
2740   }
2741
2742   protected void jpred_actionPerformed(ActionEvent e)
2743   {
2744   }
2745
2746   protected void scaleAbove_actionPerformed(ActionEvent e)
2747   {
2748   }
2749
2750   protected void scaleLeft_actionPerformed(ActionEvent e)
2751   {
2752   }
2753
2754   protected void scaleRight_actionPerformed(ActionEvent e)
2755   {
2756   }
2757
2758   protected void modifyPID_actionPerformed(ActionEvent e)
2759   {
2760   }
2761
2762   protected void modifyConservation_actionPerformed(ActionEvent e)
2763   {
2764   }
2765
2766   protected void saveAs_actionPerformed(ActionEvent e)
2767   {
2768   }
2769
2770   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2771   {
2772   }
2773
2774   public void vamsasStore_actionPerformed(ActionEvent e)
2775   {
2776
2777   }
2778
2779   public void vamsasLoad_actionPerformed(ActionEvent e)
2780   {
2781
2782   }
2783
2784   public void showTranslation_actionPerformed(ActionEvent e)
2785   {
2786
2787   }
2788
2789   public void featureSettings_actionPerformed(ActionEvent e)
2790   {
2791
2792   }
2793
2794   public void fetchSequence_actionPerformed(ActionEvent e)
2795   {
2796
2797   }
2798
2799   public void smoothFont_actionPerformed(ActionEvent e)
2800   {
2801
2802   }
2803
2804   public void annotationColour_actionPerformed(ActionEvent e)
2805   {
2806
2807   }
2808
2809   public void rnahelicesColour_actionPerformed(ActionEvent e)
2810   {
2811
2812   }
2813
2814   public void associatedData_actionPerformed(ActionEvent e)
2815   {
2816
2817   }
2818
2819   public void autoCalculate_actionPerformed(ActionEvent e)
2820   {
2821
2822   }
2823
2824   public void sortByTreeOption_actionPerformed(ActionEvent e)
2825   {
2826
2827   }
2828
2829   public void showAllSeqs_actionPerformed(ActionEvent e)
2830   {
2831
2832   }
2833
2834   public void showAllColumns_actionPerformed(ActionEvent e)
2835   {
2836
2837   }
2838
2839   public void hideSelSequences_actionPerformed(ActionEvent e)
2840   {
2841
2842   }
2843
2844   public void hideSelColumns_actionPerformed(ActionEvent e)
2845   {
2846
2847   }
2848
2849   public void hiddenMarkers_actionPerformed(ActionEvent e)
2850   {
2851
2852   }
2853
2854   public void findPdbId_actionPerformed(ActionEvent e)
2855   {
2856
2857   }
2858
2859   public void enterPdbId_actionPerformed(ActionEvent e)
2860   {
2861
2862   }
2863
2864   public void pdbFile_actionPerformed(ActionEvent e)
2865   {
2866
2867   }
2868
2869   public void invertColSel_actionPerformed(ActionEvent e)
2870   {
2871
2872   }
2873
2874   public void tabSelectionChanged(int sel)
2875   {
2876
2877   }
2878
2879   public void tabbedPane_mousePressed(MouseEvent e)
2880   {
2881
2882   }
2883
2884   public void tabbedPane_focusGained(FocusEvent e)
2885   {
2886     requestFocus();
2887   }
2888
2889   public void save_actionPerformed(ActionEvent e)
2890   {
2891
2892   }
2893
2894   public void reload_actionPerformed(ActionEvent e)
2895   {
2896
2897   }
2898
2899   public void newView_actionPerformed(ActionEvent e)
2900   {
2901
2902   }
2903
2904   public void textColour_actionPerformed(ActionEvent e)
2905   {
2906
2907   }
2908
2909   public void idRightAlign_actionPerformed(ActionEvent e)
2910   {
2911
2912   }
2913
2914   public void expandViews_actionPerformed(ActionEvent e)
2915   {
2916
2917   }
2918
2919   public void gatherViews_actionPerformed(ActionEvent e)
2920   {
2921
2922   }
2923
2924   public void buildTreeMenu()
2925   {
2926
2927   }
2928
2929   public void pageSetup_actionPerformed(ActionEvent e)
2930   {
2931
2932   }
2933
2934   public void alignmentProperties()
2935   {
2936
2937   }
2938
2939   protected void expand_newalign(ActionEvent e)
2940   {
2941     // TODO Auto-generated method stub
2942
2943   }
2944 }