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