src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
   3  * Copyright (C) 2014 The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.jbgui;
  22
  23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  24 import jalview.bin.Cache;
  25 import jalview.gui.JvSwingUtils;
  26 import jalview.gui.Preferences;
  27 import jalview.schemes.ColourSchemeProperty;
  28 import jalview.util.MessageManager;
  29
  30 import java.awt.BorderLayout;
  31 import java.awt.Color;
  32 import java.awt.GridLayout;
  33 import java.awt.Toolkit;
  34 import java.awt.event.ActionEvent;
  35 import java.awt.event.ActionListener;
  36 import java.awt.event.FocusAdapter;
  37 import java.awt.event.FocusEvent;
  38 import java.awt.event.MouseAdapter;
  39 import java.awt.event.MouseEvent;
  40
  41 import javax.swing.BorderFactory;
  42 import javax.swing.ButtonGroup;
  43 import javax.swing.JCheckBoxMenuItem;
  44 import javax.swing.JInternalFrame;
  45 import javax.swing.JLabel;
  46 import javax.swing.JMenu;
  47 import javax.swing.JMenuBar;
  48 import javax.swing.JMenuItem;
  49 import javax.swing.JOptionPane;
  50 import javax.swing.JPanel;
  51 import javax.swing.JRadioButtonMenuItem;
  52 import javax.swing.JTabbedPane;
  53 import javax.swing.SwingUtilities;
  54 import javax.swing.event.ChangeEvent;
  55 import javax.swing.event.MenuEvent;
  56 import javax.swing.event.MenuListener;
  57
  58 public class GAlignFrame extends JInternalFrame
  59 {
  60   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  61
  62   protected JMenu fileMenu = new JMenu();
  63
  64   protected JMenuItem closeMenuItem = new JMenuItem();
  65
  66   protected JMenu editMenu = new JMenu();
  67
  68   protected JMenu viewMenu = new JMenu();
  69
  70   protected JMenu annotationsMenu = new JMenu();
  71
  72   protected JMenu colourMenu = new JMenu();
  73
  74   protected JMenu calculateMenu = new JMenu();
  75
  76   protected JMenu webService = new JMenu();
  77
  78   protected JMenuItem webServiceNoServices;
  79
  80   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  81
  82   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  83
  84   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  85
  86   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  87
  88   protected JMenuItem remove2RightMenuItem = new JMenuItem();
  89
  90   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  91
  92   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  93
  94   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  95
  96   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  97
  98   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  99
 100   protected JMenuItem sortIDMenuItem = new JMenuItem();
 101
 102   protected JMenuItem sortLengthMenuItem = new JMenuItem();
 103
 104   protected JMenuItem sortGroupMenuItem = new JMenuItem();
 105
 106   protected JMenu sortByAnnotScore = new JMenu();
 107
 108   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
 109
 110   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
 111
 112   protected JMenuItem PCAMenuItem = new JMenuItem();
 113
 114   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
 115
 116   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
 117
 118   BorderLayout borderLayout1 = new BorderLayout();
 119
 120   public JLabel statusBar = new JLabel();
 121
 122   protected JMenuItem saveAs = new JMenuItem();
 123
 124   protected JMenu outputTextboxMenu = new JMenu();
 125
 126   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
 127
 128   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
 129
 130   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
 131
 132   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
 133
 134   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
 135
 136   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
 137
 138   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
 139
 140   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 141
 142   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
 143
 144   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
 145
 146   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 147
 148   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
 149
 150   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
 151
 152   protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
 153
 154   // protected JRadioButtonMenuItem covariationColour = new
 155   // JRadioButtonMenuItem();
 156
 157   protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
 158
 159   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 160
 161   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
 162
 163   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 164
 165   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 166
 167   public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
 168
 169   JMenuItem htmlMenuItem = new JMenuItem();
 170
 171   JMenuItem overviewMenuItem = new JMenuItem();
 172
 173   protected JMenuItem undoMenuItem = new JMenuItem();
 174
 175   protected JMenuItem redoMenuItem = new JMenuItem();
 176
 177   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 178
 179   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 180
 181   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 182
 183   JMenuItem printMenuItem = new JMenuItem();
 184
 185   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 186
 187   JMenuItem findMenuItem = new JMenuItem();
 188
 189   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 190
 191   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 192
 193   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 194
 195   JMenuItem deleteGroups = new JMenuItem();
 196
 197   JMenuItem createGroup = new JMenuItem();
 198
 199   JMenuItem unGroup = new JMenuItem();
 200
 201   JMenuItem delete = new JMenuItem();
 202
 203   JMenuItem copy = new JMenuItem();
 204
 205   JMenuItem cut = new JMenuItem();
 206
 207   JMenu pasteMenu = new JMenu();
 208
 209   JMenuItem pasteNew = new JMenuItem();
 210
 211   JMenuItem pasteThis = new JMenuItem();
 212
 213   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
 214
 215   JMenuItem createPNG = new JMenuItem();
 216
 217   JMenuItem createSVG = new JMenuItem();
 218
 219   protected JMenuItem font = new JMenuItem();
 220
 221   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 222
 223   JMenuItem epsFile = new JMenuItem();
 224
 225   JMenuItem LoadtreeMenuItem = new JMenuItem();
 226
 227   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 228
 229   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 230
 231   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 232
 233   protected JMenuItem modifyPID = new JMenuItem();
 234
 235   protected JMenuItem modifyConservation = new JMenuItem();
 236
 237   protected JMenu sortByTreeMenu = new JMenu();
 238
 239   protected JMenu sort = new JMenu();
 240
 241   protected JMenu calculateTree = new JMenu();
 242
 243   JMenu jMenu2 = new JMenu();
 244
 245   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 246
 247   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 248
 249   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 250
 251   protected ButtonGroup colours = new ButtonGroup();
 252
 253   JMenuItem vamsasStore = new JMenuItem();
 254
 255   protected JMenuItem showTranslation = new JMenuItem();
 256
 257   protected JMenuItem extractScores = new JMenuItem();
 258
 259   protected JMenuItem expandAlignment = new JMenuItem();
 260
 261   protected JMenu showProducts = new JMenu();
 262
 263   public JMenuItem openFeatureSettings = new JMenuItem();
 264
 265   JMenuItem fetchSequence = new JMenuItem();
 266
 267   JMenuItem annotationColour = new JMenuItem();
 268
 269   protected JMenuItem rnahelicesColour = new JMenuItem();
 270
 271   JMenuItem associatedData = new JMenuItem();
 272
 273   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 274
 275   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 276
 277   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 278
 279   JMenu addSequenceMenu = new JMenu();
 280
 281   JMenuItem addFromFile = new JMenuItem();
 282
 283   JMenuItem addFromText = new JMenuItem();
 284
 285   JMenuItem addFromURL = new JMenuItem();
 286
 287   JMenuItem exportAnnotations = new JMenuItem();
 288
 289   JMenuItem exportFeatures = new JMenuItem();
 290
 291   protected JPanel statusPanel = new JPanel();
 292
 293   GridLayout gridLayout1 = new GridLayout();
 294
 295   JMenu jMenu3 = new JMenu();
 296
 297   JMenuItem showAllSeqs = new JMenuItem();
 298
 299   JMenuItem showAllColumns = new JMenuItem();
 300
 301   JMenu hideMenu = new JMenu();
 302
 303   JMenuItem hideSelSequences = new JMenuItem();
 304
 305   JMenuItem hideSelColumns = new JMenuItem();
 306
 307   JMenuItem hideAllButSelection = new JMenuItem();
 308
 309   JMenuItem hideAllSelection = new JMenuItem();
 310
 311   JMenuItem showAllhidden = new JMenuItem();
 312
 313   protected JMenuItem showAllSeqAnnotations = new JMenuItem();
 314
 315   protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
 316
 317   protected JMenuItem showAllAlAnnotations = new JMenuItem();
 318
 319   protected JMenuItem hideAllAlAnnotations = new JMenuItem();
 320
 321   protected JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem();
 322
 323   protected JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem();
 324
 325   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 326
 327   JMenuItem invertColSel = new JMenuItem();
 328
 329   protected JTabbedPane tabbedPane = new JTabbedPane();
 330
 331   JMenuItem save = new JMenuItem();
 332
 333   protected JMenuItem reload = new JMenuItem();
 334
 335   JMenuItem newView = new JMenuItem();
 336
 337   JMenuItem textColour = new JMenuItem();
 338
 339   JMenu formatMenu = new JMenu();
 340
 341   JMenu selectMenu = new JMenu();
 342
 343   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 344
 345   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 346
 347   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 348
 349   protected JMenuItem gatherViews = new JMenuItem();
 350
 351   protected JMenuItem expandViews = new JMenuItem();
 352
 353   JMenuItem pageSetup = new JMenuItem();
 354
 355   JMenuItem alignmentProperties = new JMenuItem();
 356
 357   JMenu tooltipSettingsMenu = new JMenu();
 358
 359   private JMenuItem justifyLeftMenuItem = new JMenuItem();
 360
 361   private JMenuItem justifyRightMenuItem = new JMenuItem();
 362
 363   JMenu autoAnnMenu = new JMenu();
 364
 365   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 366
 367   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 368
 369   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 370
 371   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 372
 373   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 374
 375   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 376
 377   protected JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem();
 378
 379   protected JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem();
 380
 381   private JMenuItem grpsFromSelection = new JMenuItem();
 382
 383   private SequenceAnnotationOrder annotationSortOrder;
 384
 385   private boolean showAutoCalculatedAbove = false;
 386
 387   public GAlignFrame()
 388   {
 389     try
 390     {
 391       jbInit();
 392       setJMenuBar(alignFrameMenuBar);
 393
 394       // dynamically fill save as menu with available formats
 395       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 396       {
 397         JMenuItem item = new JMenuItem(
 398                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 399
 400         item.addActionListener(new java.awt.event.ActionListener()
 401         {
 402           @Override
 403           public void actionPerformed(ActionEvent e)
 404           {
 405             outputText_actionPerformed(e);
 406           }
 407         });
 408
 409         outputTextboxMenu.add(item);
 410       }
 411     } catch (Exception e)
 412     {
 413       System.err.println(e.toString());
 414     }
 415
 416     if (!new jalview.util.Platform().isAMac())
 417     {
 418       closeMenuItem.setMnemonic('C');
 419       outputTextboxMenu.setMnemonic('T');
 420       undoMenuItem.setMnemonic('Z');
 421       redoMenuItem.setMnemonic('0');
 422       copy.setMnemonic('C');
 423       cut.setMnemonic('U');
 424       pasteMenu.setMnemonic('P');
 425       reload.setMnemonic('R');
 426     }
 427
 428     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 429     {
 430       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 431               .getUserColourSchemes().keys();
 432
 433       while (userColours.hasMoreElements())
 434       {
 435         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 436                 userColours.nextElement().toString());
 437         radioItem.setName("USER_DEFINED");
 438         radioItem.addMouseListener(new MouseAdapter()
 439         {
 440           @Override
 441           public void mousePressed(MouseEvent evt)
 442           {
 443             if (evt.isControlDown()
 444                     || SwingUtilities.isRightMouseButton(evt))
 445             {
 446               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 447
 448               int option = JOptionPane.showInternalConfirmDialog(
 449                       jalview.gui.Desktop.desktop,
 450                       MessageManager
 451                               .getString("label.remove_from_default_list"),
 452                       MessageManager
 453                               .getString("label.remove_user_defined_colour"),
 454                       JOptionPane.YES_NO_OPTION);
 455               if (option == JOptionPane.YES_OPTION)
 456               {
 457                 jalview.gui.UserDefinedColours
 458                         .removeColourFromDefaults(radioItem.getText());
 459                 colourMenu.remove(radioItem);
 460               }
 461               else
 462               {
 463                 radioItem.addActionListener(new ActionListener()
 464                 {
 465                   @Override
 466                   public void actionPerformed(ActionEvent evt)
 467                   {
 468                     userDefinedColour_actionPerformed(evt);
 469                   }
 470                 });
 471               }
 472             }
 473           }
 474         });
 475         radioItem.addActionListener(new ActionListener()
 476         {
 477           @Override
 478           public void actionPerformed(ActionEvent evt)
 479           {
 480             userDefinedColour_actionPerformed(evt);
 481           }
 482         });
 483         colourMenu.insert(radioItem, 15);
 484         colours.add(radioItem);
 485       }
 486     }
 487     colours.add(noColourmenuItem);
 488     colours.add(clustalColour);
 489     colours.add(zappoColour);
 490     colours.add(taylorColour);
 491     colours.add(hydrophobicityColour);
 492     colours.add(helixColour);
 493     colours.add(strandColour);
 494     colours.add(turnColour);
 495     colours.add(buriedColour);
 496     colours.add(userDefinedColour);
 497     colours.add(PIDColour);
 498     colours.add(BLOSUM62Colour);
 499     colours.add(nucleotideColour);
 500     colours.add(purinePyrimidineColour);
 501     // colours.add(covariationColour);
 502     colours.add(tcoffeeColour);
 503     colours.add(RNAInteractionColour);
 504     setColourSelected(jalview.bin.Cache
 505             .getDefault("DEFAULT_COLOUR", "None"));
 506
 507   }
 508
 509   public void setColourSelected(String defaultColour)
 510   {
 511
 512     if (defaultColour != null)
 513     {
 514       int index = ColourSchemeProperty
 515               .getColourIndexFromName(defaultColour);
 516
 517       switch (index)
 518       {
 519       case ColourSchemeProperty.CLUSTAL:
 520         clustalColour.setSelected(true);
 521
 522         break;
 523
 524       case ColourSchemeProperty.BLOSUM:
 525         BLOSUM62Colour.setSelected(true);
 526
 527         break;
 528
 529       case ColourSchemeProperty.PID:
 530         PIDColour.setSelected(true);
 531
 532         break;
 533
 534       case ColourSchemeProperty.ZAPPO:
 535         zappoColour.setSelected(true);
 536
 537         break;
 538
 539       case ColourSchemeProperty.TAYLOR:
 540         taylorColour.setSelected(true);
 541         break;
 542
 543       case ColourSchemeProperty.HYDROPHOBIC:
 544         hydrophobicityColour.setSelected(true);
 545
 546         break;
 547
 548       case ColourSchemeProperty.HELIX:
 549         helixColour.setSelected(true);
 550
 551         break;
 552
 553       case ColourSchemeProperty.STRAND:
 554         strandColour.setSelected(true);
 555
 556         break;
 557
 558       case ColourSchemeProperty.TURN:
 559         turnColour.setSelected(true);
 560
 561         break;
 562
 563       case ColourSchemeProperty.BURIED:
 564         buriedColour.setSelected(true);
 565
 566         break;
 567
 568       case ColourSchemeProperty.NUCLEOTIDE:
 569         nucleotideColour.setSelected(true);
 570
 571         break;
 572
 573       case ColourSchemeProperty.TCOFFEE:
 574         tcoffeeColour.setSelected(true);
 575         break;
 576
 577       case ColourSchemeProperty.PURINEPYRIMIDINE:
 578         purinePyrimidineColour.setSelected(true);
 579
 580         break;
 581
 582       case ColourSchemeProperty.RNAINTERACTION:
 583         RNAInteractionColour.setSelected(true);
 584
 585         break;
 586       /*
 587        * case ColourSchemeProperty.COVARIATION:
 588        * covariationColour.setSelected(true);
 589        *
 590        * break;
 591        */
 592       case ColourSchemeProperty.USER_DEFINED:
 593         userDefinedColour.setSelected(true);
 594
 595         break;
 596       case ColourSchemeProperty.NONE:
 597       default:
 598         noColourmenuItem.setSelected(true);
 599         break;
 600
 601       }
 602     }
 603
 604   }
 605
 606   private void jbInit() throws Exception
 607   {
 608     fileMenu.setText(MessageManager.getString("action.file"));
 609     saveAs.setText(MessageManager.getString("action.save_as") + "...");
 610     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 611             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
 612                     .getMenuShortcutKeyMask()
 613                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 614     saveAs.addActionListener(new ActionListener()
 615     {
 616       @Override
 617       public void actionPerformed(ActionEvent e)
 618       {
 619         saveAs_actionPerformed(e);
 620       }
 621     });
 622     closeMenuItem.setText(MessageManager.getString("action.close"));
 623     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 624             java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
 625                     .getMenuShortcutKeyMask(), false));
 626     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 627     {
 628       @Override
 629       public void actionPerformed(ActionEvent e)
 630       {
 631         closeMenuItem_actionPerformed(false);
 632       }
 633     });
 634     editMenu.setText(MessageManager.getString("action.edit"));
 635     viewMenu.setText(MessageManager.getString("action.view"));
 636     annotationsMenu.setText(MessageManager.getString("action.annotations"));
 637     colourMenu.setText(MessageManager.getString("action.colour"));
 638     calculateMenu.setText(MessageManager.getString("action.calculate"));
 639     webService.setText(MessageManager.getString("action.web_service"));
 640     selectAllSequenceMenuItem.setText(MessageManager
 641             .getString("action.select_all"));
 642     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 643             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
 644                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 645     selectAllSequenceMenuItem
 646             .addActionListener(new java.awt.event.ActionListener()
 647             {
 648               @Override
 649               public void actionPerformed(ActionEvent e)
 650               {
 651                 selectAllSequenceMenuItem_actionPerformed(e);
 652               }
 653             });
 654     deselectAllSequenceMenuItem.setText(MessageManager
 655             .getString("action.deselect_all"));
 656     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 657             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 658     deselectAllSequenceMenuItem
 659             .addActionListener(new java.awt.event.ActionListener()
 660             {
 661               @Override
 662               public void actionPerformed(ActionEvent e)
 663               {
 664                 deselectAllSequenceMenuItem_actionPerformed(e);
 665               }
 666             });
 667     invertSequenceMenuItem.setText(MessageManager
 668             .getString("action.invert_sequence_selection"));
 669     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 670             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
 671                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 672     invertSequenceMenuItem
 673             .addActionListener(new java.awt.event.ActionListener()
 674             {
 675               @Override
 676               public void actionPerformed(ActionEvent e)
 677               {
 678                 invertSequenceMenuItem_actionPerformed(e);
 679               }
 680             });
 681     grpsFromSelection.setText(MessageManager
 682             .getString("action.make_groups_selection"));
 683     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
 684     {
 685       @Override
 686       public void actionPerformed(ActionEvent e)
 687       {
 688         makeGrpsFromSelection_actionPerformed(e);
 689       }
 690     });
 691     expandAlignment.setText(MessageManager
 692             .getString("action.view_flanking_regions"));
 693     expandAlignment.setToolTipText(MessageManager
 694             .getString("label.view_flanking_regions"));
 695     expandAlignment.addActionListener(new java.awt.event.ActionListener()
 696     {
 697       @Override
 698       public void actionPerformed(ActionEvent e)
 699       {
 700         expand_newalign(e);
 701       }
 702     });
 703     remove2LeftMenuItem.setText(MessageManager
 704             .getString("action.remove_left"));
 705     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 706             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
 707                     .getMenuShortcutKeyMask(), false));
 708     remove2LeftMenuItem
 709             .addActionListener(new java.awt.event.ActionListener()
 710             {
 711               @Override
 712               public void actionPerformed(ActionEvent e)
 713               {
 714                 remove2LeftMenuItem_actionPerformed(e);
 715               }
 716             });
 717     remove2RightMenuItem.setText(MessageManager
 718             .getString("action.remove_right"));
 719     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 720             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
 721                     .getMenuShortcutKeyMask(), false));
 722     remove2RightMenuItem
 723             .addActionListener(new java.awt.event.ActionListener()
 724             {
 725               @Override
 726               public void actionPerformed(ActionEvent e)
 727               {
 728                 remove2RightMenuItem_actionPerformed(e);
 729               }
 730             });
 731     removeGappedColumnMenuItem.setText(MessageManager
 732             .getString("action.remove_empty_columns"));
 733     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
 734             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 735                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 736     removeGappedColumnMenuItem
 737             .addActionListener(new java.awt.event.ActionListener()
 738             {
 739               @Override
 740               public void actionPerformed(ActionEvent e)
 741               {
 742                 removeGappedColumnMenuItem_actionPerformed(e);
 743               }
 744             });
 745     removeAllGapsMenuItem.setText(MessageManager
 746             .getString("action.remove_all_gaps"));
 747     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
 748             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 749                     .getDefaultToolkit().getMenuShortcutKeyMask()
 750                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 751     removeAllGapsMenuItem
 752             .addActionListener(new java.awt.event.ActionListener()
 753             {
 754               @Override
 755               public void actionPerformed(ActionEvent e)
 756               {
 757                 removeAllGapsMenuItem_actionPerformed(e);
 758               }
 759             });
 760     justifyLeftMenuItem.setText(MessageManager
 761             .getString("action.left_justify_alignment"));
 762     justifyLeftMenuItem
 763             .addActionListener(new java.awt.event.ActionListener()
 764             {
 765               @Override
 766               public void actionPerformed(ActionEvent e)
 767               {
 768                 justifyLeftMenuItem_actionPerformed(e);
 769               }
 770             });
 771     justifyRightMenuItem.setText(MessageManager
 772             .getString("action.right_justify_alignment"));
 773     justifyRightMenuItem
 774             .addActionListener(new java.awt.event.ActionListener()
 775             {
 776               @Override
 777               public void actionPerformed(ActionEvent e)
 778               {
 779                 justifyRightMenuItem_actionPerformed(e);
 780               }
 781             });
 782     viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
 783     viewBoxesMenuItem.setState(true);
 784     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 785     {
 786       @Override
 787       public void actionPerformed(ActionEvent e)
 788       {
 789         viewBoxesMenuItem_actionPerformed(e);
 790       }
 791     });
 792     viewTextMenuItem.setText(MessageManager.getString("action.text"));
 793     viewTextMenuItem.setState(true);
 794     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 795     {
 796       @Override
 797       public void actionPerformed(ActionEvent e)
 798       {
 799         viewTextMenuItem_actionPerformed(e);
 800       }
 801     });
 802     showNonconservedMenuItem.setText(MessageManager
 803             .getString("label.show_non_conversed"));
 804     showNonconservedMenuItem.setState(false);
 805     showNonconservedMenuItem
 806             .addActionListener(new java.awt.event.ActionListener()
 807             {
 808               @Override
 809               public void actionPerformed(ActionEvent e)
 810               {
 811                 showUnconservedMenuItem_actionPerformed(e);
 812               }
 813             });
 814     sortPairwiseMenuItem.setText(MessageManager
 815             .getString("action.by_pairwise_id"));
 816     sortPairwiseMenuItem
 817             .addActionListener(new java.awt.event.ActionListener()
 818             {
 819               @Override
 820               public void actionPerformed(ActionEvent e)
 821               {
 822                 sortPairwiseMenuItem_actionPerformed(e);
 823               }
 824             });
 825     sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
 826     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 827     {
 828       @Override
 829       public void actionPerformed(ActionEvent e)
 830       {
 831         sortIDMenuItem_actionPerformed(e);
 832       }
 833     });
 834     sortLengthMenuItem
 835             .setText(MessageManager.getString("action.by_length"));
 836     sortLengthMenuItem
 837             .addActionListener(new java.awt.event.ActionListener()
 838             {
 839               @Override
 840               public void actionPerformed(ActionEvent e)
 841               {
 842                 sortLengthMenuItem_actionPerformed(e);
 843               }
 844             });
 845     sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
 846     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 847     {
 848       @Override
 849       public void actionPerformed(ActionEvent e)
 850       {
 851         sortGroupMenuItem_actionPerformed(e);
 852       }
 853     });
 854     removeRedundancyMenuItem.setText(MessageManager
 855             .getString("action.remove_redundancy").concat("..."));
 856     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
 857             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
 858                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 859     removeRedundancyMenuItem
 860             .addActionListener(new java.awt.event.ActionListener()
 861             {
 862               @Override
 863               public void actionPerformed(ActionEvent e)
 864               {
 865                 removeRedundancyMenuItem_actionPerformed(e);
 866               }
 867             });
 868     pairwiseAlignmentMenuItem.setText(MessageManager
 869             .getString("action.pairwise_alignment"));
 870     pairwiseAlignmentMenuItem
 871             .addActionListener(new java.awt.event.ActionListener()
 872             {
 873               @Override
 874               public void actionPerformed(ActionEvent e)
 875               {
 876                 pairwiseAlignmentMenuItem_actionPerformed(e);
 877               }
 878             });
 879     PCAMenuItem.setText(MessageManager
 880             .getString("label.principal_component_analysis"));
 881     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 882     {
 883       @Override
 884       public void actionPerformed(ActionEvent e)
 885       {
 886         PCAMenuItem_actionPerformed(e);
 887       }
 888     });
 889     averageDistanceTreeMenuItem.setText(MessageManager
 890             .getString("label.average_distance_identity"));
 891     averageDistanceTreeMenuItem
 892             .addActionListener(new java.awt.event.ActionListener()
 893             {
 894               @Override
 895               public void actionPerformed(ActionEvent e)
 896               {
 897                 averageDistanceTreeMenuItem_actionPerformed(e);
 898               }
 899             });
 900     neighbourTreeMenuItem.setText(MessageManager
 901             .getString("label.neighbour_joining_identity"));
 902     neighbourTreeMenuItem
 903             .addActionListener(new java.awt.event.ActionListener()
 904             {
 905               @Override
 906               public void actionPerformed(ActionEvent e)
 907               {
 908                 neighbourTreeMenuItem_actionPerformed(e);
 909               }
 910             });
 911     this.getContentPane().setLayout(borderLayout1);
 912     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 913     statusBar.setBackground(Color.white);
 914     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 915     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 916     statusBar.setText(MessageManager.getString("label.status_bar"));
 917     outputTextboxMenu.setText(MessageManager
 918             .getString("label.out_to_textbox"));
 919     clustalColour.setText(MessageManager.getString("label.clustalx"));
 920
 921     clustalColour.addActionListener(new java.awt.event.ActionListener()
 922     {
 923       @Override
 924       public void actionPerformed(ActionEvent e)
 925       {
 926         clustalColour_actionPerformed(e);
 927       }
 928     });
 929     zappoColour.setText(MessageManager.getString("label.zappo"));
 930     zappoColour.addActionListener(new java.awt.event.ActionListener()
 931     {
 932       @Override
 933       public void actionPerformed(ActionEvent e)
 934       {
 935         zappoColour_actionPerformed(e);
 936       }
 937     });
 938     taylorColour.setText(MessageManager.getString("label.taylor"));
 939     taylorColour.addActionListener(new java.awt.event.ActionListener()
 940     {
 941       @Override
 942       public void actionPerformed(ActionEvent e)
 943       {
 944         taylorColour_actionPerformed(e);
 945       }
 946     });
 947     hydrophobicityColour.setText(MessageManager
 948             .getString("label.hydrophobicity"));
 949     hydrophobicityColour
 950             .addActionListener(new java.awt.event.ActionListener()
 951             {
 952               @Override
 953               public void actionPerformed(ActionEvent e)
 954               {
 955                 hydrophobicityColour_actionPerformed(e);
 956               }
 957             });
 958     helixColour.setText(MessageManager.getString("label.helix_propensity"));
 959     helixColour.addActionListener(new java.awt.event.ActionListener()
 960     {
 961       @Override
 962       public void actionPerformed(ActionEvent e)
 963       {
 964         helixColour_actionPerformed(e);
 965       }
 966     });
 967     strandColour.setText(MessageManager
 968             .getString("label.strand_propensity"));
 969     strandColour.addActionListener(new java.awt.event.ActionListener()
 970     {
 971       @Override
 972       public void actionPerformed(ActionEvent e)
 973       {
 974         strandColour_actionPerformed(e);
 975       }
 976     });
 977     turnColour.setText(MessageManager.getString("label.turn_propensity"));
 978     turnColour.addActionListener(new java.awt.event.ActionListener()
 979     {
 980       @Override
 981       public void actionPerformed(ActionEvent e)
 982       {
 983         turnColour_actionPerformed(e);
 984       }
 985     });
 986     buriedColour.setText(MessageManager.getString("label.buried_index"));
 987     buriedColour.addActionListener(new java.awt.event.ActionListener()
 988     {
 989       @Override
 990       public void actionPerformed(ActionEvent e)
 991       {
 992         buriedColour_actionPerformed(e);
 993       }
 994     });
 995     userDefinedColour.setText(MessageManager
 996             .getString("action.user_defined"));
 997     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 998     {
 999       @Override
1000       public void actionPerformed(ActionEvent e)
1001       {
1002         userDefinedColour_actionPerformed(e);
1003       }
1004     });
1005     PIDColour
1006             .setText(MessageManager.getString("label.percentage_identity"));
1007     PIDColour.addActionListener(new java.awt.event.ActionListener()
1008     {
1009       @Override
1010       public void actionPerformed(ActionEvent e)
1011       {
1012         PIDColour_actionPerformed(e);
1013       }
1014     });
1015     BLOSUM62Colour
1016             .setText(MessageManager.getString("label.blosum62_score"));
1017     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1018     {
1019       @Override
1020       public void actionPerformed(ActionEvent e)
1021       {
1022         BLOSUM62Colour_actionPerformed(e);
1023       }
1024     });
1025     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1026     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1027     {
1028       @Override
1029       public void actionPerformed(ActionEvent e)
1030       {
1031         nucleotideColour_actionPerformed(e);
1032       }
1033     });
1034
1035     purinePyrimidineColour.setText(MessageManager
1036             .getString("label.purine_pyrimidine"));
1037     purinePyrimidineColour
1038             .addActionListener(new java.awt.event.ActionListener()
1039             {
1040               @Override
1041               public void actionPerformed(ActionEvent e)
1042               {
1043                 purinePyrimidineColour_actionPerformed(e);
1044               }
1045             });
1046
1047     RNAInteractionColour.setText("RNA Interaction type");
1048     RNAInteractionColour
1049             .addActionListener(new java.awt.event.ActionListener()
1050             {
1051               @Override
1052               public void actionPerformed(ActionEvent e)
1053               {
1054                 RNAInteractionColour_actionPerformed(e);
1055               }
1056             });
1057     /*
1058      * covariationColour.setText("Covariation");
1059      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1060      * public void actionPerformed(ActionEvent e) {
1061      * covariationColour_actionPerformed(e); } });
1062      */
1063
1064     avDistanceTreeBlosumMenuItem.setText(MessageManager
1065             .getString("label.average_distance_bloslum62"));
1066     avDistanceTreeBlosumMenuItem
1067             .addActionListener(new java.awt.event.ActionListener()
1068             {
1069               @Override
1070               public void actionPerformed(ActionEvent e)
1071               {
1072                 avTreeBlosumMenuItem_actionPerformed(e);
1073               }
1074             });
1075     njTreeBlosumMenuItem.setText(MessageManager
1076             .getString("label.neighbour_blosum62"));
1077     njTreeBlosumMenuItem
1078             .addActionListener(new java.awt.event.ActionListener()
1079             {
1080               @Override
1081               public void actionPerformed(ActionEvent e)
1082               {
1083                 njTreeBlosumMenuItem_actionPerformed(e);
1084               }
1085             });
1086     annotationPanelMenuItem.setActionCommand("");
1087     annotationPanelMenuItem.setText(MessageManager
1088             .getString("label.show_annotations"));
1089     annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
1090             true));
1091     annotationPanelMenuItem.addActionListener(new ActionListener()
1092     {
1093       @Override
1094       public void actionPerformed(ActionEvent e)
1095       {
1096         annotationPanelMenuItem_actionPerformed(e);
1097       }
1098     });
1099     showAllAlAnnotations.setText(MessageManager
1100             .getString("label.show_all_al_annotations"));
1101     final boolean isAnnotationPanelShown = annotationPanelMenuItem
1102             .getState();
1103     showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
1104     showAllAlAnnotations.addActionListener(new ActionListener()
1105     {
1106       @Override
1107       public void actionPerformed(ActionEvent e)
1108       {
1109         showAllAnnotations_actionPerformed(false, true);
1110       }
1111     });
1112     hideAllAlAnnotations.setText(MessageManager
1113             .getString("label.hide_all_al_annotations"));
1114     hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
1115     hideAllAlAnnotations.addActionListener(new ActionListener()
1116     {
1117       @Override
1118       public void actionPerformed(ActionEvent e)
1119       {
1120         hideAllAnnotations_actionPerformed(false, true);
1121       }
1122     });
1123     showAllSeqAnnotations.setText(MessageManager
1124             .getString("label.show_all_seq_annotations"));
1125     showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
1126     showAllSeqAnnotations.addActionListener(new ActionListener()
1127     {
1128       @Override
1129       public void actionPerformed(ActionEvent e)
1130       {
1131         showAllAnnotations_actionPerformed(true, false);
1132       }
1133     });
1134     hideAllSeqAnnotations.setText(MessageManager
1135             .getString("label.hide_all_seq_annotations"));
1136     hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
1137     hideAllSeqAnnotations.addActionListener(new ActionListener()
1138     {
1139       @Override
1140       public void actionPerformed(ActionEvent e)
1141       {
1142         hideAllAnnotations_actionPerformed(true, false);
1143       }
1144     });
1145     SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
1146             .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
1147                     SequenceAnnotationOrder.NONE.name()));
1148     sortAnnBySequence.setText(MessageManager
1149             .getString("label.sort_annotations_by_sequence"));
1150     sortAnnBySequence
1151             .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
1152     sortAnnBySequence.addActionListener(new ActionListener()
1153     {
1154       @Override
1155       public void actionPerformed(ActionEvent e)
1156       {
1157         boolean newState = sortAnnBySequence.getState();
1158         sortAnnByLabel.setSelected(false);
1159         setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
1160                 : SequenceAnnotationOrder.NONE);
1161         sortAnnotations_actionPerformed();
1162       }
1163     });
1164     sortAnnByLabel.setText(MessageManager
1165             .getString("label.sort_annotations_by_label"));
1166     sortAnnByLabel
1167             .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
1168     sortAnnByLabel.addActionListener(new ActionListener()
1169     {
1170       @Override
1171       public void actionPerformed(ActionEvent e)
1172       {
1173         boolean newState = sortAnnByLabel.getState();
1174         sortAnnBySequence.setSelected(false);
1175         setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
1176                 : SequenceAnnotationOrder.NONE);
1177         sortAnnotations_actionPerformed();
1178       }
1179     });
1180     colourTextMenuItem.setText(MessageManager
1181             .getString("label.colour_text"));
1182     colourTextMenuItem
1183             .addActionListener(new java.awt.event.ActionListener()
1184             {
1185               @Override
1186               public void actionPerformed(ActionEvent e)
1187               {
1188                 colourTextMenuItem_actionPerformed(e);
1189               }
1190             });
1191     htmlMenuItem.setText(MessageManager.getString("label.html"));
1192     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
1193     {
1194       @Override
1195       public void actionPerformed(ActionEvent e)
1196       {
1197         htmlMenuItem_actionPerformed(e);
1198       }
1199     });
1200     overviewMenuItem.setText(MessageManager
1201             .getString("label.overview_window"));
1202     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
1203     {
1204       @Override
1205       public void actionPerformed(ActionEvent e)
1206       {
1207         overviewMenuItem_actionPerformed(e);
1208       }
1209     });
1210     undoMenuItem.setEnabled(false);
1211     undoMenuItem.setText(MessageManager.getString("action.undo"));
1212     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1213             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1214                     .getMenuShortcutKeyMask(), false));
1215     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1216     {
1217       @Override
1218       public void actionPerformed(ActionEvent e)
1219       {
1220         undoMenuItem_actionPerformed(e);
1221       }
1222     });
1223     redoMenuItem.setEnabled(false);
1224     redoMenuItem.setText(MessageManager.getString("action.redo"));
1225     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1226             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1227                     .getMenuShortcutKeyMask(), false));
1228     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1229     {
1230       @Override
1231       public void actionPerformed(ActionEvent e)
1232       {
1233         redoMenuItem_actionPerformed(e);
1234       }
1235     });
1236     conservationMenuItem.setText(MessageManager
1237             .getString("action.by_conservation"));
1238     conservationMenuItem
1239             .addActionListener(new java.awt.event.ActionListener()
1240             {
1241               @Override
1242               public void actionPerformed(ActionEvent e)
1243               {
1244                 conservationMenuItem_actionPerformed(e);
1245               }
1246             });
1247     noColourmenuItem.setText(MessageManager.getString("label.none"));
1248     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1249     {
1250       @Override
1251       public void actionPerformed(ActionEvent e)
1252       {
1253         noColourmenuItem_actionPerformed(e);
1254       }
1255     });
1256     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1257     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1258     {
1259       @Override
1260       public void actionPerformed(ActionEvent e)
1261       {
1262         wrapMenuItem_actionPerformed(e);
1263       }
1264     });
1265     printMenuItem.setText(MessageManager.getString("action.print") + "...");
1266     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1267             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1268                     .getMenuShortcutKeyMask(), false));
1269     printMenuItem.addActionListener(new java.awt.event.ActionListener()
1270     {
1271       @Override
1272       public void actionPerformed(ActionEvent e)
1273       {
1274         printMenuItem_actionPerformed(e);
1275       }
1276     });
1277     renderGapsMenuItem
1278             .setText(MessageManager.getString("action.show_gaps"));
1279     renderGapsMenuItem.setState(true);
1280     renderGapsMenuItem
1281             .addActionListener(new java.awt.event.ActionListener()
1282             {
1283               @Override
1284               public void actionPerformed(ActionEvent e)
1285               {
1286                 renderGapsMenuItem_actionPerformed(e);
1287               }
1288             });
1289     findMenuItem.setText(MessageManager.getString("action.find"));
1290     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1291             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1292                     .getMenuShortcutKeyMask(), false));
1293     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
1294             MessageManager.getString("label.find_tip")));
1295     findMenuItem.addActionListener(new java.awt.event.ActionListener()
1296     {
1297       @Override
1298       public void actionPerformed(ActionEvent e)
1299       {
1300         findMenuItem_actionPerformed(e);
1301       }
1302     });
1303     abovePIDThreshold.setText(MessageManager
1304             .getString("label.above_identity_threshold"));
1305     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1306     {
1307       @Override
1308       public void actionPerformed(ActionEvent e)
1309       {
1310         abovePIDThreshold_actionPerformed(e);
1311       }
1312     });
1313     showSeqFeatures.setText(MessageManager
1314             .getString("label.show_sequence_features"));
1315     showSeqFeatures.addActionListener(new ActionListener()
1316     {
1317       @Override
1318       public void actionPerformed(ActionEvent actionEvent)
1319       {
1320         showSeqFeatures_actionPerformed(actionEvent);
1321       }
1322     });
1323     /*
1324      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1325      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1326      * void actionPerformed(ActionEvent actionEvent) {
1327      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1328      */
1329     showDbRefsMenuitem.setText(MessageManager
1330             .getString("label.show_database_refs"));
1331     showDbRefsMenuitem.addActionListener(new ActionListener()
1332     {
1333
1334       @Override
1335       public void actionPerformed(ActionEvent e)
1336       {
1337         showDbRefs_actionPerformed(e);
1338       }
1339
1340     });
1341     showNpFeatsMenuitem.setText(MessageManager
1342             .getString("label.show_non_positional_features"));
1343     showNpFeatsMenuitem.addActionListener(new ActionListener()
1344     {
1345
1346       @Override
1347       public void actionPerformed(ActionEvent e)
1348       {
1349         showNpFeats_actionPerformed(e);
1350       }
1351
1352     });
1353     showGroupConservation.setText(MessageManager
1354             .getString("label.group_conservation"));
1355     showGroupConservation.addActionListener(new ActionListener()
1356     {
1357
1358       @Override
1359       public void actionPerformed(ActionEvent e)
1360       {
1361         showGroupConservation_actionPerformed(e);
1362       }
1363
1364     });
1365
1366     showGroupConsensus.setText(MessageManager
1367             .getString("label.group_consensus"));
1368     showGroupConsensus.addActionListener(new ActionListener()
1369     {
1370
1371       @Override
1372       public void actionPerformed(ActionEvent e)
1373       {
1374         showGroupConsensus_actionPerformed(e);
1375       }
1376
1377     });
1378     showConsensusHistogram.setText(MessageManager
1379             .getString("label.show_consensus_histogram"));
1380     showConsensusHistogram.addActionListener(new ActionListener()
1381     {
1382
1383       @Override
1384       public void actionPerformed(ActionEvent e)
1385       {
1386         showConsensusHistogram_actionPerformed(e);
1387       }
1388
1389     });
1390     showSequenceLogo.setText(MessageManager
1391             .getString("label.show_consensus_logo"));
1392     showSequenceLogo.addActionListener(new ActionListener()
1393     {
1394
1395       @Override
1396       public void actionPerformed(ActionEvent e)
1397       {
1398         showSequenceLogo_actionPerformed(e);
1399       }
1400
1401     });
1402     normaliseSequenceLogo.setText(MessageManager
1403             .getString("label.norm_consensus_logo"));
1404     normaliseSequenceLogo.addActionListener(new ActionListener()
1405     {
1406
1407       @Override
1408       public void actionPerformed(ActionEvent e)
1409       {
1410         normaliseSequenceLogo_actionPerformed(e);
1411       }
1412
1413     });
1414     applyAutoAnnotationSettings.setText(MessageManager
1415             .getString("label.apply_all_groups"));
1416     applyAutoAnnotationSettings.setState(false);
1417     applyAutoAnnotationSettings.setVisible(true);
1418     applyAutoAnnotationSettings.addActionListener(new ActionListener()
1419     {
1420       @Override
1421       public void actionPerformed(ActionEvent e)
1422       {
1423         applyAutoAnnotationSettings_actionPerformed(e);
1424       }
1425     });
1426
1427     ButtonGroup buttonGroup = new ButtonGroup();
1428     buttonGroup.add(showAutoFirst);
1429     buttonGroup.add(showAutoLast);
1430     showAutoFirst.setText(MessageManager.getString("label.show_first"));
1431     showAutoFirst.setSelected(Cache.getDefault(
1432             Preferences.SHOW_AUTOCALC_ABOVE,
1433             false));
1434     showAutoFirst.addActionListener(new ActionListener()
1435     {
1436       @Override
1437       public void actionPerformed(ActionEvent e)
1438       {
1439         setShowAutoCalculatedAbove(showAutoFirst.isSelected());
1440         sortAnnotations_actionPerformed();
1441       }
1442     });
1443     showAutoLast.setText(MessageManager.getString("label.show_last"));
1444     showAutoLast.setSelected(!showAutoFirst.isSelected());
1445     showAutoLast.addActionListener(new ActionListener()
1446     {
1447       @Override
1448       public void actionPerformed(ActionEvent e)
1449       {
1450         setShowAutoCalculatedAbove(!showAutoLast.isSelected());
1451         sortAnnotations_actionPerformed();
1452       }
1453     });
1454
1455     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1456     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1457     {
1458       @Override
1459       public void actionPerformed(ActionEvent e)
1460       {
1461         nucleotideColour_actionPerformed(e);
1462       }
1463     });
1464
1465     tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1466     tcoffeeColour.setEnabled(false);
1467     tcoffeeColour.addActionListener(new ActionListener()
1468     {
1469
1470       @Override
1471       public void actionPerformed(ActionEvent e)
1472       {
1473         tcoffeeColorScheme_actionPerformed(e);
1474       }
1475     });
1476
1477     deleteGroups
1478             .setText(MessageManager.getString("action.undefine_groups"));
1479     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1480             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1481                     .getMenuShortcutKeyMask(), false));
1482     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1483     {
1484       @Override
1485       public void actionPerformed(ActionEvent e)
1486       {
1487         deleteGroups_actionPerformed(e);
1488       }
1489     });
1490     createGroup.setText(MessageManager.getString("action.create_groups"));
1491     createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1492             java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1493                     .getMenuShortcutKeyMask(), false));
1494     createGroup.addActionListener(new java.awt.event.ActionListener()
1495     {
1496       @Override
1497       public void actionPerformed(ActionEvent e)
1498       {
1499         createGroup_actionPerformed(e);
1500       }
1501     });
1502     unGroup.setText(MessageManager.getString("action.remove_group"));
1503     unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1504             java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1505                     .getMenuShortcutKeyMask()
1506                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1507     unGroup.addActionListener(new java.awt.event.ActionListener()
1508     {
1509       @Override
1510       public void actionPerformed(ActionEvent e)
1511       {
1512         unGroup_actionPerformed(e);
1513       }
1514     });
1515     copy.setText(MessageManager.getString("action.copy"));
1516     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1517             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1518                     .getMenuShortcutKeyMask(), false));
1519
1520     copy.addActionListener(new java.awt.event.ActionListener()
1521     {
1522       @Override
1523       public void actionPerformed(ActionEvent e)
1524       {
1525         copy_actionPerformed(e);
1526       }
1527     });
1528     cut.setText(MessageManager.getString("action.cut"));
1529     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1530             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1531                     .getMenuShortcutKeyMask(), false));
1532     cut.addActionListener(new java.awt.event.ActionListener()
1533     {
1534       @Override
1535       public void actionPerformed(ActionEvent e)
1536       {
1537         cut_actionPerformed(e);
1538       }
1539     });
1540     delete.setText(MessageManager.getString("action.delete"));
1541     delete.addActionListener(new java.awt.event.ActionListener()
1542     {
1543       @Override
1544       public void actionPerformed(ActionEvent e)
1545       {
1546         delete_actionPerformed(e);
1547       }
1548     });
1549     pasteMenu.setText(MessageManager.getString("action.paste"));
1550     pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1551     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1552             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1553                     .getMenuShortcutKeyMask()
1554                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1555     pasteNew.addActionListener(new java.awt.event.ActionListener()
1556     {
1557       @Override
1558       public void actionPerformed(ActionEvent e)
1559       {
1560         pasteNew_actionPerformed(e);
1561       }
1562     });
1563     pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1564     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1565             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1566                     .getMenuShortcutKeyMask(), false));
1567     pasteThis.addActionListener(new java.awt.event.ActionListener()
1568     {
1569       @Override
1570       public void actionPerformed(ActionEvent e)
1571       {
1572         pasteThis_actionPerformed(e);
1573       }
1574     });
1575     applyToAllGroups.setText(MessageManager
1576             .getString("label.apply_colour_to_all_groups"));
1577     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1578     {
1579       @Override
1580       public void actionPerformed(ActionEvent e)
1581       {
1582         applyToAllGroups_actionPerformed(e);
1583       }
1584     });
1585     createPNG.addActionListener(new java.awt.event.ActionListener()
1586     {
1587       @Override
1588       public void actionPerformed(ActionEvent e)
1589       {
1590         createPNG(null);
1591       }
1592     });
1593     createPNG.setActionCommand(MessageManager
1594             .getString("label.save_png_image"));
1595     createPNG.setText("PNG");
1596
1597     font.setText(MessageManager.getString("action.font"));
1598     font.addActionListener(new java.awt.event.ActionListener()
1599     {
1600       @Override
1601       public void actionPerformed(ActionEvent e)
1602       {
1603         font_actionPerformed(e);
1604       }
1605     });
1606
1607     seqLimits.setText(MessageManager
1608             .getString("label.show_sequence_limits"));
1609     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1610     seqLimits.addActionListener(new java.awt.event.ActionListener()
1611     {
1612       @Override
1613       public void actionPerformed(ActionEvent e)
1614       {
1615         seqLimit_actionPerformed(e);
1616       }
1617     });
1618     epsFile.setText("EPS");
1619     epsFile.addActionListener(new java.awt.event.ActionListener()
1620     {
1621       @Override
1622       public void actionPerformed(ActionEvent e)
1623       {
1624         createEPS(null);
1625       }
1626     });
1627
1628     createSVG.setText("SVG");
1629     createSVG.addActionListener(new java.awt.event.ActionListener()
1630     {
1631       @Override
1632       public void actionPerformed(ActionEvent e)
1633       {
1634         createSVG(null);
1635       }
1636     });
1637
1638     LoadtreeMenuItem.setActionCommand(MessageManager
1639             .getString("label.load_tree_for_sequence_set"));
1640     LoadtreeMenuItem.setText(MessageManager
1641             .getString("label.load_associated_tree"));
1642     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1643     {
1644       @Override
1645       public void actionPerformed(ActionEvent e)
1646       {
1647         LoadtreeMenuItem_actionPerformed(e);
1648       }
1649     });
1650
1651     scaleAbove.setVisible(false);
1652     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1653     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1654     {
1655       @Override
1656       public void actionPerformed(ActionEvent e)
1657       {
1658         scaleAbove_actionPerformed(e);
1659       }
1660     });
1661     scaleLeft.setVisible(false);
1662     scaleLeft.setSelected(true);
1663     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1664     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1665     {
1666       @Override
1667       public void actionPerformed(ActionEvent e)
1668       {
1669         scaleLeft_actionPerformed(e);
1670       }
1671     });
1672     scaleRight.setVisible(false);
1673     scaleRight.setSelected(true);
1674     scaleRight.setText(MessageManager.getString("action.scale_right"));
1675     scaleRight.addActionListener(new java.awt.event.ActionListener()
1676     {
1677       @Override
1678       public void actionPerformed(ActionEvent e)
1679       {
1680         scaleRight_actionPerformed(e);
1681       }
1682     });
1683     centreColumnLabelsMenuItem.setVisible(true);
1684     centreColumnLabelsMenuItem.setState(false);
1685     centreColumnLabelsMenuItem.setText(MessageManager
1686             .getString("label.centre_column_labels"));
1687     centreColumnLabelsMenuItem
1688             .addActionListener(new java.awt.event.ActionListener()
1689             {
1690               @Override
1691               public void actionPerformed(ActionEvent e)
1692               {
1693                 centreColumnLabels_actionPerformed(e);
1694               }
1695             });
1696     followHighlightMenuItem.setVisible(true);
1697     followHighlightMenuItem.setState(true);
1698     followHighlightMenuItem.setText(MessageManager
1699             .getString("label.automatic_scrolling"));
1700     followHighlightMenuItem.addActionListener(new ActionListener()
1701     {
1702
1703       @Override
1704       public void actionPerformed(ActionEvent e)
1705       {
1706         followHighlight_actionPerformed();
1707       }
1708
1709     });
1710
1711     modifyPID.setText(MessageManager
1712             .getString("label.modify_identity_thereshold"));
1713     modifyPID.addActionListener(new java.awt.event.ActionListener()
1714     {
1715       @Override
1716       public void actionPerformed(ActionEvent e)
1717       {
1718         modifyPID_actionPerformed(e);
1719       }
1720     });
1721     modifyConservation.setText(MessageManager
1722             .getString("label.modify_conservation_thereshold"));
1723     modifyConservation
1724             .addActionListener(new java.awt.event.ActionListener()
1725             {
1726               @Override
1727               public void actionPerformed(ActionEvent e)
1728               {
1729                 modifyConservation_actionPerformed(e);
1730               }
1731             });
1732     sortByTreeMenu
1733             .setText(MessageManager.getString("action.by_tree_order"));
1734     sort.setText(MessageManager.getString("action.sort"));
1735     sort.addMenuListener(new MenuListener()
1736     {
1737       @Override
1738       public void menuSelected(MenuEvent e)
1739       {
1740         buildTreeMenu();
1741       }
1742
1743       @Override
1744       public void menuDeselected(MenuEvent e)
1745       {
1746       }
1747
1748       @Override
1749       public void menuCanceled(MenuEvent e)
1750       {
1751       }
1752     });
1753     sortByAnnotScore.setText(MessageManager
1754             .getString("label.sort_by_score"));
1755     sort.add(sortByAnnotScore);
1756     sort.addMenuListener(new javax.swing.event.MenuListener()
1757     {
1758
1759       @Override
1760       public void menuCanceled(MenuEvent e)
1761       {
1762       }
1763
1764       @Override
1765       public void menuDeselected(MenuEvent e)
1766       {
1767       }
1768
1769       @Override
1770       public void menuSelected(MenuEvent e)
1771       {
1772         buildSortByAnnotationScoresMenu();
1773       }
1774     });
1775     sortByAnnotScore.setVisible(false);
1776
1777     calculateTree
1778             .setText(MessageManager.getString("action.calculate_tree"));
1779
1780     jMenu2.setText(MessageManager.getString("label.export_image"));
1781     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1782     padGapsMenuitem.setState(jalview.bin.Cache
1783             .getDefault("PAD_GAPS", false));
1784     padGapsMenuitem.addActionListener(new ActionListener()
1785     {
1786       @Override
1787       public void actionPerformed(ActionEvent e)
1788       {
1789         padGapsMenuitem_actionPerformed(e);
1790       }
1791     });
1792     vamsasStore.setVisible(false);
1793     vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1794     vamsasStore.addActionListener(new ActionListener()
1795     {
1796       @Override
1797       public void actionPerformed(ActionEvent e)
1798       {
1799         vamsasStore_actionPerformed(e);
1800       }
1801     });
1802     showTranslation.setText(MessageManager
1803             .getString("label.translate_cDNA"));
1804     showTranslation.addActionListener(new ActionListener()
1805     {
1806       @Override
1807       public void actionPerformed(ActionEvent e)
1808       {
1809         showTranslation_actionPerformed(e);
1810       }
1811     });
1812     extractScores.setText(MessageManager.getString("label.extract_scores")
1813             + "...");
1814     extractScores.addActionListener(new ActionListener()
1815     {
1816       @Override
1817       public void actionPerformed(ActionEvent e)
1818       {
1819         extractScores_actionPerformed(e);
1820       }
1821     });
1822     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1823     // score extraction
1824     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1825     /*
1826      * showProducts.addActionListener(new ActionListener() {
1827      *
1828      * public void actionPerformed(ActionEvent e) {
1829      * showProducts_actionPerformed(e); } });
1830      */
1831     openFeatureSettings.setText(MessageManager
1832             .getString("label.feature_settings"));
1833     openFeatureSettings.addActionListener(new ActionListener()
1834     {
1835       @Override
1836       public void actionPerformed(ActionEvent e)
1837       {
1838         featureSettings_actionPerformed(e);
1839       }
1840     });
1841     fetchSequence
1842             .setText(MessageManager.getString("label.fetch_sequences"));
1843     fetchSequence.addActionListener(new ActionListener()
1844     {
1845       @Override
1846       public void actionPerformed(ActionEvent e)
1847       {
1848         fetchSequence_actionPerformed(e);
1849       }
1850     });
1851
1852     annotationColour.setText(MessageManager
1853             .getString("action.by_annotation"));
1854     annotationColour.addActionListener(new ActionListener()
1855     {
1856       @Override
1857       public void actionPerformed(ActionEvent e)
1858       {
1859         annotationColour_actionPerformed(e);
1860       }
1861     });
1862
1863     rnahelicesColour.setText(MessageManager
1864             .getString("action.by_rna_helixes"));
1865     rnahelicesColour.addActionListener(new ActionListener()
1866     {
1867       @Override
1868       public void actionPerformed(ActionEvent e)
1869       {
1870         rnahelicesColour_actionPerformed(e);
1871       }
1872     });
1873
1874     associatedData.setText(MessageManager
1875             .getString("label.load_features_annotations"));
1876     associatedData.addActionListener(new ActionListener()
1877     {
1878       @Override
1879       public void actionPerformed(ActionEvent e)
1880       {
1881         associatedData_actionPerformed(e);
1882       }
1883     });
1884     autoCalculate.setText(MessageManager
1885             .getString("label.autocalculate_consensus"));
1886     autoCalculate.setState(jalview.bin.Cache.getDefault(
1887             "AUTO_CALC_CONSENSUS", true));
1888     autoCalculate.addActionListener(new ActionListener()
1889     {
1890       @Override
1891       public void actionPerformed(ActionEvent e)
1892       {
1893         autoCalculate_actionPerformed(e);
1894       }
1895     });
1896     sortByTree.setText(MessageManager
1897             .getString("label.sort_alignment_new_tree"));
1898     sortByTree
1899             .setToolTipText("<html>"
1900                     + MessageManager
1901                             .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1902     sortByTree
1903             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1904     sortByTree.addActionListener(new ActionListener()
1905     {
1906       @Override
1907       public void actionPerformed(ActionEvent e)
1908       {
1909         sortByTreeOption_actionPerformed(e);
1910       }
1911     });
1912
1913     listenToViewSelections.setText(MessageManager
1914             .getString("label.listen_for_selections"));
1915     listenToViewSelections
1916             .setToolTipText("<html>"
1917                     + MessageManager
1918                             .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1919     listenToViewSelections.setState(false);
1920     listenToViewSelections.addActionListener(new ActionListener()
1921     {
1922       @Override
1923       public void actionPerformed(ActionEvent e)
1924       {
1925         listenToViewSelections_actionPerformed(e);
1926       }
1927     });
1928
1929     addSequenceMenu
1930             .setText(MessageManager.getString("label.add_sequences"));
1931     addFromFile.setText(MessageManager.getString("label.from_file"));
1932     addFromFile.addActionListener(new ActionListener()
1933     {
1934       @Override
1935       public void actionPerformed(ActionEvent e)
1936       {
1937         addFromFile_actionPerformed(e);
1938       }
1939     });
1940     addFromText.setText(MessageManager.getString("label.from_textbox"));
1941     addFromText.addActionListener(new ActionListener()
1942     {
1943       @Override
1944       public void actionPerformed(ActionEvent e)
1945       {
1946         addFromText_actionPerformed(e);
1947       }
1948     });
1949     addFromURL.setText(MessageManager.getString("label.from_url"));
1950     addFromURL.addActionListener(new ActionListener()
1951     {
1952       @Override
1953       public void actionPerformed(ActionEvent e)
1954       {
1955         addFromURL_actionPerformed(e);
1956       }
1957     });
1958     exportFeatures.setText(MessageManager
1959             .getString("label.export_features"));
1960     exportFeatures.addActionListener(new ActionListener()
1961     {
1962       @Override
1963       public void actionPerformed(ActionEvent e)
1964       {
1965         exportFeatures_actionPerformed(e);
1966       }
1967     });
1968     exportAnnotations.setText(MessageManager
1969             .getString("label.export_annotations"));
1970     exportAnnotations.addActionListener(new ActionListener()
1971     {
1972       @Override
1973       public void actionPerformed(ActionEvent e)
1974       {
1975         exportAnnotations_actionPerformed(e);
1976       }
1977     });
1978     statusPanel.setLayout(gridLayout1);
1979     jMenu3.setText(MessageManager.getString("action.show"));
1980     showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
1981     showAllSeqs.setToolTipText(MessageManager
1982             .getString("label.toggle_sequence_visibility"));
1983     showAllSeqs.addActionListener(new ActionListener()
1984     {
1985       @Override
1986       public void actionPerformed(ActionEvent e)
1987       {
1988         showAllSeqs_actionPerformed(e);
1989       }
1990     });
1991     showAllColumns.setText(MessageManager.getString("label.all_columns"));
1992     showAllColumns.setToolTipText(MessageManager
1993             .getString("label.toggle_columns_visibility"));
1994     showAllColumns.addActionListener(new ActionListener()
1995     {
1996       @Override
1997       public void actionPerformed(ActionEvent e)
1998       {
1999         showAllColumns_actionPerformed(e);
2000       }
2001     });
2002     hideMenu.setText(MessageManager.getString("action.hide"));
2003     hideSelSequences.setText(MessageManager
2004             .getString("label.selected_sequences"));
2005     hideSelSequences.setToolTipText(MessageManager
2006             .getString("label.toggle_sequence_visibility"));
2007     hideSelSequences.addActionListener(new ActionListener()
2008     {
2009       @Override
2010       public void actionPerformed(ActionEvent e)
2011       {
2012         hideSelSequences_actionPerformed(e);
2013       }
2014     });
2015     hideSelColumns.setText(MessageManager
2016             .getString("label.selected_columns"));
2017     hideSelColumns.setToolTipText(MessageManager
2018             .getString("label.toggle_columns_visibility"));
2019     hideSelColumns.addActionListener(new ActionListener()
2020     {
2021       @Override
2022       public void actionPerformed(ActionEvent e)
2023       {
2024         hideSelColumns_actionPerformed(e);
2025       }
2026     });
2027     hideAllSelection.setText(MessageManager
2028             .getString("label.selected_region"));
2029     hideAllSelection.addActionListener(new ActionListener()
2030     {
2031       @Override
2032       public void actionPerformed(ActionEvent e)
2033       {
2034         hideAllSelection_actionPerformed(e);
2035       }
2036     });
2037     // TODO: should be hidden if no selection exists.
2038     hideAllButSelection.setText(MessageManager
2039             .getString("label.all_but_selected_region"));
2040     hideAllButSelection.addActionListener(new ActionListener()
2041     {
2042       @Override
2043       public void actionPerformed(ActionEvent e)
2044       {
2045         hideAllButSelection_actionPerformed(e);
2046       }
2047     });
2048     showAllhidden.setText(MessageManager
2049             .getString("label.all_sequences_columns"));
2050     showAllhidden.setToolTipText(MessageManager
2051             .getString("label.toggles_visibility_hidden_selected_regions"));
2052     showAllhidden.addActionListener(new ActionListener()
2053     {
2054       @Override
2055       public void actionPerformed(ActionEvent e)
2056       {
2057         showAllhidden_actionPerformed(e);
2058       }
2059     });
2060     hiddenMarkers.setText(MessageManager
2061             .getString("action.show_hidden_markers"));
2062     hiddenMarkers.addActionListener(new ActionListener()
2063     {
2064       @Override
2065       public void actionPerformed(ActionEvent e)
2066       {
2067         hiddenMarkers_actionPerformed(e);
2068       }
2069     });
2070     invertColSel.setText(MessageManager
2071             .getString("action.invert_column_selection"));
2072     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2073             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
2074                     .getMenuShortcutKeyMask()
2075                     | java.awt.event.KeyEvent.ALT_MASK, false));
2076     invertColSel.addActionListener(new ActionListener()
2077     {
2078       @Override
2079       public void actionPerformed(ActionEvent e)
2080       {
2081         invertColSel_actionPerformed(e);
2082       }
2083     });
2084     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
2085     {
2086       @Override
2087       public void stateChanged(ChangeEvent evt)
2088       {
2089         JTabbedPane pane = (JTabbedPane) evt.getSource();
2090         int sel = pane.getSelectedIndex();
2091         tabSelectionChanged(sel);
2092       }
2093     });
2094     tabbedPane.addMouseListener(new MouseAdapter()
2095     {
2096       @Override
2097       public void mousePressed(MouseEvent e)
2098       {
2099         tabbedPane_mousePressed(e);
2100       }
2101     });
2102     tabbedPane.addFocusListener(new FocusAdapter()
2103     {
2104       @Override
2105       public void focusGained(FocusEvent e)
2106       {
2107         tabbedPane_focusGained(e);
2108       }
2109     });
2110     save.setText(MessageManager.getString("action.save"));
2111     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2112             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
2113                     .getMenuShortcutKeyMask(), false));
2114     save.addActionListener(new ActionListener()
2115     {
2116       @Override
2117       public void actionPerformed(ActionEvent e)
2118       {
2119         save_actionPerformed(e);
2120       }
2121     });
2122     reload.setEnabled(false);
2123     reload.setText(MessageManager.getString("action.reload"));
2124     reload.addActionListener(new ActionListener()
2125     {
2126       @Override
2127       public void actionPerformed(ActionEvent e)
2128       {
2129         reload_actionPerformed(e);
2130       }
2131     });
2132     newView.setText(MessageManager.getString("action.new_view"));
2133     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2134             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
2135                     .getMenuShortcutKeyMask(), false));
2136     newView.addActionListener(new ActionListener()
2137     {
2138       @Override
2139       public void actionPerformed(ActionEvent e)
2140       {
2141         newView_actionPerformed(e);
2142       }
2143     });
2144     tabbedPane.setToolTipText("<html><i>"
2145             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2146             + "</i></html>");
2147     textColour.setText(MessageManager.getString("label.colour_text")
2148             + "...");
2149     textColour.addActionListener(new ActionListener()
2150     {
2151       @Override
2152       public void actionPerformed(ActionEvent e)
2153       {
2154         textColour_actionPerformed(e);
2155       }
2156     });
2157     formatMenu.setText(MessageManager.getString("action.format"));
2158     selectMenu.setText(MessageManager.getString("action.select"));
2159     idRightAlign.setText(MessageManager
2160             .getString("label.right_align_sequence_id"));
2161     idRightAlign.addActionListener(new ActionListener()
2162     {
2163       @Override
2164       public void actionPerformed(ActionEvent e)
2165       {
2166         idRightAlign_actionPerformed(e);
2167       }
2168     });
2169     gatherViews.setEnabled(false);
2170     gatherViews.setText(MessageManager.getString("action.gather_views"));
2171     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2172             java.awt.event.KeyEvent.VK_G, 0, false));
2173     gatherViews.addActionListener(new ActionListener()
2174     {
2175       @Override
2176       public void actionPerformed(ActionEvent e)
2177       {
2178         gatherViews_actionPerformed(e);
2179       }
2180     });
2181     expandViews.setEnabled(false);
2182     expandViews.setText(MessageManager.getString("action.expand_views"));
2183     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2184             java.awt.event.KeyEvent.VK_X, 0, false));
2185     expandViews.addActionListener(new ActionListener()
2186     {
2187       @Override
2188       public void actionPerformed(ActionEvent e)
2189       {
2190         expandViews_actionPerformed(e);
2191       }
2192     });
2193     pageSetup
2194             .setText(MessageManager.getString("action.page_setup") + "...");
2195     pageSetup.addActionListener(new ActionListener()
2196     {
2197       @Override
2198       public void actionPerformed(ActionEvent e)
2199       {
2200         pageSetup_actionPerformed(e);
2201       }
2202     });
2203     alignmentProperties.setText(MessageManager
2204             .getString("label.alignment_props") + "...");
2205     alignmentProperties.addActionListener(new ActionListener()
2206     {
2207       @Override
2208       public void actionPerformed(ActionEvent actionEvent)
2209       {
2210         alignmentProperties();
2211       }
2212     });
2213     tooltipSettingsMenu.setText(MessageManager
2214             .getString("label.sequence_id_tooltip"));
2215     autoAnnMenu.setText(MessageManager
2216             .getString("label.autocalculated_annotation"));
2217     alignFrameMenuBar.add(fileMenu);
2218     alignFrameMenuBar.add(editMenu);
2219     alignFrameMenuBar.add(selectMenu);
2220     alignFrameMenuBar.add(viewMenu);
2221     alignFrameMenuBar.add(annotationsMenu);
2222     alignFrameMenuBar.add(formatMenu);
2223     alignFrameMenuBar.add(colourMenu);
2224     alignFrameMenuBar.add(calculateMenu);
2225     alignFrameMenuBar.add(webService);
2226     fileMenu.add(fetchSequence);
2227     fileMenu.add(addSequenceMenu);
2228     fileMenu.add(reload);
2229     fileMenu.addSeparator();
2230     fileMenu.add(vamsasStore);
2231     fileMenu.add(save);
2232     fileMenu.add(saveAs);
2233     fileMenu.add(outputTextboxMenu);
2234     fileMenu.add(pageSetup);
2235     fileMenu.add(printMenuItem);
2236     fileMenu.addSeparator();
2237     fileMenu.add(jMenu2);
2238     fileMenu.add(exportFeatures);
2239     fileMenu.add(exportAnnotations);
2240     fileMenu.add(LoadtreeMenuItem);
2241     fileMenu.add(associatedData);
2242     fileMenu.addSeparator();
2243     fileMenu.add(closeMenuItem);
2244     editMenu.add(undoMenuItem);
2245     editMenu.add(redoMenuItem);
2246     editMenu.add(cut);
2247     editMenu.add(copy);
2248     editMenu.add(pasteMenu);
2249     editMenu.add(delete);
2250     editMenu.addSeparator();
2251     editMenu.add(remove2LeftMenuItem);
2252     editMenu.add(remove2RightMenuItem);
2253     editMenu.add(removeGappedColumnMenuItem);
2254     editMenu.add(removeAllGapsMenuItem);
2255     editMenu.add(removeRedundancyMenuItem);
2256     editMenu.addSeparator();
2257     // dont add these yet in the CVS build - they cannot be undone!
2258     // Excluded from Jalview 2.5 release - undo needs to be implemented.
2259     // editMenu.add(justifyLeftMenuItem);
2260     // editMenu.add(justifyRightMenuItem);
2261     // editMenu.addSeparator();
2262     editMenu.add(padGapsMenuitem);
2263     viewMenu.add(newView);
2264     viewMenu.add(expandViews);
2265     viewMenu.add(gatherViews);
2266     viewMenu.addSeparator();
2267     viewMenu.add(jMenu3);
2268     viewMenu.add(hideMenu);
2269     viewMenu.addSeparator();
2270     viewMenu.add(followHighlightMenuItem);
2271     annotationsMenu.add(annotationPanelMenuItem);
2272     annotationsMenu.addSeparator();
2273     annotationsMenu.add(showAllAlAnnotations);
2274     annotationsMenu.add(hideAllAlAnnotations);
2275     annotationsMenu.addSeparator();
2276     annotationsMenu.add(showAllSeqAnnotations);
2277     annotationsMenu.add(hideAllSeqAnnotations);
2278     annotationsMenu.add(sortAnnBySequence);
2279     annotationsMenu.add(sortAnnByLabel);
2280     annotationsMenu.addSeparator();
2281     autoAnnMenu.add(showAutoFirst);
2282     autoAnnMenu.add(showAutoLast);
2283     autoAnnMenu.addSeparator();
2284     autoAnnMenu.add(applyAutoAnnotationSettings);
2285     autoAnnMenu.add(showConsensusHistogram);
2286     autoAnnMenu.add(showSequenceLogo);
2287     autoAnnMenu.add(normaliseSequenceLogo);
2288     autoAnnMenu.addSeparator();
2289     autoAnnMenu.add(showGroupConservation);
2290     autoAnnMenu.add(showGroupConsensus);
2291     annotationsMenu.add(autoAnnMenu);
2292     viewMenu.addSeparator();
2293     viewMenu.add(showSeqFeatures);
2294     // viewMenu.add(showSeqFeaturesHeight);
2295
2296     viewMenu.add(openFeatureSettings);
2297     tooltipSettingsMenu.add(showDbRefsMenuitem);
2298     tooltipSettingsMenu.add(showNpFeatsMenuitem);
2299     viewMenu.add(tooltipSettingsMenu);
2300     viewMenu.addSeparator();
2301     viewMenu.add(alignmentProperties);
2302     viewMenu.addSeparator();
2303     viewMenu.add(overviewMenuItem);
2304     colourMenu.add(applyToAllGroups);
2305     colourMenu.add(textColour);
2306     colourMenu.addSeparator();
2307     colourMenu.add(noColourmenuItem);
2308     colourMenu.add(clustalColour);
2309     colourMenu.add(BLOSUM62Colour);
2310     colourMenu.add(PIDColour);
2311     colourMenu.add(zappoColour);
2312     colourMenu.add(taylorColour);
2313     colourMenu.add(hydrophobicityColour);
2314     colourMenu.add(helixColour);
2315     colourMenu.add(strandColour);
2316     colourMenu.add(turnColour);
2317     colourMenu.add(buriedColour);
2318     colourMenu.add(nucleotideColour);
2319     colourMenu.add(purinePyrimidineColour);
2320     colourMenu.add(RNAInteractionColour);
2321     // colourMenu.add(covariationColour);
2322     colourMenu.add(tcoffeeColour);
2323     colourMenu.add(userDefinedColour);
2324     colourMenu.addSeparator();
2325     colourMenu.add(conservationMenuItem);
2326     colourMenu.add(modifyConservation);
2327     colourMenu.add(abovePIDThreshold);
2328     colourMenu.add(modifyPID);
2329     colourMenu.add(annotationColour);
2330     colourMenu.add(rnahelicesColour);
2331     calculateMenu.add(sort);
2332     calculateMenu.add(calculateTree);
2333     calculateMenu.addSeparator();
2334     calculateMenu.add(pairwiseAlignmentMenuItem);
2335     calculateMenu.add(PCAMenuItem);
2336     calculateMenu.addSeparator();
2337     calculateMenu.add(showTranslation);
2338     calculateMenu.add(showProducts);
2339     calculateMenu.add(autoCalculate);
2340     calculateMenu.add(sortByTree);
2341     calculateMenu.addSeparator();
2342     calculateMenu.add(extractScores);
2343     webServiceNoServices = new JMenuItem(
2344             MessageManager.getString("label.no_services"));
2345     webService.add(webServiceNoServices);
2346     pasteMenu.add(pasteNew);
2347     pasteMenu.add(pasteThis);
2348     sort.add(sortIDMenuItem);
2349     sort.add(sortLengthMenuItem);
2350     sort.add(sortGroupMenuItem);
2351     sort.add(sortPairwiseMenuItem);
2352     sort.add(sortByTreeMenu);
2353     jMenu2.add(htmlMenuItem);
2354     jMenu2.add(epsFile);
2355     jMenu2.add(createPNG);
2356     jMenu2.add(createSVG);
2357     addSequenceMenu.add(addFromFile);
2358     addSequenceMenu.add(addFromText);
2359     addSequenceMenu.add(addFromURL);
2360     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2361     statusPanel.add(statusBar, null);
2362     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2363     jMenu3.add(showAllColumns);
2364     jMenu3.add(showAllSeqs);
2365     jMenu3.add(showAllhidden);
2366     hideMenu.add(hideSelColumns);
2367     hideMenu.add(hideSelSequences);
2368     hideMenu.add(hideAllSelection);
2369     hideMenu.add(hideAllButSelection);
2370
2371     formatMenu.add(font);
2372     formatMenu.addSeparator();
2373     formatMenu.add(wrapMenuItem);
2374     formatMenu.add(scaleAbove);
2375     formatMenu.add(scaleLeft);
2376     formatMenu.add(scaleRight);
2377     formatMenu.add(seqLimits);
2378     formatMenu.add(idRightAlign);
2379     formatMenu.add(hiddenMarkers);
2380     formatMenu.add(viewBoxesMenuItem);
2381     formatMenu.add(viewTextMenuItem);
2382     formatMenu.add(colourTextMenuItem);
2383     formatMenu.add(renderGapsMenuItem);
2384     formatMenu.add(centreColumnLabelsMenuItem);
2385     formatMenu.add(showNonconservedMenuItem);
2386     selectMenu.add(findMenuItem);
2387     selectMenu.addSeparator();
2388     selectMenu.add(selectAllSequenceMenuItem);
2389     selectMenu.add(deselectAllSequenceMenuItem);
2390     selectMenu.add(invertSequenceMenuItem);
2391     selectMenu.add(invertColSel);
2392     selectMenu.add(createGroup);
2393     selectMenu.add(unGroup);
2394     selectMenu.add(grpsFromSelection);
2395     selectMenu.add(deleteGroups);
2396     calculateMenu.add(expandAlignment);
2397     // TODO - determine if the listenToViewSelections button is needed : see bug
2398     // JAL-574
2399     // selectMenu.addSeparator();
2400     // selectMenu.add(listenToViewSelections);
2401   }
2402
2403   /**
2404    * Action on clicking sort annotations by type.
2405    *
2406    * @param sortOrder
2407    */
2408   protected void sortAnnotations_actionPerformed()
2409   {
2410   }
2411
2412   /**
2413    * Action on clicking Show all annotations.
2414    *
2415    * @param forSequences
2416    *          update sequence-related annotations
2417    * @param forAlignment
2418    *          update non-sequence-related annotations
2419    */
2420   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2421           boolean forAlignment)
2422   {
2423     setAnnotationsVisibility(true, forSequences, forAlignment);
2424   }
2425
2426   /**
2427    * Action on clicking Hide all annotations.
2428    *
2429    * @param forSequences
2430    *          update sequence-related annotations
2431    * @param forAlignment
2432    *          update non-sequence-related annotations
2433    */
2434   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2435           boolean forAlignment)
2436   {
2437     setAnnotationsVisibility(false, forSequences, forAlignment);
2438   }
2439
2440   /**
2441    * Set the visibility of annotations to true or false. Can act on
2442    * sequence-related annotations, or alignment-related, or both.
2443    *
2444    * @param visible
2445    * @param forSequences
2446    *          update sequence-related annotations
2447    * @param forAlignment
2448    *          update non-sequence-related annotations
2449    */
2450   protected void setAnnotationsVisibility(boolean visible,
2451           boolean forSequences, boolean forAlignment)
2452   {
2453
2454   }
2455
2456   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2457   {
2458     // TODO Auto-generated method stub
2459
2460   }
2461
2462   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2463   {
2464     // TODO Auto-generated method stub
2465
2466   }
2467
2468   protected void showAllhidden_actionPerformed(ActionEvent e)
2469   {
2470     // TODO Auto-generated method stub
2471
2472   }
2473
2474   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2475   {
2476     // TODO Auto-generated method stub
2477
2478   }
2479
2480   protected void hideAllSelection_actionPerformed(ActionEvent e)
2481   {
2482     // TODO Auto-generated method stub
2483
2484   }
2485
2486   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2487   {
2488     // TODO Auto-generated method stub
2489
2490   }
2491
2492   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2493   {
2494     // TODO Auto-generated method stub
2495
2496   }
2497
2498   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2499   {
2500     // TODO Auto-generated method stub
2501
2502   }
2503
2504   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2505   {
2506     // TODO Auto-generated method stub
2507
2508   }
2509
2510   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2511   {
2512     // TODO Auto-generated method stub
2513
2514   }
2515
2516   protected void showGroupConservation_actionPerformed(ActionEvent e)
2517   {
2518     // TODO Auto-generated method stub
2519
2520   }
2521
2522   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2523   {
2524     // TODO Auto-generated method stub
2525
2526   }
2527
2528   protected void showSeqFeaturesHeight_actionPerformed(
2529           ActionEvent actionEvent)
2530   {
2531     // TODO Auto-generated method stub
2532
2533   }
2534
2535   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2536   {
2537     // TODO Auto-generated method stub
2538
2539   }
2540
2541   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2542   {
2543     // TODO Auto-generated method stub
2544
2545   }
2546
2547   protected void followHighlight_actionPerformed()
2548   {
2549     // TODO Auto-generated method stub
2550
2551   }
2552
2553   protected void showNpFeats_actionPerformed(ActionEvent e)
2554   {
2555     // TODO Auto-generated method stub
2556
2557   }
2558
2559   protected void showDbRefs_actionPerformed(ActionEvent e)
2560   {
2561     // TODO Auto-generated method stub
2562
2563   }
2564
2565   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2566   {
2567   }
2568
2569   protected void showProducts_actionPerformed(ActionEvent e)
2570   {
2571   }
2572
2573   protected void buildSortByAnnotationScoresMenu()
2574   {
2575   }
2576
2577   protected void extractScores_actionPerformed(ActionEvent e)
2578   {
2579   }
2580
2581   protected void outputText_actionPerformed(ActionEvent e)
2582   {
2583   }
2584
2585   public void addFromFile_actionPerformed(ActionEvent e)
2586   {
2587
2588   }
2589
2590   public void addFromText_actionPerformed(ActionEvent e)
2591   {
2592
2593   }
2594
2595   public void addFromURL_actionPerformed(ActionEvent e)
2596   {
2597
2598   }
2599
2600   public void exportFeatures_actionPerformed(ActionEvent e)
2601   {
2602
2603   }
2604
2605   public void exportAnnotations_actionPerformed(ActionEvent e)
2606   {
2607
2608   }
2609
2610   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2611   {
2612   }
2613
2614   protected void closeMenuItem_actionPerformed(boolean b)
2615   {
2616   }
2617
2618   protected void redoMenuItem_actionPerformed(ActionEvent e)
2619   {
2620   }
2621
2622   protected void undoMenuItem_actionPerformed(ActionEvent e)
2623   {
2624   }
2625
2626   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2627   {
2628   }
2629
2630   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2631   {
2632   }
2633
2634   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2635   {
2636   }
2637
2638   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2639   {
2640   }
2641
2642   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2643   {
2644   }
2645
2646   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2647   {
2648   }
2649
2650   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2651   {
2652   }
2653
2654   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2655   {
2656   }
2657
2658   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2659   {
2660   }
2661
2662   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2663   {
2664   }
2665
2666   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2667   {
2668   }
2669
2670   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2671   {
2672   }
2673
2674   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2675   {
2676   }
2677
2678   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2679   {
2680   }
2681
2682   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2683   {
2684   }
2685
2686   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2687   {
2688   }
2689
2690   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2691   {
2692   }
2693
2694   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2695   {
2696   }
2697
2698   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2699   {
2700   }
2701
2702   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2703   {
2704   }
2705
2706   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2707   {
2708   }
2709
2710   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2711   {
2712   }
2713
2714   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2715   {
2716   }
2717
2718   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2719   {
2720   }
2721
2722   protected void clustalColour_actionPerformed(ActionEvent e)
2723   {
2724   }
2725
2726   protected void zappoColour_actionPerformed(ActionEvent e)
2727   {
2728   }
2729
2730   protected void taylorColour_actionPerformed(ActionEvent e)
2731   {
2732   }
2733
2734   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2735   {
2736   }
2737
2738   protected void helixColour_actionPerformed(ActionEvent e)
2739   {
2740   }
2741
2742   protected void strandColour_actionPerformed(ActionEvent e)
2743   {
2744   }
2745
2746   protected void turnColour_actionPerformed(ActionEvent e)
2747   {
2748   }
2749
2750   protected void buriedColour_actionPerformed(ActionEvent e)
2751   {
2752   }
2753
2754   protected void userDefinedColour_actionPerformed(ActionEvent e)
2755   {
2756   }
2757
2758   protected void PIDColour_actionPerformed(ActionEvent e)
2759   {
2760   }
2761
2762   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2763   {
2764   }
2765
2766   protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2767   {
2768   }
2769
2770   protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2771   {
2772   }
2773
2774   /*
2775    * protected void covariationColour_actionPerformed(ActionEvent e) { }
2776    */
2777
2778   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2779   {
2780   }
2781
2782   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2783   {
2784   }
2785
2786   protected void printMenuItem_actionPerformed(ActionEvent e)
2787   {
2788   }
2789
2790   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2791   {
2792   }
2793
2794   protected void findMenuItem_actionPerformed(ActionEvent e)
2795   {
2796   }
2797
2798   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2799   {
2800   }
2801
2802   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2803   {
2804   }
2805
2806   protected void nucleotideColour_actionPerformed(ActionEvent e)
2807   {
2808   }
2809
2810   protected void deleteGroups_actionPerformed(ActionEvent e)
2811   {
2812   }
2813
2814   protected void createGroup_actionPerformed(ActionEvent e)
2815   {
2816   }
2817
2818   protected void unGroup_actionPerformed(ActionEvent e)
2819   {
2820   }
2821
2822   protected void copy_actionPerformed(ActionEvent e)
2823   {
2824   }
2825
2826   protected void cut_actionPerformed(ActionEvent e)
2827   {
2828   }
2829
2830   protected void delete_actionPerformed(ActionEvent e)
2831   {
2832   }
2833
2834   protected void pasteNew_actionPerformed(ActionEvent e)
2835   {
2836   }
2837
2838   protected void pasteThis_actionPerformed(ActionEvent e)
2839   {
2840   }
2841
2842   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2843   {
2844   }
2845
2846   public void createPNG(java.io.File f)
2847   {
2848   }
2849
2850   protected void font_actionPerformed(ActionEvent e)
2851   {
2852   }
2853
2854   protected void seqLimit_actionPerformed(ActionEvent e)
2855   {
2856   }
2857
2858   public void seqDBRef_actionPerformed(ActionEvent e)
2859   {
2860
2861   }
2862
2863   public void createEPS(java.io.File f)
2864   {
2865   }
2866
2867   public void createSVG(java.io.File f)
2868   {
2869
2870   }
2871   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2872   {
2873
2874   }
2875
2876   /**
2877    * Template method to handle the 'load T-Coffee scores' menu event.
2878    * <p>
2879    * Subclasses override this method to provide a custom action.
2880    *
2881    * @param event
2882    *          The raised event
2883    */
2884   protected void loadScores_actionPerformed(ActionEvent event)
2885   {
2886
2887   }
2888
2889   /**
2890    * Template method to handle the 'Color T-Coffee scores' menu event.
2891    * <p>
2892    * Subclasses override this method to provide a custom action.
2893    *
2894    * @param event
2895    *          The raised event
2896    */
2897   protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2898   {
2899
2900   }
2901
2902   protected void jpred_actionPerformed(ActionEvent e)
2903   {
2904   }
2905
2906   protected void scaleAbove_actionPerformed(ActionEvent e)
2907   {
2908   }
2909
2910   protected void scaleLeft_actionPerformed(ActionEvent e)
2911   {
2912   }
2913
2914   protected void scaleRight_actionPerformed(ActionEvent e)
2915   {
2916   }
2917
2918   protected void modifyPID_actionPerformed(ActionEvent e)
2919   {
2920   }
2921
2922   protected void modifyConservation_actionPerformed(ActionEvent e)
2923   {
2924   }
2925
2926   protected void saveAs_actionPerformed(ActionEvent e)
2927   {
2928   }
2929
2930   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2931   {
2932   }
2933
2934   public void vamsasStore_actionPerformed(ActionEvent e)
2935   {
2936
2937   }
2938
2939   public void vamsasLoad_actionPerformed(ActionEvent e)
2940   {
2941
2942   }
2943
2944   public void showTranslation_actionPerformed(ActionEvent e)
2945   {
2946
2947   }
2948
2949   public void featureSettings_actionPerformed(ActionEvent e)
2950   {
2951
2952   }
2953
2954   public void fetchSequence_actionPerformed(ActionEvent e)
2955   {
2956
2957   }
2958
2959   public void smoothFont_actionPerformed(ActionEvent e)
2960   {
2961
2962   }
2963
2964   public void annotationColour_actionPerformed(ActionEvent e)
2965   {
2966
2967   }
2968
2969   public void rnahelicesColour_actionPerformed(ActionEvent e)
2970   {
2971
2972   }
2973
2974   public void associatedData_actionPerformed(ActionEvent e)
2975   {
2976
2977   }
2978
2979   public void autoCalculate_actionPerformed(ActionEvent e)
2980   {
2981
2982   }
2983
2984   public void sortByTreeOption_actionPerformed(ActionEvent e)
2985   {
2986
2987   }
2988
2989   public void showAllSeqs_actionPerformed(ActionEvent e)
2990   {
2991
2992   }
2993
2994   public void showAllColumns_actionPerformed(ActionEvent e)
2995   {
2996
2997   }
2998
2999   public void hideSelSequences_actionPerformed(ActionEvent e)
3000   {
3001
3002   }
3003
3004   public void hideSelColumns_actionPerformed(ActionEvent e)
3005   {
3006
3007   }
3008
3009   public void hiddenMarkers_actionPerformed(ActionEvent e)
3010   {
3011
3012   }
3013
3014   public void findPdbId_actionPerformed(ActionEvent e)
3015   {
3016
3017   }
3018
3019   public void enterPdbId_actionPerformed(ActionEvent e)
3020   {
3021
3022   }
3023
3024   public void pdbFile_actionPerformed(ActionEvent e)
3025   {
3026
3027   }
3028
3029   public void invertColSel_actionPerformed(ActionEvent e)
3030   {
3031
3032   }
3033
3034   public void tabSelectionChanged(int sel)
3035   {
3036
3037   }
3038
3039   public void tabbedPane_mousePressed(MouseEvent e)
3040   {
3041
3042   }
3043
3044   public void tabbedPane_focusGained(FocusEvent e)
3045   {
3046     requestFocus();
3047   }
3048
3049   public void save_actionPerformed(ActionEvent e)
3050   {
3051
3052   }
3053
3054   public void reload_actionPerformed(ActionEvent e)
3055   {
3056
3057   }
3058
3059   public void newView_actionPerformed(ActionEvent e)
3060   {
3061
3062   }
3063
3064   public void textColour_actionPerformed(ActionEvent e)
3065   {
3066
3067   }
3068
3069   public void idRightAlign_actionPerformed(ActionEvent e)
3070   {
3071
3072   }
3073
3074   public void expandViews_actionPerformed(ActionEvent e)
3075   {
3076
3077   }
3078
3079   public void gatherViews_actionPerformed(ActionEvent e)
3080   {
3081
3082   }
3083
3084   public void buildTreeMenu()
3085   {
3086
3087   }
3088
3089   public void pageSetup_actionPerformed(ActionEvent e)
3090   {
3091
3092   }
3093
3094   public void alignmentProperties()
3095   {
3096
3097   }
3098
3099   protected void expand_newalign(ActionEvent e)
3100   {
3101     // TODO Auto-generated method stub
3102
3103   }
3104
3105   protected boolean isShowAutoCalculatedAbove()
3106   {
3107     return showAutoCalculatedAbove;
3108   }
3109
3110   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
3111   {
3112     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
3113   }
3114
3115   protected SequenceAnnotationOrder getAnnotationSortOrder()
3116   {
3117     return annotationSortOrder;
3118   }
3119
3120   protected void setAnnotationSortOrder(SequenceAnnotationOrder annotationSortOrder)
3121   {
3122     this.annotationSortOrder = annotationSortOrder;
3123   }
3124 }