src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.jbgui;
  22
  23 import jalview.analysis.AnnotationSorter.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 createBioJS = new JMenuItem();
 218
 219   JMenuItem createSVG = new JMenuItem();
 220
 221   protected JMenuItem font = new JMenuItem();
 222
 223   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 224
 225   JMenuItem epsFile = new JMenuItem();
 226
 227   JMenuItem LoadtreeMenuItem = new JMenuItem();
 228
 229   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 230
 231   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 232
 233   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 234
 235   protected JMenuItem modifyPID = new JMenuItem();
 236
 237   protected JMenuItem modifyConservation = new JMenuItem();
 238
 239   protected JMenu sortByTreeMenu = new JMenu();
 240
 241   protected JMenu sort = new JMenu();
 242
 243   protected JMenu calculateTree = new JMenu();
 244
 245   JMenu jMenu2 = new JMenu();
 246
 247   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 248
 249   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 250
 251   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 252
 253   protected ButtonGroup colours = new ButtonGroup();
 254
 255   JMenuItem vamsasStore = new JMenuItem();
 256
 257   protected JMenuItem showTranslation = new JMenuItem();
 258
 259   protected JMenuItem extractScores = new JMenuItem();
 260
 261   protected JMenuItem expandAlignment = new JMenuItem();
 262
 263   protected JMenu showProducts = new JMenu();
 264
 265   public JMenuItem openFeatureSettings = new JMenuItem();
 266
 267   JMenuItem fetchSequence = new JMenuItem();
 268
 269   JMenuItem annotationColour = new JMenuItem();
 270
 271   protected JMenuItem rnahelicesColour = new JMenuItem();
 272
 273   JMenuItem associatedData = new JMenuItem();
 274
 275   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 276
 277   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 278
 279   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 280
 281   JMenu addSequenceMenu = new JMenu();
 282
 283   JMenuItem addFromFile = new JMenuItem();
 284
 285   JMenuItem addFromText = new JMenuItem();
 286
 287   JMenuItem addFromURL = new JMenuItem();
 288
 289   JMenuItem exportAnnotations = new JMenuItem();
 290
 291   JMenuItem exportFeatures = new JMenuItem();
 292
 293   protected JPanel statusPanel = new JPanel();
 294
 295   GridLayout gridLayout1 = new GridLayout();
 296
 297   JMenu jMenu3 = new JMenu();
 298
 299   JMenuItem showAllSeqs = new JMenuItem();
 300
 301   JMenuItem showAllColumns = new JMenuItem();
 302
 303   JMenu hideMenu = new JMenu();
 304
 305   JMenuItem hideSelSequences = new JMenuItem();
 306
 307   JMenuItem hideSelColumns = new JMenuItem();
 308
 309   JMenuItem hideAllButSelection = new JMenuItem();
 310
 311   JMenuItem hideAllSelection = new JMenuItem();
 312
 313   JMenuItem showAllhidden = new JMenuItem();
 314
 315   protected JMenuItem showAllSeqAnnotations = new JMenuItem();
 316
 317   protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
 318
 319   protected JMenuItem showAllAlAnnotations = new JMenuItem();
 320
 321   protected JMenuItem hideAllAlAnnotations = new JMenuItem();
 322
 323   protected JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem();
 324
 325   protected JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem();
 326
 327   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 328
 329   JMenuItem invertColSel = new JMenuItem();
 330
 331   protected JTabbedPane tabbedPane = new JTabbedPane();
 332
 333   JMenuItem save = new JMenuItem();
 334
 335   protected JMenuItem reload = new JMenuItem();
 336
 337   JMenuItem newView = new JMenuItem();
 338
 339   JMenuItem textColour = new JMenuItem();
 340
 341   JMenu formatMenu = new JMenu();
 342
 343   JMenu selectMenu = new JMenu();
 344
 345   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 346
 347   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 348
 349   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 350
 351   protected JMenuItem gatherViews = new JMenuItem();
 352
 353   protected JMenuItem expandViews = new JMenuItem();
 354
 355   JMenuItem pageSetup = new JMenuItem();
 356
 357   JMenuItem alignmentProperties = new JMenuItem();
 358
 359   JMenu tooltipSettingsMenu = new JMenu();
 360
 361   private JMenuItem justifyLeftMenuItem = new JMenuItem();
 362
 363   private JMenuItem justifyRightMenuItem = new JMenuItem();
 364
 365   JMenu autoAnnMenu = new JMenu();
 366
 367   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 368
 369   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 370
 371   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 372
 373   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 374
 375   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 376
 377   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 378
 379   protected JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem();
 380
 381   protected JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem();
 382
 383   private JMenuItem grpsFromSelection = new JMenuItem();
 384
 385   private SequenceAnnotationOrder annotationSortOrder;
 386
 387   private boolean showAutoCalculatedAbove = false;
 388
 389   public GAlignFrame()
 390   {
 391     try
 392     {
 393       jbInit();
 394       setJMenuBar(alignFrameMenuBar);
 395
 396       // dynamically fill save as menu with available formats
 397       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 398       {
 399         JMenuItem item = new JMenuItem(
 400                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 401
 402         item.addActionListener(new java.awt.event.ActionListener()
 403         {
 404           @Override
 405           public void actionPerformed(ActionEvent e)
 406           {
 407             outputText_actionPerformed(e);
 408           }
 409         });
 410
 411         outputTextboxMenu.add(item);
 412       }
 413     } catch (Exception e)
 414     {
 415       System.err.println(e.toString());
 416     }
 417
 418     if (!new jalview.util.Platform().isAMac())
 419     {
 420       closeMenuItem.setMnemonic('C');
 421       outputTextboxMenu.setMnemonic('T');
 422       undoMenuItem.setMnemonic('Z');
 423       redoMenuItem.setMnemonic('0');
 424       copy.setMnemonic('C');
 425       cut.setMnemonic('U');
 426       pasteMenu.setMnemonic('P');
 427       reload.setMnemonic('R');
 428     }
 429
 430     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 431     {
 432       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 433               .getUserColourSchemes().keys();
 434
 435       while (userColours.hasMoreElements())
 436       {
 437         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 438                 userColours.nextElement().toString());
 439         radioItem.setName("USER_DEFINED");
 440         radioItem.addMouseListener(new MouseAdapter()
 441         {
 442           @Override
 443           public void mousePressed(MouseEvent evt)
 444           {
 445             if (evt.isControlDown()
 446                     || SwingUtilities.isRightMouseButton(evt))
 447             {
 448               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 449
 450               int option = JOptionPane.showInternalConfirmDialog(
 451                       jalview.gui.Desktop.desktop,
 452                       MessageManager
 453                               .getString("label.remove_from_default_list"),
 454                       MessageManager
 455                               .getString("label.remove_user_defined_colour"),
 456                       JOptionPane.YES_NO_OPTION);
 457               if (option == JOptionPane.YES_OPTION)
 458               {
 459                 jalview.gui.UserDefinedColours
 460                         .removeColourFromDefaults(radioItem.getText());
 461                 colourMenu.remove(radioItem);
 462               }
 463               else
 464               {
 465                 radioItem.addActionListener(new ActionListener()
 466                 {
 467                   @Override
 468                   public void actionPerformed(ActionEvent evt)
 469                   {
 470                     userDefinedColour_actionPerformed(evt);
 471                   }
 472                 });
 473               }
 474             }
 475           }
 476         });
 477         radioItem.addActionListener(new ActionListener()
 478         {
 479           @Override
 480           public void actionPerformed(ActionEvent evt)
 481           {
 482             userDefinedColour_actionPerformed(evt);
 483           }
 484         });
 485         colourMenu.insert(radioItem, 15);
 486         colours.add(radioItem);
 487       }
 488     }
 489     colours.add(noColourmenuItem);
 490     colours.add(clustalColour);
 491     colours.add(zappoColour);
 492     colours.add(taylorColour);
 493     colours.add(hydrophobicityColour);
 494     colours.add(helixColour);
 495     colours.add(strandColour);
 496     colours.add(turnColour);
 497     colours.add(buriedColour);
 498     colours.add(userDefinedColour);
 499     colours.add(PIDColour);
 500     colours.add(BLOSUM62Colour);
 501     colours.add(nucleotideColour);
 502     colours.add(purinePyrimidineColour);
 503     // colours.add(covariationColour);
 504     colours.add(tcoffeeColour);
 505     colours.add(RNAInteractionColour);
 506     setColourSelected(jalview.bin.Cache
 507             .getDefault("DEFAULT_COLOUR", "None"));
 508
 509   }
 510
 511   public void setColourSelected(String defaultColour)
 512   {
 513
 514     if (defaultColour != null)
 515     {
 516       int index = ColourSchemeProperty
 517               .getColourIndexFromName(defaultColour);
 518
 519       switch (index)
 520       {
 521       case ColourSchemeProperty.CLUSTAL:
 522         clustalColour.setSelected(true);
 523
 524         break;
 525
 526       case ColourSchemeProperty.BLOSUM:
 527         BLOSUM62Colour.setSelected(true);
 528
 529         break;
 530
 531       case ColourSchemeProperty.PID:
 532         PIDColour.setSelected(true);
 533
 534         break;
 535
 536       case ColourSchemeProperty.ZAPPO:
 537         zappoColour.setSelected(true);
 538
 539         break;
 540
 541       case ColourSchemeProperty.TAYLOR:
 542         taylorColour.setSelected(true);
 543         break;
 544
 545       case ColourSchemeProperty.HYDROPHOBIC:
 546         hydrophobicityColour.setSelected(true);
 547
 548         break;
 549
 550       case ColourSchemeProperty.HELIX:
 551         helixColour.setSelected(true);
 552
 553         break;
 554
 555       case ColourSchemeProperty.STRAND:
 556         strandColour.setSelected(true);
 557
 558         break;
 559
 560       case ColourSchemeProperty.TURN:
 561         turnColour.setSelected(true);
 562
 563         break;
 564
 565       case ColourSchemeProperty.BURIED:
 566         buriedColour.setSelected(true);
 567
 568         break;
 569
 570       case ColourSchemeProperty.NUCLEOTIDE:
 571         nucleotideColour.setSelected(true);
 572
 573         break;
 574
 575       case ColourSchemeProperty.TCOFFEE:
 576         tcoffeeColour.setSelected(true);
 577         break;
 578
 579       case ColourSchemeProperty.PURINEPYRIMIDINE:
 580         purinePyrimidineColour.setSelected(true);
 581
 582         break;
 583
 584       case ColourSchemeProperty.RNAINTERACTION:
 585         RNAInteractionColour.setSelected(true);
 586
 587         break;
 588       /*
 589        * case ColourSchemeProperty.COVARIATION:
 590        * covariationColour.setSelected(true);
 591        *
 592        * break;
 593        */
 594       case ColourSchemeProperty.USER_DEFINED:
 595         userDefinedColour.setSelected(true);
 596
 597         break;
 598       case ColourSchemeProperty.NONE:
 599       default:
 600         noColourmenuItem.setSelected(true);
 601         break;
 602
 603       }
 604     }
 605
 606   }
 607
 608   private void jbInit() throws Exception
 609   {
 610     fileMenu.setText(MessageManager.getString("action.file"));
 611     saveAs.setText(MessageManager.getString("action.save_as") + "...");
 612     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 613             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
 614                     .getMenuShortcutKeyMask()
 615                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 616     saveAs.addActionListener(new ActionListener()
 617     {
 618       @Override
 619       public void actionPerformed(ActionEvent e)
 620       {
 621         saveAs_actionPerformed(e);
 622       }
 623     });
 624     closeMenuItem.setText(MessageManager.getString("action.close"));
 625     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 626             java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
 627                     .getMenuShortcutKeyMask(), false));
 628     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 629     {
 630       @Override
 631       public void actionPerformed(ActionEvent e)
 632       {
 633         closeMenuItem_actionPerformed(false);
 634       }
 635     });
 636     editMenu.setText(MessageManager.getString("action.edit"));
 637     viewMenu.setText(MessageManager.getString("action.view"));
 638     annotationsMenu.setText(MessageManager.getString("action.annotations"));
 639     colourMenu.setText(MessageManager.getString("action.colour"));
 640     calculateMenu.setText(MessageManager.getString("action.calculate"));
 641     webService.setText(MessageManager.getString("action.web_service"));
 642     selectAllSequenceMenuItem.setText(MessageManager
 643             .getString("action.select_all"));
 644     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 645             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
 646                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 647     selectAllSequenceMenuItem
 648             .addActionListener(new java.awt.event.ActionListener()
 649             {
 650               @Override
 651               public void actionPerformed(ActionEvent e)
 652               {
 653                 selectAllSequenceMenuItem_actionPerformed(e);
 654               }
 655             });
 656     deselectAllSequenceMenuItem.setText(MessageManager
 657             .getString("action.deselect_all"));
 658     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 659             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 660     deselectAllSequenceMenuItem
 661             .addActionListener(new java.awt.event.ActionListener()
 662             {
 663               @Override
 664               public void actionPerformed(ActionEvent e)
 665               {
 666                 deselectAllSequenceMenuItem_actionPerformed(e);
 667               }
 668             });
 669     invertSequenceMenuItem.setText(MessageManager
 670             .getString("action.invert_sequence_selection"));
 671     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 672             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
 673                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 674     invertSequenceMenuItem
 675             .addActionListener(new java.awt.event.ActionListener()
 676             {
 677               @Override
 678               public void actionPerformed(ActionEvent e)
 679               {
 680                 invertSequenceMenuItem_actionPerformed(e);
 681               }
 682             });
 683     grpsFromSelection.setText(MessageManager
 684             .getString("action.make_groups_selection"));
 685     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
 686     {
 687       @Override
 688       public void actionPerformed(ActionEvent e)
 689       {
 690         makeGrpsFromSelection_actionPerformed(e);
 691       }
 692     });
 693     expandAlignment.setText(MessageManager
 694             .getString("action.view_flanking_regions"));
 695     expandAlignment.setToolTipText(MessageManager
 696             .getString("label.view_flanking_regions"));
 697     expandAlignment.addActionListener(new java.awt.event.ActionListener()
 698     {
 699       @Override
 700       public void actionPerformed(ActionEvent e)
 701       {
 702         expand_newalign(e);
 703       }
 704     });
 705     remove2LeftMenuItem.setText(MessageManager
 706             .getString("action.remove_left"));
 707     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 708             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
 709                     .getMenuShortcutKeyMask(), false));
 710     remove2LeftMenuItem
 711             .addActionListener(new java.awt.event.ActionListener()
 712             {
 713               @Override
 714               public void actionPerformed(ActionEvent e)
 715               {
 716                 remove2LeftMenuItem_actionPerformed(e);
 717               }
 718             });
 719     remove2RightMenuItem.setText(MessageManager
 720             .getString("action.remove_right"));
 721     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 722             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
 723                     .getMenuShortcutKeyMask(), false));
 724     remove2RightMenuItem
 725             .addActionListener(new java.awt.event.ActionListener()
 726             {
 727               @Override
 728               public void actionPerformed(ActionEvent e)
 729               {
 730                 remove2RightMenuItem_actionPerformed(e);
 731               }
 732             });
 733     removeGappedColumnMenuItem.setText(MessageManager
 734             .getString("action.remove_empty_columns"));
 735     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
 736             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 737                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 738     removeGappedColumnMenuItem
 739             .addActionListener(new java.awt.event.ActionListener()
 740             {
 741               @Override
 742               public void actionPerformed(ActionEvent e)
 743               {
 744                 removeGappedColumnMenuItem_actionPerformed(e);
 745               }
 746             });
 747     removeAllGapsMenuItem.setText(MessageManager
 748             .getString("action.remove_all_gaps"));
 749     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
 750             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 751                     .getDefaultToolkit().getMenuShortcutKeyMask()
 752                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 753     removeAllGapsMenuItem
 754             .addActionListener(new java.awt.event.ActionListener()
 755             {
 756               @Override
 757               public void actionPerformed(ActionEvent e)
 758               {
 759                 removeAllGapsMenuItem_actionPerformed(e);
 760               }
 761             });
 762     justifyLeftMenuItem.setText(MessageManager
 763             .getString("action.left_justify_alignment"));
 764     justifyLeftMenuItem
 765             .addActionListener(new java.awt.event.ActionListener()
 766             {
 767               @Override
 768               public void actionPerformed(ActionEvent e)
 769               {
 770                 justifyLeftMenuItem_actionPerformed(e);
 771               }
 772             });
 773     justifyRightMenuItem.setText(MessageManager
 774             .getString("action.right_justify_alignment"));
 775     justifyRightMenuItem
 776             .addActionListener(new java.awt.event.ActionListener()
 777             {
 778               @Override
 779               public void actionPerformed(ActionEvent e)
 780               {
 781                 justifyRightMenuItem_actionPerformed(e);
 782               }
 783             });
 784     viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
 785     viewBoxesMenuItem.setState(true);
 786     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 787     {
 788       @Override
 789       public void actionPerformed(ActionEvent e)
 790       {
 791         viewBoxesMenuItem_actionPerformed(e);
 792       }
 793     });
 794     viewTextMenuItem.setText(MessageManager.getString("action.text"));
 795     viewTextMenuItem.setState(true);
 796     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 797     {
 798       @Override
 799       public void actionPerformed(ActionEvent e)
 800       {
 801         viewTextMenuItem_actionPerformed(e);
 802       }
 803     });
 804     showNonconservedMenuItem.setText(MessageManager
 805             .getString("label.show_non_conversed"));
 806     showNonconservedMenuItem.setState(false);
 807     showNonconservedMenuItem
 808             .addActionListener(new java.awt.event.ActionListener()
 809             {
 810               @Override
 811               public void actionPerformed(ActionEvent e)
 812               {
 813                 showUnconservedMenuItem_actionPerformed(e);
 814               }
 815             });
 816     sortPairwiseMenuItem.setText(MessageManager
 817             .getString("action.by_pairwise_id"));
 818     sortPairwiseMenuItem
 819             .addActionListener(new java.awt.event.ActionListener()
 820             {
 821               @Override
 822               public void actionPerformed(ActionEvent e)
 823               {
 824                 sortPairwiseMenuItem_actionPerformed(e);
 825               }
 826             });
 827     sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
 828     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 829     {
 830       @Override
 831       public void actionPerformed(ActionEvent e)
 832       {
 833         sortIDMenuItem_actionPerformed(e);
 834       }
 835     });
 836     sortLengthMenuItem
 837             .setText(MessageManager.getString("action.by_length"));
 838     sortLengthMenuItem
 839             .addActionListener(new java.awt.event.ActionListener()
 840             {
 841               @Override
 842               public void actionPerformed(ActionEvent e)
 843               {
 844                 sortLengthMenuItem_actionPerformed(e);
 845               }
 846             });
 847     sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
 848     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 849     {
 850       @Override
 851       public void actionPerformed(ActionEvent e)
 852       {
 853         sortGroupMenuItem_actionPerformed(e);
 854       }
 855     });
 856     removeRedundancyMenuItem.setText(MessageManager
 857             .getString("action.remove_redundancy").concat("..."));
 858     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
 859             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
 860                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 861     removeRedundancyMenuItem
 862             .addActionListener(new java.awt.event.ActionListener()
 863             {
 864               @Override
 865               public void actionPerformed(ActionEvent e)
 866               {
 867                 removeRedundancyMenuItem_actionPerformed(e);
 868               }
 869             });
 870     pairwiseAlignmentMenuItem.setText(MessageManager
 871             .getString("action.pairwise_alignment"));
 872     pairwiseAlignmentMenuItem
 873             .addActionListener(new java.awt.event.ActionListener()
 874             {
 875               @Override
 876               public void actionPerformed(ActionEvent e)
 877               {
 878                 pairwiseAlignmentMenuItem_actionPerformed(e);
 879               }
 880             });
 881     PCAMenuItem.setText(MessageManager
 882             .getString("label.principal_component_analysis"));
 883     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 884     {
 885       @Override
 886       public void actionPerformed(ActionEvent e)
 887       {
 888         PCAMenuItem_actionPerformed(e);
 889       }
 890     });
 891     averageDistanceTreeMenuItem.setText(MessageManager
 892             .getString("label.average_distance_identity"));
 893     averageDistanceTreeMenuItem
 894             .addActionListener(new java.awt.event.ActionListener()
 895             {
 896               @Override
 897               public void actionPerformed(ActionEvent e)
 898               {
 899                 averageDistanceTreeMenuItem_actionPerformed(e);
 900               }
 901             });
 902     neighbourTreeMenuItem.setText(MessageManager
 903             .getString("label.neighbour_joining_identity"));
 904     neighbourTreeMenuItem
 905             .addActionListener(new java.awt.event.ActionListener()
 906             {
 907               @Override
 908               public void actionPerformed(ActionEvent e)
 909               {
 910                 neighbourTreeMenuItem_actionPerformed(e);
 911               }
 912             });
 913     this.getContentPane().setLayout(borderLayout1);
 914     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 915     statusBar.setBackground(Color.white);
 916     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 917     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 918     statusBar.setText(MessageManager.getString("label.status_bar"));
 919     outputTextboxMenu.setText(MessageManager
 920             .getString("label.out_to_textbox"));
 921     clustalColour.setText(MessageManager.getString("label.clustalx"));
 922
 923     clustalColour.addActionListener(new java.awt.event.ActionListener()
 924     {
 925       @Override
 926       public void actionPerformed(ActionEvent e)
 927       {
 928         clustalColour_actionPerformed(e);
 929       }
 930     });
 931     zappoColour.setText(MessageManager.getString("label.zappo"));
 932     zappoColour.addActionListener(new java.awt.event.ActionListener()
 933     {
 934       @Override
 935       public void actionPerformed(ActionEvent e)
 936       {
 937         zappoColour_actionPerformed(e);
 938       }
 939     });
 940     taylorColour.setText(MessageManager.getString("label.taylor"));
 941     taylorColour.addActionListener(new java.awt.event.ActionListener()
 942     {
 943       @Override
 944       public void actionPerformed(ActionEvent e)
 945       {
 946         taylorColour_actionPerformed(e);
 947       }
 948     });
 949     hydrophobicityColour.setText(MessageManager
 950             .getString("label.hydrophobicity"));
 951     hydrophobicityColour
 952             .addActionListener(new java.awt.event.ActionListener()
 953             {
 954               @Override
 955               public void actionPerformed(ActionEvent e)
 956               {
 957                 hydrophobicityColour_actionPerformed(e);
 958               }
 959             });
 960     helixColour.setText(MessageManager.getString("label.helix_propensity"));
 961     helixColour.addActionListener(new java.awt.event.ActionListener()
 962     {
 963       @Override
 964       public void actionPerformed(ActionEvent e)
 965       {
 966         helixColour_actionPerformed(e);
 967       }
 968     });
 969     strandColour.setText(MessageManager
 970             .getString("label.strand_propensity"));
 971     strandColour.addActionListener(new java.awt.event.ActionListener()
 972     {
 973       @Override
 974       public void actionPerformed(ActionEvent e)
 975       {
 976         strandColour_actionPerformed(e);
 977       }
 978     });
 979     turnColour.setText(MessageManager.getString("label.turn_propensity"));
 980     turnColour.addActionListener(new java.awt.event.ActionListener()
 981     {
 982       @Override
 983       public void actionPerformed(ActionEvent e)
 984       {
 985         turnColour_actionPerformed(e);
 986       }
 987     });
 988     buriedColour.setText(MessageManager.getString("label.buried_index"));
 989     buriedColour.addActionListener(new java.awt.event.ActionListener()
 990     {
 991       @Override
 992       public void actionPerformed(ActionEvent e)
 993       {
 994         buriedColour_actionPerformed(e);
 995       }
 996     });
 997     userDefinedColour.setText(MessageManager
 998             .getString("action.user_defined"));
 999     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1000     {
1001       @Override
1002       public void actionPerformed(ActionEvent e)
1003       {
1004         userDefinedColour_actionPerformed(e);
1005       }
1006     });
1007     PIDColour
1008             .setText(MessageManager.getString("label.percentage_identity"));
1009     PIDColour.addActionListener(new java.awt.event.ActionListener()
1010     {
1011       @Override
1012       public void actionPerformed(ActionEvent e)
1013       {
1014         PIDColour_actionPerformed(e);
1015       }
1016     });
1017     BLOSUM62Colour
1018             .setText(MessageManager.getString("label.blosum62_score"));
1019     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1020     {
1021       @Override
1022       public void actionPerformed(ActionEvent e)
1023       {
1024         BLOSUM62Colour_actionPerformed(e);
1025       }
1026     });
1027     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1028     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1029     {
1030       @Override
1031       public void actionPerformed(ActionEvent e)
1032       {
1033         nucleotideColour_actionPerformed(e);
1034       }
1035     });
1036
1037     purinePyrimidineColour.setText(MessageManager
1038             .getString("label.purine_pyrimidine"));
1039     purinePyrimidineColour
1040             .addActionListener(new java.awt.event.ActionListener()
1041             {
1042               @Override
1043               public void actionPerformed(ActionEvent e)
1044               {
1045                 purinePyrimidineColour_actionPerformed(e);
1046               }
1047             });
1048
1049     RNAInteractionColour.setText("RNA Interaction type");
1050     RNAInteractionColour
1051             .addActionListener(new java.awt.event.ActionListener()
1052             {
1053               @Override
1054               public void actionPerformed(ActionEvent e)
1055               {
1056                 RNAInteractionColour_actionPerformed(e);
1057               }
1058             });
1059     /*
1060      * covariationColour.setText("Covariation");
1061      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1062      * public void actionPerformed(ActionEvent e) {
1063      * covariationColour_actionPerformed(e); } });
1064      */
1065
1066     avDistanceTreeBlosumMenuItem.setText(MessageManager
1067             .getString("label.average_distance_bloslum62"));
1068     avDistanceTreeBlosumMenuItem
1069             .addActionListener(new java.awt.event.ActionListener()
1070             {
1071               @Override
1072               public void actionPerformed(ActionEvent e)
1073               {
1074                 avTreeBlosumMenuItem_actionPerformed(e);
1075               }
1076             });
1077     njTreeBlosumMenuItem.setText(MessageManager
1078             .getString("label.neighbour_blosum62"));
1079     njTreeBlosumMenuItem
1080             .addActionListener(new java.awt.event.ActionListener()
1081             {
1082               @Override
1083               public void actionPerformed(ActionEvent e)
1084               {
1085                 njTreeBlosumMenuItem_actionPerformed(e);
1086               }
1087             });
1088     annotationPanelMenuItem.setActionCommand("");
1089     annotationPanelMenuItem.setText(MessageManager
1090             .getString("label.show_annotations"));
1091     annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
1092             true));
1093     annotationPanelMenuItem.addActionListener(new ActionListener()
1094     {
1095       @Override
1096       public void actionPerformed(ActionEvent e)
1097       {
1098         annotationPanelMenuItem_actionPerformed(e);
1099       }
1100     });
1101     showAllAlAnnotations.setText(MessageManager
1102             .getString("label.show_all_al_annotations"));
1103     final boolean isAnnotationPanelShown = annotationPanelMenuItem
1104             .getState();
1105     showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
1106     showAllAlAnnotations.addActionListener(new ActionListener()
1107     {
1108       @Override
1109       public void actionPerformed(ActionEvent e)
1110       {
1111         showAllAnnotations_actionPerformed(false, true);
1112       }
1113     });
1114     hideAllAlAnnotations.setText(MessageManager
1115             .getString("label.hide_all_al_annotations"));
1116     hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
1117     hideAllAlAnnotations.addActionListener(new ActionListener()
1118     {
1119       @Override
1120       public void actionPerformed(ActionEvent e)
1121       {
1122         hideAllAnnotations_actionPerformed(false, true);
1123       }
1124     });
1125     showAllSeqAnnotations.setText(MessageManager
1126             .getString("label.show_all_seq_annotations"));
1127     showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
1128     showAllSeqAnnotations.addActionListener(new ActionListener()
1129     {
1130       @Override
1131       public void actionPerformed(ActionEvent e)
1132       {
1133         showAllAnnotations_actionPerformed(true, false);
1134       }
1135     });
1136     hideAllSeqAnnotations.setText(MessageManager
1137             .getString("label.hide_all_seq_annotations"));
1138     hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
1139     hideAllSeqAnnotations.addActionListener(new ActionListener()
1140     {
1141       @Override
1142       public void actionPerformed(ActionEvent e)
1143       {
1144         hideAllAnnotations_actionPerformed(true, false);
1145       }
1146     });
1147     SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
1148             .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
1149                     SequenceAnnotationOrder.NONE.name()));
1150     sortAnnBySequence.setText(MessageManager
1151             .getString("label.sort_annotations_by_sequence"));
1152     sortAnnBySequence
1153             .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
1154     sortAnnBySequence.addActionListener(new ActionListener()
1155     {
1156       @Override
1157       public void actionPerformed(ActionEvent e)
1158       {
1159         boolean newState = sortAnnBySequence.getState();
1160         sortAnnByLabel.setSelected(false);
1161         setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
1162                 : SequenceAnnotationOrder.NONE);
1163         sortAnnotations_actionPerformed();
1164       }
1165     });
1166     sortAnnByLabel.setText(MessageManager
1167             .getString("label.sort_annotations_by_label"));
1168     sortAnnByLabel
1169             .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
1170     sortAnnByLabel.addActionListener(new ActionListener()
1171     {
1172       @Override
1173       public void actionPerformed(ActionEvent e)
1174       {
1175         boolean newState = sortAnnByLabel.getState();
1176         sortAnnBySequence.setSelected(false);
1177         setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
1178                 : SequenceAnnotationOrder.NONE);
1179         sortAnnotations_actionPerformed();
1180       }
1181     });
1182     colourTextMenuItem.setText(MessageManager
1183             .getString("label.colour_text"));
1184     colourTextMenuItem
1185             .addActionListener(new java.awt.event.ActionListener()
1186             {
1187               @Override
1188               public void actionPerformed(ActionEvent e)
1189               {
1190                 colourTextMenuItem_actionPerformed(e);
1191               }
1192             });
1193     htmlMenuItem.setText(MessageManager.getString("label.html"));
1194     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
1195     {
1196       @Override
1197       public void actionPerformed(ActionEvent e)
1198       {
1199         htmlMenuItem_actionPerformed(e);
1200       }
1201     });
1202
1203     // TODO uncomment when supported by MassageManager
1204     // createBioJS.setText(MessageManager.getString("label.biojs_html_export"));
1205     createBioJS.setText("BioJS");
1206     createBioJS.addActionListener(new java.awt.event.ActionListener()
1207     {
1208       @Override
1209       public void actionPerformed(ActionEvent e)
1210       {
1211         bioJSMenuItem_actionPerformed(e);
1212       }
1213     });
1214
1215     overviewMenuItem.setText(MessageManager
1216             .getString("label.overview_window"));
1217     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
1218     {
1219       @Override
1220       public void actionPerformed(ActionEvent e)
1221       {
1222         overviewMenuItem_actionPerformed(e);
1223       }
1224     });
1225     undoMenuItem.setEnabled(false);
1226     undoMenuItem.setText(MessageManager.getString("action.undo"));
1227     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1228             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1229                     .getMenuShortcutKeyMask(), false));
1230     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1231     {
1232       @Override
1233       public void actionPerformed(ActionEvent e)
1234       {
1235         undoMenuItem_actionPerformed(e);
1236       }
1237     });
1238     redoMenuItem.setEnabled(false);
1239     redoMenuItem.setText(MessageManager.getString("action.redo"));
1240     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1241             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1242                     .getMenuShortcutKeyMask(), false));
1243     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1244     {
1245       @Override
1246       public void actionPerformed(ActionEvent e)
1247       {
1248         redoMenuItem_actionPerformed(e);
1249       }
1250     });
1251     conservationMenuItem.setText(MessageManager
1252             .getString("action.by_conservation"));
1253     conservationMenuItem
1254             .addActionListener(new java.awt.event.ActionListener()
1255             {
1256               @Override
1257               public void actionPerformed(ActionEvent e)
1258               {
1259                 conservationMenuItem_actionPerformed(e);
1260               }
1261             });
1262     noColourmenuItem.setText(MessageManager.getString("label.none"));
1263     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1264     {
1265       @Override
1266       public void actionPerformed(ActionEvent e)
1267       {
1268         noColourmenuItem_actionPerformed(e);
1269       }
1270     });
1271     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1272     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1273     {
1274       @Override
1275       public void actionPerformed(ActionEvent e)
1276       {
1277         wrapMenuItem_actionPerformed(e);
1278       }
1279     });
1280     printMenuItem.setText(MessageManager.getString("action.print") + "...");
1281     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1282             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1283                     .getMenuShortcutKeyMask(), false));
1284     printMenuItem.addActionListener(new java.awt.event.ActionListener()
1285     {
1286       @Override
1287       public void actionPerformed(ActionEvent e)
1288       {
1289         printMenuItem_actionPerformed(e);
1290       }
1291     });
1292     renderGapsMenuItem
1293             .setText(MessageManager.getString("action.show_gaps"));
1294     renderGapsMenuItem.setState(true);
1295     renderGapsMenuItem
1296             .addActionListener(new java.awt.event.ActionListener()
1297             {
1298               @Override
1299               public void actionPerformed(ActionEvent e)
1300               {
1301                 renderGapsMenuItem_actionPerformed(e);
1302               }
1303             });
1304     findMenuItem.setText(MessageManager.getString("action.find"));
1305     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1306             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1307                     .getMenuShortcutKeyMask(), false));
1308     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
1309             MessageManager.getString("label.find_tip")));
1310     findMenuItem.addActionListener(new java.awt.event.ActionListener()
1311     {
1312       @Override
1313       public void actionPerformed(ActionEvent e)
1314       {
1315         findMenuItem_actionPerformed(e);
1316       }
1317     });
1318     abovePIDThreshold.setText(MessageManager
1319             .getString("label.above_identity_threshold"));
1320     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1321     {
1322       @Override
1323       public void actionPerformed(ActionEvent e)
1324       {
1325         abovePIDThreshold_actionPerformed(e);
1326       }
1327     });
1328     showSeqFeatures.setText(MessageManager
1329             .getString("label.show_sequence_features"));
1330     showSeqFeatures.addActionListener(new ActionListener()
1331     {
1332       @Override
1333       public void actionPerformed(ActionEvent actionEvent)
1334       {
1335         showSeqFeatures_actionPerformed(actionEvent);
1336       }
1337     });
1338     /*
1339      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1340      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1341      * void actionPerformed(ActionEvent actionEvent) {
1342      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1343      */
1344     showDbRefsMenuitem.setText(MessageManager
1345             .getString("label.show_database_refs"));
1346     showDbRefsMenuitem.addActionListener(new ActionListener()
1347     {
1348
1349       @Override
1350       public void actionPerformed(ActionEvent e)
1351       {
1352         showDbRefs_actionPerformed(e);
1353       }
1354
1355     });
1356     showNpFeatsMenuitem.setText(MessageManager
1357             .getString("label.show_non_positional_features"));
1358     showNpFeatsMenuitem.addActionListener(new ActionListener()
1359     {
1360
1361       @Override
1362       public void actionPerformed(ActionEvent e)
1363       {
1364         showNpFeats_actionPerformed(e);
1365       }
1366
1367     });
1368     showGroupConservation.setText(MessageManager
1369             .getString("label.group_conservation"));
1370     showGroupConservation.addActionListener(new ActionListener()
1371     {
1372
1373       @Override
1374       public void actionPerformed(ActionEvent e)
1375       {
1376         showGroupConservation_actionPerformed(e);
1377       }
1378
1379     });
1380
1381     showGroupConsensus.setText(MessageManager
1382             .getString("label.group_consensus"));
1383     showGroupConsensus.addActionListener(new ActionListener()
1384     {
1385
1386       @Override
1387       public void actionPerformed(ActionEvent e)
1388       {
1389         showGroupConsensus_actionPerformed(e);
1390       }
1391
1392     });
1393     showConsensusHistogram.setText(MessageManager
1394             .getString("label.show_consensus_histogram"));
1395     showConsensusHistogram.addActionListener(new ActionListener()
1396     {
1397
1398       @Override
1399       public void actionPerformed(ActionEvent e)
1400       {
1401         showConsensusHistogram_actionPerformed(e);
1402       }
1403
1404     });
1405     showSequenceLogo.setText(MessageManager
1406             .getString("label.show_consensus_logo"));
1407     showSequenceLogo.addActionListener(new ActionListener()
1408     {
1409
1410       @Override
1411       public void actionPerformed(ActionEvent e)
1412       {
1413         showSequenceLogo_actionPerformed(e);
1414       }
1415
1416     });
1417     normaliseSequenceLogo.setText(MessageManager
1418             .getString("label.norm_consensus_logo"));
1419     normaliseSequenceLogo.addActionListener(new ActionListener()
1420     {
1421
1422       @Override
1423       public void actionPerformed(ActionEvent e)
1424       {
1425         normaliseSequenceLogo_actionPerformed(e);
1426       }
1427
1428     });
1429     applyAutoAnnotationSettings.setText(MessageManager
1430             .getString("label.apply_all_groups"));
1431     applyAutoAnnotationSettings.setState(false);
1432     applyAutoAnnotationSettings.setVisible(true);
1433     applyAutoAnnotationSettings.addActionListener(new ActionListener()
1434     {
1435       @Override
1436       public void actionPerformed(ActionEvent e)
1437       {
1438         applyAutoAnnotationSettings_actionPerformed(e);
1439       }
1440     });
1441
1442     ButtonGroup buttonGroup = new ButtonGroup();
1443     buttonGroup.add(showAutoFirst);
1444     buttonGroup.add(showAutoLast);
1445     showAutoFirst.setText(MessageManager.getString("label.show_first"));
1446     showAutoFirst.setSelected(Cache.getDefault(
1447             Preferences.SHOW_AUTOCALC_ABOVE,
1448             false));
1449     showAutoFirst.addActionListener(new ActionListener()
1450     {
1451       @Override
1452       public void actionPerformed(ActionEvent e)
1453       {
1454         setShowAutoCalculatedAbove(showAutoFirst.isSelected());
1455         sortAnnotations_actionPerformed();
1456       }
1457     });
1458     showAutoLast.setText(MessageManager.getString("label.show_last"));
1459     showAutoLast.setSelected(!showAutoFirst.isSelected());
1460     showAutoLast.addActionListener(new ActionListener()
1461     {
1462       @Override
1463       public void actionPerformed(ActionEvent e)
1464       {
1465         setShowAutoCalculatedAbove(!showAutoLast.isSelected());
1466         sortAnnotations_actionPerformed();
1467       }
1468     });
1469
1470     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1471     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1472     {
1473       @Override
1474       public void actionPerformed(ActionEvent e)
1475       {
1476         nucleotideColour_actionPerformed(e);
1477       }
1478     });
1479
1480     tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1481     tcoffeeColour.setEnabled(false);
1482     tcoffeeColour.addActionListener(new ActionListener()
1483     {
1484
1485       @Override
1486       public void actionPerformed(ActionEvent e)
1487       {
1488         tcoffeeColorScheme_actionPerformed(e);
1489       }
1490     });
1491
1492     deleteGroups
1493             .setText(MessageManager.getString("action.undefine_groups"));
1494     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1495             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1496                     .getMenuShortcutKeyMask(), false));
1497     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1498     {
1499       @Override
1500       public void actionPerformed(ActionEvent e)
1501       {
1502         deleteGroups_actionPerformed(e);
1503       }
1504     });
1505     createGroup.setText(MessageManager.getString("action.create_groups"));
1506     createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1507             java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1508                     .getMenuShortcutKeyMask(), false));
1509     createGroup.addActionListener(new java.awt.event.ActionListener()
1510     {
1511       @Override
1512       public void actionPerformed(ActionEvent e)
1513       {
1514         createGroup_actionPerformed(e);
1515       }
1516     });
1517     unGroup.setText(MessageManager.getString("action.remove_group"));
1518     unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1519             java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1520                     .getMenuShortcutKeyMask()
1521                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1522     unGroup.addActionListener(new java.awt.event.ActionListener()
1523     {
1524       @Override
1525       public void actionPerformed(ActionEvent e)
1526       {
1527         unGroup_actionPerformed(e);
1528       }
1529     });
1530     copy.setText(MessageManager.getString("action.copy"));
1531     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1532             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1533                     .getMenuShortcutKeyMask(), false));
1534
1535     copy.addActionListener(new java.awt.event.ActionListener()
1536     {
1537       @Override
1538       public void actionPerformed(ActionEvent e)
1539       {
1540         copy_actionPerformed(e);
1541       }
1542     });
1543     cut.setText(MessageManager.getString("action.cut"));
1544     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1545             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1546                     .getMenuShortcutKeyMask(), false));
1547     cut.addActionListener(new java.awt.event.ActionListener()
1548     {
1549       @Override
1550       public void actionPerformed(ActionEvent e)
1551       {
1552         cut_actionPerformed(e);
1553       }
1554     });
1555     delete.setText(MessageManager.getString("action.delete"));
1556     delete.addActionListener(new java.awt.event.ActionListener()
1557     {
1558       @Override
1559       public void actionPerformed(ActionEvent e)
1560       {
1561         delete_actionPerformed(e);
1562       }
1563     });
1564     pasteMenu.setText(MessageManager.getString("action.paste"));
1565     pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1566     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1567             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1568                     .getMenuShortcutKeyMask()
1569                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1570     pasteNew.addActionListener(new java.awt.event.ActionListener()
1571     {
1572       @Override
1573       public void actionPerformed(ActionEvent e)
1574       {
1575         pasteNew_actionPerformed(e);
1576       }
1577     });
1578     pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1579     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1580             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1581                     .getMenuShortcutKeyMask(), false));
1582     pasteThis.addActionListener(new java.awt.event.ActionListener()
1583     {
1584       @Override
1585       public void actionPerformed(ActionEvent e)
1586       {
1587         pasteThis_actionPerformed(e);
1588       }
1589     });
1590     applyToAllGroups.setText(MessageManager
1591             .getString("label.apply_colour_to_all_groups"));
1592     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1593     {
1594       @Override
1595       public void actionPerformed(ActionEvent e)
1596       {
1597         applyToAllGroups_actionPerformed(e);
1598       }
1599     });
1600     createPNG.addActionListener(new java.awt.event.ActionListener()
1601     {
1602       @Override
1603       public void actionPerformed(ActionEvent e)
1604       {
1605         createPNG(null);
1606       }
1607     });
1608     createPNG.setActionCommand(MessageManager
1609             .getString("label.save_png_image"));
1610     createPNG.setText("PNG");
1611
1612     font.setText(MessageManager.getString("action.font"));
1613     font.addActionListener(new java.awt.event.ActionListener()
1614     {
1615       @Override
1616       public void actionPerformed(ActionEvent e)
1617       {
1618         font_actionPerformed(e);
1619       }
1620     });
1621     seqLimits.setText(MessageManager
1622             .getString("label.show_sequence_limits"));
1623     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1624     seqLimits.addActionListener(new java.awt.event.ActionListener()
1625     {
1626       @Override
1627       public void actionPerformed(ActionEvent e)
1628       {
1629         seqLimit_actionPerformed(e);
1630       }
1631     });
1632     epsFile.setText("EPS");
1633     epsFile.addActionListener(new java.awt.event.ActionListener()
1634     {
1635       @Override
1636       public void actionPerformed(ActionEvent e)
1637       {
1638         createEPS(null);
1639       }
1640     });
1641
1642     createSVG.setText("SVG");
1643     createSVG.addActionListener(new java.awt.event.ActionListener()
1644     {
1645       @Override
1646       public void actionPerformed(ActionEvent e)
1647       {
1648         createSVG(null);
1649       }
1650     });
1651
1652     LoadtreeMenuItem.setActionCommand(MessageManager
1653             .getString("label.load_tree_for_sequence_set"));
1654     LoadtreeMenuItem.setText(MessageManager
1655             .getString("label.load_associated_tree"));
1656     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1657     {
1658       @Override
1659       public void actionPerformed(ActionEvent e)
1660       {
1661         LoadtreeMenuItem_actionPerformed(e);
1662       }
1663     });
1664
1665     scaleAbove.setVisible(false);
1666     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1667     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1668     {
1669       @Override
1670       public void actionPerformed(ActionEvent e)
1671       {
1672         scaleAbove_actionPerformed(e);
1673       }
1674     });
1675     scaleLeft.setVisible(false);
1676     scaleLeft.setSelected(true);
1677     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1678     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1679     {
1680       @Override
1681       public void actionPerformed(ActionEvent e)
1682       {
1683         scaleLeft_actionPerformed(e);
1684       }
1685     });
1686     scaleRight.setVisible(false);
1687     scaleRight.setSelected(true);
1688     scaleRight.setText(MessageManager.getString("action.scale_right"));
1689     scaleRight.addActionListener(new java.awt.event.ActionListener()
1690     {
1691       @Override
1692       public void actionPerformed(ActionEvent e)
1693       {
1694         scaleRight_actionPerformed(e);
1695       }
1696     });
1697     centreColumnLabelsMenuItem.setVisible(true);
1698     centreColumnLabelsMenuItem.setState(false);
1699     centreColumnLabelsMenuItem.setText(MessageManager
1700             .getString("label.centre_column_labels"));
1701     centreColumnLabelsMenuItem
1702             .addActionListener(new java.awt.event.ActionListener()
1703             {
1704               @Override
1705               public void actionPerformed(ActionEvent e)
1706               {
1707                 centreColumnLabels_actionPerformed(e);
1708               }
1709             });
1710     followHighlightMenuItem.setVisible(true);
1711     followHighlightMenuItem.setState(true);
1712     followHighlightMenuItem.setText(MessageManager
1713             .getString("label.automatic_scrolling"));
1714     followHighlightMenuItem.addActionListener(new ActionListener()
1715     {
1716
1717       @Override
1718       public void actionPerformed(ActionEvent e)
1719       {
1720         followHighlight_actionPerformed();
1721       }
1722
1723     });
1724
1725     modifyPID.setText(MessageManager
1726             .getString("label.modify_identity_thereshold"));
1727     modifyPID.addActionListener(new java.awt.event.ActionListener()
1728     {
1729       @Override
1730       public void actionPerformed(ActionEvent e)
1731       {
1732         modifyPID_actionPerformed(e);
1733       }
1734     });
1735     modifyConservation.setText(MessageManager
1736             .getString("label.modify_conservation_thereshold"));
1737     modifyConservation
1738             .addActionListener(new java.awt.event.ActionListener()
1739             {
1740               @Override
1741               public void actionPerformed(ActionEvent e)
1742               {
1743                 modifyConservation_actionPerformed(e);
1744               }
1745             });
1746     sortByTreeMenu
1747             .setText(MessageManager.getString("action.by_tree_order"));
1748     sort.setText(MessageManager.getString("action.sort"));
1749     sort.addMenuListener(new MenuListener()
1750     {
1751       @Override
1752       public void menuSelected(MenuEvent e)
1753       {
1754         buildTreeMenu();
1755       }
1756
1757       @Override
1758       public void menuDeselected(MenuEvent e)
1759       {
1760       }
1761
1762       @Override
1763       public void menuCanceled(MenuEvent e)
1764       {
1765       }
1766     });
1767     sortByAnnotScore.setText(MessageManager
1768             .getString("label.sort_by_score"));
1769     sort.add(sortByAnnotScore);
1770     sort.addMenuListener(new javax.swing.event.MenuListener()
1771     {
1772
1773       @Override
1774       public void menuCanceled(MenuEvent e)
1775       {
1776       }
1777
1778       @Override
1779       public void menuDeselected(MenuEvent e)
1780       {
1781       }
1782
1783       @Override
1784       public void menuSelected(MenuEvent e)
1785       {
1786         buildSortByAnnotationScoresMenu();
1787       }
1788     });
1789     sortByAnnotScore.setVisible(false);
1790
1791     calculateTree
1792             .setText(MessageManager.getString("action.calculate_tree"));
1793
1794     jMenu2.setText(MessageManager.getString("label.export_image"));
1795     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1796     padGapsMenuitem.setState(jalview.bin.Cache
1797             .getDefault("PAD_GAPS", false));
1798     padGapsMenuitem.addActionListener(new ActionListener()
1799     {
1800       @Override
1801       public void actionPerformed(ActionEvent e)
1802       {
1803         padGapsMenuitem_actionPerformed(e);
1804       }
1805     });
1806     vamsasStore.setVisible(false);
1807     vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1808     vamsasStore.addActionListener(new ActionListener()
1809     {
1810       @Override
1811       public void actionPerformed(ActionEvent e)
1812       {
1813         vamsasStore_actionPerformed(e);
1814       }
1815     });
1816     showTranslation.setText(MessageManager
1817             .getString("label.translate_cDNA"));
1818     showTranslation.addActionListener(new ActionListener()
1819     {
1820       @Override
1821       public void actionPerformed(ActionEvent e)
1822       {
1823         showTranslation_actionPerformed(e);
1824       }
1825     });
1826     extractScores.setText(MessageManager.getString("label.extract_scores")
1827             + "...");
1828     extractScores.addActionListener(new ActionListener()
1829     {
1830       @Override
1831       public void actionPerformed(ActionEvent e)
1832       {
1833         extractScores_actionPerformed(e);
1834       }
1835     });
1836     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1837     // score extraction
1838     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1839     /*
1840      * showProducts.addActionListener(new ActionListener() {
1841      *
1842      * public void actionPerformed(ActionEvent e) {
1843      * showProducts_actionPerformed(e); } });
1844      */
1845     openFeatureSettings.setText(MessageManager
1846             .getString("label.feature_settings"));
1847     openFeatureSettings.addActionListener(new ActionListener()
1848     {
1849       @Override
1850       public void actionPerformed(ActionEvent e)
1851       {
1852         featureSettings_actionPerformed(e);
1853       }
1854     });
1855     fetchSequence
1856             .setText(MessageManager.getString("label.fetch_sequences"));
1857     fetchSequence.addActionListener(new ActionListener()
1858     {
1859       @Override
1860       public void actionPerformed(ActionEvent e)
1861       {
1862         fetchSequence_actionPerformed(e);
1863       }
1864     });
1865
1866     annotationColour.setText(MessageManager
1867             .getString("action.by_annotation"));
1868     annotationColour.addActionListener(new ActionListener()
1869     {
1870       @Override
1871       public void actionPerformed(ActionEvent e)
1872       {
1873         annotationColour_actionPerformed(e);
1874       }
1875     });
1876
1877     rnahelicesColour.setText(MessageManager
1878             .getString("action.by_rna_helixes"));
1879     rnahelicesColour.addActionListener(new ActionListener()
1880     {
1881       @Override
1882       public void actionPerformed(ActionEvent e)
1883       {
1884         rnahelicesColour_actionPerformed(e);
1885       }
1886     });
1887
1888     associatedData.setText(MessageManager
1889             .getString("label.load_features_annotations"));
1890     associatedData.addActionListener(new ActionListener()
1891     {
1892       @Override
1893       public void actionPerformed(ActionEvent e)
1894       {
1895         associatedData_actionPerformed(e);
1896       }
1897     });
1898     autoCalculate.setText(MessageManager
1899             .getString("label.autocalculate_consensus"));
1900     autoCalculate.setState(jalview.bin.Cache.getDefault(
1901             "AUTO_CALC_CONSENSUS", true));
1902     autoCalculate.addActionListener(new ActionListener()
1903     {
1904       @Override
1905       public void actionPerformed(ActionEvent e)
1906       {
1907         autoCalculate_actionPerformed(e);
1908       }
1909     });
1910     sortByTree.setText(MessageManager
1911             .getString("label.sort_alignment_new_tree"));
1912     sortByTree
1913             .setToolTipText("<html>"
1914                     + MessageManager
1915                             .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1916     sortByTree
1917             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1918     sortByTree.addActionListener(new ActionListener()
1919     {
1920       @Override
1921       public void actionPerformed(ActionEvent e)
1922       {
1923         sortByTreeOption_actionPerformed(e);
1924       }
1925     });
1926
1927     listenToViewSelections.setText(MessageManager
1928             .getString("label.listen_for_selections"));
1929     listenToViewSelections
1930             .setToolTipText("<html>"
1931                     + MessageManager
1932                             .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1933     listenToViewSelections.setState(false);
1934     listenToViewSelections.addActionListener(new ActionListener()
1935     {
1936       @Override
1937       public void actionPerformed(ActionEvent e)
1938       {
1939         listenToViewSelections_actionPerformed(e);
1940       }
1941     });
1942
1943     addSequenceMenu
1944             .setText(MessageManager.getString("label.add_sequences"));
1945     addFromFile.setText(MessageManager.getString("label.from_file"));
1946     addFromFile.addActionListener(new ActionListener()
1947     {
1948       @Override
1949       public void actionPerformed(ActionEvent e)
1950       {
1951         addFromFile_actionPerformed(e);
1952       }
1953     });
1954     addFromText.setText(MessageManager.getString("label.from_textbox"));
1955     addFromText.addActionListener(new ActionListener()
1956     {
1957       @Override
1958       public void actionPerformed(ActionEvent e)
1959       {
1960         addFromText_actionPerformed(e);
1961       }
1962     });
1963     addFromURL.setText(MessageManager.getString("label.from_url"));
1964     addFromURL.addActionListener(new ActionListener()
1965     {
1966       @Override
1967       public void actionPerformed(ActionEvent e)
1968       {
1969         addFromURL_actionPerformed(e);
1970       }
1971     });
1972     exportFeatures.setText(MessageManager
1973             .getString("label.export_features"));
1974     exportFeatures.addActionListener(new ActionListener()
1975     {
1976       @Override
1977       public void actionPerformed(ActionEvent e)
1978       {
1979         exportFeatures_actionPerformed(e);
1980       }
1981     });
1982     exportAnnotations.setText(MessageManager
1983             .getString("label.export_annotations"));
1984     exportAnnotations.addActionListener(new ActionListener()
1985     {
1986       @Override
1987       public void actionPerformed(ActionEvent e)
1988       {
1989         exportAnnotations_actionPerformed(e);
1990       }
1991     });
1992     statusPanel.setLayout(gridLayout1);
1993     jMenu3.setText(MessageManager.getString("action.show"));
1994     showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
1995     showAllSeqs.setToolTipText(MessageManager
1996             .getString("label.toggle_sequence_visibility"));
1997     showAllSeqs.addActionListener(new ActionListener()
1998     {
1999       @Override
2000       public void actionPerformed(ActionEvent e)
2001       {
2002         showAllSeqs_actionPerformed(e);
2003       }
2004     });
2005     showAllColumns.setText(MessageManager.getString("label.all_columns"));
2006     showAllColumns.setToolTipText(MessageManager
2007             .getString("label.toggle_columns_visibility"));
2008     showAllColumns.addActionListener(new ActionListener()
2009     {
2010       @Override
2011       public void actionPerformed(ActionEvent e)
2012       {
2013         showAllColumns_actionPerformed(e);
2014       }
2015     });
2016     hideMenu.setText(MessageManager.getString("action.hide"));
2017     hideSelSequences.setText(MessageManager
2018             .getString("label.selected_sequences"));
2019     hideSelSequences.setToolTipText(MessageManager
2020             .getString("label.toggle_sequence_visibility"));
2021     hideSelSequences.addActionListener(new ActionListener()
2022     {
2023       @Override
2024       public void actionPerformed(ActionEvent e)
2025       {
2026         hideSelSequences_actionPerformed(e);
2027       }
2028     });
2029     hideSelColumns.setText(MessageManager
2030             .getString("label.selected_columns"));
2031     hideSelColumns.setToolTipText(MessageManager
2032             .getString("label.toggle_columns_visibility"));
2033     hideSelColumns.addActionListener(new ActionListener()
2034     {
2035       @Override
2036       public void actionPerformed(ActionEvent e)
2037       {
2038         hideSelColumns_actionPerformed(e);
2039       }
2040     });
2041     hideAllSelection.setText(MessageManager
2042             .getString("label.selected_region"));
2043     hideAllSelection.addActionListener(new ActionListener()
2044     {
2045       @Override
2046       public void actionPerformed(ActionEvent e)
2047       {
2048         hideAllSelection_actionPerformed(e);
2049       }
2050     });
2051     // TODO: should be hidden if no selection exists.
2052     hideAllButSelection.setText(MessageManager
2053             .getString("label.all_but_selected_region"));
2054     hideAllButSelection.addActionListener(new ActionListener()
2055     {
2056       @Override
2057       public void actionPerformed(ActionEvent e)
2058       {
2059         hideAllButSelection_actionPerformed(e);
2060       }
2061     });
2062     showAllhidden.setText(MessageManager
2063             .getString("label.all_sequences_columns"));
2064     showAllhidden.setToolTipText(MessageManager
2065             .getString("label.toggles_visibility_hidden_selected_regions"));
2066     showAllhidden.addActionListener(new ActionListener()
2067     {
2068       @Override
2069       public void actionPerformed(ActionEvent e)
2070       {
2071         showAllhidden_actionPerformed(e);
2072       }
2073     });
2074     hiddenMarkers.setText(MessageManager
2075             .getString("action.show_hidden_markers"));
2076     hiddenMarkers.addActionListener(new ActionListener()
2077     {
2078       @Override
2079       public void actionPerformed(ActionEvent e)
2080       {
2081         hiddenMarkers_actionPerformed(e);
2082       }
2083     });
2084     invertColSel.setText(MessageManager
2085             .getString("action.invert_column_selection"));
2086     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2087             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
2088                     .getMenuShortcutKeyMask()
2089                     | java.awt.event.KeyEvent.ALT_MASK, false));
2090     invertColSel.addActionListener(new ActionListener()
2091     {
2092       @Override
2093       public void actionPerformed(ActionEvent e)
2094       {
2095         invertColSel_actionPerformed(e);
2096       }
2097     });
2098     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
2099     {
2100       @Override
2101       public void stateChanged(ChangeEvent evt)
2102       {
2103         JTabbedPane pane = (JTabbedPane) evt.getSource();
2104         int sel = pane.getSelectedIndex();
2105         tabSelectionChanged(sel);
2106       }
2107     });
2108     tabbedPane.addMouseListener(new MouseAdapter()
2109     {
2110       @Override
2111       public void mousePressed(MouseEvent e)
2112       {
2113         tabbedPane_mousePressed(e);
2114       }
2115     });
2116     tabbedPane.addFocusListener(new FocusAdapter()
2117     {
2118       @Override
2119       public void focusGained(FocusEvent e)
2120       {
2121         tabbedPane_focusGained(e);
2122       }
2123     });
2124     save.setText(MessageManager.getString("action.save"));
2125     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2126             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
2127                     .getMenuShortcutKeyMask(), false));
2128     save.addActionListener(new ActionListener()
2129     {
2130       @Override
2131       public void actionPerformed(ActionEvent e)
2132       {
2133         save_actionPerformed(e);
2134       }
2135     });
2136     reload.setEnabled(false);
2137     reload.setText(MessageManager.getString("action.reload"));
2138     reload.addActionListener(new ActionListener()
2139     {
2140       @Override
2141       public void actionPerformed(ActionEvent e)
2142       {
2143         reload_actionPerformed(e);
2144       }
2145     });
2146     newView.setText(MessageManager.getString("action.new_view"));
2147     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2148             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
2149                     .getMenuShortcutKeyMask(), false));
2150     newView.addActionListener(new ActionListener()
2151     {
2152       @Override
2153       public void actionPerformed(ActionEvent e)
2154       {
2155         newView_actionPerformed(e);
2156       }
2157     });
2158     tabbedPane.setToolTipText("<html><i>"
2159             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2160             + "</i></html>");
2161     textColour.setText(MessageManager.getString("label.colour_text")
2162             + "...");
2163     textColour.addActionListener(new ActionListener()
2164     {
2165       @Override
2166       public void actionPerformed(ActionEvent e)
2167       {
2168         textColour_actionPerformed(e);
2169       }
2170     });
2171     formatMenu.setText(MessageManager.getString("action.format"));
2172     selectMenu.setText(MessageManager.getString("action.select"));
2173     idRightAlign.setText(MessageManager
2174             .getString("label.right_align_sequence_id"));
2175     idRightAlign.addActionListener(new ActionListener()
2176     {
2177       @Override
2178       public void actionPerformed(ActionEvent e)
2179       {
2180         idRightAlign_actionPerformed(e);
2181       }
2182     });
2183     gatherViews.setEnabled(false);
2184     gatherViews.setText(MessageManager.getString("action.gather_views"));
2185     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2186             java.awt.event.KeyEvent.VK_G, 0, false));
2187     gatherViews.addActionListener(new ActionListener()
2188     {
2189       @Override
2190       public void actionPerformed(ActionEvent e)
2191       {
2192         gatherViews_actionPerformed(e);
2193       }
2194     });
2195     expandViews.setEnabled(false);
2196     expandViews.setText(MessageManager.getString("action.expand_views"));
2197     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2198             java.awt.event.KeyEvent.VK_X, 0, false));
2199     expandViews.addActionListener(new ActionListener()
2200     {
2201       @Override
2202       public void actionPerformed(ActionEvent e)
2203       {
2204         expandViews_actionPerformed(e);
2205       }
2206     });
2207     pageSetup
2208             .setText(MessageManager.getString("action.page_setup") + "...");
2209     pageSetup.addActionListener(new ActionListener()
2210     {
2211       @Override
2212       public void actionPerformed(ActionEvent e)
2213       {
2214         pageSetup_actionPerformed(e);
2215       }
2216     });
2217     alignmentProperties.setText(MessageManager
2218             .getString("label.alignment_props") + "...");
2219     alignmentProperties.addActionListener(new ActionListener()
2220     {
2221       @Override
2222       public void actionPerformed(ActionEvent actionEvent)
2223       {
2224         alignmentProperties();
2225       }
2226     });
2227     tooltipSettingsMenu.setText(MessageManager
2228             .getString("label.sequence_id_tooltip"));
2229     autoAnnMenu.setText(MessageManager
2230             .getString("label.autocalculated_annotation"));
2231     alignFrameMenuBar.add(fileMenu);
2232     alignFrameMenuBar.add(editMenu);
2233     alignFrameMenuBar.add(selectMenu);
2234     alignFrameMenuBar.add(viewMenu);
2235     alignFrameMenuBar.add(annotationsMenu);
2236     alignFrameMenuBar.add(formatMenu);
2237     alignFrameMenuBar.add(colourMenu);
2238     alignFrameMenuBar.add(calculateMenu);
2239     alignFrameMenuBar.add(webService);
2240     fileMenu.add(fetchSequence);
2241     fileMenu.add(addSequenceMenu);
2242     fileMenu.add(reload);
2243     fileMenu.addSeparator();
2244     fileMenu.add(vamsasStore);
2245     fileMenu.add(save);
2246     fileMenu.add(saveAs);
2247     fileMenu.add(outputTextboxMenu);
2248     fileMenu.add(pageSetup);
2249     fileMenu.add(printMenuItem);
2250     fileMenu.addSeparator();
2251     fileMenu.add(jMenu2);
2252     fileMenu.add(exportFeatures);
2253     fileMenu.add(exportAnnotations);
2254     fileMenu.add(LoadtreeMenuItem);
2255     fileMenu.add(associatedData);
2256     fileMenu.addSeparator();
2257     fileMenu.add(closeMenuItem);
2258     editMenu.add(undoMenuItem);
2259     editMenu.add(redoMenuItem);
2260     editMenu.add(cut);
2261     editMenu.add(copy);
2262     editMenu.add(pasteMenu);
2263     editMenu.add(delete);
2264     editMenu.addSeparator();
2265     editMenu.add(remove2LeftMenuItem);
2266     editMenu.add(remove2RightMenuItem);
2267     editMenu.add(removeGappedColumnMenuItem);
2268     editMenu.add(removeAllGapsMenuItem);
2269     editMenu.add(removeRedundancyMenuItem);
2270     editMenu.addSeparator();
2271     // dont add these yet in the CVS build - they cannot be undone!
2272     // Excluded from Jalview 2.5 release - undo needs to be implemented.
2273     // editMenu.add(justifyLeftMenuItem);
2274     // editMenu.add(justifyRightMenuItem);
2275     // editMenu.addSeparator();
2276     editMenu.add(padGapsMenuitem);
2277     viewMenu.add(newView);
2278     viewMenu.add(expandViews);
2279     viewMenu.add(gatherViews);
2280     viewMenu.addSeparator();
2281     viewMenu.add(jMenu3);
2282     viewMenu.add(hideMenu);
2283     viewMenu.addSeparator();
2284     viewMenu.add(followHighlightMenuItem);
2285     annotationsMenu.add(annotationPanelMenuItem);
2286     annotationsMenu.addSeparator();
2287     annotationsMenu.add(showAllAlAnnotations);
2288     annotationsMenu.add(hideAllAlAnnotations);
2289     annotationsMenu.addSeparator();
2290     annotationsMenu.add(showAllSeqAnnotations);
2291     annotationsMenu.add(hideAllSeqAnnotations);
2292     annotationsMenu.add(sortAnnBySequence);
2293     annotationsMenu.add(sortAnnByLabel);
2294     annotationsMenu.addSeparator();
2295     autoAnnMenu.add(showAutoFirst);
2296     autoAnnMenu.add(showAutoLast);
2297     autoAnnMenu.addSeparator();
2298     autoAnnMenu.add(applyAutoAnnotationSettings);
2299     autoAnnMenu.add(showConsensusHistogram);
2300     autoAnnMenu.add(showSequenceLogo);
2301     autoAnnMenu.add(normaliseSequenceLogo);
2302     autoAnnMenu.addSeparator();
2303     autoAnnMenu.add(showGroupConservation);
2304     autoAnnMenu.add(showGroupConsensus);
2305     annotationsMenu.add(autoAnnMenu);
2306     viewMenu.addSeparator();
2307     viewMenu.add(showSeqFeatures);
2308     // viewMenu.add(showSeqFeaturesHeight);
2309
2310     viewMenu.add(openFeatureSettings);
2311     tooltipSettingsMenu.add(showDbRefsMenuitem);
2312     tooltipSettingsMenu.add(showNpFeatsMenuitem);
2313     viewMenu.add(tooltipSettingsMenu);
2314     viewMenu.addSeparator();
2315     viewMenu.add(alignmentProperties);
2316     viewMenu.addSeparator();
2317     viewMenu.add(overviewMenuItem);
2318     colourMenu.add(applyToAllGroups);
2319     colourMenu.add(textColour);
2320     colourMenu.addSeparator();
2321     colourMenu.add(noColourmenuItem);
2322     colourMenu.add(clustalColour);
2323     colourMenu.add(BLOSUM62Colour);
2324     colourMenu.add(PIDColour);
2325     colourMenu.add(zappoColour);
2326     colourMenu.add(taylorColour);
2327     colourMenu.add(hydrophobicityColour);
2328     colourMenu.add(helixColour);
2329     colourMenu.add(strandColour);
2330     colourMenu.add(turnColour);
2331     colourMenu.add(buriedColour);
2332     colourMenu.add(nucleotideColour);
2333     colourMenu.add(purinePyrimidineColour);
2334     colourMenu.add(RNAInteractionColour);
2335     // colourMenu.add(covariationColour);
2336     colourMenu.add(tcoffeeColour);
2337     colourMenu.add(userDefinedColour);
2338     colourMenu.addSeparator();
2339     colourMenu.add(conservationMenuItem);
2340     colourMenu.add(modifyConservation);
2341     colourMenu.add(abovePIDThreshold);
2342     colourMenu.add(modifyPID);
2343     colourMenu.add(annotationColour);
2344     colourMenu.add(rnahelicesColour);
2345     calculateMenu.add(sort);
2346     calculateMenu.add(calculateTree);
2347     calculateMenu.addSeparator();
2348     calculateMenu.add(pairwiseAlignmentMenuItem);
2349     calculateMenu.add(PCAMenuItem);
2350     calculateMenu.addSeparator();
2351     calculateMenu.add(showTranslation);
2352     calculateMenu.add(showProducts);
2353     calculateMenu.add(autoCalculate);
2354     calculateMenu.add(sortByTree);
2355     calculateMenu.addSeparator();
2356     calculateMenu.add(extractScores);
2357     webServiceNoServices = new JMenuItem(
2358             MessageManager.getString("label.no_services"));
2359     webService.add(webServiceNoServices);
2360     pasteMenu.add(pasteNew);
2361     pasteMenu.add(pasteThis);
2362     sort.add(sortIDMenuItem);
2363     sort.add(sortLengthMenuItem);
2364     sort.add(sortGroupMenuItem);
2365     sort.add(sortPairwiseMenuItem);
2366     sort.add(sortByTreeMenu);
2367     jMenu2.add(htmlMenuItem);
2368     jMenu2.add(epsFile);
2369     jMenu2.add(createPNG);
2370     jMenu2.add(createBioJS);
2371     jMenu2.add(createSVG);
2372     addSequenceMenu.add(addFromFile);
2373     addSequenceMenu.add(addFromText);
2374     addSequenceMenu.add(addFromURL);
2375     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2376     statusPanel.add(statusBar, null);
2377     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2378     jMenu3.add(showAllColumns);
2379     jMenu3.add(showAllSeqs);
2380     jMenu3.add(showAllhidden);
2381     hideMenu.add(hideSelColumns);
2382     hideMenu.add(hideSelSequences);
2383     hideMenu.add(hideAllSelection);
2384     hideMenu.add(hideAllButSelection);
2385
2386     formatMenu.add(font);
2387     formatMenu.addSeparator();
2388     formatMenu.add(wrapMenuItem);
2389     formatMenu.add(scaleAbove);
2390     formatMenu.add(scaleLeft);
2391     formatMenu.add(scaleRight);
2392     formatMenu.add(seqLimits);
2393     formatMenu.add(idRightAlign);
2394     formatMenu.add(hiddenMarkers);
2395     formatMenu.add(viewBoxesMenuItem);
2396     formatMenu.add(viewTextMenuItem);
2397     formatMenu.add(colourTextMenuItem);
2398     formatMenu.add(renderGapsMenuItem);
2399     formatMenu.add(centreColumnLabelsMenuItem);
2400     formatMenu.add(showNonconservedMenuItem);
2401     selectMenu.add(findMenuItem);
2402     selectMenu.addSeparator();
2403     selectMenu.add(selectAllSequenceMenuItem);
2404     selectMenu.add(deselectAllSequenceMenuItem);
2405     selectMenu.add(invertSequenceMenuItem);
2406     selectMenu.add(invertColSel);
2407     selectMenu.add(createGroup);
2408     selectMenu.add(unGroup);
2409     selectMenu.add(grpsFromSelection);
2410     selectMenu.add(deleteGroups);
2411     calculateMenu.add(expandAlignment);
2412     // TODO - determine if the listenToViewSelections button is needed : see bug
2413     // JAL-574
2414     // selectMenu.addSeparator();
2415     // selectMenu.add(listenToViewSelections);
2416   }
2417
2418   /**
2419    * Action on clicking sort annotations by type.
2420    *
2421    * @param sortOrder
2422    */
2423   protected void sortAnnotations_actionPerformed()
2424   {
2425   }
2426
2427   /**
2428    * Action on clicking Show all annotations.
2429    *
2430    * @param forSequences
2431    *          update sequence-related annotations
2432    * @param forAlignment
2433    *          update non-sequence-related annotations
2434    */
2435   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2436           boolean forAlignment)
2437   {
2438     setAnnotationsVisibility(true, forSequences, forAlignment);
2439   }
2440
2441   /**
2442    * Action on clicking Hide all annotations.
2443    *
2444    * @param forSequences
2445    *          update sequence-related annotations
2446    * @param forAlignment
2447    *          update non-sequence-related annotations
2448    */
2449   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2450           boolean forAlignment)
2451   {
2452     setAnnotationsVisibility(false, forSequences, forAlignment);
2453   }
2454
2455   /**
2456    * Set the visibility of annotations to true or false. Can act on
2457    * sequence-related annotations, or alignment-related, or both.
2458    *
2459    * @param visible
2460    * @param forSequences
2461    *          update sequence-related annotations
2462    * @param forAlignment
2463    *          update non-sequence-related annotations
2464    */
2465   protected void setAnnotationsVisibility(boolean visible,
2466           boolean forSequences, boolean forAlignment)
2467   {
2468
2469   }
2470
2471   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2472   {
2473     // TODO Auto-generated method stub
2474
2475   }
2476
2477   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2478   {
2479     // TODO Auto-generated method stub
2480
2481   }
2482
2483   protected void showAllhidden_actionPerformed(ActionEvent e)
2484   {
2485     // TODO Auto-generated method stub
2486
2487   }
2488
2489   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2490   {
2491     // TODO Auto-generated method stub
2492
2493   }
2494
2495   protected void hideAllSelection_actionPerformed(ActionEvent e)
2496   {
2497     // TODO Auto-generated method stub
2498
2499   }
2500
2501   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2502   {
2503     // TODO Auto-generated method stub
2504
2505   }
2506
2507   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2508   {
2509     // TODO Auto-generated method stub
2510
2511   }
2512
2513   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2514   {
2515     // TODO Auto-generated method stub
2516
2517   }
2518
2519   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2520   {
2521     // TODO Auto-generated method stub
2522
2523   }
2524
2525   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2526   {
2527     // TODO Auto-generated method stub
2528
2529   }
2530
2531   protected void showGroupConservation_actionPerformed(ActionEvent e)
2532   {
2533     // TODO Auto-generated method stub
2534
2535   }
2536
2537   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2538   {
2539     // TODO Auto-generated method stub
2540
2541   }
2542
2543   protected void showSeqFeaturesHeight_actionPerformed(
2544           ActionEvent actionEvent)
2545   {
2546     // TODO Auto-generated method stub
2547
2548   }
2549
2550   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2551   {
2552     // TODO Auto-generated method stub
2553
2554   }
2555
2556   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2557   {
2558     // TODO Auto-generated method stub
2559
2560   }
2561
2562   protected void followHighlight_actionPerformed()
2563   {
2564     // TODO Auto-generated method stub
2565
2566   }
2567
2568   protected void showNpFeats_actionPerformed(ActionEvent e)
2569   {
2570     // TODO Auto-generated method stub
2571
2572   }
2573
2574   protected void showDbRefs_actionPerformed(ActionEvent e)
2575   {
2576     // TODO Auto-generated method stub
2577
2578   }
2579
2580   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2581   {
2582   }
2583
2584   protected void showProducts_actionPerformed(ActionEvent e)
2585   {
2586   }
2587
2588   protected void buildSortByAnnotationScoresMenu()
2589   {
2590   }
2591
2592   protected void extractScores_actionPerformed(ActionEvent e)
2593   {
2594   }
2595
2596   protected void outputText_actionPerformed(ActionEvent e)
2597   {
2598   }
2599
2600   public void addFromFile_actionPerformed(ActionEvent e)
2601   {
2602
2603   }
2604
2605   public void addFromText_actionPerformed(ActionEvent e)
2606   {
2607
2608   }
2609
2610   public void addFromURL_actionPerformed(ActionEvent e)
2611   {
2612
2613   }
2614
2615   public void exportFeatures_actionPerformed(ActionEvent e)
2616   {
2617
2618   }
2619
2620   public void exportAnnotations_actionPerformed(ActionEvent e)
2621   {
2622
2623   }
2624
2625   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2626   {
2627   }
2628
2629   protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2630   {
2631
2632   }
2633
2634   protected void closeMenuItem_actionPerformed(boolean b)
2635   {
2636   }
2637
2638   protected void redoMenuItem_actionPerformed(ActionEvent e)
2639   {
2640   }
2641
2642   protected void undoMenuItem_actionPerformed(ActionEvent e)
2643   {
2644   }
2645
2646   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2647   {
2648   }
2649
2650   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2651   {
2652   }
2653
2654   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2655   {
2656   }
2657
2658   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2659   {
2660   }
2661
2662   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2663   {
2664   }
2665
2666   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2667   {
2668   }
2669
2670   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2671   {
2672   }
2673
2674   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2675   {
2676   }
2677
2678   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2679   {
2680   }
2681
2682   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2683   {
2684   }
2685
2686   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2687   {
2688   }
2689
2690   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2691   {
2692   }
2693
2694   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2695   {
2696   }
2697
2698   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2699   {
2700   }
2701
2702   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2703   {
2704   }
2705
2706   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2707   {
2708   }
2709
2710   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2711   {
2712   }
2713
2714   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2715   {
2716   }
2717
2718   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2719   {
2720   }
2721
2722   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2723   {
2724   }
2725
2726   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2727   {
2728   }
2729
2730   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2731   {
2732   }
2733
2734   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2735   {
2736   }
2737
2738   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2739   {
2740   }
2741
2742   protected void clustalColour_actionPerformed(ActionEvent e)
2743   {
2744   }
2745
2746   protected void zappoColour_actionPerformed(ActionEvent e)
2747   {
2748   }
2749
2750   protected void taylorColour_actionPerformed(ActionEvent e)
2751   {
2752   }
2753
2754   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2755   {
2756   }
2757
2758   protected void helixColour_actionPerformed(ActionEvent e)
2759   {
2760   }
2761
2762   protected void strandColour_actionPerformed(ActionEvent e)
2763   {
2764   }
2765
2766   protected void turnColour_actionPerformed(ActionEvent e)
2767   {
2768   }
2769
2770   protected void buriedColour_actionPerformed(ActionEvent e)
2771   {
2772   }
2773
2774   protected void userDefinedColour_actionPerformed(ActionEvent e)
2775   {
2776   }
2777
2778   protected void PIDColour_actionPerformed(ActionEvent e)
2779   {
2780   }
2781
2782   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2783   {
2784   }
2785
2786   protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2787   {
2788   }
2789
2790   protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2791   {
2792   }
2793
2794   /*
2795    * protected void covariationColour_actionPerformed(ActionEvent e) { }
2796    */
2797
2798   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2799   {
2800   }
2801
2802   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2803   {
2804   }
2805
2806   protected void printMenuItem_actionPerformed(ActionEvent e)
2807   {
2808   }
2809
2810   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2811   {
2812   }
2813
2814   protected void findMenuItem_actionPerformed(ActionEvent e)
2815   {
2816   }
2817
2818   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2819   {
2820   }
2821
2822   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2823   {
2824   }
2825
2826   protected void nucleotideColour_actionPerformed(ActionEvent e)
2827   {
2828   }
2829
2830   protected void deleteGroups_actionPerformed(ActionEvent e)
2831   {
2832   }
2833
2834   protected void createGroup_actionPerformed(ActionEvent e)
2835   {
2836   }
2837
2838   protected void unGroup_actionPerformed(ActionEvent e)
2839   {
2840   }
2841
2842   protected void copy_actionPerformed(ActionEvent e)
2843   {
2844   }
2845
2846   protected void cut_actionPerformed(ActionEvent e)
2847   {
2848   }
2849
2850   protected void delete_actionPerformed(ActionEvent e)
2851   {
2852   }
2853
2854   protected void pasteNew_actionPerformed(ActionEvent e)
2855   {
2856   }
2857
2858   protected void pasteThis_actionPerformed(ActionEvent e)
2859   {
2860   }
2861
2862   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2863   {
2864   }
2865
2866   public void createPNG(java.io.File f)
2867   {
2868   }
2869
2870   protected void font_actionPerformed(ActionEvent e)
2871   {
2872   }
2873
2874   protected void seqLimit_actionPerformed(ActionEvent e)
2875   {
2876   }
2877
2878   public void seqDBRef_actionPerformed(ActionEvent e)
2879   {
2880
2881   }
2882
2883   public void createEPS(java.io.File f)
2884   {
2885   }
2886
2887   public void createSVG(java.io.File f)
2888   {
2889
2890   }
2891   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2892   {
2893
2894   }
2895
2896   /**
2897    * Template method to handle the 'load T-Coffee scores' menu event.
2898    * <p>
2899    * Subclasses override this method to provide a custom action.
2900    *
2901    * @param event
2902    *          The raised event
2903    */
2904   protected void loadScores_actionPerformed(ActionEvent event)
2905   {
2906
2907   }
2908
2909   /**
2910    * Template method to handle the 'Color T-Coffee scores' menu event.
2911    * <p>
2912    * Subclasses override this method to provide a custom action.
2913    *
2914    * @param event
2915    *          The raised event
2916    */
2917   protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2918   {
2919
2920   }
2921
2922   protected void jpred_actionPerformed(ActionEvent e)
2923   {
2924   }
2925
2926   protected void scaleAbove_actionPerformed(ActionEvent e)
2927   {
2928   }
2929
2930   protected void scaleLeft_actionPerformed(ActionEvent e)
2931   {
2932   }
2933
2934   protected void scaleRight_actionPerformed(ActionEvent e)
2935   {
2936   }
2937
2938   protected void modifyPID_actionPerformed(ActionEvent e)
2939   {
2940   }
2941
2942   protected void modifyConservation_actionPerformed(ActionEvent e)
2943   {
2944   }
2945
2946   protected void saveAs_actionPerformed(ActionEvent e)
2947   {
2948   }
2949
2950   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2951   {
2952   }
2953
2954   public void vamsasStore_actionPerformed(ActionEvent e)
2955   {
2956
2957   }
2958
2959   public void vamsasLoad_actionPerformed(ActionEvent e)
2960   {
2961
2962   }
2963
2964   public void showTranslation_actionPerformed(ActionEvent e)
2965   {
2966
2967   }
2968
2969   public void featureSettings_actionPerformed(ActionEvent e)
2970   {
2971
2972   }
2973
2974   public void fetchSequence_actionPerformed(ActionEvent e)
2975   {
2976
2977   }
2978
2979   public void smoothFont_actionPerformed(ActionEvent e)
2980   {
2981
2982   }
2983
2984   public void annotationColour_actionPerformed(ActionEvent e)
2985   {
2986
2987   }
2988
2989   public void rnahelicesColour_actionPerformed(ActionEvent e)
2990   {
2991
2992   }
2993
2994   public void associatedData_actionPerformed(ActionEvent e)
2995   {
2996
2997   }
2998
2999   public void autoCalculate_actionPerformed(ActionEvent e)
3000   {
3001
3002   }
3003
3004   public void sortByTreeOption_actionPerformed(ActionEvent e)
3005   {
3006
3007   }
3008
3009   public void showAllSeqs_actionPerformed(ActionEvent e)
3010   {
3011
3012   }
3013
3014   public void showAllColumns_actionPerformed(ActionEvent e)
3015   {
3016
3017   }
3018
3019   public void hideSelSequences_actionPerformed(ActionEvent e)
3020   {
3021
3022   }
3023
3024   public void hideSelColumns_actionPerformed(ActionEvent e)
3025   {
3026
3027   }
3028
3029   public void hiddenMarkers_actionPerformed(ActionEvent e)
3030   {
3031
3032   }
3033
3034   public void findPdbId_actionPerformed(ActionEvent e)
3035   {
3036
3037   }
3038
3039   public void enterPdbId_actionPerformed(ActionEvent e)
3040   {
3041
3042   }
3043
3044   public void pdbFile_actionPerformed(ActionEvent e)
3045   {
3046
3047   }
3048
3049   public void invertColSel_actionPerformed(ActionEvent e)
3050   {
3051
3052   }
3053
3054   public void tabSelectionChanged(int sel)
3055   {
3056
3057   }
3058
3059   public void tabbedPane_mousePressed(MouseEvent e)
3060   {
3061
3062   }
3063
3064   public void tabbedPane_focusGained(FocusEvent e)
3065   {
3066     requestFocus();
3067   }
3068
3069   public void save_actionPerformed(ActionEvent e)
3070   {
3071
3072   }
3073
3074   public void reload_actionPerformed(ActionEvent e)
3075   {
3076
3077   }
3078
3079   public void newView_actionPerformed(ActionEvent e)
3080   {
3081
3082   }
3083
3084   public void textColour_actionPerformed(ActionEvent e)
3085   {
3086
3087   }
3088
3089   public void idRightAlign_actionPerformed(ActionEvent e)
3090   {
3091
3092   }
3093
3094   public void expandViews_actionPerformed(ActionEvent e)
3095   {
3096
3097   }
3098
3099   public void gatherViews_actionPerformed(ActionEvent e)
3100   {
3101
3102   }
3103
3104   public void buildTreeMenu()
3105   {
3106
3107   }
3108
3109   public void pageSetup_actionPerformed(ActionEvent e)
3110   {
3111
3112   }
3113
3114   public void alignmentProperties()
3115   {
3116
3117   }
3118
3119   protected void expand_newalign(ActionEvent e)
3120   {
3121     // TODO Auto-generated method stub
3122
3123   }
3124
3125   protected boolean isShowAutoCalculatedAbove()
3126   {
3127     return showAutoCalculatedAbove;
3128   }
3129
3130   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
3131   {
3132     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
3133   }
3134
3135   protected SequenceAnnotationOrder getAnnotationSortOrder()
3136   {
3137     return annotationSortOrder;
3138   }
3139
3140   protected void setAnnotationSortOrder(SequenceAnnotationOrder annotationSortOrder)
3141   {
3142     this.annotationSortOrder = annotationSortOrder;
3143   }
3144 }