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 createSVG = new JMenuItem();
 218
 219   protected JMenuItem font = new JMenuItem();
 220
 221   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 222
 223   JMenuItem epsFile = new JMenuItem();
 224
 225   JMenuItem LoadtreeMenuItem = new JMenuItem();
 226
 227   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 228
 229   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 230
 231   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 232
 233   protected JMenuItem modifyPID = new JMenuItem();
 234
 235   protected JMenuItem modifyConservation = new JMenuItem();
 236
 237   protected JMenu sortByTreeMenu = new JMenu();
 238
 239   protected JMenu sort = new JMenu();
 240
 241   protected JMenu calculateTree = new JMenu();
 242
 243   JMenu jMenu2 = new JMenu();
 244
 245   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 246
 247   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 248
 249   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 250
 251   protected ButtonGroup colours = new ButtonGroup();
 252
 253   JMenuItem vamsasStore = new JMenuItem();
 254
 255   protected JMenuItem showTranslation = new JMenuItem();
 256
 257   protected JMenu cdna = new JMenu();
 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     overviewMenuItem.setText(MessageManager
1203             .getString("label.overview_window"));
1204     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
1205     {
1206       @Override
1207       public void actionPerformed(ActionEvent e)
1208       {
1209         overviewMenuItem_actionPerformed(e);
1210       }
1211     });
1212     undoMenuItem.setEnabled(false);
1213     undoMenuItem.setText(MessageManager.getString("action.undo"));
1214     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1215             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1216                     .getMenuShortcutKeyMask(), false));
1217     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1218     {
1219       @Override
1220       public void actionPerformed(ActionEvent e)
1221       {
1222         undoMenuItem_actionPerformed(e);
1223       }
1224     });
1225     redoMenuItem.setEnabled(false);
1226     redoMenuItem.setText(MessageManager.getString("action.redo"));
1227     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1228             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1229                     .getMenuShortcutKeyMask(), false));
1230     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1231     {
1232       @Override
1233       public void actionPerformed(ActionEvent e)
1234       {
1235         redoMenuItem_actionPerformed(e);
1236       }
1237     });
1238     conservationMenuItem.setText(MessageManager
1239             .getString("action.by_conservation"));
1240     conservationMenuItem
1241             .addActionListener(new java.awt.event.ActionListener()
1242             {
1243               @Override
1244               public void actionPerformed(ActionEvent e)
1245               {
1246                 conservationMenuItem_actionPerformed(e);
1247               }
1248             });
1249     noColourmenuItem.setText(MessageManager.getString("label.none"));
1250     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1251     {
1252       @Override
1253       public void actionPerformed(ActionEvent e)
1254       {
1255         noColourmenuItem_actionPerformed(e);
1256       }
1257     });
1258     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1259     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1260     {
1261       @Override
1262       public void actionPerformed(ActionEvent e)
1263       {
1264         wrapMenuItem_actionPerformed(e);
1265       }
1266     });
1267     printMenuItem.setText(MessageManager.getString("action.print") + "...");
1268     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1269             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1270                     .getMenuShortcutKeyMask(), false));
1271     printMenuItem.addActionListener(new java.awt.event.ActionListener()
1272     {
1273       @Override
1274       public void actionPerformed(ActionEvent e)
1275       {
1276         printMenuItem_actionPerformed(e);
1277       }
1278     });
1279     renderGapsMenuItem
1280             .setText(MessageManager.getString("action.show_gaps"));
1281     renderGapsMenuItem.setState(true);
1282     renderGapsMenuItem
1283             .addActionListener(new java.awt.event.ActionListener()
1284             {
1285               @Override
1286               public void actionPerformed(ActionEvent e)
1287               {
1288                 renderGapsMenuItem_actionPerformed(e);
1289               }
1290             });
1291     findMenuItem.setText(MessageManager.getString("action.find"));
1292     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1293             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1294                     .getMenuShortcutKeyMask(), false));
1295     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
1296             MessageManager.getString("label.find_tip")));
1297     findMenuItem.addActionListener(new java.awt.event.ActionListener()
1298     {
1299       @Override
1300       public void actionPerformed(ActionEvent e)
1301       {
1302         findMenuItem_actionPerformed(e);
1303       }
1304     });
1305     abovePIDThreshold.setText(MessageManager
1306             .getString("label.above_identity_threshold"));
1307     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1308     {
1309       @Override
1310       public void actionPerformed(ActionEvent e)
1311       {
1312         abovePIDThreshold_actionPerformed(e);
1313       }
1314     });
1315     showSeqFeatures.setText(MessageManager
1316             .getString("label.show_sequence_features"));
1317     showSeqFeatures.addActionListener(new ActionListener()
1318     {
1319       @Override
1320       public void actionPerformed(ActionEvent actionEvent)
1321       {
1322         showSeqFeatures_actionPerformed(actionEvent);
1323       }
1324     });
1325     /*
1326      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1327      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1328      * void actionPerformed(ActionEvent actionEvent) {
1329      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1330      */
1331     showDbRefsMenuitem.setText(MessageManager
1332             .getString("label.show_database_refs"));
1333     showDbRefsMenuitem.addActionListener(new ActionListener()
1334     {
1335
1336       @Override
1337       public void actionPerformed(ActionEvent e)
1338       {
1339         showDbRefs_actionPerformed(e);
1340       }
1341
1342     });
1343     showNpFeatsMenuitem.setText(MessageManager
1344             .getString("label.show_non_positional_features"));
1345     showNpFeatsMenuitem.addActionListener(new ActionListener()
1346     {
1347
1348       @Override
1349       public void actionPerformed(ActionEvent e)
1350       {
1351         showNpFeats_actionPerformed(e);
1352       }
1353
1354     });
1355     showGroupConservation.setText(MessageManager
1356             .getString("label.group_conservation"));
1357     showGroupConservation.addActionListener(new ActionListener()
1358     {
1359
1360       @Override
1361       public void actionPerformed(ActionEvent e)
1362       {
1363         showGroupConservation_actionPerformed(e);
1364       }
1365
1366     });
1367
1368     showGroupConsensus.setText(MessageManager
1369             .getString("label.group_consensus"));
1370     showGroupConsensus.addActionListener(new ActionListener()
1371     {
1372
1373       @Override
1374       public void actionPerformed(ActionEvent e)
1375       {
1376         showGroupConsensus_actionPerformed(e);
1377       }
1378
1379     });
1380     showConsensusHistogram.setText(MessageManager
1381             .getString("label.show_consensus_histogram"));
1382     showConsensusHistogram.addActionListener(new ActionListener()
1383     {
1384
1385       @Override
1386       public void actionPerformed(ActionEvent e)
1387       {
1388         showConsensusHistogram_actionPerformed(e);
1389       }
1390
1391     });
1392     showSequenceLogo.setText(MessageManager
1393             .getString("label.show_consensus_logo"));
1394     showSequenceLogo.addActionListener(new ActionListener()
1395     {
1396
1397       @Override
1398       public void actionPerformed(ActionEvent e)
1399       {
1400         showSequenceLogo_actionPerformed(e);
1401       }
1402
1403     });
1404     normaliseSequenceLogo.setText(MessageManager
1405             .getString("label.norm_consensus_logo"));
1406     normaliseSequenceLogo.addActionListener(new ActionListener()
1407     {
1408
1409       @Override
1410       public void actionPerformed(ActionEvent e)
1411       {
1412         normaliseSequenceLogo_actionPerformed(e);
1413       }
1414
1415     });
1416     applyAutoAnnotationSettings.setText(MessageManager
1417             .getString("label.apply_all_groups"));
1418     applyAutoAnnotationSettings.setState(false);
1419     applyAutoAnnotationSettings.setVisible(true);
1420     applyAutoAnnotationSettings.addActionListener(new ActionListener()
1421     {
1422       @Override
1423       public void actionPerformed(ActionEvent e)
1424       {
1425         applyAutoAnnotationSettings_actionPerformed(e);
1426       }
1427     });
1428
1429     ButtonGroup buttonGroup = new ButtonGroup();
1430     buttonGroup.add(showAutoFirst);
1431     buttonGroup.add(showAutoLast);
1432     showAutoFirst.setText(MessageManager.getString("label.show_first"));
1433     showAutoFirst.setSelected(Cache.getDefault(
1434             Preferences.SHOW_AUTOCALC_ABOVE,
1435             false));
1436     showAutoFirst.addActionListener(new ActionListener()
1437     {
1438       @Override
1439       public void actionPerformed(ActionEvent e)
1440       {
1441         setShowAutoCalculatedAbove(showAutoFirst.isSelected());
1442         sortAnnotations_actionPerformed();
1443       }
1444     });
1445     showAutoLast.setText(MessageManager.getString("label.show_last"));
1446     showAutoLast.setSelected(!showAutoFirst.isSelected());
1447     showAutoLast.addActionListener(new ActionListener()
1448     {
1449       @Override
1450       public void actionPerformed(ActionEvent e)
1451       {
1452         setShowAutoCalculatedAbove(!showAutoLast.isSelected());
1453         sortAnnotations_actionPerformed();
1454       }
1455     });
1456
1457     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1458     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1459     {
1460       @Override
1461       public void actionPerformed(ActionEvent e)
1462       {
1463         nucleotideColour_actionPerformed(e);
1464       }
1465     });
1466
1467     tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1468     tcoffeeColour.setEnabled(false);
1469     tcoffeeColour.addActionListener(new ActionListener()
1470     {
1471
1472       @Override
1473       public void actionPerformed(ActionEvent e)
1474       {
1475         tcoffeeColorScheme_actionPerformed(e);
1476       }
1477     });
1478
1479     deleteGroups
1480             .setText(MessageManager.getString("action.undefine_groups"));
1481     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1482             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1483                     .getMenuShortcutKeyMask(), false));
1484     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1485     {
1486       @Override
1487       public void actionPerformed(ActionEvent e)
1488       {
1489         deleteGroups_actionPerformed(e);
1490       }
1491     });
1492     createGroup.setText(MessageManager.getString("action.create_groups"));
1493     createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1494             java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1495                     .getMenuShortcutKeyMask(), false));
1496     createGroup.addActionListener(new java.awt.event.ActionListener()
1497     {
1498       @Override
1499       public void actionPerformed(ActionEvent e)
1500       {
1501         createGroup_actionPerformed(e);
1502       }
1503     });
1504     unGroup.setText(MessageManager.getString("action.remove_group"));
1505     unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1506             java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1507                     .getMenuShortcutKeyMask()
1508                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1509     unGroup.addActionListener(new java.awt.event.ActionListener()
1510     {
1511       @Override
1512       public void actionPerformed(ActionEvent e)
1513       {
1514         unGroup_actionPerformed(e);
1515       }
1516     });
1517     copy.setText(MessageManager.getString("action.copy"));
1518     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1519             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1520                     .getMenuShortcutKeyMask(), false));
1521
1522     copy.addActionListener(new java.awt.event.ActionListener()
1523     {
1524       @Override
1525       public void actionPerformed(ActionEvent e)
1526       {
1527         copy_actionPerformed(e);
1528       }
1529     });
1530     cut.setText(MessageManager.getString("action.cut"));
1531     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1532             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1533                     .getMenuShortcutKeyMask(), false));
1534     cut.addActionListener(new java.awt.event.ActionListener()
1535     {
1536       @Override
1537       public void actionPerformed(ActionEvent e)
1538       {
1539         cut_actionPerformed(e);
1540       }
1541     });
1542     delete.setText(MessageManager.getString("action.delete"));
1543     delete.addActionListener(new java.awt.event.ActionListener()
1544     {
1545       @Override
1546       public void actionPerformed(ActionEvent e)
1547       {
1548         delete_actionPerformed(e);
1549       }
1550     });
1551     pasteMenu.setText(MessageManager.getString("action.paste"));
1552     pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1553     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1554             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1555                     .getMenuShortcutKeyMask()
1556                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1557     pasteNew.addActionListener(new java.awt.event.ActionListener()
1558     {
1559       @Override
1560       public void actionPerformed(ActionEvent e)
1561       {
1562         pasteNew_actionPerformed(e);
1563       }
1564     });
1565     pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1566     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1567             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1568                     .getMenuShortcutKeyMask(), false));
1569     pasteThis.addActionListener(new java.awt.event.ActionListener()
1570     {
1571       @Override
1572       public void actionPerformed(ActionEvent e)
1573       {
1574         pasteThis_actionPerformed(e);
1575       }
1576     });
1577     applyToAllGroups.setText(MessageManager
1578             .getString("label.apply_colour_to_all_groups"));
1579     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1580     {
1581       @Override
1582       public void actionPerformed(ActionEvent e)
1583       {
1584         applyToAllGroups_actionPerformed(e);
1585       }
1586     });
1587     createPNG.addActionListener(new java.awt.event.ActionListener()
1588     {
1589       @Override
1590       public void actionPerformed(ActionEvent e)
1591       {
1592         createPNG(null);
1593       }
1594     });
1595     createPNG.setActionCommand(MessageManager
1596             .getString("label.save_png_image"));
1597     createPNG.setText("PNG");
1598
1599     font.setText(MessageManager.getString("action.font"));
1600     font.addActionListener(new java.awt.event.ActionListener()
1601     {
1602       @Override
1603       public void actionPerformed(ActionEvent e)
1604       {
1605         font_actionPerformed(e);
1606       }
1607     });
1608
1609     seqLimits.setText(MessageManager
1610             .getString("label.show_sequence_limits"));
1611     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1612     seqLimits.addActionListener(new java.awt.event.ActionListener()
1613     {
1614       @Override
1615       public void actionPerformed(ActionEvent e)
1616       {
1617         seqLimit_actionPerformed(e);
1618       }
1619     });
1620     epsFile.setText("EPS");
1621     epsFile.addActionListener(new java.awt.event.ActionListener()
1622     {
1623       @Override
1624       public void actionPerformed(ActionEvent e)
1625       {
1626         createEPS(null);
1627       }
1628     });
1629
1630     createSVG.setText("SVG");
1631     createSVG.addActionListener(new java.awt.event.ActionListener()
1632     {
1633       @Override
1634       public void actionPerformed(ActionEvent e)
1635       {
1636         createSVG(null);
1637       }
1638     });
1639
1640     LoadtreeMenuItem.setActionCommand(MessageManager
1641             .getString("label.load_tree_for_sequence_set"));
1642     LoadtreeMenuItem.setText(MessageManager
1643             .getString("label.load_associated_tree"));
1644     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1645     {
1646       @Override
1647       public void actionPerformed(ActionEvent e)
1648       {
1649         LoadtreeMenuItem_actionPerformed(e);
1650       }
1651     });
1652
1653     scaleAbove.setVisible(false);
1654     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1655     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1656     {
1657       @Override
1658       public void actionPerformed(ActionEvent e)
1659       {
1660         scaleAbove_actionPerformed(e);
1661       }
1662     });
1663     scaleLeft.setVisible(false);
1664     scaleLeft.setSelected(true);
1665     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1666     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1667     {
1668       @Override
1669       public void actionPerformed(ActionEvent e)
1670       {
1671         scaleLeft_actionPerformed(e);
1672       }
1673     });
1674     scaleRight.setVisible(false);
1675     scaleRight.setSelected(true);
1676     scaleRight.setText(MessageManager.getString("action.scale_right"));
1677     scaleRight.addActionListener(new java.awt.event.ActionListener()
1678     {
1679       @Override
1680       public void actionPerformed(ActionEvent e)
1681       {
1682         scaleRight_actionPerformed(e);
1683       }
1684     });
1685     centreColumnLabelsMenuItem.setVisible(true);
1686     centreColumnLabelsMenuItem.setState(false);
1687     centreColumnLabelsMenuItem.setText(MessageManager
1688             .getString("label.centre_column_labels"));
1689     centreColumnLabelsMenuItem
1690             .addActionListener(new java.awt.event.ActionListener()
1691             {
1692               @Override
1693               public void actionPerformed(ActionEvent e)
1694               {
1695                 centreColumnLabels_actionPerformed(e);
1696               }
1697             });
1698     followHighlightMenuItem.setVisible(true);
1699     followHighlightMenuItem.setState(true);
1700     followHighlightMenuItem.setText(MessageManager
1701             .getString("label.automatic_scrolling"));
1702     followHighlightMenuItem.addActionListener(new ActionListener()
1703     {
1704
1705       @Override
1706       public void actionPerformed(ActionEvent e)
1707       {
1708         followHighlight_actionPerformed();
1709       }
1710
1711     });
1712
1713     modifyPID.setText(MessageManager
1714             .getString("label.modify_identity_thereshold"));
1715     modifyPID.addActionListener(new java.awt.event.ActionListener()
1716     {
1717       @Override
1718       public void actionPerformed(ActionEvent e)
1719       {
1720         modifyPID_actionPerformed(e);
1721       }
1722     });
1723     modifyConservation.setText(MessageManager
1724             .getString("label.modify_conservation_thereshold"));
1725     modifyConservation
1726             .addActionListener(new java.awt.event.ActionListener()
1727             {
1728               @Override
1729               public void actionPerformed(ActionEvent e)
1730               {
1731                 modifyConservation_actionPerformed(e);
1732               }
1733             });
1734     sortByTreeMenu
1735             .setText(MessageManager.getString("action.by_tree_order"));
1736     sort.setText(MessageManager.getString("action.sort"));
1737     sort.addMenuListener(new MenuListener()
1738     {
1739       @Override
1740       public void menuSelected(MenuEvent e)
1741       {
1742         buildTreeMenu();
1743       }
1744
1745       @Override
1746       public void menuDeselected(MenuEvent e)
1747       {
1748       }
1749
1750       @Override
1751       public void menuCanceled(MenuEvent e)
1752       {
1753       }
1754     });
1755     sortByAnnotScore.setText(MessageManager
1756             .getString("label.sort_by_score"));
1757     sort.add(sortByAnnotScore);
1758     sort.addMenuListener(new javax.swing.event.MenuListener()
1759     {
1760
1761       @Override
1762       public void menuCanceled(MenuEvent e)
1763       {
1764       }
1765
1766       @Override
1767       public void menuDeselected(MenuEvent e)
1768       {
1769       }
1770
1771       @Override
1772       public void menuSelected(MenuEvent e)
1773       {
1774         buildSortByAnnotationScoresMenu();
1775       }
1776     });
1777     sortByAnnotScore.setVisible(false);
1778
1779     calculateTree
1780             .setText(MessageManager.getString("action.calculate_tree"));
1781
1782     jMenu2.setText(MessageManager.getString("label.export_image"));
1783     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1784     padGapsMenuitem.setState(jalview.bin.Cache
1785             .getDefault("PAD_GAPS", false));
1786     padGapsMenuitem.addActionListener(new ActionListener()
1787     {
1788       @Override
1789       public void actionPerformed(ActionEvent e)
1790       {
1791         padGapsMenuitem_actionPerformed(e);
1792       }
1793     });
1794     vamsasStore.setVisible(false);
1795     vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1796     vamsasStore.addActionListener(new ActionListener()
1797     {
1798       @Override
1799       public void actionPerformed(ActionEvent e)
1800       {
1801         vamsasStore_actionPerformed(e);
1802       }
1803     });
1804     showTranslation.setText(MessageManager
1805             .getString("label.translate_cDNA"));
1806     showTranslation.addActionListener(new ActionListener()
1807     {
1808       @Override
1809       public void actionPerformed(ActionEvent e)
1810       {
1811         showTranslation_actionPerformed(e);
1812       }
1813     });
1814     cdna.setText(MessageManager.getString("label.cDNA"));
1815     extractScores.setText(MessageManager.getString("label.extract_scores")
1816             + "...");
1817     extractScores.addActionListener(new ActionListener()
1818     {
1819       @Override
1820       public void actionPerformed(ActionEvent e)
1821       {
1822         extractScores_actionPerformed(e);
1823       }
1824     });
1825     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1826     // score extraction
1827     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1828     /*
1829      * showProducts.addActionListener(new ActionListener() {
1830      *
1831      * public void actionPerformed(ActionEvent e) {
1832      * showProducts_actionPerformed(e); } });
1833      */
1834     openFeatureSettings.setText(MessageManager
1835             .getString("label.feature_settings"));
1836     openFeatureSettings.addActionListener(new ActionListener()
1837     {
1838       @Override
1839       public void actionPerformed(ActionEvent e)
1840       {
1841         featureSettings_actionPerformed(e);
1842       }
1843     });
1844     fetchSequence
1845             .setText(MessageManager.getString("label.fetch_sequences"));
1846     fetchSequence.addActionListener(new ActionListener()
1847     {
1848       @Override
1849       public void actionPerformed(ActionEvent e)
1850       {
1851         fetchSequence_actionPerformed(e);
1852       }
1853     });
1854
1855     annotationColour.setText(MessageManager
1856             .getString("action.by_annotation"));
1857     annotationColour.addActionListener(new ActionListener()
1858     {
1859       @Override
1860       public void actionPerformed(ActionEvent e)
1861       {
1862         annotationColour_actionPerformed(e);
1863       }
1864     });
1865
1866     rnahelicesColour.setText(MessageManager
1867             .getString("action.by_rna_helixes"));
1868     rnahelicesColour.addActionListener(new ActionListener()
1869     {
1870       @Override
1871       public void actionPerformed(ActionEvent e)
1872       {
1873         rnahelicesColour_actionPerformed(e);
1874       }
1875     });
1876
1877     associatedData.setText(MessageManager
1878             .getString("label.load_features_annotations"));
1879     associatedData.addActionListener(new ActionListener()
1880     {
1881       @Override
1882       public void actionPerformed(ActionEvent e)
1883       {
1884         associatedData_actionPerformed(e);
1885       }
1886     });
1887     autoCalculate.setText(MessageManager
1888             .getString("label.autocalculate_consensus"));
1889     autoCalculate.setState(jalview.bin.Cache.getDefault(
1890             "AUTO_CALC_CONSENSUS", true));
1891     autoCalculate.addActionListener(new ActionListener()
1892     {
1893       @Override
1894       public void actionPerformed(ActionEvent e)
1895       {
1896         autoCalculate_actionPerformed(e);
1897       }
1898     });
1899     sortByTree.setText(MessageManager
1900             .getString("label.sort_alignment_new_tree"));
1901     sortByTree
1902             .setToolTipText("<html>"
1903                     + MessageManager
1904                             .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1905     sortByTree
1906             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1907     sortByTree.addActionListener(new ActionListener()
1908     {
1909       @Override
1910       public void actionPerformed(ActionEvent e)
1911       {
1912         sortByTreeOption_actionPerformed(e);
1913       }
1914     });
1915
1916     listenToViewSelections.setText(MessageManager
1917             .getString("label.listen_for_selections"));
1918     listenToViewSelections
1919             .setToolTipText("<html>"
1920                     + MessageManager
1921                             .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1922     listenToViewSelections.setState(false);
1923     listenToViewSelections.addActionListener(new ActionListener()
1924     {
1925       @Override
1926       public void actionPerformed(ActionEvent e)
1927       {
1928         listenToViewSelections_actionPerformed(e);
1929       }
1930     });
1931
1932     addSequenceMenu
1933             .setText(MessageManager.getString("label.add_sequences"));
1934     addFromFile.setText(MessageManager.getString("label.from_file"));
1935     addFromFile.addActionListener(new ActionListener()
1936     {
1937       @Override
1938       public void actionPerformed(ActionEvent e)
1939       {
1940         addFromFile_actionPerformed(e);
1941       }
1942     });
1943     addFromText.setText(MessageManager.getString("label.from_textbox"));
1944     addFromText.addActionListener(new ActionListener()
1945     {
1946       @Override
1947       public void actionPerformed(ActionEvent e)
1948       {
1949         addFromText_actionPerformed(e);
1950       }
1951     });
1952     addFromURL.setText(MessageManager.getString("label.from_url"));
1953     addFromURL.addActionListener(new ActionListener()
1954     {
1955       @Override
1956       public void actionPerformed(ActionEvent e)
1957       {
1958         addFromURL_actionPerformed(e);
1959       }
1960     });
1961     exportFeatures.setText(MessageManager
1962             .getString("label.export_features"));
1963     exportFeatures.addActionListener(new ActionListener()
1964     {
1965       @Override
1966       public void actionPerformed(ActionEvent e)
1967       {
1968         exportFeatures_actionPerformed(e);
1969       }
1970     });
1971     exportAnnotations.setText(MessageManager
1972             .getString("label.export_annotations"));
1973     exportAnnotations.addActionListener(new ActionListener()
1974     {
1975       @Override
1976       public void actionPerformed(ActionEvent e)
1977       {
1978         exportAnnotations_actionPerformed(e);
1979       }
1980     });
1981     statusPanel.setLayout(gridLayout1);
1982     jMenu3.setText(MessageManager.getString("action.show"));
1983     showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
1984     showAllSeqs.setToolTipText(MessageManager
1985             .getString("label.toggle_sequence_visibility"));
1986     showAllSeqs.addActionListener(new ActionListener()
1987     {
1988       @Override
1989       public void actionPerformed(ActionEvent e)
1990       {
1991         showAllSeqs_actionPerformed(e);
1992       }
1993     });
1994     showAllColumns.setText(MessageManager.getString("label.all_columns"));
1995     showAllColumns.setToolTipText(MessageManager
1996             .getString("label.toggle_columns_visibility"));
1997     showAllColumns.addActionListener(new ActionListener()
1998     {
1999       @Override
2000       public void actionPerformed(ActionEvent e)
2001       {
2002         showAllColumns_actionPerformed(e);
2003       }
2004     });
2005     hideMenu.setText(MessageManager.getString("action.hide"));
2006     hideSelSequences.setText(MessageManager
2007             .getString("label.selected_sequences"));
2008     hideSelSequences.setToolTipText(MessageManager
2009             .getString("label.toggle_sequence_visibility"));
2010     hideSelSequences.addActionListener(new ActionListener()
2011     {
2012       @Override
2013       public void actionPerformed(ActionEvent e)
2014       {
2015         hideSelSequences_actionPerformed(e);
2016       }
2017     });
2018     hideSelColumns.setText(MessageManager
2019             .getString("label.selected_columns"));
2020     hideSelColumns.setToolTipText(MessageManager
2021             .getString("label.toggle_columns_visibility"));
2022     hideSelColumns.addActionListener(new ActionListener()
2023     {
2024       @Override
2025       public void actionPerformed(ActionEvent e)
2026       {
2027         hideSelColumns_actionPerformed(e);
2028       }
2029     });
2030     hideAllSelection.setText(MessageManager
2031             .getString("label.selected_region"));
2032     hideAllSelection.addActionListener(new ActionListener()
2033     {
2034       @Override
2035       public void actionPerformed(ActionEvent e)
2036       {
2037         hideAllSelection_actionPerformed(e);
2038       }
2039     });
2040     // TODO: should be hidden if no selection exists.
2041     hideAllButSelection.setText(MessageManager
2042             .getString("label.all_but_selected_region"));
2043     hideAllButSelection.addActionListener(new ActionListener()
2044     {
2045       @Override
2046       public void actionPerformed(ActionEvent e)
2047       {
2048         hideAllButSelection_actionPerformed(e);
2049       }
2050     });
2051     showAllhidden.setText(MessageManager
2052             .getString("label.all_sequences_columns"));
2053     showAllhidden.setToolTipText(MessageManager
2054             .getString("label.toggles_visibility_hidden_selected_regions"));
2055     showAllhidden.addActionListener(new ActionListener()
2056     {
2057       @Override
2058       public void actionPerformed(ActionEvent e)
2059       {
2060         showAllhidden_actionPerformed(e);
2061       }
2062     });
2063     hiddenMarkers.setText(MessageManager
2064             .getString("action.show_hidden_markers"));
2065     hiddenMarkers.addActionListener(new ActionListener()
2066     {
2067       @Override
2068       public void actionPerformed(ActionEvent e)
2069       {
2070         hiddenMarkers_actionPerformed(e);
2071       }
2072     });
2073     invertColSel.setText(MessageManager
2074             .getString("action.invert_column_selection"));
2075     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2076             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
2077                     .getMenuShortcutKeyMask()
2078                     | java.awt.event.KeyEvent.ALT_MASK, false));
2079     invertColSel.addActionListener(new ActionListener()
2080     {
2081       @Override
2082       public void actionPerformed(ActionEvent e)
2083       {
2084         invertColSel_actionPerformed(e);
2085       }
2086     });
2087     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
2088     {
2089       @Override
2090       public void stateChanged(ChangeEvent evt)
2091       {
2092         JTabbedPane pane = (JTabbedPane) evt.getSource();
2093         int sel = pane.getSelectedIndex();
2094         tabSelectionChanged(sel);
2095       }
2096     });
2097     tabbedPane.addMouseListener(new MouseAdapter()
2098     {
2099       @Override
2100       public void mousePressed(MouseEvent e)
2101       {
2102         tabbedPane_mousePressed(e);
2103       }
2104     });
2105     tabbedPane.addFocusListener(new FocusAdapter()
2106     {
2107       @Override
2108       public void focusGained(FocusEvent e)
2109       {
2110         tabbedPane_focusGained(e);
2111       }
2112     });
2113     save.setText(MessageManager.getString("action.save"));
2114     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2115             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
2116                     .getMenuShortcutKeyMask(), false));
2117     save.addActionListener(new ActionListener()
2118     {
2119       @Override
2120       public void actionPerformed(ActionEvent e)
2121       {
2122         save_actionPerformed(e);
2123       }
2124     });
2125     reload.setEnabled(false);
2126     reload.setText(MessageManager.getString("action.reload"));
2127     reload.addActionListener(new ActionListener()
2128     {
2129       @Override
2130       public void actionPerformed(ActionEvent e)
2131       {
2132         reload_actionPerformed(e);
2133       }
2134     });
2135     newView.setText(MessageManager.getString("action.new_view"));
2136     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2137             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
2138                     .getMenuShortcutKeyMask(), false));
2139     newView.addActionListener(new ActionListener()
2140     {
2141       @Override
2142       public void actionPerformed(ActionEvent e)
2143       {
2144         newView_actionPerformed(e);
2145       }
2146     });
2147     tabbedPane.setToolTipText("<html><i>"
2148             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2149             + "</i></html>");
2150     textColour.setText(MessageManager.getString("label.colour_text")
2151             + "...");
2152     textColour.addActionListener(new ActionListener()
2153     {
2154       @Override
2155       public void actionPerformed(ActionEvent e)
2156       {
2157         textColour_actionPerformed(e);
2158       }
2159     });
2160     formatMenu.setText(MessageManager.getString("action.format"));
2161     selectMenu.setText(MessageManager.getString("action.select"));
2162     idRightAlign.setText(MessageManager
2163             .getString("label.right_align_sequence_id"));
2164     idRightAlign.addActionListener(new ActionListener()
2165     {
2166       @Override
2167       public void actionPerformed(ActionEvent e)
2168       {
2169         idRightAlign_actionPerformed(e);
2170       }
2171     });
2172     gatherViews.setEnabled(false);
2173     gatherViews.setText(MessageManager.getString("action.gather_views"));
2174     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2175             java.awt.event.KeyEvent.VK_G, 0, false));
2176     gatherViews.addActionListener(new ActionListener()
2177     {
2178       @Override
2179       public void actionPerformed(ActionEvent e)
2180       {
2181         gatherViews_actionPerformed(e);
2182       }
2183     });
2184     expandViews.setEnabled(false);
2185     expandViews.setText(MessageManager.getString("action.expand_views"));
2186     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2187             java.awt.event.KeyEvent.VK_X, 0, false));
2188     expandViews.addActionListener(new ActionListener()
2189     {
2190       @Override
2191       public void actionPerformed(ActionEvent e)
2192       {
2193         expandViews_actionPerformed(e);
2194       }
2195     });
2196     pageSetup
2197             .setText(MessageManager.getString("action.page_setup") + "...");
2198     pageSetup.addActionListener(new ActionListener()
2199     {
2200       @Override
2201       public void actionPerformed(ActionEvent e)
2202       {
2203         pageSetup_actionPerformed(e);
2204       }
2205     });
2206     alignmentProperties.setText(MessageManager
2207             .getString("label.alignment_props") + "...");
2208     alignmentProperties.addActionListener(new ActionListener()
2209     {
2210       @Override
2211       public void actionPerformed(ActionEvent actionEvent)
2212       {
2213         alignmentProperties();
2214       }
2215     });
2216     tooltipSettingsMenu.setText(MessageManager
2217             .getString("label.sequence_id_tooltip"));
2218     autoAnnMenu.setText(MessageManager
2219             .getString("label.autocalculated_annotation"));
2220     alignFrameMenuBar.add(fileMenu);
2221     alignFrameMenuBar.add(editMenu);
2222     alignFrameMenuBar.add(selectMenu);
2223     alignFrameMenuBar.add(viewMenu);
2224     alignFrameMenuBar.add(annotationsMenu);
2225     alignFrameMenuBar.add(formatMenu);
2226     alignFrameMenuBar.add(colourMenu);
2227     alignFrameMenuBar.add(calculateMenu);
2228     alignFrameMenuBar.add(webService);
2229     fileMenu.add(fetchSequence);
2230     fileMenu.add(addSequenceMenu);
2231     fileMenu.add(reload);
2232     fileMenu.addSeparator();
2233     fileMenu.add(vamsasStore);
2234     fileMenu.add(save);
2235     fileMenu.add(saveAs);
2236     fileMenu.add(outputTextboxMenu);
2237     fileMenu.add(pageSetup);
2238     fileMenu.add(printMenuItem);
2239     fileMenu.addSeparator();
2240     fileMenu.add(jMenu2);
2241     fileMenu.add(exportFeatures);
2242     fileMenu.add(exportAnnotations);
2243     fileMenu.add(LoadtreeMenuItem);
2244     fileMenu.add(associatedData);
2245     fileMenu.addSeparator();
2246     fileMenu.add(closeMenuItem);
2247     editMenu.add(undoMenuItem);
2248     editMenu.add(redoMenuItem);
2249     editMenu.add(cut);
2250     editMenu.add(copy);
2251     editMenu.add(pasteMenu);
2252     editMenu.add(delete);
2253     editMenu.addSeparator();
2254     editMenu.add(remove2LeftMenuItem);
2255     editMenu.add(remove2RightMenuItem);
2256     editMenu.add(removeGappedColumnMenuItem);
2257     editMenu.add(removeAllGapsMenuItem);
2258     editMenu.add(removeRedundancyMenuItem);
2259     editMenu.addSeparator();
2260     // dont add these yet in the CVS build - they cannot be undone!
2261     // Excluded from Jalview 2.5 release - undo needs to be implemented.
2262     // editMenu.add(justifyLeftMenuItem);
2263     // editMenu.add(justifyRightMenuItem);
2264     // editMenu.addSeparator();
2265     editMenu.add(padGapsMenuitem);
2266     viewMenu.add(newView);
2267     viewMenu.add(expandViews);
2268     viewMenu.add(gatherViews);
2269     viewMenu.addSeparator();
2270     viewMenu.add(jMenu3);
2271     viewMenu.add(hideMenu);
2272     viewMenu.addSeparator();
2273     viewMenu.add(followHighlightMenuItem);
2274     annotationsMenu.add(annotationPanelMenuItem);
2275     annotationsMenu.addSeparator();
2276     annotationsMenu.add(showAllAlAnnotations);
2277     annotationsMenu.add(hideAllAlAnnotations);
2278     annotationsMenu.addSeparator();
2279     annotationsMenu.add(showAllSeqAnnotations);
2280     annotationsMenu.add(hideAllSeqAnnotations);
2281     annotationsMenu.add(sortAnnBySequence);
2282     annotationsMenu.add(sortAnnByLabel);
2283     annotationsMenu.addSeparator();
2284     autoAnnMenu.add(showAutoFirst);
2285     autoAnnMenu.add(showAutoLast);
2286     autoAnnMenu.addSeparator();
2287     autoAnnMenu.add(applyAutoAnnotationSettings);
2288     autoAnnMenu.add(showConsensusHistogram);
2289     autoAnnMenu.add(showSequenceLogo);
2290     autoAnnMenu.add(normaliseSequenceLogo);
2291     autoAnnMenu.addSeparator();
2292     autoAnnMenu.add(showGroupConservation);
2293     autoAnnMenu.add(showGroupConsensus);
2294     annotationsMenu.add(autoAnnMenu);
2295     viewMenu.addSeparator();
2296     viewMenu.add(showSeqFeatures);
2297     // viewMenu.add(showSeqFeaturesHeight);
2298
2299     viewMenu.add(openFeatureSettings);
2300     tooltipSettingsMenu.add(showDbRefsMenuitem);
2301     tooltipSettingsMenu.add(showNpFeatsMenuitem);
2302     viewMenu.add(tooltipSettingsMenu);
2303     viewMenu.addSeparator();
2304     viewMenu.add(alignmentProperties);
2305     viewMenu.addSeparator();
2306     viewMenu.add(overviewMenuItem);
2307     colourMenu.add(applyToAllGroups);
2308     colourMenu.add(textColour);
2309     colourMenu.addSeparator();
2310     colourMenu.add(noColourmenuItem);
2311     colourMenu.add(clustalColour);
2312     colourMenu.add(BLOSUM62Colour);
2313     colourMenu.add(PIDColour);
2314     colourMenu.add(zappoColour);
2315     colourMenu.add(taylorColour);
2316     colourMenu.add(hydrophobicityColour);
2317     colourMenu.add(helixColour);
2318     colourMenu.add(strandColour);
2319     colourMenu.add(turnColour);
2320     colourMenu.add(buriedColour);
2321     colourMenu.add(nucleotideColour);
2322     colourMenu.add(purinePyrimidineColour);
2323     colourMenu.add(RNAInteractionColour);
2324     // colourMenu.add(covariationColour);
2325     colourMenu.add(tcoffeeColour);
2326     colourMenu.add(userDefinedColour);
2327     colourMenu.addSeparator();
2328     colourMenu.add(conservationMenuItem);
2329     colourMenu.add(modifyConservation);
2330     colourMenu.add(abovePIDThreshold);
2331     colourMenu.add(modifyPID);
2332     colourMenu.add(annotationColour);
2333     colourMenu.add(rnahelicesColour);
2334     calculateMenu.add(sort);
2335     calculateMenu.add(calculateTree);
2336     calculateMenu.addSeparator();
2337     calculateMenu.add(pairwiseAlignmentMenuItem);
2338     calculateMenu.add(PCAMenuItem);
2339     calculateMenu.addSeparator();
2340     calculateMenu.add(showTranslation);
2341     calculateMenu.add(cdna);
2342     calculateMenu.add(showProducts);
2343     calculateMenu.add(autoCalculate);
2344     calculateMenu.add(sortByTree);
2345     calculateMenu.addSeparator();
2346     calculateMenu.add(extractScores);
2347     webServiceNoServices = new JMenuItem(
2348             MessageManager.getString("label.no_services"));
2349     webService.add(webServiceNoServices);
2350     pasteMenu.add(pasteNew);
2351     pasteMenu.add(pasteThis);
2352     sort.add(sortIDMenuItem);
2353     sort.add(sortLengthMenuItem);
2354     sort.add(sortGroupMenuItem);
2355     sort.add(sortPairwiseMenuItem);
2356     sort.add(sortByTreeMenu);
2357     jMenu2.add(htmlMenuItem);
2358     jMenu2.add(epsFile);
2359     jMenu2.add(createPNG);
2360     jMenu2.add(createSVG);
2361     addSequenceMenu.add(addFromFile);
2362     addSequenceMenu.add(addFromText);
2363     addSequenceMenu.add(addFromURL);
2364     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2365     statusPanel.add(statusBar, null);
2366     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2367     jMenu3.add(showAllColumns);
2368     jMenu3.add(showAllSeqs);
2369     jMenu3.add(showAllhidden);
2370     hideMenu.add(hideSelColumns);
2371     hideMenu.add(hideSelSequences);
2372     hideMenu.add(hideAllSelection);
2373     hideMenu.add(hideAllButSelection);
2374
2375     formatMenu.add(font);
2376     formatMenu.addSeparator();
2377     formatMenu.add(wrapMenuItem);
2378     formatMenu.add(scaleAbove);
2379     formatMenu.add(scaleLeft);
2380     formatMenu.add(scaleRight);
2381     formatMenu.add(seqLimits);
2382     formatMenu.add(idRightAlign);
2383     formatMenu.add(hiddenMarkers);
2384     formatMenu.add(viewBoxesMenuItem);
2385     formatMenu.add(viewTextMenuItem);
2386     formatMenu.add(colourTextMenuItem);
2387     formatMenu.add(renderGapsMenuItem);
2388     formatMenu.add(centreColumnLabelsMenuItem);
2389     formatMenu.add(showNonconservedMenuItem);
2390     selectMenu.add(findMenuItem);
2391     selectMenu.addSeparator();
2392     selectMenu.add(selectAllSequenceMenuItem);
2393     selectMenu.add(deselectAllSequenceMenuItem);
2394     selectMenu.add(invertSequenceMenuItem);
2395     selectMenu.add(invertColSel);
2396     selectMenu.add(createGroup);
2397     selectMenu.add(unGroup);
2398     selectMenu.add(grpsFromSelection);
2399     selectMenu.add(deleteGroups);
2400     calculateMenu.add(expandAlignment);
2401     // TODO - determine if the listenToViewSelections button is needed : see bug
2402     // JAL-574
2403     // selectMenu.addSeparator();
2404     // selectMenu.add(listenToViewSelections);
2405   }
2406
2407   /**
2408    * Action on clicking sort annotations by type.
2409    *
2410    * @param sortOrder
2411    */
2412   protected void sortAnnotations_actionPerformed()
2413   {
2414   }
2415
2416   /**
2417    * Action on clicking Show all annotations.
2418    *
2419    * @param forSequences
2420    *          update sequence-related annotations
2421    * @param forAlignment
2422    *          update non-sequence-related annotations
2423    */
2424   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2425           boolean forAlignment)
2426   {
2427     setAnnotationsVisibility(true, forSequences, forAlignment);
2428   }
2429
2430   /**
2431    * Action on clicking Hide all annotations.
2432    *
2433    * @param forSequences
2434    *          update sequence-related annotations
2435    * @param forAlignment
2436    *          update non-sequence-related annotations
2437    */
2438   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2439           boolean forAlignment)
2440   {
2441     setAnnotationsVisibility(false, forSequences, forAlignment);
2442   }
2443
2444   /**
2445    * Set the visibility of annotations to true or false. Can act on
2446    * sequence-related annotations, or alignment-related, or both.
2447    *
2448    * @param visible
2449    * @param forSequences
2450    *          update sequence-related annotations
2451    * @param forAlignment
2452    *          update non-sequence-related annotations
2453    */
2454   protected void setAnnotationsVisibility(boolean visible,
2455           boolean forSequences, boolean forAlignment)
2456   {
2457
2458   }
2459
2460   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2461   {
2462     // TODO Auto-generated method stub
2463
2464   }
2465
2466   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2467   {
2468     // TODO Auto-generated method stub
2469
2470   }
2471
2472   protected void showAllhidden_actionPerformed(ActionEvent e)
2473   {
2474     // TODO Auto-generated method stub
2475
2476   }
2477
2478   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2479   {
2480     // TODO Auto-generated method stub
2481
2482   }
2483
2484   protected void hideAllSelection_actionPerformed(ActionEvent e)
2485   {
2486     // TODO Auto-generated method stub
2487
2488   }
2489
2490   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2491   {
2492     // TODO Auto-generated method stub
2493
2494   }
2495
2496   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2497   {
2498     // TODO Auto-generated method stub
2499
2500   }
2501
2502   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2503   {
2504     // TODO Auto-generated method stub
2505
2506   }
2507
2508   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2509   {
2510     // TODO Auto-generated method stub
2511
2512   }
2513
2514   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2515   {
2516     // TODO Auto-generated method stub
2517
2518   }
2519
2520   protected void showGroupConservation_actionPerformed(ActionEvent e)
2521   {
2522     // TODO Auto-generated method stub
2523
2524   }
2525
2526   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2527   {
2528     // TODO Auto-generated method stub
2529
2530   }
2531
2532   protected void showSeqFeaturesHeight_actionPerformed(
2533           ActionEvent actionEvent)
2534   {
2535     // TODO Auto-generated method stub
2536
2537   }
2538
2539   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2540   {
2541     // TODO Auto-generated method stub
2542
2543   }
2544
2545   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2546   {
2547     // TODO Auto-generated method stub
2548
2549   }
2550
2551   protected void followHighlight_actionPerformed()
2552   {
2553     // TODO Auto-generated method stub
2554
2555   }
2556
2557   protected void showNpFeats_actionPerformed(ActionEvent e)
2558   {
2559     // TODO Auto-generated method stub
2560
2561   }
2562
2563   protected void showDbRefs_actionPerformed(ActionEvent e)
2564   {
2565     // TODO Auto-generated method stub
2566
2567   }
2568
2569   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2570   {
2571   }
2572
2573   protected void showProducts_actionPerformed(ActionEvent e)
2574   {
2575   }
2576
2577   protected void buildSortByAnnotationScoresMenu()
2578   {
2579   }
2580
2581   protected void extractScores_actionPerformed(ActionEvent e)
2582   {
2583   }
2584
2585   protected void outputText_actionPerformed(ActionEvent e)
2586   {
2587   }
2588
2589   public void addFromFile_actionPerformed(ActionEvent e)
2590   {
2591
2592   }
2593
2594   public void addFromText_actionPerformed(ActionEvent e)
2595   {
2596
2597   }
2598
2599   public void addFromURL_actionPerformed(ActionEvent e)
2600   {
2601
2602   }
2603
2604   public void exportFeatures_actionPerformed(ActionEvent e)
2605   {
2606
2607   }
2608
2609   public void exportAnnotations_actionPerformed(ActionEvent e)
2610   {
2611
2612   }
2613
2614   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2615   {
2616   }
2617
2618   protected void closeMenuItem_actionPerformed(boolean b)
2619   {
2620   }
2621
2622   protected void redoMenuItem_actionPerformed(ActionEvent e)
2623   {
2624   }
2625
2626   protected void undoMenuItem_actionPerformed(ActionEvent e)
2627   {
2628   }
2629
2630   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2631   {
2632   }
2633
2634   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2635   {
2636   }
2637
2638   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2639   {
2640   }
2641
2642   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2643   {
2644   }
2645
2646   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2647   {
2648   }
2649
2650   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2651   {
2652   }
2653
2654   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2655   {
2656   }
2657
2658   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2659   {
2660   }
2661
2662   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2663   {
2664   }
2665
2666   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2667   {
2668   }
2669
2670   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2671   {
2672   }
2673
2674   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2675   {
2676   }
2677
2678   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2679   {
2680   }
2681
2682   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2683   {
2684   }
2685
2686   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2687   {
2688   }
2689
2690   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2691   {
2692   }
2693
2694   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2695   {
2696   }
2697
2698   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2699   {
2700   }
2701
2702   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2703   {
2704   }
2705
2706   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2707   {
2708   }
2709
2710   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2711   {
2712   }
2713
2714   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2715   {
2716   }
2717
2718   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2719   {
2720   }
2721
2722   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2723   {
2724   }
2725
2726   protected void clustalColour_actionPerformed(ActionEvent e)
2727   {
2728   }
2729
2730   protected void zappoColour_actionPerformed(ActionEvent e)
2731   {
2732   }
2733
2734   protected void taylorColour_actionPerformed(ActionEvent e)
2735   {
2736   }
2737
2738   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2739   {
2740   }
2741
2742   protected void helixColour_actionPerformed(ActionEvent e)
2743   {
2744   }
2745
2746   protected void strandColour_actionPerformed(ActionEvent e)
2747   {
2748   }
2749
2750   protected void turnColour_actionPerformed(ActionEvent e)
2751   {
2752   }
2753
2754   protected void buriedColour_actionPerformed(ActionEvent e)
2755   {
2756   }
2757
2758   protected void userDefinedColour_actionPerformed(ActionEvent e)
2759   {
2760   }
2761
2762   protected void PIDColour_actionPerformed(ActionEvent e)
2763   {
2764   }
2765
2766   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2767   {
2768   }
2769
2770   protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2771   {
2772   }
2773
2774   protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2775   {
2776   }
2777
2778   /*
2779    * protected void covariationColour_actionPerformed(ActionEvent e) { }
2780    */
2781
2782   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2783   {
2784   }
2785
2786   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2787   {
2788   }
2789
2790   protected void printMenuItem_actionPerformed(ActionEvent e)
2791   {
2792   }
2793
2794   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2795   {
2796   }
2797
2798   protected void findMenuItem_actionPerformed(ActionEvent e)
2799   {
2800   }
2801
2802   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2803   {
2804   }
2805
2806   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2807   {
2808   }
2809
2810   protected void nucleotideColour_actionPerformed(ActionEvent e)
2811   {
2812   }
2813
2814   protected void deleteGroups_actionPerformed(ActionEvent e)
2815   {
2816   }
2817
2818   protected void createGroup_actionPerformed(ActionEvent e)
2819   {
2820   }
2821
2822   protected void unGroup_actionPerformed(ActionEvent e)
2823   {
2824   }
2825
2826   protected void copy_actionPerformed(ActionEvent e)
2827   {
2828   }
2829
2830   protected void cut_actionPerformed(ActionEvent e)
2831   {
2832   }
2833
2834   protected void delete_actionPerformed(ActionEvent e)
2835   {
2836   }
2837
2838   protected void pasteNew_actionPerformed(ActionEvent e)
2839   {
2840   }
2841
2842   protected void pasteThis_actionPerformed(ActionEvent e)
2843   {
2844   }
2845
2846   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2847   {
2848   }
2849
2850   public void createPNG(java.io.File f)
2851   {
2852   }
2853
2854   protected void font_actionPerformed(ActionEvent e)
2855   {
2856   }
2857
2858   protected void seqLimit_actionPerformed(ActionEvent e)
2859   {
2860   }
2861
2862   public void seqDBRef_actionPerformed(ActionEvent e)
2863   {
2864
2865   }
2866
2867   public void createEPS(java.io.File f)
2868   {
2869   }
2870
2871   public void createSVG(java.io.File f)
2872   {
2873
2874   }
2875   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2876   {
2877
2878   }
2879
2880   /**
2881    * Template method to handle the 'load T-Coffee scores' menu event.
2882    * <p>
2883    * Subclasses override this method to provide a custom action.
2884    *
2885    * @param event
2886    *          The raised event
2887    */
2888   protected void loadScores_actionPerformed(ActionEvent event)
2889   {
2890
2891   }
2892
2893   /**
2894    * Template method to handle the 'Color T-Coffee scores' menu event.
2895    * <p>
2896    * Subclasses override this method to provide a custom action.
2897    *
2898    * @param event
2899    *          The raised event
2900    */
2901   protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2902   {
2903
2904   }
2905
2906   protected void jpred_actionPerformed(ActionEvent e)
2907   {
2908   }
2909
2910   protected void scaleAbove_actionPerformed(ActionEvent e)
2911   {
2912   }
2913
2914   protected void scaleLeft_actionPerformed(ActionEvent e)
2915   {
2916   }
2917
2918   protected void scaleRight_actionPerformed(ActionEvent e)
2919   {
2920   }
2921
2922   protected void modifyPID_actionPerformed(ActionEvent e)
2923   {
2924   }
2925
2926   protected void modifyConservation_actionPerformed(ActionEvent e)
2927   {
2928   }
2929
2930   protected void saveAs_actionPerformed(ActionEvent e)
2931   {
2932   }
2933
2934   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2935   {
2936   }
2937
2938   public void vamsasStore_actionPerformed(ActionEvent e)
2939   {
2940
2941   }
2942
2943   public void vamsasLoad_actionPerformed(ActionEvent e)
2944   {
2945
2946   }
2947
2948   public void showTranslation_actionPerformed(ActionEvent e)
2949   {
2950
2951   }
2952
2953   public void featureSettings_actionPerformed(ActionEvent e)
2954   {
2955
2956   }
2957
2958   public void fetchSequence_actionPerformed(ActionEvent e)
2959   {
2960
2961   }
2962
2963   public void smoothFont_actionPerformed(ActionEvent e)
2964   {
2965
2966   }
2967
2968   public void annotationColour_actionPerformed(ActionEvent e)
2969   {
2970
2971   }
2972
2973   public void rnahelicesColour_actionPerformed(ActionEvent e)
2974   {
2975
2976   }
2977
2978   public void associatedData_actionPerformed(ActionEvent e)
2979   {
2980
2981   }
2982
2983   public void autoCalculate_actionPerformed(ActionEvent e)
2984   {
2985
2986   }
2987
2988   public void sortByTreeOption_actionPerformed(ActionEvent e)
2989   {
2990
2991   }
2992
2993   public void showAllSeqs_actionPerformed(ActionEvent e)
2994   {
2995
2996   }
2997
2998   public void showAllColumns_actionPerformed(ActionEvent e)
2999   {
3000
3001   }
3002
3003   public void hideSelSequences_actionPerformed(ActionEvent e)
3004   {
3005
3006   }
3007
3008   public void hideSelColumns_actionPerformed(ActionEvent e)
3009   {
3010
3011   }
3012
3013   public void hiddenMarkers_actionPerformed(ActionEvent e)
3014   {
3015
3016   }
3017
3018   public void findPdbId_actionPerformed(ActionEvent e)
3019   {
3020
3021   }
3022
3023   public void enterPdbId_actionPerformed(ActionEvent e)
3024   {
3025
3026   }
3027
3028   public void pdbFile_actionPerformed(ActionEvent e)
3029   {
3030
3031   }
3032
3033   public void invertColSel_actionPerformed(ActionEvent e)
3034   {
3035
3036   }
3037
3038   public void tabSelectionChanged(int sel)
3039   {
3040
3041   }
3042
3043   public void tabbedPane_mousePressed(MouseEvent e)
3044   {
3045
3046   }
3047
3048   public void tabbedPane_focusGained(FocusEvent e)
3049   {
3050     requestFocus();
3051   }
3052
3053   public void save_actionPerformed(ActionEvent e)
3054   {
3055
3056   }
3057
3058   public void reload_actionPerformed(ActionEvent e)
3059   {
3060
3061   }
3062
3063   public void newView_actionPerformed(ActionEvent e)
3064   {
3065
3066   }
3067
3068   public void textColour_actionPerformed(ActionEvent e)
3069   {
3070
3071   }
3072
3073   public void idRightAlign_actionPerformed(ActionEvent e)
3074   {
3075
3076   }
3077
3078   public void expandViews_actionPerformed(ActionEvent e)
3079   {
3080
3081   }
3082
3083   public void gatherViews_actionPerformed(ActionEvent e)
3084   {
3085
3086   }
3087
3088   public void buildTreeMenu()
3089   {
3090
3091   }
3092
3093   public void pageSetup_actionPerformed(ActionEvent e)
3094   {
3095
3096   }
3097
3098   public void alignmentProperties()
3099   {
3100
3101   }
3102
3103   protected void expand_newalign(ActionEvent e)
3104   {
3105     // TODO Auto-generated method stub
3106
3107   }
3108
3109   protected boolean isShowAutoCalculatedAbove()
3110   {
3111     return showAutoCalculatedAbove;
3112   }
3113
3114   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
3115   {
3116     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
3117   }
3118
3119   protected SequenceAnnotationOrder getAnnotationSortOrder()
3120   {
3121     return annotationSortOrder;
3122   }
3123
3124   protected void setAnnotationSortOrder(SequenceAnnotationOrder annotationSortOrder)
3125   {
3126     this.annotationSortOrder = annotationSortOrder;
3127   }
3128 }