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
1815     /*
1816      * cDNA menu options
1817      */
1818     cdna.setText(MessageManager.getString("label.cdna"));
1819     JMenuItem linkCdna = new JMenuItem(
1820             MessageManager.getString("label.link_cdna"));
1821     linkCdna.setToolTipText(JvSwingUtils.wrapTooltip(true,
1822             MessageManager.getString("label.link_cdna_tip")));
1823     linkCdna.addActionListener(new ActionListener()
1824     {
1825       @Override
1826       public void actionPerformed(ActionEvent e)
1827       {
1828         linkCdna_actionPerformed();
1829       }
1830     });
1831     cdna.add(linkCdna);
1832     JMenuItem alignCdna = new JMenuItem(
1833             MessageManager.getString("label.align_cdna"));
1834     alignCdna.setToolTipText(JvSwingUtils.wrapTooltip(true,
1835             MessageManager.getString("label.align_cdna_tip")));
1836     alignCdna.addActionListener(new ActionListener()
1837     {
1838       @Override
1839       public void actionPerformed(ActionEvent e)
1840       {
1841         alignCdna_actionPerformed();
1842       }
1843     });
1844     cdna.add(alignCdna);
1845
1846     extractScores.setText(MessageManager.getString("label.extract_scores")
1847             + "...");
1848     extractScores.addActionListener(new ActionListener()
1849     {
1850       @Override
1851       public void actionPerformed(ActionEvent e)
1852       {
1853         extractScores_actionPerformed(e);
1854       }
1855     });
1856     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1857     // score extraction
1858     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1859     /*
1860      * showProducts.addActionListener(new ActionListener() {
1861      *
1862      * public void actionPerformed(ActionEvent e) {
1863      * showProducts_actionPerformed(e); } });
1864      */
1865     openFeatureSettings.setText(MessageManager
1866             .getString("label.feature_settings"));
1867     openFeatureSettings.addActionListener(new ActionListener()
1868     {
1869       @Override
1870       public void actionPerformed(ActionEvent e)
1871       {
1872         featureSettings_actionPerformed(e);
1873       }
1874     });
1875     fetchSequence
1876             .setText(MessageManager.getString("label.fetch_sequences"));
1877     fetchSequence.addActionListener(new ActionListener()
1878     {
1879       @Override
1880       public void actionPerformed(ActionEvent e)
1881       {
1882         fetchSequence_actionPerformed(e);
1883       }
1884     });
1885
1886     annotationColour.setText(MessageManager
1887             .getString("action.by_annotation"));
1888     annotationColour.addActionListener(new ActionListener()
1889     {
1890       @Override
1891       public void actionPerformed(ActionEvent e)
1892       {
1893         annotationColour_actionPerformed(e);
1894       }
1895     });
1896
1897     rnahelicesColour.setText(MessageManager
1898             .getString("action.by_rna_helixes"));
1899     rnahelicesColour.addActionListener(new ActionListener()
1900     {
1901       @Override
1902       public void actionPerformed(ActionEvent e)
1903       {
1904         rnahelicesColour_actionPerformed(e);
1905       }
1906     });
1907
1908     associatedData.setText(MessageManager
1909             .getString("label.load_features_annotations"));
1910     associatedData.addActionListener(new ActionListener()
1911     {
1912       @Override
1913       public void actionPerformed(ActionEvent e)
1914       {
1915         associatedData_actionPerformed(e);
1916       }
1917     });
1918     autoCalculate.setText(MessageManager
1919             .getString("label.autocalculate_consensus"));
1920     autoCalculate.setState(jalview.bin.Cache.getDefault(
1921             "AUTO_CALC_CONSENSUS", true));
1922     autoCalculate.addActionListener(new ActionListener()
1923     {
1924       @Override
1925       public void actionPerformed(ActionEvent e)
1926       {
1927         autoCalculate_actionPerformed(e);
1928       }
1929     });
1930     sortByTree.setText(MessageManager
1931             .getString("label.sort_alignment_new_tree"));
1932     sortByTree
1933             .setToolTipText("<html>"
1934                     + MessageManager
1935                             .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1936     sortByTree
1937             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1938     sortByTree.addActionListener(new ActionListener()
1939     {
1940       @Override
1941       public void actionPerformed(ActionEvent e)
1942       {
1943         sortByTreeOption_actionPerformed(e);
1944       }
1945     });
1946
1947     listenToViewSelections.setText(MessageManager
1948             .getString("label.listen_for_selections"));
1949     listenToViewSelections
1950             .setToolTipText("<html>"
1951                     + MessageManager
1952                             .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1953     listenToViewSelections.setState(false);
1954     listenToViewSelections.addActionListener(new ActionListener()
1955     {
1956       @Override
1957       public void actionPerformed(ActionEvent e)
1958       {
1959         listenToViewSelections_actionPerformed(e);
1960       }
1961     });
1962
1963     addSequenceMenu
1964             .setText(MessageManager.getString("label.add_sequences"));
1965     addFromFile.setText(MessageManager.getString("label.from_file"));
1966     addFromFile.addActionListener(new ActionListener()
1967     {
1968       @Override
1969       public void actionPerformed(ActionEvent e)
1970       {
1971         addFromFile_actionPerformed(e);
1972       }
1973     });
1974     addFromText.setText(MessageManager.getString("label.from_textbox"));
1975     addFromText.addActionListener(new ActionListener()
1976     {
1977       @Override
1978       public void actionPerformed(ActionEvent e)
1979       {
1980         addFromText_actionPerformed(e);
1981       }
1982     });
1983     addFromURL.setText(MessageManager.getString("label.from_url"));
1984     addFromURL.addActionListener(new ActionListener()
1985     {
1986       @Override
1987       public void actionPerformed(ActionEvent e)
1988       {
1989         addFromURL_actionPerformed(e);
1990       }
1991     });
1992     exportFeatures.setText(MessageManager
1993             .getString("label.export_features"));
1994     exportFeatures.addActionListener(new ActionListener()
1995     {
1996       @Override
1997       public void actionPerformed(ActionEvent e)
1998       {
1999         exportFeatures_actionPerformed(e);
2000       }
2001     });
2002     exportAnnotations.setText(MessageManager
2003             .getString("label.export_annotations"));
2004     exportAnnotations.addActionListener(new ActionListener()
2005     {
2006       @Override
2007       public void actionPerformed(ActionEvent e)
2008       {
2009         exportAnnotations_actionPerformed(e);
2010       }
2011     });
2012     statusPanel.setLayout(gridLayout1);
2013     jMenu3.setText(MessageManager.getString("action.show"));
2014     showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
2015     showAllSeqs.setToolTipText(MessageManager
2016             .getString("label.toggle_sequence_visibility"));
2017     showAllSeqs.addActionListener(new ActionListener()
2018     {
2019       @Override
2020       public void actionPerformed(ActionEvent e)
2021       {
2022         showAllSeqs_actionPerformed(e);
2023       }
2024     });
2025     showAllColumns.setText(MessageManager.getString("label.all_columns"));
2026     showAllColumns.setToolTipText(MessageManager
2027             .getString("label.toggle_columns_visibility"));
2028     showAllColumns.addActionListener(new ActionListener()
2029     {
2030       @Override
2031       public void actionPerformed(ActionEvent e)
2032       {
2033         showAllColumns_actionPerformed(e);
2034       }
2035     });
2036     hideMenu.setText(MessageManager.getString("action.hide"));
2037     hideSelSequences.setText(MessageManager
2038             .getString("label.selected_sequences"));
2039     hideSelSequences.setToolTipText(MessageManager
2040             .getString("label.toggle_sequence_visibility"));
2041     hideSelSequences.addActionListener(new ActionListener()
2042     {
2043       @Override
2044       public void actionPerformed(ActionEvent e)
2045       {
2046         hideSelSequences_actionPerformed(e);
2047       }
2048     });
2049     hideSelColumns.setText(MessageManager
2050             .getString("label.selected_columns"));
2051     hideSelColumns.setToolTipText(MessageManager
2052             .getString("label.toggle_columns_visibility"));
2053     hideSelColumns.addActionListener(new ActionListener()
2054     {
2055       @Override
2056       public void actionPerformed(ActionEvent e)
2057       {
2058         hideSelColumns_actionPerformed(e);
2059       }
2060     });
2061     hideAllSelection.setText(MessageManager
2062             .getString("label.selected_region"));
2063     hideAllSelection.addActionListener(new ActionListener()
2064     {
2065       @Override
2066       public void actionPerformed(ActionEvent e)
2067       {
2068         hideAllSelection_actionPerformed(e);
2069       }
2070     });
2071     // TODO: should be hidden if no selection exists.
2072     hideAllButSelection.setText(MessageManager
2073             .getString("label.all_but_selected_region"));
2074     hideAllButSelection.addActionListener(new ActionListener()
2075     {
2076       @Override
2077       public void actionPerformed(ActionEvent e)
2078       {
2079         hideAllButSelection_actionPerformed(e);
2080       }
2081     });
2082     showAllhidden.setText(MessageManager
2083             .getString("label.all_sequences_columns"));
2084     showAllhidden.setToolTipText(MessageManager
2085             .getString("label.toggles_visibility_hidden_selected_regions"));
2086     showAllhidden.addActionListener(new ActionListener()
2087     {
2088       @Override
2089       public void actionPerformed(ActionEvent e)
2090       {
2091         showAllhidden_actionPerformed(e);
2092       }
2093     });
2094     hiddenMarkers.setText(MessageManager
2095             .getString("action.show_hidden_markers"));
2096     hiddenMarkers.addActionListener(new ActionListener()
2097     {
2098       @Override
2099       public void actionPerformed(ActionEvent e)
2100       {
2101         hiddenMarkers_actionPerformed(e);
2102       }
2103     });
2104     invertColSel.setText(MessageManager
2105             .getString("action.invert_column_selection"));
2106     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2107             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
2108                     .getMenuShortcutKeyMask()
2109                     | java.awt.event.KeyEvent.ALT_MASK, false));
2110     invertColSel.addActionListener(new ActionListener()
2111     {
2112       @Override
2113       public void actionPerformed(ActionEvent e)
2114       {
2115         invertColSel_actionPerformed(e);
2116       }
2117     });
2118     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
2119     {
2120       @Override
2121       public void stateChanged(ChangeEvent evt)
2122       {
2123         JTabbedPane pane = (JTabbedPane) evt.getSource();
2124         int sel = pane.getSelectedIndex();
2125         tabSelectionChanged(sel);
2126       }
2127     });
2128     tabbedPane.addMouseListener(new MouseAdapter()
2129     {
2130       @Override
2131       public void mousePressed(MouseEvent e)
2132       {
2133         tabbedPane_mousePressed(e);
2134       }
2135     });
2136     tabbedPane.addFocusListener(new FocusAdapter()
2137     {
2138       @Override
2139       public void focusGained(FocusEvent e)
2140       {
2141         tabbedPane_focusGained(e);
2142       }
2143     });
2144     save.setText(MessageManager.getString("action.save"));
2145     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2146             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
2147                     .getMenuShortcutKeyMask(), false));
2148     save.addActionListener(new ActionListener()
2149     {
2150       @Override
2151       public void actionPerformed(ActionEvent e)
2152       {
2153         save_actionPerformed(e);
2154       }
2155     });
2156     reload.setEnabled(false);
2157     reload.setText(MessageManager.getString("action.reload"));
2158     reload.addActionListener(new ActionListener()
2159     {
2160       @Override
2161       public void actionPerformed(ActionEvent e)
2162       {
2163         reload_actionPerformed(e);
2164       }
2165     });
2166     newView.setText(MessageManager.getString("action.new_view"));
2167     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2168             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
2169                     .getMenuShortcutKeyMask(), false));
2170     newView.addActionListener(new ActionListener()
2171     {
2172       @Override
2173       public void actionPerformed(ActionEvent e)
2174       {
2175         newView_actionPerformed(e);
2176       }
2177     });
2178     tabbedPane.setToolTipText("<html><i>"
2179             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2180             + "</i></html>");
2181     textColour.setText(MessageManager.getString("label.colour_text")
2182             + "...");
2183     textColour.addActionListener(new ActionListener()
2184     {
2185       @Override
2186       public void actionPerformed(ActionEvent e)
2187       {
2188         textColour_actionPerformed(e);
2189       }
2190     });
2191     formatMenu.setText(MessageManager.getString("action.format"));
2192     selectMenu.setText(MessageManager.getString("action.select"));
2193     idRightAlign.setText(MessageManager
2194             .getString("label.right_align_sequence_id"));
2195     idRightAlign.addActionListener(new ActionListener()
2196     {
2197       @Override
2198       public void actionPerformed(ActionEvent e)
2199       {
2200         idRightAlign_actionPerformed(e);
2201       }
2202     });
2203     gatherViews.setEnabled(false);
2204     gatherViews.setText(MessageManager.getString("action.gather_views"));
2205     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2206             java.awt.event.KeyEvent.VK_G, 0, false));
2207     gatherViews.addActionListener(new ActionListener()
2208     {
2209       @Override
2210       public void actionPerformed(ActionEvent e)
2211       {
2212         gatherViews_actionPerformed(e);
2213       }
2214     });
2215     expandViews.setEnabled(false);
2216     expandViews.setText(MessageManager.getString("action.expand_views"));
2217     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2218             java.awt.event.KeyEvent.VK_X, 0, false));
2219     expandViews.addActionListener(new ActionListener()
2220     {
2221       @Override
2222       public void actionPerformed(ActionEvent e)
2223       {
2224         expandViews_actionPerformed(e);
2225       }
2226     });
2227     pageSetup
2228             .setText(MessageManager.getString("action.page_setup") + "...");
2229     pageSetup.addActionListener(new ActionListener()
2230     {
2231       @Override
2232       public void actionPerformed(ActionEvent e)
2233       {
2234         pageSetup_actionPerformed(e);
2235       }
2236     });
2237     alignmentProperties.setText(MessageManager
2238             .getString("label.alignment_props") + "...");
2239     alignmentProperties.addActionListener(new ActionListener()
2240     {
2241       @Override
2242       public void actionPerformed(ActionEvent actionEvent)
2243       {
2244         alignmentProperties();
2245       }
2246     });
2247     tooltipSettingsMenu.setText(MessageManager
2248             .getString("label.sequence_id_tooltip"));
2249     autoAnnMenu.setText(MessageManager
2250             .getString("label.autocalculated_annotation"));
2251     alignFrameMenuBar.add(fileMenu);
2252     alignFrameMenuBar.add(editMenu);
2253     alignFrameMenuBar.add(selectMenu);
2254     alignFrameMenuBar.add(viewMenu);
2255     alignFrameMenuBar.add(annotationsMenu);
2256     alignFrameMenuBar.add(formatMenu);
2257     alignFrameMenuBar.add(colourMenu);
2258     alignFrameMenuBar.add(calculateMenu);
2259     alignFrameMenuBar.add(webService);
2260     fileMenu.add(fetchSequence);
2261     fileMenu.add(addSequenceMenu);
2262     fileMenu.add(reload);
2263     fileMenu.addSeparator();
2264     fileMenu.add(vamsasStore);
2265     fileMenu.add(save);
2266     fileMenu.add(saveAs);
2267     fileMenu.add(outputTextboxMenu);
2268     fileMenu.add(pageSetup);
2269     fileMenu.add(printMenuItem);
2270     fileMenu.addSeparator();
2271     fileMenu.add(jMenu2);
2272     fileMenu.add(exportFeatures);
2273     fileMenu.add(exportAnnotations);
2274     fileMenu.add(LoadtreeMenuItem);
2275     fileMenu.add(associatedData);
2276     fileMenu.addSeparator();
2277     fileMenu.add(closeMenuItem);
2278     editMenu.add(undoMenuItem);
2279     editMenu.add(redoMenuItem);
2280     editMenu.add(cut);
2281     editMenu.add(copy);
2282     editMenu.add(pasteMenu);
2283     editMenu.add(delete);
2284     editMenu.addSeparator();
2285     editMenu.add(remove2LeftMenuItem);
2286     editMenu.add(remove2RightMenuItem);
2287     editMenu.add(removeGappedColumnMenuItem);
2288     editMenu.add(removeAllGapsMenuItem);
2289     editMenu.add(removeRedundancyMenuItem);
2290     editMenu.addSeparator();
2291     // dont add these yet in the CVS build - they cannot be undone!
2292     // Excluded from Jalview 2.5 release - undo needs to be implemented.
2293     // editMenu.add(justifyLeftMenuItem);
2294     // editMenu.add(justifyRightMenuItem);
2295     // editMenu.addSeparator();
2296     editMenu.add(padGapsMenuitem);
2297     viewMenu.add(newView);
2298     viewMenu.add(expandViews);
2299     viewMenu.add(gatherViews);
2300     viewMenu.addSeparator();
2301     viewMenu.add(jMenu3);
2302     viewMenu.add(hideMenu);
2303     viewMenu.addSeparator();
2304     viewMenu.add(followHighlightMenuItem);
2305     annotationsMenu.add(annotationPanelMenuItem);
2306     annotationsMenu.addSeparator();
2307     annotationsMenu.add(showAllAlAnnotations);
2308     annotationsMenu.add(hideAllAlAnnotations);
2309     annotationsMenu.addSeparator();
2310     annotationsMenu.add(showAllSeqAnnotations);
2311     annotationsMenu.add(hideAllSeqAnnotations);
2312     annotationsMenu.add(sortAnnBySequence);
2313     annotationsMenu.add(sortAnnByLabel);
2314     annotationsMenu.addSeparator();
2315     autoAnnMenu.add(showAutoFirst);
2316     autoAnnMenu.add(showAutoLast);
2317     autoAnnMenu.addSeparator();
2318     autoAnnMenu.add(applyAutoAnnotationSettings);
2319     autoAnnMenu.add(showConsensusHistogram);
2320     autoAnnMenu.add(showSequenceLogo);
2321     autoAnnMenu.add(normaliseSequenceLogo);
2322     autoAnnMenu.addSeparator();
2323     autoAnnMenu.add(showGroupConservation);
2324     autoAnnMenu.add(showGroupConsensus);
2325     annotationsMenu.add(autoAnnMenu);
2326     viewMenu.addSeparator();
2327     viewMenu.add(showSeqFeatures);
2328     // viewMenu.add(showSeqFeaturesHeight);
2329
2330     viewMenu.add(openFeatureSettings);
2331     tooltipSettingsMenu.add(showDbRefsMenuitem);
2332     tooltipSettingsMenu.add(showNpFeatsMenuitem);
2333     viewMenu.add(tooltipSettingsMenu);
2334     viewMenu.addSeparator();
2335     viewMenu.add(alignmentProperties);
2336     viewMenu.addSeparator();
2337     viewMenu.add(overviewMenuItem);
2338     colourMenu.add(applyToAllGroups);
2339     colourMenu.add(textColour);
2340     colourMenu.addSeparator();
2341     colourMenu.add(noColourmenuItem);
2342     colourMenu.add(clustalColour);
2343     colourMenu.add(BLOSUM62Colour);
2344     colourMenu.add(PIDColour);
2345     colourMenu.add(zappoColour);
2346     colourMenu.add(taylorColour);
2347     colourMenu.add(hydrophobicityColour);
2348     colourMenu.add(helixColour);
2349     colourMenu.add(strandColour);
2350     colourMenu.add(turnColour);
2351     colourMenu.add(buriedColour);
2352     colourMenu.add(nucleotideColour);
2353     colourMenu.add(purinePyrimidineColour);
2354     colourMenu.add(RNAInteractionColour);
2355     // colourMenu.add(covariationColour);
2356     colourMenu.add(tcoffeeColour);
2357     colourMenu.add(userDefinedColour);
2358     colourMenu.addSeparator();
2359     colourMenu.add(conservationMenuItem);
2360     colourMenu.add(modifyConservation);
2361     colourMenu.add(abovePIDThreshold);
2362     colourMenu.add(modifyPID);
2363     colourMenu.add(annotationColour);
2364     colourMenu.add(rnahelicesColour);
2365     calculateMenu.add(sort);
2366     calculateMenu.add(calculateTree);
2367     calculateMenu.addSeparator();
2368     calculateMenu.add(pairwiseAlignmentMenuItem);
2369     calculateMenu.add(PCAMenuItem);
2370     calculateMenu.addSeparator();
2371     calculateMenu.add(showTranslation);
2372     calculateMenu.add(cdna);
2373     calculateMenu.add(showProducts);
2374     calculateMenu.add(autoCalculate);
2375     calculateMenu.add(sortByTree);
2376     calculateMenu.addSeparator();
2377     calculateMenu.add(extractScores);
2378     webServiceNoServices = new JMenuItem(
2379             MessageManager.getString("label.no_services"));
2380     webService.add(webServiceNoServices);
2381     pasteMenu.add(pasteNew);
2382     pasteMenu.add(pasteThis);
2383     sort.add(sortIDMenuItem);
2384     sort.add(sortLengthMenuItem);
2385     sort.add(sortGroupMenuItem);
2386     sort.add(sortPairwiseMenuItem);
2387     sort.add(sortByTreeMenu);
2388     jMenu2.add(htmlMenuItem);
2389     jMenu2.add(epsFile);
2390     jMenu2.add(createPNG);
2391     jMenu2.add(createSVG);
2392     addSequenceMenu.add(addFromFile);
2393     addSequenceMenu.add(addFromText);
2394     addSequenceMenu.add(addFromURL);
2395     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2396     statusPanel.add(statusBar, null);
2397     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2398     jMenu3.add(showAllColumns);
2399     jMenu3.add(showAllSeqs);
2400     jMenu3.add(showAllhidden);
2401     hideMenu.add(hideSelColumns);
2402     hideMenu.add(hideSelSequences);
2403     hideMenu.add(hideAllSelection);
2404     hideMenu.add(hideAllButSelection);
2405
2406     formatMenu.add(font);
2407     formatMenu.addSeparator();
2408     formatMenu.add(wrapMenuItem);
2409     formatMenu.add(scaleAbove);
2410     formatMenu.add(scaleLeft);
2411     formatMenu.add(scaleRight);
2412     formatMenu.add(seqLimits);
2413     formatMenu.add(idRightAlign);
2414     formatMenu.add(hiddenMarkers);
2415     formatMenu.add(viewBoxesMenuItem);
2416     formatMenu.add(viewTextMenuItem);
2417     formatMenu.add(colourTextMenuItem);
2418     formatMenu.add(renderGapsMenuItem);
2419     formatMenu.add(centreColumnLabelsMenuItem);
2420     formatMenu.add(showNonconservedMenuItem);
2421     selectMenu.add(findMenuItem);
2422     selectMenu.addSeparator();
2423     selectMenu.add(selectAllSequenceMenuItem);
2424     selectMenu.add(deselectAllSequenceMenuItem);
2425     selectMenu.add(invertSequenceMenuItem);
2426     selectMenu.add(invertColSel);
2427     selectMenu.add(createGroup);
2428     selectMenu.add(unGroup);
2429     selectMenu.add(grpsFromSelection);
2430     selectMenu.add(deleteGroups);
2431     calculateMenu.add(expandAlignment);
2432     // TODO - determine if the listenToViewSelections button is needed : see bug
2433     // JAL-574
2434     // selectMenu.addSeparator();
2435     // selectMenu.add(listenToViewSelections);
2436   }
2437
2438   protected void alignCdna_actionPerformed()
2439   {
2440     // TODO Auto-generated method stub
2441
2442   }
2443
2444   protected void linkCdna_actionPerformed()
2445   {
2446     // TODO Auto-generated method stub
2447
2448   }
2449
2450   /**
2451    * Action on clicking sort annotations by type.
2452    *
2453    * @param sortOrder
2454    */
2455   protected void sortAnnotations_actionPerformed()
2456   {
2457   }
2458
2459   /**
2460    * Action on clicking Show all annotations.
2461    *
2462    * @param forSequences
2463    *          update sequence-related annotations
2464    * @param forAlignment
2465    *          update non-sequence-related annotations
2466    */
2467   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2468           boolean forAlignment)
2469   {
2470     setAnnotationsVisibility(true, forSequences, forAlignment);
2471   }
2472
2473   /**
2474    * Action on clicking Hide all annotations.
2475    *
2476    * @param forSequences
2477    *          update sequence-related annotations
2478    * @param forAlignment
2479    *          update non-sequence-related annotations
2480    */
2481   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2482           boolean forAlignment)
2483   {
2484     setAnnotationsVisibility(false, forSequences, forAlignment);
2485   }
2486
2487   /**
2488    * Set the visibility of annotations to true or false. Can act on
2489    * sequence-related annotations, or alignment-related, or both.
2490    *
2491    * @param visible
2492    * @param forSequences
2493    *          update sequence-related annotations
2494    * @param forAlignment
2495    *          update non-sequence-related annotations
2496    */
2497   protected void setAnnotationsVisibility(boolean visible,
2498           boolean forSequences, boolean forAlignment)
2499   {
2500
2501   }
2502
2503   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2504   {
2505     // TODO Auto-generated method stub
2506
2507   }
2508
2509   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2510   {
2511     // TODO Auto-generated method stub
2512
2513   }
2514
2515   protected void showAllhidden_actionPerformed(ActionEvent e)
2516   {
2517     // TODO Auto-generated method stub
2518
2519   }
2520
2521   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2522   {
2523     // TODO Auto-generated method stub
2524
2525   }
2526
2527   protected void hideAllSelection_actionPerformed(ActionEvent e)
2528   {
2529     // TODO Auto-generated method stub
2530
2531   }
2532
2533   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2534   {
2535     // TODO Auto-generated method stub
2536
2537   }
2538
2539   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2540   {
2541     // TODO Auto-generated method stub
2542
2543   }
2544
2545   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2546   {
2547     // TODO Auto-generated method stub
2548
2549   }
2550
2551   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2552   {
2553     // TODO Auto-generated method stub
2554
2555   }
2556
2557   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2558   {
2559     // TODO Auto-generated method stub
2560
2561   }
2562
2563   protected void showGroupConservation_actionPerformed(ActionEvent e)
2564   {
2565     // TODO Auto-generated method stub
2566
2567   }
2568
2569   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2570   {
2571     // TODO Auto-generated method stub
2572
2573   }
2574
2575   protected void showSeqFeaturesHeight_actionPerformed(
2576           ActionEvent actionEvent)
2577   {
2578     // TODO Auto-generated method stub
2579
2580   }
2581
2582   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2583   {
2584     // TODO Auto-generated method stub
2585
2586   }
2587
2588   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2589   {
2590     // TODO Auto-generated method stub
2591
2592   }
2593
2594   protected void followHighlight_actionPerformed()
2595   {
2596     // TODO Auto-generated method stub
2597
2598   }
2599
2600   protected void showNpFeats_actionPerformed(ActionEvent e)
2601   {
2602     // TODO Auto-generated method stub
2603
2604   }
2605
2606   protected void showDbRefs_actionPerformed(ActionEvent e)
2607   {
2608     // TODO Auto-generated method stub
2609
2610   }
2611
2612   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2613   {
2614   }
2615
2616   protected void showProducts_actionPerformed(ActionEvent e)
2617   {
2618   }
2619
2620   protected void buildSortByAnnotationScoresMenu()
2621   {
2622   }
2623
2624   protected void extractScores_actionPerformed(ActionEvent e)
2625   {
2626   }
2627
2628   protected void outputText_actionPerformed(ActionEvent e)
2629   {
2630   }
2631
2632   public void addFromFile_actionPerformed(ActionEvent e)
2633   {
2634
2635   }
2636
2637   public void addFromText_actionPerformed(ActionEvent e)
2638   {
2639
2640   }
2641
2642   public void addFromURL_actionPerformed(ActionEvent e)
2643   {
2644
2645   }
2646
2647   public void exportFeatures_actionPerformed(ActionEvent e)
2648   {
2649
2650   }
2651
2652   public void exportAnnotations_actionPerformed(ActionEvent e)
2653   {
2654
2655   }
2656
2657   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2658   {
2659   }
2660
2661   protected void closeMenuItem_actionPerformed(boolean b)
2662   {
2663   }
2664
2665   protected void redoMenuItem_actionPerformed(ActionEvent e)
2666   {
2667   }
2668
2669   protected void undoMenuItem_actionPerformed(ActionEvent e)
2670   {
2671   }
2672
2673   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2674   {
2675   }
2676
2677   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2678   {
2679   }
2680
2681   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2682   {
2683   }
2684
2685   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2686   {
2687   }
2688
2689   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2690   {
2691   }
2692
2693   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2694   {
2695   }
2696
2697   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2698   {
2699   }
2700
2701   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2702   {
2703   }
2704
2705   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2706   {
2707   }
2708
2709   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2710   {
2711   }
2712
2713   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2714   {
2715   }
2716
2717   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2718   {
2719   }
2720
2721   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2722   {
2723   }
2724
2725   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2726   {
2727   }
2728
2729   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2730   {
2731   }
2732
2733   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2734   {
2735   }
2736
2737   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2738   {
2739   }
2740
2741   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2742   {
2743   }
2744
2745   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2746   {
2747   }
2748
2749   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2750   {
2751   }
2752
2753   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2754   {
2755   }
2756
2757   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2758   {
2759   }
2760
2761   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2762   {
2763   }
2764
2765   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2766   {
2767   }
2768
2769   protected void clustalColour_actionPerformed(ActionEvent e)
2770   {
2771   }
2772
2773   protected void zappoColour_actionPerformed(ActionEvent e)
2774   {
2775   }
2776
2777   protected void taylorColour_actionPerformed(ActionEvent e)
2778   {
2779   }
2780
2781   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2782   {
2783   }
2784
2785   protected void helixColour_actionPerformed(ActionEvent e)
2786   {
2787   }
2788
2789   protected void strandColour_actionPerformed(ActionEvent e)
2790   {
2791   }
2792
2793   protected void turnColour_actionPerformed(ActionEvent e)
2794   {
2795   }
2796
2797   protected void buriedColour_actionPerformed(ActionEvent e)
2798   {
2799   }
2800
2801   protected void userDefinedColour_actionPerformed(ActionEvent e)
2802   {
2803   }
2804
2805   protected void PIDColour_actionPerformed(ActionEvent e)
2806   {
2807   }
2808
2809   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2810   {
2811   }
2812
2813   protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2814   {
2815   }
2816
2817   protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2818   {
2819   }
2820
2821   /*
2822    * protected void covariationColour_actionPerformed(ActionEvent e) { }
2823    */
2824
2825   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2826   {
2827   }
2828
2829   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2830   {
2831   }
2832
2833   protected void printMenuItem_actionPerformed(ActionEvent e)
2834   {
2835   }
2836
2837   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2838   {
2839   }
2840
2841   protected void findMenuItem_actionPerformed(ActionEvent e)
2842   {
2843   }
2844
2845   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2846   {
2847   }
2848
2849   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2850   {
2851   }
2852
2853   protected void nucleotideColour_actionPerformed(ActionEvent e)
2854   {
2855   }
2856
2857   protected void deleteGroups_actionPerformed(ActionEvent e)
2858   {
2859   }
2860
2861   protected void createGroup_actionPerformed(ActionEvent e)
2862   {
2863   }
2864
2865   protected void unGroup_actionPerformed(ActionEvent e)
2866   {
2867   }
2868
2869   protected void copy_actionPerformed(ActionEvent e)
2870   {
2871   }
2872
2873   protected void cut_actionPerformed(ActionEvent e)
2874   {
2875   }
2876
2877   protected void delete_actionPerformed(ActionEvent e)
2878   {
2879   }
2880
2881   protected void pasteNew_actionPerformed(ActionEvent e)
2882   {
2883   }
2884
2885   protected void pasteThis_actionPerformed(ActionEvent e)
2886   {
2887   }
2888
2889   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2890   {
2891   }
2892
2893   public void createPNG(java.io.File f)
2894   {
2895   }
2896
2897   protected void font_actionPerformed(ActionEvent e)
2898   {
2899   }
2900
2901   protected void seqLimit_actionPerformed(ActionEvent e)
2902   {
2903   }
2904
2905   public void seqDBRef_actionPerformed(ActionEvent e)
2906   {
2907
2908   }
2909
2910   public void createEPS(java.io.File f)
2911   {
2912   }
2913
2914   public void createSVG(java.io.File f)
2915   {
2916
2917   }
2918   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2919   {
2920
2921   }
2922
2923   /**
2924    * Template method to handle the 'load T-Coffee scores' menu event.
2925    * <p>
2926    * Subclasses override this method to provide a custom action.
2927    *
2928    * @param event
2929    *          The raised event
2930    */
2931   protected void loadScores_actionPerformed(ActionEvent event)
2932   {
2933
2934   }
2935
2936   /**
2937    * Template method to handle the 'Color T-Coffee scores' menu event.
2938    * <p>
2939    * Subclasses override this method to provide a custom action.
2940    *
2941    * @param event
2942    *          The raised event
2943    */
2944   protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2945   {
2946
2947   }
2948
2949   protected void jpred_actionPerformed(ActionEvent e)
2950   {
2951   }
2952
2953   protected void scaleAbove_actionPerformed(ActionEvent e)
2954   {
2955   }
2956
2957   protected void scaleLeft_actionPerformed(ActionEvent e)
2958   {
2959   }
2960
2961   protected void scaleRight_actionPerformed(ActionEvent e)
2962   {
2963   }
2964
2965   protected void modifyPID_actionPerformed(ActionEvent e)
2966   {
2967   }
2968
2969   protected void modifyConservation_actionPerformed(ActionEvent e)
2970   {
2971   }
2972
2973   protected void saveAs_actionPerformed(ActionEvent e)
2974   {
2975   }
2976
2977   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2978   {
2979   }
2980
2981   public void vamsasStore_actionPerformed(ActionEvent e)
2982   {
2983
2984   }
2985
2986   public void vamsasLoad_actionPerformed(ActionEvent e)
2987   {
2988
2989   }
2990
2991   public void showTranslation_actionPerformed(ActionEvent e)
2992   {
2993
2994   }
2995
2996   public void featureSettings_actionPerformed(ActionEvent e)
2997   {
2998
2999   }
3000
3001   public void fetchSequence_actionPerformed(ActionEvent e)
3002   {
3003
3004   }
3005
3006   public void smoothFont_actionPerformed(ActionEvent e)
3007   {
3008
3009   }
3010
3011   public void annotationColour_actionPerformed(ActionEvent e)
3012   {
3013
3014   }
3015
3016   public void rnahelicesColour_actionPerformed(ActionEvent e)
3017   {
3018
3019   }
3020
3021   public void associatedData_actionPerformed(ActionEvent e)
3022   {
3023
3024   }
3025
3026   public void autoCalculate_actionPerformed(ActionEvent e)
3027   {
3028
3029   }
3030
3031   public void sortByTreeOption_actionPerformed(ActionEvent e)
3032   {
3033
3034   }
3035
3036   public void showAllSeqs_actionPerformed(ActionEvent e)
3037   {
3038
3039   }
3040
3041   public void showAllColumns_actionPerformed(ActionEvent e)
3042   {
3043
3044   }
3045
3046   public void hideSelSequences_actionPerformed(ActionEvent e)
3047   {
3048
3049   }
3050
3051   public void hideSelColumns_actionPerformed(ActionEvent e)
3052   {
3053
3054   }
3055
3056   public void hiddenMarkers_actionPerformed(ActionEvent e)
3057   {
3058
3059   }
3060
3061   public void findPdbId_actionPerformed(ActionEvent e)
3062   {
3063
3064   }
3065
3066   public void enterPdbId_actionPerformed(ActionEvent e)
3067   {
3068
3069   }
3070
3071   public void pdbFile_actionPerformed(ActionEvent e)
3072   {
3073
3074   }
3075
3076   public void invertColSel_actionPerformed(ActionEvent e)
3077   {
3078
3079   }
3080
3081   public void tabSelectionChanged(int sel)
3082   {
3083
3084   }
3085
3086   public void tabbedPane_mousePressed(MouseEvent e)
3087   {
3088
3089   }
3090
3091   public void tabbedPane_focusGained(FocusEvent e)
3092   {
3093     requestFocus();
3094   }
3095
3096   public void save_actionPerformed(ActionEvent e)
3097   {
3098
3099   }
3100
3101   public void reload_actionPerformed(ActionEvent e)
3102   {
3103
3104   }
3105
3106   public void newView_actionPerformed(ActionEvent e)
3107   {
3108
3109   }
3110
3111   public void textColour_actionPerformed(ActionEvent e)
3112   {
3113
3114   }
3115
3116   public void idRightAlign_actionPerformed(ActionEvent e)
3117   {
3118
3119   }
3120
3121   public void expandViews_actionPerformed(ActionEvent e)
3122   {
3123
3124   }
3125
3126   public void gatherViews_actionPerformed(ActionEvent e)
3127   {
3128
3129   }
3130
3131   public void buildTreeMenu()
3132   {
3133
3134   }
3135
3136   public void pageSetup_actionPerformed(ActionEvent e)
3137   {
3138
3139   }
3140
3141   public void alignmentProperties()
3142   {
3143
3144   }
3145
3146   protected void expand_newalign(ActionEvent e)
3147   {
3148     // TODO Auto-generated method stub
3149
3150   }
3151
3152   protected boolean isShowAutoCalculatedAbove()
3153   {
3154     return showAutoCalculatedAbove;
3155   }
3156
3157   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
3158   {
3159     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
3160   }
3161
3162   protected SequenceAnnotationOrder getAnnotationSortOrder()
3163   {
3164     return annotationSortOrder;
3165   }
3166
3167   protected void setAnnotationSortOrder(SequenceAnnotationOrder annotationSortOrder)
3168   {
3169     this.annotationSortOrder = annotationSortOrder;
3170   }
3171 }