src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
   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 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  * The Jalview Authors are detailed in the 'AUTHORS' file.
  18  */
  19 package jalview.jbgui;
  20
  21 import jalview.schemes.ColourSchemeProperty;
  22 import jalview.util.MessageManager;
  23
  24 import java.awt.BorderLayout;
  25 import java.awt.Color;
  26 import java.awt.GridLayout;
  27 import java.awt.Toolkit;
  28 import java.awt.event.ActionEvent;
  29 import java.awt.event.ActionListener;
  30 import java.awt.event.FocusAdapter;
  31 import java.awt.event.FocusEvent;
  32 import java.awt.event.MouseAdapter;
  33 import java.awt.event.MouseEvent;
  34
  35 import javax.swing.BorderFactory;
  36 import javax.swing.ButtonGroup;
  37 import javax.swing.JCheckBoxMenuItem;
  38 import javax.swing.JInternalFrame;
  39 import javax.swing.JLabel;
  40 import javax.swing.JMenu;
  41 import javax.swing.JMenuBar;
  42 import javax.swing.JMenuItem;
  43 import javax.swing.JOptionPane;
  44 import javax.swing.JPanel;
  45 import javax.swing.JRadioButtonMenuItem;
  46 import javax.swing.JTabbedPane;
  47 import javax.swing.SwingUtilities;
  48 import javax.swing.event.ChangeEvent;
  49 import javax.swing.event.MenuEvent;
  50 import javax.swing.event.MenuListener;
  51
  52 public class GAlignFrame extends JInternalFrame
  53 {
  54   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  55
  56   protected JMenu fileMenu = new JMenu();
  57
  58   protected JMenuItem closeMenuItem = new JMenuItem();
  59
  60   protected JMenu editMenu = new JMenu();
  61
  62   protected JMenu viewMenu = new JMenu();
  63
  64   protected JMenu colourMenu = new JMenu();
  65
  66   protected JMenu calculateMenu = new JMenu();
  67
  68   protected JMenu webService = new JMenu();
  69
  70   protected JMenuItem webServiceNoServices;
  71
  72   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  73
  74   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  75
  76   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  77
  78   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  79
  80   protected JMenuItem remove2RightMenuItem = new JMenuItem();
  81
  82   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  83
  84   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  85
  86   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  87
  88   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  89
  90   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  91
  92   protected JMenuItem sortIDMenuItem = new JMenuItem();
  93
  94   protected JMenuItem sortLengthMenuItem = new JMenuItem();
  95
  96   protected JMenuItem sortGroupMenuItem = new JMenuItem();
  97
  98   protected JMenu sortByAnnotScore = new JMenu();
  99
 100   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
 101
 102   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
 103
 104   protected JMenuItem PCAMenuItem = new JMenuItem();
 105
 106   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
 107
 108   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
 109
 110   BorderLayout borderLayout1 = new BorderLayout();
 111
 112   public JLabel statusBar = new JLabel();
 113
 114   protected JMenuItem saveAs = new JMenuItem();
 115
 116   protected JMenu outputTextboxMenu = new JMenu();
 117
 118   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
 119
 120   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
 121
 122   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
 123
 124   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
 125
 126   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
 127
 128   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
 129
 130   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
 131
 132   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 133
 134   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
 135
 136   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
 137
 138   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 139
 140   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
 141
 142   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
 143
 144   // protected JRadioButtonMenuItem covariationColour = new
 145   // JRadioButtonMenuItem();
 146
 147   protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
 148
 149   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 150
 151   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
 152
 153   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 154
 155   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 156
 157   public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
 158
 159   JMenuItem htmlMenuItem = new JMenuItem();
 160
 161   JMenuItem overviewMenuItem = new JMenuItem();
 162
 163   protected JMenuItem undoMenuItem = new JMenuItem();
 164
 165   protected JMenuItem redoMenuItem = new JMenuItem();
 166
 167   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 168
 169   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 170
 171   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 172
 173   JMenuItem printMenuItem = new JMenuItem();
 174
 175   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 176
 177   JMenuItem findMenuItem = new JMenuItem();
 178
 179   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 180
 181   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 182
 183   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 184
 185   JMenuItem deleteGroups = new JMenuItem();
 186
 187   JMenuItem createGroup = new JMenuItem();
 188   JMenuItem unGroup = new JMenuItem();
 189
 190   JMenuItem delete = new JMenuItem();
 191
 192   JMenuItem copy = new JMenuItem();
 193
 194   JMenuItem cut = new JMenuItem();
 195
 196   JMenu pasteMenu = new JMenu();
 197
 198   JMenuItem pasteNew = new JMenuItem();
 199
 200   JMenuItem pasteThis = new JMenuItem();
 201
 202   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
 203
 204   JMenuItem createPNG = new JMenuItem();
 205
 206   protected JMenuItem font = new JMenuItem();
 207
 208   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 209
 210   JMenuItem epsFile = new JMenuItem();
 211
 212   JMenuItem LoadtreeMenuItem = new JMenuItem();
 213
 214   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 215
 216   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 217
 218   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 219
 220   protected JMenuItem modifyPID = new JMenuItem();
 221
 222   protected JMenuItem modifyConservation = new JMenuItem();
 223
 224   protected JMenu sortByTreeMenu = new JMenu();
 225
 226   protected JMenu sort = new JMenu();
 227
 228   protected JMenu calculateTree = new JMenu();
 229
 230   JMenu jMenu2 = new JMenu();
 231
 232   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 233
 234   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 235
 236   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 237
 238   protected ButtonGroup colours = new ButtonGroup();
 239
 240   JMenuItem vamsasStore = new JMenuItem();
 241
 242   protected JMenuItem showTranslation = new JMenuItem();
 243
 244   protected JMenuItem extractScores = new JMenuItem();
 245
 246   protected JMenuItem expandAlignment = new JMenuItem();
 247
 248   protected JMenu showProducts = new JMenu();
 249
 250   public JMenuItem openFeatureSettings = new JMenuItem();
 251
 252   JMenuItem fetchSequence = new JMenuItem();
 253
 254   JMenuItem annotationColour = new JMenuItem();
 255
 256   protected JMenuItem rnahelicesColour = new JMenuItem();
 257
 258   JMenuItem associatedData = new JMenuItem();
 259
 260   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 261
 262   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 263
 264   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 265
 266   JMenu addSequenceMenu = new JMenu();
 267
 268   JMenuItem addFromFile = new JMenuItem();
 269
 270   JMenuItem addFromText = new JMenuItem();
 271
 272   JMenuItem addFromURL = new JMenuItem();
 273
 274   JMenuItem exportAnnotations = new JMenuItem();
 275
 276   JMenuItem exportFeatures = new JMenuItem();
 277
 278   protected JPanel statusPanel = new JPanel();
 279
 280   GridLayout gridLayout1 = new GridLayout();
 281
 282   JMenu jMenu3 = new JMenu();
 283
 284   JMenuItem showAllSeqs = new JMenuItem();
 285
 286   JMenuItem showAllColumns = new JMenuItem();
 287
 288   JMenu hideMenu = new JMenu();
 289
 290   JMenuItem hideSelSequences = new JMenuItem();
 291
 292   JMenuItem hideSelColumns = new JMenuItem();
 293
 294   JMenuItem hideAllButSelection = new JMenuItem();
 295
 296   JMenuItem hideAllSelection = new JMenuItem();
 297
 298   JMenuItem showAllhidden = new JMenuItem();
 299
 300   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 301
 302   JMenuItem invertColSel = new JMenuItem();
 303
 304   protected JTabbedPane tabbedPane = new JTabbedPane();
 305
 306   JMenuItem save = new JMenuItem();
 307
 308   protected JMenuItem reload = new JMenuItem();
 309
 310   JMenuItem newView = new JMenuItem();
 311
 312   JMenuItem textColour = new JMenuItem();
 313
 314   JMenu formatMenu = new JMenu();
 315
 316   JMenu selectMenu = new JMenu();
 317
 318   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 319
 320   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 321
 322   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 323
 324   protected JMenuItem gatherViews = new JMenuItem();
 325
 326   protected JMenuItem expandViews = new JMenuItem();
 327
 328   JMenuItem pageSetup = new JMenuItem();
 329
 330   JMenuItem alignmentProperties = new JMenuItem();
 331
 332   JMenu tooltipSettingsMenu = new JMenu();
 333
 334   private JMenuItem justifyLeftMenuItem = new JMenuItem();
 335
 336   private JMenuItem justifyRightMenuItem = new JMenuItem();
 337
 338   JMenu autoAnnMenu = new JMenu();
 339
 340   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 341
 342   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 343
 344   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 345
 346   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 347
 348   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 349
 350   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 351
 352   private JMenuItem grpsFromSelection = new JMenuItem();
 353
 354   public GAlignFrame()
 355   {
 356     try
 357     {
 358       jbInit();
 359       setJMenuBar(alignFrameMenuBar);
 360
 361       // dynamically fill save as menu with available formats
 362       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 363       {
 364         JMenuItem item = new JMenuItem(
 365                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 366
 367         item.addActionListener(new java.awt.event.ActionListener()
 368         {
 369           public void actionPerformed(ActionEvent e)
 370           {
 371             outputText_actionPerformed(e);
 372           }
 373         });
 374
 375         outputTextboxMenu.add(item);
 376       }
 377     } catch (Exception e)
 378     {
 379     }
 380
 381     if (!new jalview.util.Platform().isAMac())
 382     {
 383       closeMenuItem.setMnemonic('C');
 384       outputTextboxMenu.setMnemonic('T');
 385       undoMenuItem.setMnemonic('Z');
 386       redoMenuItem.setMnemonic('0');
 387       copy.setMnemonic('C');
 388       cut.setMnemonic('U');
 389       pasteMenu.setMnemonic('P');
 390       reload.setMnemonic('R');
 391     }
 392
 393     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 394     {
 395       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 396               .getUserColourSchemes().keys();
 397
 398       while (userColours.hasMoreElements())
 399       {
 400         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 401                 userColours.nextElement().toString());
 402         radioItem.setName("USER_DEFINED");
 403         radioItem.addMouseListener(new MouseAdapter()
 404         {
 405           public void mousePressed(MouseEvent evt)
 406           {
 407             if (evt.isControlDown()
 408                     || SwingUtilities.isRightMouseButton(evt))
 409             {
 410               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 411
 412               int option = JOptionPane.showInternalConfirmDialog(
 413                       jalview.gui.Desktop.desktop,
 414                       MessageManager.getString("label.remove_from_default_list"),
 415                       MessageManager.getString("label.remove_user_defined_colour"),
 416                       JOptionPane.YES_NO_OPTION);
 417               if (option == JOptionPane.YES_OPTION)
 418               {
 419                 jalview.gui.UserDefinedColours
 420                         .removeColourFromDefaults(radioItem.getText());
 421                 colourMenu.remove(radioItem);
 422               }
 423               else
 424               {
 425                 radioItem.addActionListener(new ActionListener()
 426                 {
 427                   public void actionPerformed(ActionEvent evt)
 428                   {
 429                     userDefinedColour_actionPerformed(evt);
 430                   }
 431                 });
 432               }
 433             }
 434           }
 435         });
 436         radioItem.addActionListener(new ActionListener()
 437         {
 438           public void actionPerformed(ActionEvent evt)
 439           {
 440             userDefinedColour_actionPerformed(evt);
 441           }
 442         });
 443         colourMenu.insert(radioItem, 15);
 444         colours.add(radioItem);
 445       }
 446     }
 447     colours.add(noColourmenuItem);
 448     colours.add(clustalColour);
 449     colours.add(zappoColour);
 450     colours.add(taylorColour);
 451     colours.add(hydrophobicityColour);
 452     colours.add(helixColour);
 453     colours.add(strandColour);
 454     colours.add(turnColour);
 455     colours.add(buriedColour);
 456     colours.add(userDefinedColour);
 457     colours.add(PIDColour);
 458     colours.add(BLOSUM62Colour);
 459     colours.add(nucleotideColour);
 460     colours.add(purinePyrimidineColour);
 461     // colours.add(covariationColour);
 462     colours.add(tcoffeeColour);
 463
 464     setColourSelected(jalview.bin.Cache
 465             .getDefault("DEFAULT_COLOUR", "None"));
 466
 467   }
 468
 469   public void setColourSelected(String defaultColour)
 470   {
 471
 472     if (defaultColour != null)
 473     {
 474       int index = ColourSchemeProperty
 475               .getColourIndexFromName(defaultColour);
 476
 477       switch (index)
 478       {
 479       case ColourSchemeProperty.CLUSTAL:
 480         clustalColour.setSelected(true);
 481
 482         break;
 483
 484       case ColourSchemeProperty.BLOSUM:
 485         BLOSUM62Colour.setSelected(true);
 486
 487         break;
 488
 489       case ColourSchemeProperty.PID:
 490         PIDColour.setSelected(true);
 491
 492         break;
 493
 494       case ColourSchemeProperty.ZAPPO:
 495         zappoColour.setSelected(true);
 496
 497         break;
 498
 499       case ColourSchemeProperty.TAYLOR:
 500         taylorColour.setSelected(true);
 501         break;
 502
 503       case ColourSchemeProperty.HYDROPHOBIC:
 504         hydrophobicityColour.setSelected(true);
 505
 506         break;
 507
 508       case ColourSchemeProperty.HELIX:
 509         helixColour.setSelected(true);
 510
 511         break;
 512
 513       case ColourSchemeProperty.STRAND:
 514         strandColour.setSelected(true);
 515
 516         break;
 517
 518       case ColourSchemeProperty.TURN:
 519         turnColour.setSelected(true);
 520
 521         break;
 522
 523       case ColourSchemeProperty.BURIED:
 524         buriedColour.setSelected(true);
 525
 526         break;
 527
 528       case ColourSchemeProperty.NUCLEOTIDE:
 529         nucleotideColour.setSelected(true);
 530
 531         break;
 532
 533       case ColourSchemeProperty.TCOFFEE:
 534         tcoffeeColour.setSelected(true);
 535         break;
 536
 537       case ColourSchemeProperty.PURINEPYRIMIDINE:
 538         purinePyrimidineColour.setSelected(true);
 539
 540         break;
 541       /*
 542        * case ColourSchemeProperty.COVARIATION:
 543        * covariationColour.setSelected(true);
 544        *
 545        * break;
 546        */
 547       case ColourSchemeProperty.USER_DEFINED:
 548         userDefinedColour.setSelected(true);
 549
 550         break;
 551       case ColourSchemeProperty.NONE:
 552       default:
 553         noColourmenuItem.setSelected(true);
 554         break;
 555
 556       }
 557     }
 558
 559   }
 560
 561   private void jbInit() throws Exception
 562   {
 563     fileMenu.setText(MessageManager.getString("action.file"));
 564     saveAs.setText(MessageManager.getString("action.save_as") + "...");
 565     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 566             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
 567                     .getMenuShortcutKeyMask()
 568                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 569     saveAs.addActionListener(new ActionListener()
 570     {
 571       public void actionPerformed(ActionEvent e)
 572       {
 573         saveAs_actionPerformed(e);
 574       }
 575     });
 576     closeMenuItem.setText(MessageManager.getString("action.close"));
 577     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 578             java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
 579                     .getMenuShortcutKeyMask(), false));
 580     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 581     {
 582       public void actionPerformed(ActionEvent e)
 583       {
 584         closeMenuItem_actionPerformed(false);
 585       }
 586     });
 587     editMenu.setText(MessageManager.getString("action.edit"));
 588     viewMenu.setText(MessageManager.getString("action.view"));
 589     colourMenu.setText(MessageManager.getString("action.colour"));
 590     calculateMenu.setText(MessageManager.getString("action.calculate"));
 591     webService.setText(MessageManager.getString("action.web_service"));
 592     selectAllSequenceMenuItem.setText(MessageManager.getString("action.select_all"));
 593     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 594             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
 595                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 596     selectAllSequenceMenuItem
 597             .addActionListener(new java.awt.event.ActionListener()
 598             {
 599               public void actionPerformed(ActionEvent e)
 600               {
 601                 selectAllSequenceMenuItem_actionPerformed(e);
 602               }
 603             });
 604     deselectAllSequenceMenuItem.setText(MessageManager.getString("action.deselect_all"));
 605     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 606             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 607     deselectAllSequenceMenuItem
 608             .addActionListener(new java.awt.event.ActionListener()
 609             {
 610               public void actionPerformed(ActionEvent e)
 611               {
 612                 deselectAllSequenceMenuItem_actionPerformed(e);
 613               }
 614             });
 615     invertSequenceMenuItem.setText(MessageManager.getString("action.invert_sequence_selection"));
 616     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 617             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
 618                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 619     invertSequenceMenuItem
 620             .addActionListener(new java.awt.event.ActionListener()
 621             {
 622               public void actionPerformed(ActionEvent e)
 623               {
 624                 invertSequenceMenuItem_actionPerformed(e);
 625               }
 626             });
 627     grpsFromSelection.setText(MessageManager.getString("action.make_groups_selection"));
 628     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
 629     {
 630       public void actionPerformed(ActionEvent e)
 631       {
 632         makeGrpsFromSelection_actionPerformed(e);
 633       }
 634     });
 635     expandAlignment.setText(MessageManager.getString("action.view_flanking_regions"));
 636     expandAlignment.setToolTipText(MessageManager.getString("label.view_flanking_regions"));
 637     expandAlignment.addActionListener(new java.awt.event.ActionListener() {
 638       @Override
 639       public void actionPerformed(ActionEvent e)
 640       {
 641         expand_newalign(e);
 642       }
 643     });
 644     remove2LeftMenuItem.setText(MessageManager.getString("action.remove_left"));
 645     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 646             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
 647                     .getMenuShortcutKeyMask(), false));
 648     remove2LeftMenuItem
 649             .addActionListener(new java.awt.event.ActionListener()
 650             {
 651               public void actionPerformed(ActionEvent e)
 652               {
 653                 remove2LeftMenuItem_actionPerformed(e);
 654               }
 655             });
 656     remove2RightMenuItem.setText(MessageManager.getString("action.remove_right"));
 657     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 658             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
 659                     .getMenuShortcutKeyMask(), false));
 660     remove2RightMenuItem
 661             .addActionListener(new java.awt.event.ActionListener()
 662             {
 663               public void actionPerformed(ActionEvent e)
 664               {
 665                 remove2RightMenuItem_actionPerformed(e);
 666               }
 667             });
 668     removeGappedColumnMenuItem.setText(MessageManager.getString("action.remove_empty_columns"));
 669     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
 670             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 671                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 672     removeGappedColumnMenuItem
 673             .addActionListener(new java.awt.event.ActionListener()
 674             {
 675               public void actionPerformed(ActionEvent e)
 676               {
 677                 removeGappedColumnMenuItem_actionPerformed(e);
 678               }
 679             });
 680     removeAllGapsMenuItem.setText(MessageManager.getString("action.remove_all_gaps"));
 681     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
 682             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 683                     .getDefaultToolkit().getMenuShortcutKeyMask()
 684                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 685     removeAllGapsMenuItem
 686             .addActionListener(new java.awt.event.ActionListener()
 687             {
 688               public void actionPerformed(ActionEvent e)
 689               {
 690                 removeAllGapsMenuItem_actionPerformed(e);
 691               }
 692             });
 693     justifyLeftMenuItem.setText(MessageManager.getString("action.left_justify_alignment"));
 694     justifyLeftMenuItem
 695             .addActionListener(new java.awt.event.ActionListener()
 696             {
 697               public void actionPerformed(ActionEvent e)
 698               {
 699                 justifyLeftMenuItem_actionPerformed(e);
 700               }
 701             });
 702     justifyRightMenuItem.setText(MessageManager.getString("action.right_justify_alignment"));
 703     justifyRightMenuItem
 704             .addActionListener(new java.awt.event.ActionListener()
 705             {
 706               public void actionPerformed(ActionEvent e)
 707               {
 708                 justifyRightMenuItem_actionPerformed(e);
 709               }
 710             });
 711     viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
 712     viewBoxesMenuItem.setState(true);
 713     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 714     {
 715       public void actionPerformed(ActionEvent e)
 716       {
 717         viewBoxesMenuItem_actionPerformed(e);
 718       }
 719     });
 720     viewTextMenuItem.setText(MessageManager.getString("action.text"));
 721     viewTextMenuItem.setState(true);
 722     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 723     {
 724       public void actionPerformed(ActionEvent e)
 725       {
 726         viewTextMenuItem_actionPerformed(e);
 727       }
 728     });
 729     showNonconservedMenuItem.setText(MessageManager.getString("label.show_non_conversed"));
 730     showNonconservedMenuItem.setState(false);
 731     showNonconservedMenuItem
 732             .addActionListener(new java.awt.event.ActionListener()
 733             {
 734               public void actionPerformed(ActionEvent e)
 735               {
 736                 showUnconservedMenuItem_actionPerformed(e);
 737               }
 738             });
 739     sortPairwiseMenuItem.setText(MessageManager.getString("action.by_pairwise_id"));
 740     sortPairwiseMenuItem
 741             .addActionListener(new java.awt.event.ActionListener()
 742             {
 743               public void actionPerformed(ActionEvent e)
 744               {
 745                 sortPairwiseMenuItem_actionPerformed(e);
 746               }
 747             });
 748     sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
 749     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 750     {
 751       public void actionPerformed(ActionEvent e)
 752       {
 753         sortIDMenuItem_actionPerformed(e);
 754       }
 755     });
 756     sortLengthMenuItem.setText(MessageManager.getString("action.by_length"));
 757     sortLengthMenuItem
 758             .addActionListener(new java.awt.event.ActionListener()
 759             {
 760               public void actionPerformed(ActionEvent e)
 761               {
 762                 sortLengthMenuItem_actionPerformed(e);
 763               }
 764             });
 765     sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
 766     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 767     {
 768       public void actionPerformed(ActionEvent e)
 769       {
 770         sortGroupMenuItem_actionPerformed(e);
 771       }
 772     });
 773     removeRedundancyMenuItem.setText(MessageManager.getString("action.remove_redundancy"));
 774     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
 775             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
 776                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 777     removeRedundancyMenuItem
 778             .addActionListener(new java.awt.event.ActionListener()
 779             {
 780               public void actionPerformed(ActionEvent e)
 781               {
 782                 removeRedundancyMenuItem_actionPerformed(e);
 783               }
 784             });
 785     pairwiseAlignmentMenuItem.setText(MessageManager.getString("action.pairwise_alignment"));
 786     pairwiseAlignmentMenuItem
 787             .addActionListener(new java.awt.event.ActionListener()
 788             {
 789               public void actionPerformed(ActionEvent e)
 790               {
 791                 pairwiseAlignmentMenuItem_actionPerformed(e);
 792               }
 793             });
 794     PCAMenuItem.setText(MessageManager.getString("label.principal_component_analysis"));
 795     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 796     {
 797       public void actionPerformed(ActionEvent e)
 798       {
 799         PCAMenuItem_actionPerformed(e);
 800       }
 801     });
 802     averageDistanceTreeMenuItem
 803             .setText(MessageManager.getString("label.average_distance_identity"));
 804     averageDistanceTreeMenuItem
 805             .addActionListener(new java.awt.event.ActionListener()
 806             {
 807               public void actionPerformed(ActionEvent e)
 808               {
 809                 averageDistanceTreeMenuItem_actionPerformed(e);
 810               }
 811             });
 812     neighbourTreeMenuItem.setText(MessageManager.getString("label.neighbour_joining_identity"));
 813     neighbourTreeMenuItem
 814             .addActionListener(new java.awt.event.ActionListener()
 815             {
 816               public void actionPerformed(ActionEvent e)
 817               {
 818                 neighbourTreeMenuItem_actionPerformed(e);
 819               }
 820             });
 821     this.getContentPane().setLayout(borderLayout1);
 822     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 823     statusBar.setBackground(Color.white);
 824     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 825     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 826     statusBar.setText(MessageManager.getString("label.status_bar"));
 827     outputTextboxMenu.setText(MessageManager.getString("label.out_to_textbox"));
 828     clustalColour.setText(MessageManager.getString("label.clustalx"));
 829
 830     clustalColour.addActionListener(new java.awt.event.ActionListener()
 831     {
 832       public void actionPerformed(ActionEvent e)
 833       {
 834         clustalColour_actionPerformed(e);
 835       }
 836     });
 837     zappoColour.setText(MessageManager.getString("label.zappo"));
 838     zappoColour.addActionListener(new java.awt.event.ActionListener()
 839     {
 840       public void actionPerformed(ActionEvent e)
 841       {
 842         zappoColour_actionPerformed(e);
 843       }
 844     });
 845     taylorColour.setText(MessageManager.getString("label.taylor"));
 846     taylorColour.addActionListener(new java.awt.event.ActionListener()
 847     {
 848       public void actionPerformed(ActionEvent e)
 849       {
 850         taylorColour_actionPerformed(e);
 851       }
 852     });
 853     hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));
 854     hydrophobicityColour
 855             .addActionListener(new java.awt.event.ActionListener()
 856             {
 857               public void actionPerformed(ActionEvent e)
 858               {
 859                 hydrophobicityColour_actionPerformed(e);
 860               }
 861             });
 862     helixColour.setText(MessageManager.getString("label.helix_propensity"));
 863     helixColour.addActionListener(new java.awt.event.ActionListener()
 864     {
 865       public void actionPerformed(ActionEvent e)
 866       {
 867         helixColour_actionPerformed(e);
 868       }
 869     });
 870     strandColour.setText(MessageManager.getString("label.strand_propensity"));
 871     strandColour.addActionListener(new java.awt.event.ActionListener()
 872     {
 873       public void actionPerformed(ActionEvent e)
 874       {
 875         strandColour_actionPerformed(e);
 876       }
 877     });
 878     turnColour.setText(MessageManager.getString("label.turn_propensity"));
 879     turnColour.addActionListener(new java.awt.event.ActionListener()
 880     {
 881       public void actionPerformed(ActionEvent e)
 882       {
 883         turnColour_actionPerformed(e);
 884       }
 885     });
 886     buriedColour.setText(MessageManager.getString("label.buried_index"));
 887     buriedColour.addActionListener(new java.awt.event.ActionListener()
 888     {
 889       public void actionPerformed(ActionEvent e)
 890       {
 891         buriedColour_actionPerformed(e);
 892       }
 893     });
 894     userDefinedColour.setText(MessageManager.getString("action.user_defined"));
 895     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 896     {
 897       public void actionPerformed(ActionEvent e)
 898       {
 899         userDefinedColour_actionPerformed(e);
 900       }
 901     });
 902     PIDColour.setText(MessageManager.getString("label.percentage_identity"));
 903     PIDColour.addActionListener(new java.awt.event.ActionListener()
 904     {
 905       public void actionPerformed(ActionEvent e)
 906       {
 907         PIDColour_actionPerformed(e);
 908       }
 909     });
 910     BLOSUM62Colour.setText(MessageManager.getString("label.blosum62_score"));
 911     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 912     {
 913       public void actionPerformed(ActionEvent e)
 914       {
 915         BLOSUM62Colour_actionPerformed(e);
 916       }
 917     });
 918     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
 919     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
 920     {
 921       public void actionPerformed(ActionEvent e)
 922       {
 923         nucleotideColour_actionPerformed(e);
 924       }
 925     });
 926
 927     purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
 928     purinePyrimidineColour
 929             .addActionListener(new java.awt.event.ActionListener()
 930             {
 931               public void actionPerformed(ActionEvent e)
 932               {
 933                 purinePyrimidineColour_actionPerformed(e);
 934               }
 935             });
 936     /*
 937      * covariationColour.setText("Covariation");
 938      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
 939      * public void actionPerformed(ActionEvent e) {
 940      * covariationColour_actionPerformed(e); } });
 941      */
 942
 943     avDistanceTreeBlosumMenuItem.setText(MessageManager.getString("label.average_distance_bloslum62"));
 944     avDistanceTreeBlosumMenuItem
 945             .addActionListener(new java.awt.event.ActionListener()
 946             {
 947               public void actionPerformed(ActionEvent e)
 948               {
 949                 avTreeBlosumMenuItem_actionPerformed(e);
 950               }
 951             });
 952     njTreeBlosumMenuItem.setText(MessageManager.getString("label.neighbour_blosum62"));
 953     njTreeBlosumMenuItem
 954             .addActionListener(new java.awt.event.ActionListener()
 955             {
 956               public void actionPerformed(ActionEvent e)
 957               {
 958                 njTreeBlosumMenuItem_actionPerformed(e);
 959               }
 960             });
 961     annotationPanelMenuItem.setActionCommand("");
 962     annotationPanelMenuItem.setText(MessageManager.getString("label.show_annotations"));
 963     annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
 964             "SHOW_ANNOTATIONS", true));
 965     annotationPanelMenuItem
 966             .addActionListener(new java.awt.event.ActionListener()
 967             {
 968               public void actionPerformed(ActionEvent e)
 969               {
 970                 annotationPanelMenuItem_actionPerformed(e);
 971               }
 972             });
 973     colourTextMenuItem.setText(MessageManager.getString("label.colour_text"));
 974     colourTextMenuItem
 975             .addActionListener(new java.awt.event.ActionListener()
 976             {
 977               public void actionPerformed(ActionEvent e)
 978               {
 979                 colourTextMenuItem_actionPerformed(e);
 980               }
 981             });
 982     htmlMenuItem.setText(MessageManager.getString("label.html"));
 983     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
 984     {
 985       public void actionPerformed(ActionEvent e)
 986       {
 987         htmlMenuItem_actionPerformed(e);
 988       }
 989     });
 990     overviewMenuItem.setText(MessageManager.getString("label.overview_window"));
 991     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
 992     {
 993       public void actionPerformed(ActionEvent e)
 994       {
 995         overviewMenuItem_actionPerformed(e);
 996       }
 997     });
 998     undoMenuItem.setEnabled(false);
 999     undoMenuItem.setText(MessageManager.getString("action.undo"));
1000     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1001             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1002                     .getMenuShortcutKeyMask(), false));
1003     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1004     {
1005       public void actionPerformed(ActionEvent e)
1006       {
1007         undoMenuItem_actionPerformed(e);
1008       }
1009     });
1010     redoMenuItem.setEnabled(false);
1011     redoMenuItem.setText(MessageManager.getString("action.redo"));
1012     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1013             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1014                     .getMenuShortcutKeyMask(), false));
1015     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1016     {
1017       public void actionPerformed(ActionEvent e)
1018       {
1019         redoMenuItem_actionPerformed(e);
1020       }
1021     });
1022     conservationMenuItem.setText(MessageManager.getString("action.by_conservation"));
1023     conservationMenuItem
1024             .addActionListener(new java.awt.event.ActionListener()
1025             {
1026               public void actionPerformed(ActionEvent e)
1027               {
1028                 conservationMenuItem_actionPerformed(e);
1029               }
1030             });
1031     noColourmenuItem.setText(MessageManager.getString("label.none"));
1032     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1033     {
1034       public void actionPerformed(ActionEvent e)
1035       {
1036         noColourmenuItem_actionPerformed(e);
1037       }
1038     });
1039     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1040     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1041     {
1042       public void actionPerformed(ActionEvent e)
1043       {
1044         wrapMenuItem_actionPerformed(e);
1045       }
1046     });
1047     printMenuItem.setText(MessageManager.getString("action.print") + "...");
1048     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1049             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1050                     .getMenuShortcutKeyMask(), false));
1051     printMenuItem.addActionListener(new java.awt.event.ActionListener()
1052     {
1053       public void actionPerformed(ActionEvent e)
1054       {
1055         printMenuItem_actionPerformed(e);
1056       }
1057     });
1058     renderGapsMenuItem.setText(MessageManager.getString("action.show_gaps"));
1059     renderGapsMenuItem.setState(true);
1060     renderGapsMenuItem
1061             .addActionListener(new java.awt.event.ActionListener()
1062             {
1063               public void actionPerformed(ActionEvent e)
1064               {
1065                 renderGapsMenuItem_actionPerformed(e);
1066               }
1067             });
1068     findMenuItem.setText(MessageManager.getString("action.find"));
1069     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1070             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1071                     .getMenuShortcutKeyMask(), false));
1072     findMenuItem.addActionListener(new java.awt.event.ActionListener()
1073     {
1074       public void actionPerformed(ActionEvent e)
1075       {
1076         findMenuItem_actionPerformed(e);
1077       }
1078     });
1079     abovePIDThreshold.setText(MessageManager.getString("label.above_identity_threshold"));
1080     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1081     {
1082       public void actionPerformed(ActionEvent e)
1083       {
1084         abovePIDThreshold_actionPerformed(e);
1085       }
1086     });
1087     showSeqFeatures.setText(MessageManager.getString("label.show_sequence_features"));
1088     showSeqFeatures.addActionListener(new ActionListener()
1089     {
1090       public void actionPerformed(ActionEvent actionEvent)
1091       {
1092         showSeqFeatures_actionPerformed(actionEvent);
1093       }
1094     });
1095     /*
1096      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1097      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1098      * void actionPerformed(ActionEvent actionEvent) {
1099      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1100      */
1101     showDbRefsMenuitem.setText(MessageManager.getString("label.show_database_refs"));
1102     showDbRefsMenuitem.addActionListener(new ActionListener()
1103     {
1104
1105       public void actionPerformed(ActionEvent e)
1106       {
1107         showDbRefs_actionPerformed(e);
1108       }
1109
1110     });
1111     showNpFeatsMenuitem.setText(MessageManager.getString("label.show_non_positional_features"));
1112     showNpFeatsMenuitem.addActionListener(new ActionListener()
1113     {
1114
1115       public void actionPerformed(ActionEvent e)
1116       {
1117         showNpFeats_actionPerformed(e);
1118       }
1119
1120     });
1121     showGroupConservation.setText(MessageManager.getString("label.group_conservation"));
1122     showGroupConservation.addActionListener(new ActionListener()
1123     {
1124
1125       public void actionPerformed(ActionEvent e)
1126       {
1127         showGroupConservation_actionPerformed(e);
1128       }
1129
1130     });
1131
1132     showGroupConsensus.setText(MessageManager.getString("label.group_consensus"));
1133     showGroupConsensus.addActionListener(new ActionListener()
1134     {
1135
1136       public void actionPerformed(ActionEvent e)
1137       {
1138         showGroupConsensus_actionPerformed(e);
1139       }
1140
1141     });
1142     showConsensusHistogram.setText(MessageManager.getString("label.show_consensus_histogram"));
1143     showConsensusHistogram.addActionListener(new ActionListener()
1144     {
1145
1146       public void actionPerformed(ActionEvent e)
1147       {
1148         showConsensusHistogram_actionPerformed(e);
1149       }
1150
1151     });
1152     showSequenceLogo.setText(MessageManager.getString("label.show_consensus_logo"));
1153     showSequenceLogo.addActionListener(new ActionListener()
1154     {
1155
1156       public void actionPerformed(ActionEvent e)
1157       {
1158         showSequenceLogo_actionPerformed(e);
1159       }
1160
1161     });
1162     normaliseSequenceLogo.setText(MessageManager.getString("label.norm_consensus_logo"));
1163     normaliseSequenceLogo.addActionListener(new ActionListener()
1164     {
1165
1166       public void actionPerformed(ActionEvent e)
1167       {
1168         normaliseSequenceLogo_actionPerformed(e);
1169       }
1170
1171     });
1172     applyAutoAnnotationSettings.setText(MessageManager.getString("label.apply_all_groups"));
1173     applyAutoAnnotationSettings.setState(false);
1174     applyAutoAnnotationSettings.setVisible(true);
1175     applyAutoAnnotationSettings.addActionListener(new ActionListener()
1176     {
1177
1178       public void actionPerformed(ActionEvent e)
1179       {
1180         applyAutoAnnotationSettings_actionPerformed(e);
1181       }
1182
1183     });
1184
1185     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1186     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1187     {
1188       public void actionPerformed(ActionEvent e)
1189       {
1190         nucleotideColour_actionPerformed(e);
1191       }
1192     });
1193
1194     tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1195     tcoffeeColour.setEnabled(false);
1196     tcoffeeColour.addActionListener(new ActionListener()
1197     {
1198
1199       @Override
1200       public void actionPerformed(ActionEvent e)
1201       {
1202         tcoffeeColorScheme_actionPerformed(e);
1203       }
1204     });
1205
1206     deleteGroups.setText(MessageManager.getString("action.undefine_groups"));
1207     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1208             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1209                     .getMenuShortcutKeyMask(), false));
1210     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1211     {
1212       public void actionPerformed(ActionEvent e)
1213       {
1214         deleteGroups_actionPerformed(e);
1215       }
1216     });
1217     createGroup.setText(MessageManager.getString("action.create_groups"));
1218     createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1219             java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1220                     .getMenuShortcutKeyMask(), false));
1221     createGroup.addActionListener(new java.awt.event.ActionListener()
1222     {
1223       public void actionPerformed(ActionEvent e)
1224       {
1225         createGroup_actionPerformed(e);
1226       }
1227     });
1228     unGroup.setText(MessageManager.getString("action.remove_group"));
1229     unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1230             java.awt.event.KeyEvent.VK_G,Toolkit.getDefaultToolkit()
1231                     .getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));
1232     unGroup.addActionListener(new java.awt.event.ActionListener()
1233     {
1234       public void actionPerformed(ActionEvent e)
1235       {
1236         unGroup_actionPerformed(e);
1237       }
1238     });
1239     copy.setText(MessageManager.getString("action.copy"));
1240     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1241             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1242                     .getMenuShortcutKeyMask(), false));
1243
1244     copy.addActionListener(new java.awt.event.ActionListener()
1245     {
1246       public void actionPerformed(ActionEvent e)
1247       {
1248         copy_actionPerformed(e);
1249       }
1250     });
1251     cut.setText(MessageManager.getString("action.cut"));
1252     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1253             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1254                     .getMenuShortcutKeyMask(), false));
1255     cut.addActionListener(new java.awt.event.ActionListener()
1256     {
1257       public void actionPerformed(ActionEvent e)
1258       {
1259         cut_actionPerformed(e);
1260       }
1261     });
1262     delete.setText(MessageManager.getString("action.delete"));
1263     delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1264             java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1265     delete.addActionListener(new java.awt.event.ActionListener()
1266     {
1267       public void actionPerformed(ActionEvent e)
1268       {
1269         delete_actionPerformed(e);
1270       }
1271     });
1272     pasteMenu.setText(MessageManager.getString("action.paste"));
1273     pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1274     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1275             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1276                     .getMenuShortcutKeyMask()
1277                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1278     pasteNew.addActionListener(new java.awt.event.ActionListener()
1279     {
1280       public void actionPerformed(ActionEvent e)
1281       {
1282         pasteNew_actionPerformed(e);
1283       }
1284     });
1285     pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1286     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1287             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1288                     .getMenuShortcutKeyMask(), false));
1289     pasteThis.addActionListener(new java.awt.event.ActionListener()
1290     {
1291       public void actionPerformed(ActionEvent e)
1292       {
1293         pasteThis_actionPerformed(e);
1294       }
1295     });
1296     applyToAllGroups.setText(MessageManager.getString("label.apply_colour_to_all_groups"));
1297     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1298     {
1299       public void actionPerformed(ActionEvent e)
1300       {
1301         applyToAllGroups_actionPerformed(e);
1302       }
1303     });
1304     createPNG.addActionListener(new java.awt.event.ActionListener()
1305     {
1306       public void actionPerformed(ActionEvent e)
1307       {
1308         createPNG(null);
1309       }
1310     });
1311     createPNG.setActionCommand(MessageManager.getString("label.save_png_image"));
1312     createPNG.setText("PNG");
1313     font.setText(MessageManager.getString("action.font"));
1314     font.addActionListener(new java.awt.event.ActionListener()
1315     {
1316       public void actionPerformed(ActionEvent e)
1317       {
1318         font_actionPerformed(e);
1319       }
1320     });
1321
1322     seqLimits.setText(MessageManager.getString("label.show_sequence_limits"));
1323     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1324     seqLimits.addActionListener(new java.awt.event.ActionListener()
1325     {
1326       public void actionPerformed(ActionEvent e)
1327       {
1328         seqLimit_actionPerformed(e);
1329       }
1330     });
1331     epsFile.setText("EPS");
1332     epsFile.addActionListener(new java.awt.event.ActionListener()
1333     {
1334       public void actionPerformed(ActionEvent e)
1335       {
1336         createEPS(null);
1337       }
1338     });
1339     LoadtreeMenuItem.setActionCommand(MessageManager.getString("label.load_tree_for_sequence_set"));
1340     LoadtreeMenuItem.setText(MessageManager.getString("label.load_associated_tree"));
1341     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1342     {
1343       public void actionPerformed(ActionEvent e)
1344       {
1345         LoadtreeMenuItem_actionPerformed(e);
1346       }
1347     });
1348
1349     scaleAbove.setVisible(false);
1350     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1351     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1352     {
1353       public void actionPerformed(ActionEvent e)
1354       {
1355         scaleAbove_actionPerformed(e);
1356       }
1357     });
1358     scaleLeft.setVisible(false);
1359     scaleLeft.setSelected(true);
1360     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1361     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1362     {
1363       public void actionPerformed(ActionEvent e)
1364       {
1365         scaleLeft_actionPerformed(e);
1366       }
1367     });
1368     scaleRight.setVisible(false);
1369     scaleRight.setSelected(true);
1370     scaleRight.setText(MessageManager.getString("action.scale_right"));
1371     scaleRight.addActionListener(new java.awt.event.ActionListener()
1372     {
1373       public void actionPerformed(ActionEvent e)
1374       {
1375         scaleRight_actionPerformed(e);
1376       }
1377     });
1378     centreColumnLabelsMenuItem.setVisible(true);
1379     centreColumnLabelsMenuItem.setState(false);
1380     centreColumnLabelsMenuItem.setText(MessageManager.getString("label.centre_column_labels"));
1381     centreColumnLabelsMenuItem
1382             .addActionListener(new java.awt.event.ActionListener()
1383             {
1384               public void actionPerformed(ActionEvent e)
1385               {
1386                 centreColumnLabels_actionPerformed(e);
1387               }
1388             });
1389     followHighlightMenuItem.setVisible(true);
1390     followHighlightMenuItem.setState(true);
1391     followHighlightMenuItem.setText(MessageManager.getString("label.automatic_scrolling"));
1392     followHighlightMenuItem.addActionListener(new ActionListener()
1393     {
1394
1395       public void actionPerformed(ActionEvent e)
1396       {
1397         followHighlight_actionPerformed();
1398       }
1399
1400     });
1401
1402     modifyPID.setText(MessageManager.getString("label.modify_identity_thereshold"));
1403     modifyPID.addActionListener(new java.awt.event.ActionListener()
1404     {
1405       public void actionPerformed(ActionEvent e)
1406       {
1407         modifyPID_actionPerformed(e);
1408       }
1409     });
1410     modifyConservation.setText(MessageManager.getString("label.modify_conservation_thereshold"));
1411     modifyConservation
1412             .addActionListener(new java.awt.event.ActionListener()
1413             {
1414               public void actionPerformed(ActionEvent e)
1415               {
1416                 modifyConservation_actionPerformed(e);
1417               }
1418             });
1419     sortByTreeMenu.setText(MessageManager.getString("action.by_tree_order"));
1420     sort.setText(MessageManager.getString("action.sort"));
1421     sort.addMenuListener(new MenuListener()
1422     {
1423       public void menuSelected(MenuEvent e)
1424       {
1425         buildTreeMenu();
1426       }
1427
1428       public void menuDeselected(MenuEvent e)
1429       {
1430       }
1431
1432       public void menuCanceled(MenuEvent e)
1433       {
1434       }
1435     });
1436     sortByAnnotScore.setText(MessageManager.getString("label.sort_by_score"));
1437     sort.add(sortByAnnotScore);
1438     sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1439     {
1440
1441       public void menuCanceled(MenuEvent e)
1442       {
1443       }
1444
1445       public void menuDeselected(MenuEvent e)
1446       {
1447       }
1448
1449       public void menuSelected(MenuEvent e)
1450       {
1451         buildSortByAnnotationScoresMenu();
1452       }
1453     });
1454     sortByAnnotScore.setVisible(false);
1455
1456     calculateTree.setText(MessageManager.getString("action.calculate_tree"));
1457
1458     jMenu2.setText(MessageManager.getString("label.export_image"));
1459     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1460     padGapsMenuitem.setState(jalview.bin.Cache
1461             .getDefault("PAD_GAPS", false));
1462     padGapsMenuitem.addActionListener(new ActionListener()
1463     {
1464       public void actionPerformed(ActionEvent e)
1465       {
1466         padGapsMenuitem_actionPerformed(e);
1467       }
1468     });
1469     vamsasStore.setVisible(false);
1470     vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1471     vamsasStore.addActionListener(new ActionListener()
1472     {
1473       public void actionPerformed(ActionEvent e)
1474       {
1475         vamsasStore_actionPerformed(e);
1476       }
1477     });
1478     showTranslation.setText(MessageManager.getString("label.translate_cDNA"));
1479     showTranslation.addActionListener(new ActionListener()
1480     {
1481       public void actionPerformed(ActionEvent e)
1482       {
1483         showTranslation_actionPerformed(e);
1484       }
1485     });
1486     extractScores.setText(MessageManager.getString("label.extract_scores") + "...");
1487     extractScores.addActionListener(new ActionListener()
1488     {
1489       public void actionPerformed(ActionEvent e)
1490       {
1491         extractScores_actionPerformed(e);
1492       }
1493     });
1494     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1495     // score extraction
1496     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1497     /*
1498      * showProducts.addActionListener(new ActionListener() {
1499      *
1500      * public void actionPerformed(ActionEvent e) {
1501      * showProducts_actionPerformed(e); } });
1502      */
1503     openFeatureSettings.setText(MessageManager.getString("label.feature_settings"));
1504     openFeatureSettings.addActionListener(new ActionListener()
1505     {
1506       public void actionPerformed(ActionEvent e)
1507       {
1508         featureSettings_actionPerformed(e);
1509       }
1510     });
1511     fetchSequence.setText(MessageManager.getString("label.fetch_sequences"));
1512     fetchSequence.addActionListener(new ActionListener()
1513     {
1514       public void actionPerformed(ActionEvent e)
1515       {
1516         fetchSequence_actionPerformed(e);
1517       }
1518     });
1519
1520     annotationColour.setText(MessageManager.getString("action.by_annotation"));
1521     annotationColour.addActionListener(new ActionListener()
1522     {
1523       public void actionPerformed(ActionEvent e)
1524       {
1525         annotationColour_actionPerformed(e);
1526       }
1527     });
1528
1529     rnahelicesColour.setText(MessageManager.getString("action.by_rna_helixes"));
1530     rnahelicesColour.addActionListener(new ActionListener()
1531     {
1532       public void actionPerformed(ActionEvent e)
1533       {
1534         rnahelicesColour_actionPerformed(e);
1535       }
1536     });
1537
1538     associatedData.setText(MessageManager.getString("label.load_features_annotations"));
1539     associatedData.addActionListener(new ActionListener()
1540     {
1541       public void actionPerformed(ActionEvent e)
1542       {
1543         associatedData_actionPerformed(e);
1544       }
1545     });
1546     autoCalculate.setText(MessageManager.getString("label.autocalculate_consensus"));
1547     autoCalculate.setState(jalview.bin.Cache.getDefault(
1548             "AUTO_CALC_CONSENSUS", true));
1549     autoCalculate.addActionListener(new ActionListener()
1550     {
1551       public void actionPerformed(ActionEvent e)
1552       {
1553         autoCalculate_actionPerformed(e);
1554       }
1555     });
1556     sortByTree.setText(MessageManager.getString("label.sort_alignment_new_tree"));
1557     sortByTree
1558             .setToolTipText("<html>" + MessageManager.getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1559     sortByTree
1560             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1561     sortByTree.addActionListener(new ActionListener()
1562     {
1563       public void actionPerformed(ActionEvent e)
1564       {
1565         sortByTreeOption_actionPerformed(e);
1566       }
1567     });
1568
1569     listenToViewSelections.setText(MessageManager.getString("label.listen_for_selections"));
1570     listenToViewSelections
1571             .setToolTipText("<html>" + MessageManager.getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1572     listenToViewSelections.setState(false);
1573     listenToViewSelections.addActionListener(new ActionListener()
1574     {
1575       public void actionPerformed(ActionEvent e)
1576       {
1577         listenToViewSelections_actionPerformed(e);
1578       }
1579     });
1580
1581     addSequenceMenu.setText(MessageManager.getString("label.add_sequences"));
1582     addFromFile.setText(MessageManager.getString("label.from_file"));
1583     addFromFile.addActionListener(new ActionListener()
1584     {
1585       public void actionPerformed(ActionEvent e)
1586       {
1587         addFromFile_actionPerformed(e);
1588       }
1589     });
1590     addFromText.setText(MessageManager.getString("label.from_textbox"));
1591     addFromText.addActionListener(new ActionListener()
1592     {
1593       public void actionPerformed(ActionEvent e)
1594       {
1595         addFromText_actionPerformed(e);
1596       }
1597     });
1598     addFromURL.setText(MessageManager.getString("label.from_url"));
1599     addFromURL.addActionListener(new ActionListener()
1600     {
1601       public void actionPerformed(ActionEvent e)
1602       {
1603         addFromURL_actionPerformed(e);
1604       }
1605     });
1606     exportFeatures.setText(MessageManager.getString("label.export_features"));
1607     exportFeatures.addActionListener(new ActionListener()
1608     {
1609       public void actionPerformed(ActionEvent e)
1610       {
1611         exportFeatures_actionPerformed(e);
1612       }
1613     });
1614     exportAnnotations.setText(MessageManager.getString("label.export_annotations"));
1615     exportAnnotations.addActionListener(new ActionListener()
1616     {
1617       public void actionPerformed(ActionEvent e)
1618       {
1619         exportAnnotations_actionPerformed(e);
1620       }
1621     });
1622     statusPanel.setLayout(gridLayout1);
1623     jMenu3.setText(MessageManager.getString("action.show"));
1624     showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
1625     showAllSeqs.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
1626     showAllSeqs.addActionListener(new ActionListener()
1627     {
1628       public void actionPerformed(ActionEvent e)
1629       {
1630         showAllSeqs_actionPerformed(e);
1631       }
1632     });
1633     showAllColumns.setText(MessageManager.getString("label.all_columns"));
1634     showAllColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
1635     showAllColumns.addActionListener(new ActionListener()
1636     {
1637       public void actionPerformed(ActionEvent e)
1638       {
1639         showAllColumns_actionPerformed(e);
1640       }
1641     });
1642     hideMenu.setText(MessageManager.getString("action.hide"));
1643     hideSelSequences.setText(MessageManager.getString("label.selected_sequences"));
1644     hideSelSequences.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
1645     hideSelSequences.addActionListener(new ActionListener()
1646     {
1647       public void actionPerformed(ActionEvent e)
1648       {
1649         hideSelSequences_actionPerformed(e);
1650       }
1651     });
1652     hideSelColumns.setText(MessageManager.getString("label.selected_columns"));
1653     hideSelColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
1654     hideSelColumns.addActionListener(new ActionListener()
1655     {
1656       public void actionPerformed(ActionEvent e)
1657       {
1658         hideSelColumns_actionPerformed(e);
1659       }
1660     });
1661     hideAllSelection.setText(MessageManager.getString("label.selected_region"));
1662     hideAllSelection.addActionListener(new ActionListener()
1663     {
1664       public void actionPerformed(ActionEvent e)
1665       {
1666         hideAllSelection_actionPerformed(e);
1667       }
1668     });
1669     // TODO: should be hidden if no selection exists.
1670     hideAllButSelection.setText(MessageManager.getString("label.all_but_selected_region"));
1671     hideAllButSelection.addActionListener(new ActionListener()
1672     {
1673       public void actionPerformed(ActionEvent e)
1674       {
1675         hideAllButSelection_actionPerformed(e);
1676       }
1677     });
1678     showAllhidden.setText(MessageManager.getString("label.all_sequences_columns"));
1679     showAllhidden
1680             .setToolTipText(MessageManager.getString("label.toggles_visibility_hidden_selected_regions"));
1681     showAllhidden.addActionListener(new ActionListener()
1682     {
1683       public void actionPerformed(ActionEvent e)
1684       {
1685         showAllhidden_actionPerformed(e);
1686       }
1687     });
1688
1689     hiddenMarkers.setText(MessageManager.getString("action.show_hidden_markers"));
1690     hiddenMarkers.addActionListener(new ActionListener()
1691     {
1692       public void actionPerformed(ActionEvent e)
1693       {
1694         hiddenMarkers_actionPerformed(e);
1695       }
1696     });
1697     invertColSel.setText(MessageManager.getString("action.invert_column_selection"));
1698     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1699             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1700                     .getMenuShortcutKeyMask()
1701                     | java.awt.event.KeyEvent.ALT_MASK, false));
1702     invertColSel.addActionListener(new ActionListener()
1703     {
1704       public void actionPerformed(ActionEvent e)
1705       {
1706         invertColSel_actionPerformed(e);
1707       }
1708     });
1709     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1710     {
1711       public void stateChanged(ChangeEvent evt)
1712       {
1713         JTabbedPane pane = (JTabbedPane) evt.getSource();
1714         int sel = pane.getSelectedIndex();
1715         tabSelectionChanged(sel);
1716       }
1717     });
1718     tabbedPane.addMouseListener(new MouseAdapter()
1719     {
1720       public void mousePressed(MouseEvent e)
1721       {
1722         tabbedPane_mousePressed(e);
1723       }
1724     });
1725     tabbedPane.addFocusListener(new FocusAdapter()
1726     {
1727       public void focusGained(FocusEvent e)
1728       {
1729         tabbedPane_focusGained(e);
1730       }
1731     });
1732     save.setText(MessageManager.getString("action.save"));
1733     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1734             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1735                     .getMenuShortcutKeyMask(), false));
1736     save.addActionListener(new ActionListener()
1737     {
1738       public void actionPerformed(ActionEvent e)
1739       {
1740         save_actionPerformed(e);
1741       }
1742     });
1743     reload.setEnabled(false);
1744     reload.setText(MessageManager.getString("action.reload"));
1745     reload.addActionListener(new ActionListener()
1746     {
1747       public void actionPerformed(ActionEvent e)
1748       {
1749         reload_actionPerformed(e);
1750       }
1751     });
1752     newView.setText(MessageManager.getString("action.new_view"));
1753     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1754             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1755                     .getMenuShortcutKeyMask(), false));
1756     newView.addActionListener(new ActionListener()
1757     {
1758       public void actionPerformed(ActionEvent e)
1759       {
1760         newView_actionPerformed(e);
1761       }
1762     });
1763     tabbedPane.setToolTipText("<html><i>" + MessageManager.getString("label.rename_tab_eXpand_reGroup") + "</i></html>");
1764     textColour.setText(MessageManager.getString("label.colour_text") + "...");
1765     textColour.addActionListener(new ActionListener()
1766     {
1767       public void actionPerformed(ActionEvent e)
1768       {
1769         textColour_actionPerformed(e);
1770       }
1771     });
1772     formatMenu.setText(MessageManager.getString("action.format"));
1773     selectMenu.setText(MessageManager.getString("action.select"));
1774     idRightAlign.setText(MessageManager.getString("label.right_align_sequence_id"));
1775     idRightAlign.addActionListener(new ActionListener()
1776     {
1777       public void actionPerformed(ActionEvent e)
1778       {
1779         idRightAlign_actionPerformed(e);
1780       }
1781     });
1782     gatherViews.setEnabled(false);
1783     gatherViews.setText(MessageManager.getString("action.gather_views"));
1784     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1785             java.awt.event.KeyEvent.VK_G, 0, false));
1786     gatherViews.addActionListener(new ActionListener()
1787     {
1788       public void actionPerformed(ActionEvent e)
1789       {
1790         gatherViews_actionPerformed(e);
1791       }
1792     });
1793     expandViews.setEnabled(false);
1794     expandViews.setText(MessageManager.getString("action.expand_views"));
1795     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1796             java.awt.event.KeyEvent.VK_X, 0, false));
1797     expandViews.addActionListener(new ActionListener()
1798     {
1799       public void actionPerformed(ActionEvent e)
1800       {
1801         expandViews_actionPerformed(e);
1802       }
1803     });
1804     pageSetup.setText(MessageManager.getString("action.page_setup") + "...");
1805     pageSetup.addActionListener(new ActionListener()
1806     {
1807       public void actionPerformed(ActionEvent e)
1808       {
1809         pageSetup_actionPerformed(e);
1810       }
1811     });
1812     alignmentProperties.setText(MessageManager.getString("label.alignment_props") + "...");
1813     alignmentProperties.addActionListener(new ActionListener()
1814     {
1815       public void actionPerformed(ActionEvent actionEvent)
1816       {
1817         alignmentProperties();
1818       }
1819     });
1820     tooltipSettingsMenu.setText(MessageManager.getString("label.sequence_id_tooltip"));
1821     autoAnnMenu.setText(MessageManager.getString("label.autocalculated_annotation"));
1822     alignFrameMenuBar.add(fileMenu);
1823     alignFrameMenuBar.add(editMenu);
1824     alignFrameMenuBar.add(selectMenu);
1825     alignFrameMenuBar.add(viewMenu);
1826     alignFrameMenuBar.add(formatMenu);
1827     alignFrameMenuBar.add(colourMenu);
1828     alignFrameMenuBar.add(calculateMenu);
1829     alignFrameMenuBar.add(webService);
1830     fileMenu.add(fetchSequence);
1831     fileMenu.add(addSequenceMenu);
1832     fileMenu.add(reload);
1833     fileMenu.addSeparator();
1834     fileMenu.add(vamsasStore);
1835     fileMenu.add(save);
1836     fileMenu.add(saveAs);
1837     fileMenu.add(outputTextboxMenu);
1838     fileMenu.add(pageSetup);
1839     fileMenu.add(printMenuItem);
1840     fileMenu.addSeparator();
1841     fileMenu.add(jMenu2);
1842     fileMenu.add(exportFeatures);
1843     fileMenu.add(exportAnnotations);
1844     fileMenu.add(LoadtreeMenuItem);
1845     fileMenu.add(associatedData);
1846     fileMenu.addSeparator();
1847     fileMenu.add(closeMenuItem);
1848     editMenu.add(undoMenuItem);
1849     editMenu.add(redoMenuItem);
1850     editMenu.add(cut);
1851     editMenu.add(copy);
1852     editMenu.add(pasteMenu);
1853     editMenu.add(delete);
1854     editMenu.addSeparator();
1855     editMenu.add(remove2LeftMenuItem);
1856     editMenu.add(remove2RightMenuItem);
1857     editMenu.add(removeGappedColumnMenuItem);
1858     editMenu.add(removeAllGapsMenuItem);
1859     editMenu.add(removeRedundancyMenuItem);
1860     editMenu.addSeparator();
1861     // dont add these yet in the CVS build - they cannot be undone!
1862     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1863     // editMenu.add(justifyLeftMenuItem);
1864     // editMenu.add(justifyRightMenuItem);
1865     // editMenu.addSeparator();
1866     editMenu.add(padGapsMenuitem);
1867     viewMenu.add(newView);
1868     viewMenu.add(expandViews);
1869     viewMenu.add(gatherViews);
1870     viewMenu.addSeparator();
1871     viewMenu.add(jMenu3);
1872     viewMenu.add(hideMenu);
1873     viewMenu.addSeparator();
1874     viewMenu.add(followHighlightMenuItem);
1875     viewMenu.add(annotationPanelMenuItem);
1876     autoAnnMenu.add(applyAutoAnnotationSettings);
1877     autoAnnMenu.add(showConsensusHistogram);
1878     autoAnnMenu.add(showSequenceLogo);
1879     autoAnnMenu.add(normaliseSequenceLogo);
1880     autoAnnMenu.addSeparator();
1881     autoAnnMenu.add(showGroupConservation);
1882     autoAnnMenu.add(showGroupConsensus);
1883     viewMenu.add(autoAnnMenu);
1884     viewMenu.addSeparator();
1885     viewMenu.add(showSeqFeatures);
1886     // viewMenu.add(showSeqFeaturesHeight);
1887
1888     viewMenu.add(openFeatureSettings);
1889     tooltipSettingsMenu.add(showDbRefsMenuitem);
1890     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1891     viewMenu.add(tooltipSettingsMenu);
1892     viewMenu.addSeparator();
1893     viewMenu.add(alignmentProperties);
1894     viewMenu.addSeparator();
1895     viewMenu.add(overviewMenuItem);
1896     colourMenu.add(applyToAllGroups);
1897     colourMenu.add(textColour);
1898     colourMenu.addSeparator();
1899     colourMenu.add(noColourmenuItem);
1900     colourMenu.add(clustalColour);
1901     colourMenu.add(BLOSUM62Colour);
1902     colourMenu.add(PIDColour);
1903     colourMenu.add(zappoColour);
1904     colourMenu.add(taylorColour);
1905     colourMenu.add(hydrophobicityColour);
1906     colourMenu.add(helixColour);
1907     colourMenu.add(strandColour);
1908     colourMenu.add(turnColour);
1909     colourMenu.add(buriedColour);
1910     colourMenu.add(nucleotideColour);
1911     colourMenu.add(purinePyrimidineColour);
1912     // colourMenu.add(covariationColour);
1913     colourMenu.add(tcoffeeColour);
1914     colourMenu.add(userDefinedColour);
1915     colourMenu.addSeparator();
1916     colourMenu.add(conservationMenuItem);
1917     colourMenu.add(modifyConservation);
1918     colourMenu.add(abovePIDThreshold);
1919     colourMenu.add(modifyPID);
1920     colourMenu.add(annotationColour);
1921     colourMenu.add(rnahelicesColour);
1922     calculateMenu.add(sort);
1923     calculateMenu.add(calculateTree);
1924     calculateMenu.addSeparator();
1925     calculateMenu.add(pairwiseAlignmentMenuItem);
1926     calculateMenu.add(PCAMenuItem);
1927     calculateMenu.addSeparator();
1928     calculateMenu.add(showTranslation);
1929     calculateMenu.add(showProducts);
1930     calculateMenu.add(autoCalculate);
1931     calculateMenu.add(sortByTree);
1932     calculateMenu.addSeparator();
1933     calculateMenu.add(extractScores);
1934     webServiceNoServices = new JMenuItem(MessageManager.getString("label.no_services"));
1935     webService.add(webServiceNoServices);
1936     pasteMenu.add(pasteNew);
1937     pasteMenu.add(pasteThis);
1938     sort.add(sortIDMenuItem);
1939     sort.add(sortLengthMenuItem);
1940     sort.add(sortGroupMenuItem);
1941     sort.add(sortPairwiseMenuItem);
1942     sort.add(sortByTreeMenu);
1943     jMenu2.add(htmlMenuItem);
1944     jMenu2.add(epsFile);
1945     jMenu2.add(createPNG);
1946     addSequenceMenu.add(addFromFile);
1947     addSequenceMenu.add(addFromText);
1948     addSequenceMenu.add(addFromURL);
1949     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1950     statusPanel.add(statusBar, null);
1951     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1952     jMenu3.add(showAllColumns);
1953     jMenu3.add(showAllSeqs);
1954     jMenu3.add(showAllhidden);
1955     hideMenu.add(hideSelColumns);
1956     hideMenu.add(hideSelSequences);
1957     hideMenu.add(hideAllSelection);
1958     hideMenu.add(hideAllButSelection);
1959
1960     formatMenu.add(font);
1961     formatMenu.addSeparator();
1962     formatMenu.add(wrapMenuItem);
1963     formatMenu.add(scaleAbove);
1964     formatMenu.add(scaleLeft);
1965     formatMenu.add(scaleRight);
1966     formatMenu.add(seqLimits);
1967     formatMenu.add(idRightAlign);
1968     formatMenu.add(hiddenMarkers);
1969     formatMenu.add(viewBoxesMenuItem);
1970     formatMenu.add(viewTextMenuItem);
1971     formatMenu.add(colourTextMenuItem);
1972     formatMenu.add(renderGapsMenuItem);
1973     formatMenu.add(centreColumnLabelsMenuItem);
1974     formatMenu.add(showNonconservedMenuItem);
1975     selectMenu.add(findMenuItem);
1976     selectMenu.addSeparator();
1977     selectMenu.add(selectAllSequenceMenuItem);
1978     selectMenu.add(deselectAllSequenceMenuItem);
1979     selectMenu.add(invertSequenceMenuItem);
1980     selectMenu.add(invertColSel);
1981     selectMenu.add(createGroup);
1982     selectMenu.add(unGroup);
1983     selectMenu.add(grpsFromSelection);
1984     selectMenu.add(deleteGroups);
1985     calculateMenu.add(expandAlignment);
1986     // TODO - determine if the listenToViewSelections button is needed : see bug
1987     // JAL-574
1988     // selectMenu.addSeparator();
1989     // selectMenu.add(listenToViewSelections);
1990   }
1991
1992   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
1993   {
1994     // TODO Auto-generated method stub
1995
1996   }
1997
1998   protected void listenToViewSelections_actionPerformed(ActionEvent e)
1999   {
2000     // TODO Auto-generated method stub
2001
2002   }
2003
2004   protected void showAllhidden_actionPerformed(ActionEvent e)
2005   {
2006     // TODO Auto-generated method stub
2007
2008   }
2009
2010   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2011   {
2012     // TODO Auto-generated method stub
2013
2014   }
2015
2016   protected void hideAllSelection_actionPerformed(ActionEvent e)
2017   {
2018     // TODO Auto-generated method stub
2019
2020   }
2021
2022   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2023   {
2024     // TODO Auto-generated method stub
2025
2026   }
2027
2028   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2029   {
2030     // TODO Auto-generated method stub
2031
2032   }
2033
2034   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2035   {
2036     // TODO Auto-generated method stub
2037
2038   }
2039
2040   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2041   {
2042     // TODO Auto-generated method stub
2043
2044   }
2045
2046   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2047   {
2048     // TODO Auto-generated method stub
2049
2050   }
2051
2052   protected void showGroupConservation_actionPerformed(ActionEvent e)
2053   {
2054     // TODO Auto-generated method stub
2055
2056   }
2057
2058   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2059   {
2060     // TODO Auto-generated method stub
2061
2062   }
2063
2064   protected void showSeqFeaturesHeight_actionPerformed(
2065           ActionEvent actionEvent)
2066   {
2067     // TODO Auto-generated method stub
2068
2069   }
2070
2071   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2072   {
2073     // TODO Auto-generated method stub
2074
2075   }
2076
2077   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2078   {
2079     // TODO Auto-generated method stub
2080
2081   }
2082
2083   protected void followHighlight_actionPerformed()
2084   {
2085     // TODO Auto-generated method stub
2086
2087   }
2088
2089   protected void showNpFeats_actionPerformed(ActionEvent e)
2090   {
2091     // TODO Auto-generated method stub
2092
2093   }
2094
2095   protected void showDbRefs_actionPerformed(ActionEvent e)
2096   {
2097     // TODO Auto-generated method stub
2098
2099   }
2100
2101   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2102   {
2103   }
2104
2105   protected void showProducts_actionPerformed(ActionEvent e)
2106   {
2107   }
2108
2109   protected void buildSortByAnnotationScoresMenu()
2110   {
2111   }
2112
2113   protected void extractScores_actionPerformed(ActionEvent e)
2114   {
2115   }
2116
2117   protected void outputText_actionPerformed(ActionEvent e)
2118   {
2119   }
2120
2121   public void addFromFile_actionPerformed(ActionEvent e)
2122   {
2123
2124   }
2125
2126   public void addFromText_actionPerformed(ActionEvent e)
2127   {
2128
2129   }
2130
2131   public void addFromURL_actionPerformed(ActionEvent e)
2132   {
2133
2134   }
2135
2136   public void exportFeatures_actionPerformed(ActionEvent e)
2137   {
2138
2139   }
2140
2141   public void exportAnnotations_actionPerformed(ActionEvent e)
2142   {
2143
2144   }
2145
2146   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2147   {
2148   }
2149
2150   protected void closeMenuItem_actionPerformed(boolean b)
2151   {
2152   }
2153
2154   protected void redoMenuItem_actionPerformed(ActionEvent e)
2155   {
2156   }
2157
2158   protected void undoMenuItem_actionPerformed(ActionEvent e)
2159   {
2160   }
2161
2162   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2163   {
2164   }
2165
2166   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2167   {
2168   }
2169
2170   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2171   {
2172   }
2173
2174   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2175   {
2176   }
2177
2178   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2179   {
2180   }
2181
2182   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2183   {
2184   }
2185
2186   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2187   {
2188   }
2189
2190   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2191   {
2192   }
2193
2194   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2195   {
2196   }
2197
2198   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2199   {
2200   }
2201
2202   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2203   {
2204   }
2205
2206   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2207   {
2208   }
2209
2210   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2211   {
2212   }
2213
2214   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2215   {
2216   }
2217
2218   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2219   {
2220   }
2221
2222   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2223   {
2224   }
2225
2226   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2227   {
2228   }
2229
2230   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2231   {
2232   }
2233
2234   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2235   {
2236   }
2237
2238   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2239   {
2240   }
2241
2242   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2243   {
2244   }
2245
2246   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2247   {
2248   }
2249
2250   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2251   {
2252   }
2253
2254   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2255   {
2256   }
2257
2258   protected void clustalColour_actionPerformed(ActionEvent e)
2259   {
2260   }
2261
2262   protected void zappoColour_actionPerformed(ActionEvent e)
2263   {
2264   }
2265
2266   protected void taylorColour_actionPerformed(ActionEvent e)
2267   {
2268   }
2269
2270   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2271   {
2272   }
2273
2274   protected void helixColour_actionPerformed(ActionEvent e)
2275   {
2276   }
2277
2278   protected void strandColour_actionPerformed(ActionEvent e)
2279   {
2280   }
2281
2282   protected void turnColour_actionPerformed(ActionEvent e)
2283   {
2284   }
2285
2286   protected void buriedColour_actionPerformed(ActionEvent e)
2287   {
2288   }
2289
2290   protected void userDefinedColour_actionPerformed(ActionEvent e)
2291   {
2292   }
2293
2294   protected void PIDColour_actionPerformed(ActionEvent e)
2295   {
2296   }
2297
2298   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2299   {
2300   }
2301
2302   protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2303   {
2304   }
2305
2306   /*
2307    * protected void covariationColour_actionPerformed(ActionEvent e) { }
2308    */
2309
2310   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2311   {
2312   }
2313
2314   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2315   {
2316   }
2317
2318   protected void printMenuItem_actionPerformed(ActionEvent e)
2319   {
2320   }
2321
2322   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2323   {
2324   }
2325
2326   protected void findMenuItem_actionPerformed(ActionEvent e)
2327   {
2328   }
2329
2330   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2331   {
2332   }
2333
2334   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2335   {
2336   }
2337
2338   protected void nucleotideColour_actionPerformed(ActionEvent e)
2339   {
2340   }
2341
2342   protected void deleteGroups_actionPerformed(ActionEvent e)
2343   {
2344   }
2345
2346   protected void createGroup_actionPerformed(ActionEvent e)
2347   {
2348   }
2349
2350   protected void unGroup_actionPerformed(ActionEvent e)
2351   {
2352   }
2353
2354   protected void copy_actionPerformed(ActionEvent e)
2355   {
2356   }
2357
2358   protected void cut_actionPerformed(ActionEvent e)
2359   {
2360   }
2361
2362   protected void delete_actionPerformed(ActionEvent e)
2363   {
2364   }
2365
2366   protected void pasteNew_actionPerformed(ActionEvent e)
2367   {
2368   }
2369
2370   protected void pasteThis_actionPerformed(ActionEvent e)
2371   {
2372   }
2373
2374   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2375   {
2376   }
2377
2378   public void createPNG(java.io.File f)
2379   {
2380   }
2381
2382   protected void font_actionPerformed(ActionEvent e)
2383   {
2384   }
2385
2386   protected void seqLimit_actionPerformed(ActionEvent e)
2387   {
2388   }
2389
2390   public void seqDBRef_actionPerformed(ActionEvent e)
2391   {
2392
2393   }
2394
2395   public void createEPS(java.io.File f)
2396   {
2397   }
2398
2399   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2400   {
2401
2402   }
2403
2404   /**
2405    * Template method to handle the 'load T-Coffee scores' menu event.
2406    * <p>
2407    * Subclasses override this method to provide a custom action.
2408    *
2409    * @param event
2410    *          The raised event
2411    */
2412   protected void loadScores_actionPerformed(ActionEvent event)
2413   {
2414
2415   }
2416
2417   /**
2418    * Template method to handle the 'Color T-Coffee scores' menu event.
2419    * <p>
2420    * Subclasses override this method to provide a custom action.
2421    *
2422    * @param event
2423    *          The raised event
2424    */
2425   protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2426   {
2427
2428   }
2429
2430   protected void jpred_actionPerformed(ActionEvent e)
2431   {
2432   }
2433
2434   protected void scaleAbove_actionPerformed(ActionEvent e)
2435   {
2436   }
2437
2438   protected void scaleLeft_actionPerformed(ActionEvent e)
2439   {
2440   }
2441
2442   protected void scaleRight_actionPerformed(ActionEvent e)
2443   {
2444   }
2445
2446   protected void modifyPID_actionPerformed(ActionEvent e)
2447   {
2448   }
2449
2450   protected void modifyConservation_actionPerformed(ActionEvent e)
2451   {
2452   }
2453
2454   protected void saveAs_actionPerformed(ActionEvent e)
2455   {
2456   }
2457
2458   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2459   {
2460   }
2461
2462   public void vamsasStore_actionPerformed(ActionEvent e)
2463   {
2464
2465   }
2466
2467   public void vamsasLoad_actionPerformed(ActionEvent e)
2468   {
2469
2470   }
2471
2472   public void showTranslation_actionPerformed(ActionEvent e)
2473   {
2474
2475   }
2476
2477   public void featureSettings_actionPerformed(ActionEvent e)
2478   {
2479
2480   }
2481
2482   public void fetchSequence_actionPerformed(ActionEvent e)
2483   {
2484
2485   }
2486
2487   public void smoothFont_actionPerformed(ActionEvent e)
2488   {
2489
2490   }
2491
2492   public void annotationColour_actionPerformed(ActionEvent e)
2493   {
2494
2495   }
2496
2497   public void rnahelicesColour_actionPerformed(ActionEvent e)
2498   {
2499
2500   }
2501
2502   public void associatedData_actionPerformed(ActionEvent e)
2503   {
2504
2505   }
2506
2507   public void autoCalculate_actionPerformed(ActionEvent e)
2508   {
2509
2510   }
2511
2512   public void sortByTreeOption_actionPerformed(ActionEvent e)
2513   {
2514
2515   }
2516
2517   public void showAllSeqs_actionPerformed(ActionEvent e)
2518   {
2519
2520   }
2521
2522   public void showAllColumns_actionPerformed(ActionEvent e)
2523   {
2524
2525   }
2526
2527   public void hideSelSequences_actionPerformed(ActionEvent e)
2528   {
2529
2530   }
2531
2532   public void hideSelColumns_actionPerformed(ActionEvent e)
2533   {
2534
2535   }
2536
2537   public void hiddenMarkers_actionPerformed(ActionEvent e)
2538   {
2539
2540   }
2541
2542   public void findPdbId_actionPerformed(ActionEvent e)
2543   {
2544
2545   }
2546
2547   public void enterPdbId_actionPerformed(ActionEvent e)
2548   {
2549
2550   }
2551
2552   public void pdbFile_actionPerformed(ActionEvent e)
2553   {
2554
2555   }
2556
2557   public void invertColSel_actionPerformed(ActionEvent e)
2558   {
2559
2560   }
2561
2562   public void tabSelectionChanged(int sel)
2563   {
2564
2565   }
2566
2567   public void tabbedPane_mousePressed(MouseEvent e)
2568   {
2569
2570   }
2571
2572   public void tabbedPane_focusGained(FocusEvent e)
2573   {
2574     requestFocus();
2575   }
2576
2577   public void save_actionPerformed(ActionEvent e)
2578   {
2579
2580   }
2581
2582   public void reload_actionPerformed(ActionEvent e)
2583   {
2584
2585   }
2586
2587   public void newView_actionPerformed(ActionEvent e)
2588   {
2589
2590   }
2591
2592   public void textColour_actionPerformed(ActionEvent e)
2593   {
2594
2595   }
2596
2597   public void idRightAlign_actionPerformed(ActionEvent e)
2598   {
2599
2600   }
2601
2602   public void expandViews_actionPerformed(ActionEvent e)
2603   {
2604
2605   }
2606
2607   public void gatherViews_actionPerformed(ActionEvent e)
2608   {
2609
2610   }
2611
2612   public void buildTreeMenu()
2613   {
2614
2615   }
2616
2617   public void pageSetup_actionPerformed(ActionEvent e)
2618   {
2619
2620   }
2621
2622   public void alignmentProperties()
2623   {
2624
2625   }
2626
2627   protected void expand_newalign(ActionEvent e)
2628   {
2629     // TODO Auto-generated method stub
2630
2631   }
2632 }