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