src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
   3  * Copyright (C) 2014 The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  * The Jalview Authors are detailed in the 'AUTHORS' file.
  18  */
  19 package jalview.jbgui;
  20
  21 import jalview.schemes.ColourSchemeProperty;
  22 import jalview.util.MessageManager;
  23
  24 import java.awt.BorderLayout;
  25 import java.awt.Color;
  26 import java.awt.GridLayout;
  27 import java.awt.Toolkit;
  28 import java.awt.event.ActionEvent;
  29 import java.awt.event.ActionListener;
  30 import java.awt.event.FocusAdapter;
  31 import java.awt.event.FocusEvent;
  32 import java.awt.event.MouseAdapter;
  33 import java.awt.event.MouseEvent;
  34
  35 import javax.swing.BorderFactory;
  36 import javax.swing.ButtonGroup;
  37 import javax.swing.JCheckBoxMenuItem;
  38 import javax.swing.JInternalFrame;
  39 import javax.swing.JLabel;
  40 import javax.swing.JMenu;
  41 import javax.swing.JMenuBar;
  42 import javax.swing.JMenuItem;
  43 import javax.swing.JOptionPane;
  44 import javax.swing.JPanel;
  45 import javax.swing.JRadioButtonMenuItem;
  46 import javax.swing.JTabbedPane;
  47 import javax.swing.SwingUtilities;
  48 import javax.swing.event.ChangeEvent;
  49 import javax.swing.event.MenuEvent;
  50 import javax.swing.event.MenuListener;
  51
  52 public class GAlignFrame extends JInternalFrame
  53 {
  54   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  55
  56   protected JMenu fileMenu = new JMenu();
  57
  58   protected JMenuItem closeMenuItem = new JMenuItem();
  59
  60   protected JMenu editMenu = new JMenu();
  61
  62   protected JMenu viewMenu = new JMenu();
  63
  64   protected JMenu colourMenu = new JMenu();
  65
  66   protected JMenu calculateMenu = new JMenu();
  67
  68   protected JMenu webService = new JMenu();
  69
  70   protected JMenuItem webServiceNoServices;
  71
  72   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  73
  74   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  75
  76   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  77
  78   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  79
  80   protected JMenuItem remove2RightMenuItem = new JMenuItem();
  81
  82   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  83
  84   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  85
  86   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  87
  88   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  89
  90   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  91
  92   protected JMenuItem sortIDMenuItem = new JMenuItem();
  93
  94   protected JMenuItem sortLengthMenuItem = new JMenuItem();
  95
  96   protected JMenuItem sortGroupMenuItem = new JMenuItem();
  97
  98   protected JMenu sortByAnnotScore = new JMenu();
  99
 100   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
 101
 102   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
 103
 104   protected JMenuItem PCAMenuItem = new JMenuItem();
 105
 106   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
 107
 108   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
 109
 110   BorderLayout borderLayout1 = new BorderLayout();
 111
 112   public JLabel statusBar = new JLabel();
 113
 114   protected JMenuItem saveAs = new JMenuItem();
 115
 116   protected JMenu outputTextboxMenu = new JMenu();
 117
 118   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
 119
 120   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
 121
 122   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
 123
 124   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
 125
 126   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
 127
 128   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
 129
 130   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
 131
 132   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 133
 134   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
 135
 136   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
 137
 138   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 139
 140   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
 141
 142   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
 143
 144   // protected JRadioButtonMenuItem covariationColour = new
 145   // JRadioButtonMenuItem();
 146
 147   protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
 148
 149   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 150
 151   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
 152
 153   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 154
 155   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 156
 157   public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
 158
 159   JMenuItem htmlMenuItem = new JMenuItem();
 160
 161   JMenuItem overviewMenuItem = new JMenuItem();
 162
 163   protected JMenuItem undoMenuItem = new JMenuItem();
 164
 165   protected JMenuItem redoMenuItem = new JMenuItem();
 166
 167   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 168
 169   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 170
 171   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 172
 173   JMenuItem printMenuItem = new JMenuItem();
 174
 175   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 176
 177   JMenuItem findMenuItem = new JMenuItem();
 178
 179   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 180
 181   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 182
 183   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 184
 185   JMenuItem deleteGroups = new JMenuItem();
 186
 187   JMenuItem createGroup = new JMenuItem();
 188   JMenuItem unGroup = new JMenuItem();
 189
 190   JMenuItem delete = new JMenuItem();
 191
 192   JMenuItem copy = new JMenuItem();
 193
 194   JMenuItem cut = new JMenuItem();
 195
 196   JMenu pasteMenu = new JMenu();
 197
 198   JMenuItem pasteNew = new JMenuItem();
 199
 200   JMenuItem pasteThis = new JMenuItem();
 201
 202   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
 203
 204   JMenuItem createPNG = new JMenuItem();
 205
 206   protected JMenuItem font = new JMenuItem();
 207
 208   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 209
 210   JMenuItem epsFile = new JMenuItem();
 211
 212   JMenuItem LoadtreeMenuItem = new JMenuItem();
 213
 214   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 215
 216   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 217
 218   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 219
 220   protected JMenuItem modifyPID = new JMenuItem();
 221
 222   protected JMenuItem modifyConservation = new JMenuItem();
 223
 224   protected JMenu sortByTreeMenu = new JMenu();
 225
 226   protected JMenu sort = new JMenu();
 227
 228   protected JMenu calculateTree = new JMenu();
 229
 230   JMenu jMenu2 = new JMenu();
 231
 232   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 233
 234   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 235
 236   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 237
 238   protected ButtonGroup colours = new ButtonGroup();
 239
 240   JMenuItem vamsasStore = new JMenuItem();
 241
 242   protected JMenuItem showTranslation = new JMenuItem();
 243
 244   protected JMenuItem extractScores = new JMenuItem();
 245
 246   protected JMenuItem expandAlignment = new JMenuItem();
 247
 248   protected JMenu showProducts = new JMenu();
 249
 250   public JMenuItem openFeatureSettings = new JMenuItem();
 251
 252   JMenuItem fetchSequence = new JMenuItem();
 253
 254   JMenuItem annotationColour = new JMenuItem();
 255
 256   protected JMenuItem rnahelicesColour = new JMenuItem();
 257
 258   JMenuItem associatedData = new JMenuItem();
 259
 260   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 261
 262   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 263
 264   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 265
 266   JMenu addSequenceMenu = new JMenu();
 267
 268   JMenuItem addFromFile = new JMenuItem();
 269
 270   JMenuItem addFromText = new JMenuItem();
 271
 272   JMenuItem addFromURL = new JMenuItem();
 273
 274   JMenuItem exportAnnotations = new JMenuItem();
 275
 276   JMenuItem exportFeatures = new JMenuItem();
 277
 278   protected JPanel statusPanel = new JPanel();
 279
 280   GridLayout gridLayout1 = new GridLayout();
 281
 282   JMenu jMenu3 = new JMenu();
 283
 284   JMenuItem showAllSeqs = new JMenuItem();
 285
 286   JMenuItem showAllColumns = new JMenuItem();
 287
 288   JMenu hideMenu = new JMenu();
 289
 290   JMenuItem hideSelSequences = new JMenuItem();
 291
 292   JMenuItem hideSelColumns = new JMenuItem();
 293
 294   JMenuItem hideAllButSelection = new JMenuItem();
 295
 296   JMenuItem hideAllSelection = new JMenuItem();
 297
 298   JMenuItem showAllhidden = new JMenuItem();
 299
 300   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 301
 302   JMenuItem invertColSel = new JMenuItem();
 303
 304   protected JTabbedPane tabbedPane = new JTabbedPane();
 305
 306   JMenuItem save = new JMenuItem();
 307
 308   protected JMenuItem reload = new JMenuItem();
 309
 310   JMenuItem newView = new JMenuItem();
 311
 312   JMenuItem textColour = new JMenuItem();
 313
 314   JMenu formatMenu = new JMenu();
 315
 316   JMenu selectMenu = new JMenu();
 317
 318   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 319
 320   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 321
 322   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 323
 324   protected JMenuItem gatherViews = new JMenuItem();
 325
 326   protected JMenuItem expandViews = new JMenuItem();
 327
 328   JMenuItem pageSetup = new JMenuItem();
 329
 330   JMenuItem alignmentProperties = new JMenuItem();
 331
 332   JMenu tooltipSettingsMenu = new JMenu();
 333
 334   private JMenuItem justifyLeftMenuItem = new JMenuItem();
 335
 336   private JMenuItem justifyRightMenuItem = new JMenuItem();
 337
 338   JMenu autoAnnMenu = new JMenu();
 339
 340   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 341
 342   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 343
 344   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 345
 346   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 347
 348   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 349
 350   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 351
 352   private JMenuItem grpsFromSelection = new JMenuItem();
 353
 354   public GAlignFrame()
 355   {
 356     try
 357     {
 358       jbInit();
 359       setJMenuBar(alignFrameMenuBar);
 360
 361       // dynamically fill save as menu with available formats
 362       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 363       {
 364         JMenuItem item = new JMenuItem(
 365                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 366
 367         item.addActionListener(new java.awt.event.ActionListener()
 368         {
 369           public void actionPerformed(ActionEvent e)
 370           {
 371             outputText_actionPerformed(e);
 372           }
 373         });
 374
 375         outputTextboxMenu.add(item);
 376       }
 377     } catch (Exception e)
 378     {
 379     }
 380
 381     if (!new jalview.util.Platform().isAMac())
 382     {
 383       closeMenuItem.setMnemonic('C');
 384       outputTextboxMenu.setMnemonic('T');
 385       undoMenuItem.setMnemonic('Z');
 386       redoMenuItem.setMnemonic('0');
 387       copy.setMnemonic('C');
 388       cut.setMnemonic('U');
 389       pasteMenu.setMnemonic('P');
 390       reload.setMnemonic('R');
 391     }
 392
 393     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 394     {
 395       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 396               .getUserColourSchemes().keys();
 397
 398       while (userColours.hasMoreElements())
 399       {
 400         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 401                 userColours.nextElement().toString());
 402         radioItem.setName("USER_DEFINED");
 403         radioItem.addMouseListener(new MouseAdapter()
 404         {
 405           public void mousePressed(MouseEvent evt)
 406           {
 407             if (evt.isControlDown()
 408                     || SwingUtilities.isRightMouseButton(evt))
 409             {
 410               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 411
 412               int option = JOptionPane.showInternalConfirmDialog(
 413                       jalview.gui.Desktop.desktop,
 414                       MessageManager.getString("label.remove_from_default_list"),
 415                       MessageManager.getString("label.remove_user_defined_colour"),
 416                       JOptionPane.YES_NO_OPTION);
 417               if (option == JOptionPane.YES_OPTION)
 418               {
 419                 jalview.gui.UserDefinedColours
 420                         .removeColourFromDefaults(radioItem.getText());
 421                 colourMenu.remove(radioItem);
 422               }
 423               else
 424               {
 425                 radioItem.addActionListener(new ActionListener()
 426                 {
 427                   public void actionPerformed(ActionEvent evt)
 428                   {
 429                     userDefinedColour_actionPerformed(evt);
 430                   }
 431                 });
 432               }
 433             }
 434           }
 435         });
 436         radioItem.addActionListener(new ActionListener()
 437         {
 438           public void actionPerformed(ActionEvent evt)
 439           {
 440             userDefinedColour_actionPerformed(evt);
 441           }
 442         });
 443         colourMenu.insert(radioItem, 15);
 444         colours.add(radioItem);
 445       }
 446     }
 447     colours.add(noColourmenuItem);
 448     colours.add(clustalColour);
 449     colours.add(zappoColour);
 450     colours.add(taylorColour);
 451     colours.add(hydrophobicityColour);
 452     colours.add(helixColour);
 453     colours.add(strandColour);
 454     colours.add(turnColour);
 455     colours.add(buriedColour);
 456     colours.add(userDefinedColour);
 457     colours.add(PIDColour);
 458     colours.add(BLOSUM62Colour);
 459     colours.add(nucleotideColour);
 460     colours.add(purinePyrimidineColour);
 461     // colours.add(covariationColour);
 462     colours.add(tcoffeeColour);
 463
 464     setColourSelected(jalview.bin.Cache
 465             .getDefault("DEFAULT_COLOUR", "None"));
 466
 467   }
 468
 469   public void setColourSelected(String defaultColour)
 470   {
 471
 472     if (defaultColour != null)
 473     {
 474       int index = ColourSchemeProperty
 475               .getColourIndexFromName(defaultColour);
 476
 477       switch (index)
 478       {
 479       case ColourSchemeProperty.CLUSTAL:
 480         clustalColour.setSelected(true);
 481
 482         break;
 483
 484       case ColourSchemeProperty.BLOSUM:
 485         BLOSUM62Colour.setSelected(true);
 486
 487         break;
 488
 489       case ColourSchemeProperty.PID:
 490         PIDColour.setSelected(true);
 491
 492         break;
 493
 494       case ColourSchemeProperty.ZAPPO:
 495         zappoColour.setSelected(true);
 496
 497         break;
 498
 499       case ColourSchemeProperty.TAYLOR:
 500         taylorColour.setSelected(true);
 501         break;
 502
 503       case ColourSchemeProperty.HYDROPHOBIC:
 504         hydrophobicityColour.setSelected(true);
 505
 506         break;
 507
 508       case ColourSchemeProperty.HELIX:
 509         helixColour.setSelected(true);
 510
 511         break;
 512
 513       case ColourSchemeProperty.STRAND:
 514         strandColour.setSelected(true);
 515
 516         break;
 517
 518       case ColourSchemeProperty.TURN:
 519         turnColour.setSelected(true);
 520
 521         break;
 522
 523       case ColourSchemeProperty.BURIED:
 524         buriedColour.setSelected(true);
 525
 526         break;
 527
 528       case ColourSchemeProperty.NUCLEOTIDE:
 529         nucleotideColour.setSelected(true);
 530
 531         break;
 532
 533       case ColourSchemeProperty.TCOFFEE:
 534         tcoffeeColour.setSelected(true);
 535         break;
 536
 537       case ColourSchemeProperty.PURINEPYRIMIDINE:
 538         purinePyrimidineColour.setSelected(true);
 539
 540         break;
 541       /*
 542        * case ColourSchemeProperty.COVARIATION:
 543        * covariationColour.setSelected(true);
 544        *
 545        * break;
 546        */
 547       case ColourSchemeProperty.USER_DEFINED:
 548         userDefinedColour.setSelected(true);
 549
 550         break;
 551       case ColourSchemeProperty.NONE:
 552       default:
 553         noColourmenuItem.setSelected(true);
 554         break;
 555
 556       }
 557     }
 558
 559   }
 560
 561   private void jbInit() throws Exception
 562   {
 563     fileMenu.setText(MessageManager.getString("action.file"));
 564     saveAs.setText(MessageManager.getString("action.save_as") + "...");
 565     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 566             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
 567                     .getMenuShortcutKeyMask()
 568                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 569     saveAs.addActionListener(new ActionListener()
 570     {
 571       public void actionPerformed(ActionEvent e)
 572       {
 573         saveAs_actionPerformed(e);
 574       }
 575     });
 576     closeMenuItem.setText(MessageManager.getString("action.close"));
 577     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 578             java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
 579                     .getMenuShortcutKeyMask(), false));
 580     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 581     {
 582       public void actionPerformed(ActionEvent e)
 583       {
 584         closeMenuItem_actionPerformed(false);
 585       }
 586     });
 587     editMenu.setText(MessageManager.getString("action.edit"));
 588     viewMenu.setText(MessageManager.getString("action.view"));
 589     colourMenu.setText(MessageManager.getString("action.colour"));
 590     calculateMenu.setText(MessageManager.getString("action.calculate"));
 591     webService.setText(MessageManager.getString("action.web_service"));
 592     selectAllSequenceMenuItem.setText(MessageManager.getString("action.select_all"));
 593     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 594             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
 595                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 596     selectAllSequenceMenuItem
 597             .addActionListener(new java.awt.event.ActionListener()
 598             {
 599               public void actionPerformed(ActionEvent e)
 600               {
 601                 selectAllSequenceMenuItem_actionPerformed(e);
 602               }
 603             });
 604     deselectAllSequenceMenuItem.setText(MessageManager.getString("action.deselect_all"));
 605     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 606             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 607     deselectAllSequenceMenuItem
 608             .addActionListener(new java.awt.event.ActionListener()
 609             {
 610               public void actionPerformed(ActionEvent e)
 611               {
 612                 deselectAllSequenceMenuItem_actionPerformed(e);
 613               }
 614             });
 615     invertSequenceMenuItem.setText(MessageManager.getString("action.invert_sequence_selection"));
 616     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 617             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
 618                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 619     invertSequenceMenuItem
 620             .addActionListener(new java.awt.event.ActionListener()
 621             {
 622               public void actionPerformed(ActionEvent e)
 623               {
 624                 invertSequenceMenuItem_actionPerformed(e);
 625               }
 626             });
 627     grpsFromSelection.setText(MessageManager.getString("action.make_groups_selection"));
 628     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
 629     {
 630       public void actionPerformed(ActionEvent e)
 631       {
 632         makeGrpsFromSelection_actionPerformed(e);
 633       }
 634     });
 635     expandAlignment.setText(MessageManager.getString("action.view_flanking_regions"));
 636     expandAlignment.addActionListener(new java.awt.event.ActionListener() {
 637       @Override
 638       public void actionPerformed(ActionEvent e)
 639       {
 640         expand_newalign(e);
 641       }
 642     });
 643     remove2LeftMenuItem.setText(MessageManager.getString("action.remove_left"));
 644     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 645             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
 646                     .getMenuShortcutKeyMask(), false));
 647     remove2LeftMenuItem
 648             .addActionListener(new java.awt.event.ActionListener()
 649             {
 650               public void actionPerformed(ActionEvent e)
 651               {
 652                 remove2LeftMenuItem_actionPerformed(e);
 653               }
 654             });
 655     remove2RightMenuItem.setText(MessageManager.getString("action.remove_right"));
 656     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 657             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
 658                     .getMenuShortcutKeyMask(), false));
 659     remove2RightMenuItem
 660             .addActionListener(new java.awt.event.ActionListener()
 661             {
 662               public void actionPerformed(ActionEvent e)
 663               {
 664                 remove2RightMenuItem_actionPerformed(e);
 665               }
 666             });
 667     removeGappedColumnMenuItem.setText(MessageManager.getString("action.remove_empty_columns"));
 668     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
 669             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 670                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 671     removeGappedColumnMenuItem
 672             .addActionListener(new java.awt.event.ActionListener()
 673             {
 674               public void actionPerformed(ActionEvent e)
 675               {
 676                 removeGappedColumnMenuItem_actionPerformed(e);
 677               }
 678             });
 679     removeAllGapsMenuItem.setText(MessageManager.getString("action.remove_all_gaps"));
 680     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
 681             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 682                     .getDefaultToolkit().getMenuShortcutKeyMask()
 683                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 684     removeAllGapsMenuItem
 685             .addActionListener(new java.awt.event.ActionListener()
 686             {
 687               public void actionPerformed(ActionEvent e)
 688               {
 689                 removeAllGapsMenuItem_actionPerformed(e);
 690               }
 691             });
 692     justifyLeftMenuItem.setText(MessageManager.getString("action.left_justify_alignment"));
 693     justifyLeftMenuItem
 694             .addActionListener(new java.awt.event.ActionListener()
 695             {
 696               public void actionPerformed(ActionEvent e)
 697               {
 698                 justifyLeftMenuItem_actionPerformed(e);
 699               }
 700             });
 701     justifyRightMenuItem.setText(MessageManager.getString("action.right_justify_alignment"));
 702     justifyRightMenuItem
 703             .addActionListener(new java.awt.event.ActionListener()
 704             {
 705               public void actionPerformed(ActionEvent e)
 706               {
 707                 justifyRightMenuItem_actionPerformed(e);
 708               }
 709             });
 710     viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
 711     viewBoxesMenuItem.setState(true);
 712     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 713     {
 714       public void actionPerformed(ActionEvent e)
 715       {
 716         viewBoxesMenuItem_actionPerformed(e);
 717       }
 718     });
 719     viewTextMenuItem.setText(MessageManager.getString("action.text"));
 720     viewTextMenuItem.setState(true);
 721     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 722     {
 723       public void actionPerformed(ActionEvent e)
 724       {
 725         viewTextMenuItem_actionPerformed(e);
 726       }
 727     });
 728     showNonconservedMenuItem.setText(MessageManager.getString("label.show_non_conversed"));
 729     showNonconservedMenuItem.setState(false);
 730     showNonconservedMenuItem
 731             .addActionListener(new java.awt.event.ActionListener()
 732             {
 733               public void actionPerformed(ActionEvent e)
 734               {
 735                 showUnconservedMenuItem_actionPerformed(e);
 736               }
 737             });
 738     sortPairwiseMenuItem.setText(MessageManager.getString("action.by_pairwise_id"));
 739     sortPairwiseMenuItem
 740             .addActionListener(new java.awt.event.ActionListener()
 741             {
 742               public void actionPerformed(ActionEvent e)
 743               {
 744                 sortPairwiseMenuItem_actionPerformed(e);
 745               }
 746             });
 747     sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
 748     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 749     {
 750       public void actionPerformed(ActionEvent e)
 751       {
 752         sortIDMenuItem_actionPerformed(e);
 753       }
 754     });
 755     sortLengthMenuItem.setText(MessageManager.getString("action.by_length"));
 756     sortLengthMenuItem
 757             .addActionListener(new java.awt.event.ActionListener()
 758             {
 759               public void actionPerformed(ActionEvent e)
 760               {
 761                 sortLengthMenuItem_actionPerformed(e);
 762               }
 763             });
 764     sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
 765     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 766     {
 767       public void actionPerformed(ActionEvent e)
 768       {
 769         sortGroupMenuItem_actionPerformed(e);
 770       }
 771     });
 772     removeRedundancyMenuItem.setText(MessageManager.getString("action.remove_redundancy"));
 773     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
 774             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
 775                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 776     removeRedundancyMenuItem
 777             .addActionListener(new java.awt.event.ActionListener()
 778             {
 779               public void actionPerformed(ActionEvent e)
 780               {
 781                 removeRedundancyMenuItem_actionPerformed(e);
 782               }
 783             });
 784     pairwiseAlignmentMenuItem.setText(MessageManager.getString("action.pairwise_alignment"));
 785     pairwiseAlignmentMenuItem
 786             .addActionListener(new java.awt.event.ActionListener()
 787             {
 788               public void actionPerformed(ActionEvent e)
 789               {
 790                 pairwiseAlignmentMenuItem_actionPerformed(e);
 791               }
 792             });
 793     PCAMenuItem.setText(MessageManager.getString("label.principal_component_analysis"));
 794     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 795     {
 796       public void actionPerformed(ActionEvent e)
 797       {
 798         PCAMenuItem_actionPerformed(e);
 799       }
 800     });
 801     averageDistanceTreeMenuItem
 802             .setText(MessageManager.getString("label.average_distance_identity"));
 803     averageDistanceTreeMenuItem
 804             .addActionListener(new java.awt.event.ActionListener()
 805             {
 806               public void actionPerformed(ActionEvent e)
 807               {
 808                 averageDistanceTreeMenuItem_actionPerformed(e);
 809               }
 810             });
 811     neighbourTreeMenuItem.setText(MessageManager.getString("label.neighbour_joining_identity"));
 812     neighbourTreeMenuItem
 813             .addActionListener(new java.awt.event.ActionListener()
 814             {
 815               public void actionPerformed(ActionEvent e)
 816               {
 817                 neighbourTreeMenuItem_actionPerformed(e);
 818               }
 819             });
 820     this.getContentPane().setLayout(borderLayout1);
 821     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 822     statusBar.setBackground(Color.white);
 823     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 824     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 825     statusBar.setText(MessageManager.getString("label.status_bar"));
 826     outputTextboxMenu.setText(MessageManager.getString("label.out_to_textbox"));
 827     clustalColour.setText(MessageManager.getString("label.clustalx"));
 828
 829     clustalColour.addActionListener(new java.awt.event.ActionListener()
 830     {
 831       public void actionPerformed(ActionEvent e)
 832       {
 833         clustalColour_actionPerformed(e);
 834       }
 835     });
 836     zappoColour.setText(MessageManager.getString("label.zappo"));
 837     zappoColour.addActionListener(new java.awt.event.ActionListener()
 838     {
 839       public void actionPerformed(ActionEvent e)
 840       {
 841         zappoColour_actionPerformed(e);
 842       }
 843     });
 844     taylorColour.setText(MessageManager.getString("label.taylor"));
 845     taylorColour.addActionListener(new java.awt.event.ActionListener()
 846     {
 847       public void actionPerformed(ActionEvent e)
 848       {
 849         taylorColour_actionPerformed(e);
 850       }
 851     });
 852     hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));
 853     hydrophobicityColour
 854             .addActionListener(new java.awt.event.ActionListener()
 855             {
 856               public void actionPerformed(ActionEvent e)
 857               {
 858                 hydrophobicityColour_actionPerformed(e);
 859               }
 860             });
 861     helixColour.setText(MessageManager.getString("label.helix_propensity"));
 862     helixColour.addActionListener(new java.awt.event.ActionListener()
 863     {
 864       public void actionPerformed(ActionEvent e)
 865       {
 866         helixColour_actionPerformed(e);
 867       }
 868     });
 869     strandColour.setText(MessageManager.getString("label.strand_propensity"));
 870     strandColour.addActionListener(new java.awt.event.ActionListener()
 871     {
 872       public void actionPerformed(ActionEvent e)
 873       {
 874         strandColour_actionPerformed(e);
 875       }
 876     });
 877     turnColour.setText(MessageManager.getString("Turn Propensity"));
 878     turnColour.addActionListener(new java.awt.event.ActionListener()
 879     {
 880       public void actionPerformed(ActionEvent e)
 881       {
 882         turnColour_actionPerformed(e);
 883       }
 884     });
 885     buriedColour.setText(MessageManager.getString("Buried Index"));
 886     buriedColour.addActionListener(new java.awt.event.ActionListener()
 887     {
 888       public void actionPerformed(ActionEvent e)
 889       {
 890         buriedColour_actionPerformed(e);
 891       }
 892     });
 893     userDefinedColour.setText(MessageManager.getString("action.user_defined"));
 894     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 895     {
 896       public void actionPerformed(ActionEvent e)
 897       {
 898         userDefinedColour_actionPerformed(e);
 899       }
 900     });
 901     PIDColour.setText(MessageManager.getString("label.percentage_identity"));
 902     PIDColour.addActionListener(new java.awt.event.ActionListener()
 903     {
 904       public void actionPerformed(ActionEvent e)
 905       {
 906         PIDColour_actionPerformed(e);
 907       }
 908     });
 909     BLOSUM62Colour.setText(MessageManager.getString("label.blosum62_score"));
 910     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 911     {
 912       public void actionPerformed(ActionEvent e)
 913       {
 914         BLOSUM62Colour_actionPerformed(e);
 915       }
 916     });
 917     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
 918     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
 919     {
 920       public void actionPerformed(ActionEvent e)
 921       {
 922         nucleotideColour_actionPerformed(e);
 923       }
 924     });
 925
 926     purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
 927     purinePyrimidineColour
 928             .addActionListener(new java.awt.event.ActionListener()
 929             {
 930               public void actionPerformed(ActionEvent e)
 931               {
 932                 purinePyrimidineColour_actionPerformed(e);
 933               }
 934             });
 935     /*
 936      * covariationColour.setText("Covariation");
 937      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
 938      * public void actionPerformed(ActionEvent e) {
 939      * covariationColour_actionPerformed(e); } });
 940      */
 941
 942     avDistanceTreeBlosumMenuItem.setText(MessageManager.getString("label.average_distance_bloslum62"));
 943     avDistanceTreeBlosumMenuItem
 944             .addActionListener(new java.awt.event.ActionListener()
 945             {
 946               public void actionPerformed(ActionEvent e)
 947               {
 948                 avTreeBlosumMenuItem_actionPerformed(e);
 949               }
 950             });
 951     njTreeBlosumMenuItem.setText(MessageManager.getString("label.neighbour_blosum62"));
 952     njTreeBlosumMenuItem
 953             .addActionListener(new java.awt.event.ActionListener()
 954             {
 955               public void actionPerformed(ActionEvent e)
 956               {
 957                 njTreeBlosumMenuItem_actionPerformed(e);
 958               }
 959             });
 960     annotationPanelMenuItem.setActionCommand("");
 961     annotationPanelMenuItem.setText(MessageManager.getString("label.show_annotations"));
 962     annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
 963             "SHOW_ANNOTATIONS", true));
 964     annotationPanelMenuItem
 965             .addActionListener(new java.awt.event.ActionListener()
 966             {
 967               public void actionPerformed(ActionEvent e)
 968               {
 969                 annotationPanelMenuItem_actionPerformed(e);
 970               }
 971             });
 972     colourTextMenuItem.setText(MessageManager.getString("label.colour_text"));
 973     colourTextMenuItem
 974             .addActionListener(new java.awt.event.ActionListener()
 975             {
 976               public void actionPerformed(ActionEvent e)
 977               {
 978                 colourTextMenuItem_actionPerformed(e);
 979               }
 980             });
 981     htmlMenuItem.setText(MessageManager.getString("label.html"));
 982     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
 983     {
 984       public void actionPerformed(ActionEvent e)
 985       {
 986         htmlMenuItem_actionPerformed(e);
 987       }
 988     });
 989     overviewMenuItem.setText(MessageManager.getString("label.overview_window"));
 990     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
 991     {
 992       public void actionPerformed(ActionEvent e)
 993       {
 994         overviewMenuItem_actionPerformed(e);
 995       }
 996     });
 997     undoMenuItem.setEnabled(false);
 998     undoMenuItem.setText(MessageManager.getString("action.undo"));
 999     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1000             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1001                     .getMenuShortcutKeyMask(), false));
1002     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1003     {
1004       public void actionPerformed(ActionEvent e)
1005       {
1006         undoMenuItem_actionPerformed(e);
1007       }
1008     });
1009     redoMenuItem.setEnabled(false);
1010     redoMenuItem.setText(MessageManager.getString("action.redo"));
1011     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1012             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1013                     .getMenuShortcutKeyMask(), false));
1014     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1015     {
1016       public void actionPerformed(ActionEvent e)
1017       {
1018         redoMenuItem_actionPerformed(e);
1019       }
1020     });
1021     conservationMenuItem.setText(MessageManager.getString("action.by_conservation"));
1022     conservationMenuItem
1023             .addActionListener(new java.awt.event.ActionListener()
1024             {
1025               public void actionPerformed(ActionEvent e)
1026               {
1027                 conservationMenuItem_actionPerformed(e);
1028               }
1029             });
1030     noColourmenuItem.setText(MessageManager.getString("label.none"));
1031     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1032     {
1033       public void actionPerformed(ActionEvent e)
1034       {
1035         noColourmenuItem_actionPerformed(e);
1036       }
1037     });
1038     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1039     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1040     {
1041       public void actionPerformed(ActionEvent e)
1042       {
1043         wrapMenuItem_actionPerformed(e);
1044       }
1045     });
1046     printMenuItem.setText(MessageManager.getString("action.print") + "...");
1047     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1048             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1049                     .getMenuShortcutKeyMask(), false));
1050     printMenuItem.addActionListener(new java.awt.event.ActionListener()
1051     {
1052       public void actionPerformed(ActionEvent e)
1053       {
1054         printMenuItem_actionPerformed(e);
1055       }
1056     });
1057     renderGapsMenuItem.setText(MessageManager.getString("action.show_gaps"));
1058     renderGapsMenuItem.setState(true);
1059     renderGapsMenuItem
1060             .addActionListener(new java.awt.event.ActionListener()
1061             {
1062               public void actionPerformed(ActionEvent e)
1063               {
1064                 renderGapsMenuItem_actionPerformed(e);
1065               }
1066             });
1067     findMenuItem.setText(MessageManager.getString("action.find"));
1068     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1069             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1070                     .getMenuShortcutKeyMask(), false));
1071     findMenuItem.addActionListener(new java.awt.event.ActionListener()
1072     {
1073       public void actionPerformed(ActionEvent e)
1074       {
1075         findMenuItem_actionPerformed(e);
1076       }
1077     });
1078     abovePIDThreshold.setText(MessageManager.getString("label.above_identity_threshold"));
1079     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1080     {
1081       public void actionPerformed(ActionEvent e)
1082       {
1083         abovePIDThreshold_actionPerformed(e);
1084       }
1085     });
1086     showSeqFeatures.setText(MessageManager.getString("label.show_sequence_features"));
1087     showSeqFeatures.addActionListener(new ActionListener()
1088     {
1089       public void actionPerformed(ActionEvent actionEvent)
1090       {
1091         showSeqFeatures_actionPerformed(actionEvent);
1092       }
1093     });
1094     /*
1095      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1096      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1097      * void actionPerformed(ActionEvent actionEvent) {
1098      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1099      */
1100     showDbRefsMenuitem.setText(MessageManager.getString("label.show_database_refs"));
1101     showDbRefsMenuitem.addActionListener(new ActionListener()
1102     {
1103
1104       public void actionPerformed(ActionEvent e)
1105       {
1106         showDbRefs_actionPerformed(e);
1107       }
1108
1109     });
1110     showNpFeatsMenuitem.setText(MessageManager.getString("label.show_non_positional_features"));
1111     showNpFeatsMenuitem.addActionListener(new ActionListener()
1112     {
1113
1114       public void actionPerformed(ActionEvent e)
1115       {
1116         showNpFeats_actionPerformed(e);
1117       }
1118
1119     });
1120     showGroupConservation.setText(MessageManager.getString("label.group_conservation"));
1121     showGroupConservation.addActionListener(new ActionListener()
1122     {
1123
1124       public void actionPerformed(ActionEvent e)
1125       {
1126         showGroupConservation_actionPerformed(e);
1127       }
1128
1129     });
1130
1131     showGroupConsensus.setText(MessageManager.getString("label.group_consensus"));
1132     showGroupConsensus.addActionListener(new ActionListener()
1133     {
1134
1135       public void actionPerformed(ActionEvent e)
1136       {
1137         showGroupConsensus_actionPerformed(e);
1138       }
1139
1140     });
1141     showConsensusHistogram.setText(MessageManager.getString("label.show_consensus_histogram"));
1142     showConsensusHistogram.addActionListener(new ActionListener()
1143     {
1144
1145       public void actionPerformed(ActionEvent e)
1146       {
1147         showConsensusHistogram_actionPerformed(e);
1148       }
1149
1150     });
1151     showSequenceLogo.setText(MessageManager.getString("label.show_consensus_logo"));
1152     showSequenceLogo.addActionListener(new ActionListener()
1153     {
1154
1155       public void actionPerformed(ActionEvent e)
1156       {
1157         showSequenceLogo_actionPerformed(e);
1158       }
1159
1160     });
1161     normaliseSequenceLogo.setText(MessageManager.getString("label.norm_consensus_logo"));
1162     normaliseSequenceLogo.addActionListener(new ActionListener()
1163     {
1164
1165       public void actionPerformed(ActionEvent e)
1166       {
1167         normaliseSequenceLogo_actionPerformed(e);
1168       }
1169
1170     });
1171     applyAutoAnnotationSettings.setText(MessageManager.getString("label.apply_all_groups"));
1172     applyAutoAnnotationSettings.setState(false);
1173     applyAutoAnnotationSettings.setVisible(true);
1174     applyAutoAnnotationSettings.addActionListener(new ActionListener()
1175     {
1176
1177       public void actionPerformed(ActionEvent e)
1178       {
1179         applyAutoAnnotationSettings_actionPerformed(e);
1180       }
1181
1182     });
1183
1184     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1185     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1186     {
1187       public void actionPerformed(ActionEvent e)
1188       {
1189         nucleotideColour_actionPerformed(e);
1190       }
1191     });
1192
1193     tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1194     tcoffeeColour.setEnabled(false);
1195     tcoffeeColour.addActionListener(new ActionListener()
1196     {
1197
1198       @Override
1199       public void actionPerformed(ActionEvent e)
1200       {
1201         tcoffeeColorScheme_actionPerformed(e);
1202       }
1203     });
1204
1205     deleteGroups.setText(MessageManager.getString("action.undefine_groups"));
1206     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1207             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1208                     .getMenuShortcutKeyMask(), false));
1209     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1210     {
1211       public void actionPerformed(ActionEvent e)
1212       {
1213         deleteGroups_actionPerformed(e);
1214       }
1215     });
1216     createGroup.setText(MessageManager.getString("action.create_groups"));
1217     createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1218             java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1219                     .getMenuShortcutKeyMask(), false));
1220     createGroup.addActionListener(new java.awt.event.ActionListener()
1221     {
1222       public void actionPerformed(ActionEvent e)
1223       {
1224         createGroup_actionPerformed(e);
1225       }
1226     });
1227     unGroup.setText(MessageManager.getString("action.remove_group"));
1228     unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1229             java.awt.event.KeyEvent.VK_G,Toolkit.getDefaultToolkit()
1230                     .getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));
1231     unGroup.addActionListener(new java.awt.event.ActionListener()
1232     {
1233       public void actionPerformed(ActionEvent e)
1234       {
1235         unGroup_actionPerformed(e);
1236       }
1237     });
1238     copy.setText(MessageManager.getString("action.copy"));
1239     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1240             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1241                     .getMenuShortcutKeyMask(), false));
1242
1243     copy.addActionListener(new java.awt.event.ActionListener()
1244     {
1245       public void actionPerformed(ActionEvent e)
1246       {
1247         copy_actionPerformed(e);
1248       }
1249     });
1250     cut.setText(MessageManager.getString("action.cut"));
1251     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1252             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1253                     .getMenuShortcutKeyMask(), false));
1254     cut.addActionListener(new java.awt.event.ActionListener()
1255     {
1256       public void actionPerformed(ActionEvent e)
1257       {
1258         cut_actionPerformed(e);
1259       }
1260     });
1261     delete.setText(MessageManager.getString("action.delete"));
1262     delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1263             java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1264     delete.addActionListener(new java.awt.event.ActionListener()
1265     {
1266       public void actionPerformed(ActionEvent e)
1267       {
1268         delete_actionPerformed(e);
1269       }
1270     });
1271     pasteMenu.setText(MessageManager.getString("action.paste"));
1272     pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1273     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1274             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1275                     .getMenuShortcutKeyMask()
1276                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1277     pasteNew.addActionListener(new java.awt.event.ActionListener()
1278     {
1279       public void actionPerformed(ActionEvent e)
1280       {
1281         pasteNew_actionPerformed(e);
1282       }
1283     });
1284     pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1285     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1286             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1287                     .getMenuShortcutKeyMask(), false));
1288     pasteThis.addActionListener(new java.awt.event.ActionListener()
1289     {
1290       public void actionPerformed(ActionEvent e)
1291       {
1292         pasteThis_actionPerformed(e);
1293       }
1294     });
1295     applyToAllGroups.setText(MessageManager.getString("label.apply_colour_to_all_groups"));
1296     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1297     {
1298       public void actionPerformed(ActionEvent e)
1299       {
1300         applyToAllGroups_actionPerformed(e);
1301       }
1302     });
1303     createPNG.addActionListener(new java.awt.event.ActionListener()
1304     {
1305       public void actionPerformed(ActionEvent e)
1306       {
1307         createPNG(null);
1308       }
1309     });
1310     createPNG.setActionCommand(MessageManager.getString("label.save_png_image"));
1311     createPNG.setText("PNG");
1312     font.setText(MessageManager.getString("action.font"));
1313     font.addActionListener(new java.awt.event.ActionListener()
1314     {
1315       public void actionPerformed(ActionEvent e)
1316       {
1317         font_actionPerformed(e);
1318       }
1319     });
1320
1321     seqLimits.setText(MessageManager.getString("label.show_sequence_limits"));
1322     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1323     seqLimits.addActionListener(new java.awt.event.ActionListener()
1324     {
1325       public void actionPerformed(ActionEvent e)
1326       {
1327         seqLimit_actionPerformed(e);
1328       }
1329     });
1330     epsFile.setText("EPS");
1331     epsFile.addActionListener(new java.awt.event.ActionListener()
1332     {
1333       public void actionPerformed(ActionEvent e)
1334       {
1335         createEPS(null);
1336       }
1337     });
1338     LoadtreeMenuItem.setActionCommand(MessageManager.getString("label.load_tree_for_sequence_set"));
1339     LoadtreeMenuItem.setText(MessageManager.getString("label.load_associated_tree"));
1340     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1341     {
1342       public void actionPerformed(ActionEvent e)
1343       {
1344         LoadtreeMenuItem_actionPerformed(e);
1345       }
1346     });
1347
1348     scaleAbove.setVisible(false);
1349     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1350     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1351     {
1352       public void actionPerformed(ActionEvent e)
1353       {
1354         scaleAbove_actionPerformed(e);
1355       }
1356     });
1357     scaleLeft.setVisible(false);
1358     scaleLeft.setSelected(true);
1359     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1360     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1361     {
1362       public void actionPerformed(ActionEvent e)
1363       {
1364         scaleLeft_actionPerformed(e);
1365       }
1366     });
1367     scaleRight.setVisible(false);
1368     scaleRight.setSelected(true);
1369     scaleRight.setText(MessageManager.getString("action.scale_right"));
1370     scaleRight.addActionListener(new java.awt.event.ActionListener()
1371     {
1372       public void actionPerformed(ActionEvent e)
1373       {
1374         scaleRight_actionPerformed(e);
1375       }
1376     });
1377     centreColumnLabelsMenuItem.setVisible(true);
1378     centreColumnLabelsMenuItem.setState(false);
1379     centreColumnLabelsMenuItem.setText(MessageManager.getString("label.centre_column_labels"));
1380     centreColumnLabelsMenuItem
1381             .addActionListener(new java.awt.event.ActionListener()
1382             {
1383               public void actionPerformed(ActionEvent e)
1384               {
1385                 centreColumnLabels_actionPerformed(e);
1386               }
1387             });
1388     followHighlightMenuItem.setVisible(true);
1389     followHighlightMenuItem.setState(true);
1390     followHighlightMenuItem.setText(MessageManager.getString("label.automatic_scrolling"));
1391     followHighlightMenuItem.addActionListener(new ActionListener()
1392     {
1393
1394       public void actionPerformed(ActionEvent e)
1395       {
1396         followHighlight_actionPerformed();
1397       }
1398
1399     });
1400
1401     modifyPID.setText(MessageManager.getString("label.modify_identity_thereshold"));
1402     modifyPID.addActionListener(new java.awt.event.ActionListener()
1403     {
1404       public void actionPerformed(ActionEvent e)
1405       {
1406         modifyPID_actionPerformed(e);
1407       }
1408     });
1409     modifyConservation.setText(MessageManager.getString("label.modify_conservation_thereshold"));
1410     modifyConservation
1411             .addActionListener(new java.awt.event.ActionListener()
1412             {
1413               public void actionPerformed(ActionEvent e)
1414               {
1415                 modifyConservation_actionPerformed(e);
1416               }
1417             });
1418     sortByTreeMenu.setText(MessageManager.getString("action.by_tree_order"));
1419     sort.setText(MessageManager.getString("action.sort"));
1420     sort.addMenuListener(new MenuListener()
1421     {
1422       public void menuSelected(MenuEvent e)
1423       {
1424         buildTreeMenu();
1425       }
1426
1427       public void menuDeselected(MenuEvent e)
1428       {
1429       }
1430
1431       public void menuCanceled(MenuEvent e)
1432       {
1433       }
1434     });
1435     sortByAnnotScore.setText(MessageManager.getString("label.sort_by_score"));
1436     sort.add(sortByAnnotScore);
1437     sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1438     {
1439
1440       public void menuCanceled(MenuEvent e)
1441       {
1442       }
1443
1444       public void menuDeselected(MenuEvent e)
1445       {
1446       }
1447
1448       public void menuSelected(MenuEvent e)
1449       {
1450         buildSortByAnnotationScoresMenu();
1451       }
1452     });
1453     sortByAnnotScore.setVisible(false);
1454
1455     calculateTree.setText(MessageManager.getString("action.calculate_tree"));
1456
1457     jMenu2.setText(MessageManager.getString("label.export_image"));
1458     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1459     padGapsMenuitem.setState(jalview.bin.Cache
1460             .getDefault("PAD_GAPS", false));
1461     padGapsMenuitem.addActionListener(new ActionListener()
1462     {
1463       public void actionPerformed(ActionEvent e)
1464       {
1465         padGapsMenuitem_actionPerformed(e);
1466       }
1467     });
1468     vamsasStore.setVisible(false);
1469     vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1470     vamsasStore.addActionListener(new ActionListener()
1471     {
1472       public void actionPerformed(ActionEvent e)
1473       {
1474         vamsasStore_actionPerformed(e);
1475       }
1476     });
1477     showTranslation.setText(MessageManager.getString("label.translate_cDNA"));
1478     showTranslation.addActionListener(new ActionListener()
1479     {
1480       public void actionPerformed(ActionEvent e)
1481       {
1482         showTranslation_actionPerformed(e);
1483       }
1484     });
1485     extractScores.setText(MessageManager.getString("label.extract_scores") + "...");
1486     extractScores.addActionListener(new ActionListener()
1487     {
1488       public void actionPerformed(ActionEvent e)
1489       {
1490         extractScores_actionPerformed(e);
1491       }
1492     });
1493     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1494     // score extraction
1495     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1496     /*
1497      * showProducts.addActionListener(new ActionListener() {
1498      *
1499      * public void actionPerformed(ActionEvent e) {
1500      * showProducts_actionPerformed(e); } });
1501      */
1502     openFeatureSettings.setText(MessageManager.getString("label.feature_settings"));
1503     openFeatureSettings.addActionListener(new ActionListener()
1504     {
1505       public void actionPerformed(ActionEvent e)
1506       {
1507         featureSettings_actionPerformed(e);
1508       }
1509     });
1510     fetchSequence.setText(MessageManager.getString("label.fetch_sequences"));
1511     fetchSequence.addActionListener(new ActionListener()
1512     {
1513       public void actionPerformed(ActionEvent e)
1514       {
1515         fetchSequence_actionPerformed(e);
1516       }
1517     });
1518
1519     annotationColour.setText(MessageManager.getString("action.by_annotation"));
1520     annotationColour.addActionListener(new ActionListener()
1521     {
1522       public void actionPerformed(ActionEvent e)
1523       {
1524         annotationColour_actionPerformed(e);
1525       }
1526     });
1527
1528     rnahelicesColour.setText(MessageManager.getString("action.by_rna_helixes"));
1529     rnahelicesColour.addActionListener(new ActionListener()
1530     {
1531       public void actionPerformed(ActionEvent e)
1532       {
1533         rnahelicesColour_actionPerformed(e);
1534       }
1535     });
1536
1537     associatedData.setText(MessageManager.getString("label.load_features_annotations"));
1538     associatedData.addActionListener(new ActionListener()
1539     {
1540       public void actionPerformed(ActionEvent e)
1541       {
1542         associatedData_actionPerformed(e);
1543       }
1544     });
1545     autoCalculate.setText(MessageManager.getString("label.autocalculate_consensus"));
1546     autoCalculate.setState(jalview.bin.Cache.getDefault(
1547             "AUTO_CALC_CONSENSUS", true));
1548     autoCalculate.addActionListener(new ActionListener()
1549     {
1550       public void actionPerformed(ActionEvent e)
1551       {
1552         autoCalculate_actionPerformed(e);
1553       }
1554     });
1555     sortByTree.setText(MessageManager.getString("label.sort_alignment_new_tree"));
1556     sortByTree
1557             .setToolTipText("<html>" + MessageManager.getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1558     sortByTree
1559             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1560     sortByTree.addActionListener(new ActionListener()
1561     {
1562       public void actionPerformed(ActionEvent e)
1563       {
1564         sortByTreeOption_actionPerformed(e);
1565       }
1566     });
1567
1568     listenToViewSelections.setText(MessageManager.getString("label.listen_for_selections"));
1569     listenToViewSelections
1570             .setToolTipText("<html>" + MessageManager.getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1571     listenToViewSelections.setState(false);
1572     listenToViewSelections.addActionListener(new ActionListener()
1573     {
1574       public void actionPerformed(ActionEvent e)
1575       {
1576         listenToViewSelections_actionPerformed(e);
1577       }
1578     });
1579
1580     addSequenceMenu.setText(MessageManager.getString("label.add_sequences"));
1581     addFromFile.setText(MessageManager.getString("label.from_file"));
1582     addFromFile.addActionListener(new ActionListener()
1583     {
1584       public void actionPerformed(ActionEvent e)
1585       {
1586         addFromFile_actionPerformed(e);
1587       }
1588     });
1589     addFromText.setText(MessageManager.getString("label.from_textbox"));
1590     addFromText.addActionListener(new ActionListener()
1591     {
1592       public void actionPerformed(ActionEvent e)
1593       {
1594         addFromText_actionPerformed(e);
1595       }
1596     });
1597     addFromURL.setText(MessageManager.getString("label.from_url"));
1598     addFromURL.addActionListener(new ActionListener()
1599     {
1600       public void actionPerformed(ActionEvent e)
1601       {
1602         addFromURL_actionPerformed(e);
1603       }
1604     });
1605     exportFeatures.setText(MessageManager.getString("label.export_features"));
1606     exportFeatures.addActionListener(new ActionListener()
1607     {
1608       public void actionPerformed(ActionEvent e)
1609       {
1610         exportFeatures_actionPerformed(e);
1611       }
1612     });
1613     exportAnnotations.setText(MessageManager.getString("label.export_annotations"));
1614     exportAnnotations.addActionListener(new ActionListener()
1615     {
1616       public void actionPerformed(ActionEvent e)
1617       {
1618         exportAnnotations_actionPerformed(e);
1619       }
1620     });
1621     statusPanel.setLayout(gridLayout1);
1622     jMenu3.setText(MessageManager.getString("action.show"));
1623     showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
1624     showAllSeqs.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
1625     showAllSeqs.addActionListener(new ActionListener()
1626     {
1627       public void actionPerformed(ActionEvent e)
1628       {
1629         showAllSeqs_actionPerformed(e);
1630       }
1631     });
1632     showAllColumns.setText(MessageManager.getString("label.all_columns"));
1633     showAllColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
1634     showAllColumns.addActionListener(new ActionListener()
1635     {
1636       public void actionPerformed(ActionEvent e)
1637       {
1638         showAllColumns_actionPerformed(e);
1639       }
1640     });
1641     hideMenu.setText(MessageManager.getString("action.hide"));
1642     hideSelSequences.setText(MessageManager.getString("label.selected_sequences"));
1643     hideSelSequences.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
1644     hideSelSequences.addActionListener(new ActionListener()
1645     {
1646       public void actionPerformed(ActionEvent e)
1647       {
1648         hideSelSequences_actionPerformed(e);
1649       }
1650     });
1651     hideSelColumns.setText(MessageManager.getString("label.selected_columns"));
1652     hideSelColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
1653     hideSelColumns.addActionListener(new ActionListener()
1654     {
1655       public void actionPerformed(ActionEvent e)
1656       {
1657         hideSelColumns_actionPerformed(e);
1658       }
1659     });
1660     hideAllSelection.setText(MessageManager.getString("label.selected_region"));
1661     hideAllSelection.addActionListener(new ActionListener()
1662     {
1663       public void actionPerformed(ActionEvent e)
1664       {
1665         hideAllSelection_actionPerformed(e);
1666       }
1667     });
1668     // TODO: should be hidden if no selection exists.
1669     hideAllButSelection.setText(MessageManager.getString("label.all_but_selected_region"));
1670     hideAllButSelection.addActionListener(new ActionListener()
1671     {
1672       public void actionPerformed(ActionEvent e)
1673       {
1674         hideAllButSelection_actionPerformed(e);
1675       }
1676     });
1677     showAllhidden.setText(MessageManager.getString("label.all_sequences_columns"));
1678     showAllhidden
1679             .setToolTipText(MessageManager.getString("label.toggles_visibility_hidden_selected_regions"));
1680     showAllhidden.addActionListener(new ActionListener()
1681     {
1682       public void actionPerformed(ActionEvent e)
1683       {
1684         showAllhidden_actionPerformed(e);
1685       }
1686     });
1687
1688     hiddenMarkers.setText(MessageManager.getString("action.show_hidden_markers"));
1689     hiddenMarkers.addActionListener(new ActionListener()
1690     {
1691       public void actionPerformed(ActionEvent e)
1692       {
1693         hiddenMarkers_actionPerformed(e);
1694       }
1695     });
1696     invertColSel.setText(MessageManager.getString("action.invert_column_selection"));
1697     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1698             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1699                     .getMenuShortcutKeyMask()
1700                     | java.awt.event.KeyEvent.ALT_MASK, false));
1701     invertColSel.addActionListener(new ActionListener()
1702     {
1703       public void actionPerformed(ActionEvent e)
1704       {
1705         invertColSel_actionPerformed(e);
1706       }
1707     });
1708     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1709     {
1710       public void stateChanged(ChangeEvent evt)
1711       {
1712         JTabbedPane pane = (JTabbedPane) evt.getSource();
1713         int sel = pane.getSelectedIndex();
1714         tabSelectionChanged(sel);
1715       }
1716     });
1717     tabbedPane.addMouseListener(new MouseAdapter()
1718     {
1719       public void mousePressed(MouseEvent e)
1720       {
1721         tabbedPane_mousePressed(e);
1722       }
1723     });
1724     tabbedPane.addFocusListener(new FocusAdapter()
1725     {
1726       public void focusGained(FocusEvent e)
1727       {
1728         tabbedPane_focusGained(e);
1729       }
1730     });
1731     save.setText(MessageManager.getString("action.save"));
1732     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1733             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1734                     .getMenuShortcutKeyMask(), false));
1735     save.addActionListener(new ActionListener()
1736     {
1737       public void actionPerformed(ActionEvent e)
1738       {
1739         save_actionPerformed(e);
1740       }
1741     });
1742     reload.setEnabled(false);
1743     reload.setText(MessageManager.getString("action.reload"));
1744     reload.addActionListener(new ActionListener()
1745     {
1746       public void actionPerformed(ActionEvent e)
1747       {
1748         reload_actionPerformed(e);
1749       }
1750     });
1751     newView.setText(MessageManager.getString("action.new_view"));
1752     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1753             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1754                     .getMenuShortcutKeyMask(), false));
1755     newView.addActionListener(new ActionListener()
1756     {
1757       public void actionPerformed(ActionEvent e)
1758       {
1759         newView_actionPerformed(e);
1760       }
1761     });
1762     tabbedPane.setToolTipText("<html><i>" + MessageManager.getString("label.rename_tab_eXpand_reGroup") + "</i></html>");
1763     textColour.setText(MessageManager.getString("label.colour_text") + "...");
1764     textColour.addActionListener(new ActionListener()
1765     {
1766       public void actionPerformed(ActionEvent e)
1767       {
1768         textColour_actionPerformed(e);
1769       }
1770     });
1771     formatMenu.setText(MessageManager.getString("action.format"));
1772     selectMenu.setText(MessageManager.getString("action.select"));
1773     idRightAlign.setText(MessageManager.getString("label.right_align_sequence_id"));
1774     idRightAlign.addActionListener(new ActionListener()
1775     {
1776       public void actionPerformed(ActionEvent e)
1777       {
1778         idRightAlign_actionPerformed(e);
1779       }
1780     });
1781     gatherViews.setEnabled(false);
1782     gatherViews.setText(MessageManager.getString("action.gather_views"));
1783     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1784             java.awt.event.KeyEvent.VK_G, 0, false));
1785     gatherViews.addActionListener(new ActionListener()
1786     {
1787       public void actionPerformed(ActionEvent e)
1788       {
1789         gatherViews_actionPerformed(e);
1790       }
1791     });
1792     expandViews.setEnabled(false);
1793     expandViews.setText(MessageManager.getString("action.expand_views"));
1794     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1795             java.awt.event.KeyEvent.VK_X, 0, false));
1796     expandViews.addActionListener(new ActionListener()
1797     {
1798       public void actionPerformed(ActionEvent e)
1799       {
1800         expandViews_actionPerformed(e);
1801       }
1802     });
1803     pageSetup.setText(MessageManager.getString("action.page_setup") + "...");
1804     pageSetup.addActionListener(new ActionListener()
1805     {
1806       public void actionPerformed(ActionEvent e)
1807       {
1808         pageSetup_actionPerformed(e);
1809       }
1810     });
1811     alignmentProperties.setText(MessageManager.getString("label.alignment_props") + "...");
1812     alignmentProperties.addActionListener(new ActionListener()
1813     {
1814       public void actionPerformed(ActionEvent actionEvent)
1815       {
1816         alignmentProperties();
1817       }
1818     });
1819     tooltipSettingsMenu.setText(MessageManager.getString("label.sequence_id_tooltip"));
1820     autoAnnMenu.setText(MessageManager.getString("label.autocalculated_annotation"));
1821     alignFrameMenuBar.add(fileMenu);
1822     alignFrameMenuBar.add(editMenu);
1823     alignFrameMenuBar.add(selectMenu);
1824     alignFrameMenuBar.add(viewMenu);
1825     alignFrameMenuBar.add(formatMenu);
1826     alignFrameMenuBar.add(colourMenu);
1827     alignFrameMenuBar.add(calculateMenu);
1828     alignFrameMenuBar.add(webService);
1829     fileMenu.add(fetchSequence);
1830     fileMenu.add(addSequenceMenu);
1831     fileMenu.add(reload);
1832     fileMenu.addSeparator();
1833     fileMenu.add(vamsasStore);
1834     fileMenu.add(save);
1835     fileMenu.add(saveAs);
1836     fileMenu.add(outputTextboxMenu);
1837     fileMenu.add(pageSetup);
1838     fileMenu.add(printMenuItem);
1839     fileMenu.addSeparator();
1840     fileMenu.add(jMenu2);
1841     fileMenu.add(exportFeatures);
1842     fileMenu.add(exportAnnotations);
1843     fileMenu.add(LoadtreeMenuItem);
1844     fileMenu.add(associatedData);
1845     fileMenu.addSeparator();
1846     fileMenu.add(closeMenuItem);
1847     editMenu.add(undoMenuItem);
1848     editMenu.add(redoMenuItem);
1849     editMenu.add(cut);
1850     editMenu.add(copy);
1851     editMenu.add(pasteMenu);
1852     editMenu.add(delete);
1853     editMenu.addSeparator();
1854     editMenu.add(remove2LeftMenuItem);
1855     editMenu.add(remove2RightMenuItem);
1856     editMenu.add(removeGappedColumnMenuItem);
1857     editMenu.add(removeAllGapsMenuItem);
1858     editMenu.add(removeRedundancyMenuItem);
1859     editMenu.addSeparator();
1860     // dont add these yet in the CVS build - they cannot be undone!
1861     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1862     // editMenu.add(justifyLeftMenuItem);
1863     // editMenu.add(justifyRightMenuItem);
1864     // editMenu.addSeparator();
1865     editMenu.add(padGapsMenuitem);
1866     viewMenu.add(newView);
1867     viewMenu.add(expandViews);
1868     viewMenu.add(gatherViews);
1869     viewMenu.addSeparator();
1870     viewMenu.add(jMenu3);
1871     viewMenu.add(hideMenu);
1872     viewMenu.addSeparator();
1873     viewMenu.add(followHighlightMenuItem);
1874     viewMenu.add(annotationPanelMenuItem);
1875     autoAnnMenu.add(applyAutoAnnotationSettings);
1876     autoAnnMenu.add(showConsensusHistogram);
1877     autoAnnMenu.add(showSequenceLogo);
1878     autoAnnMenu.add(normaliseSequenceLogo);
1879     autoAnnMenu.addSeparator();
1880     autoAnnMenu.add(showGroupConservation);
1881     autoAnnMenu.add(showGroupConsensus);
1882     viewMenu.add(autoAnnMenu);
1883     viewMenu.addSeparator();
1884     viewMenu.add(showSeqFeatures);
1885     // viewMenu.add(showSeqFeaturesHeight);
1886
1887     viewMenu.add(openFeatureSettings);
1888     tooltipSettingsMenu.add(showDbRefsMenuitem);
1889     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1890     viewMenu.add(tooltipSettingsMenu);
1891     viewMenu.addSeparator();
1892     viewMenu.add(alignmentProperties);
1893     viewMenu.addSeparator();
1894     viewMenu.add(overviewMenuItem);
1895     colourMenu.add(applyToAllGroups);
1896     colourMenu.add(textColour);
1897     colourMenu.addSeparator();
1898     colourMenu.add(noColourmenuItem);
1899     colourMenu.add(clustalColour);
1900     colourMenu.add(BLOSUM62Colour);
1901     colourMenu.add(PIDColour);
1902     colourMenu.add(zappoColour);
1903     colourMenu.add(taylorColour);
1904     colourMenu.add(hydrophobicityColour);
1905     colourMenu.add(helixColour);
1906     colourMenu.add(strandColour);
1907     colourMenu.add(turnColour);
1908     colourMenu.add(buriedColour);
1909     colourMenu.add(nucleotideColour);
1910     colourMenu.add(purinePyrimidineColour);
1911     // colourMenu.add(covariationColour);
1912     colourMenu.add(tcoffeeColour);
1913     colourMenu.add(userDefinedColour);
1914     colourMenu.addSeparator();
1915     colourMenu.add(conservationMenuItem);
1916     colourMenu.add(modifyConservation);
1917     colourMenu.add(abovePIDThreshold);
1918     colourMenu.add(modifyPID);
1919     colourMenu.add(annotationColour);
1920     colourMenu.add(rnahelicesColour);
1921     calculateMenu.add(sort);
1922     calculateMenu.add(calculateTree);
1923     calculateMenu.addSeparator();
1924     calculateMenu.add(pairwiseAlignmentMenuItem);
1925     calculateMenu.add(PCAMenuItem);
1926     calculateMenu.addSeparator();
1927     calculateMenu.add(showTranslation);
1928     calculateMenu.add(showProducts);
1929     calculateMenu.add(autoCalculate);
1930     calculateMenu.add(sortByTree);
1931     calculateMenu.addSeparator();
1932     calculateMenu.add(extractScores);
1933     webServiceNoServices = new JMenuItem(MessageManager.getString("label.no_services"));
1934     webService.add(webServiceNoServices);
1935     pasteMenu.add(pasteNew);
1936     pasteMenu.add(pasteThis);
1937     sort.add(sortIDMenuItem);
1938     sort.add(sortLengthMenuItem);
1939     sort.add(sortGroupMenuItem);
1940     sort.add(sortPairwiseMenuItem);
1941     sort.add(sortByTreeMenu);
1942     jMenu2.add(htmlMenuItem);
1943     jMenu2.add(epsFile);
1944     jMenu2.add(createPNG);
1945     addSequenceMenu.add(addFromFile);
1946     addSequenceMenu.add(addFromText);
1947     addSequenceMenu.add(addFromURL);
1948     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1949     statusPanel.add(statusBar, null);
1950     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1951     jMenu3.add(showAllColumns);
1952     jMenu3.add(showAllSeqs);
1953     jMenu3.add(showAllhidden);
1954     hideMenu.add(hideSelColumns);
1955     hideMenu.add(hideSelSequences);
1956     hideMenu.add(hideAllSelection);
1957     hideMenu.add(hideAllButSelection);
1958
1959     formatMenu.add(font);
1960     formatMenu.addSeparator();
1961     formatMenu.add(wrapMenuItem);
1962     formatMenu.add(scaleAbove);
1963     formatMenu.add(scaleLeft);
1964     formatMenu.add(scaleRight);
1965     formatMenu.add(seqLimits);
1966     formatMenu.add(idRightAlign);
1967     formatMenu.add(hiddenMarkers);
1968     formatMenu.add(viewBoxesMenuItem);
1969     formatMenu.add(viewTextMenuItem);
1970     formatMenu.add(colourTextMenuItem);
1971     formatMenu.add(renderGapsMenuItem);
1972     formatMenu.add(centreColumnLabelsMenuItem);
1973     formatMenu.add(showNonconservedMenuItem);
1974     selectMenu.add(findMenuItem);
1975     selectMenu.addSeparator();
1976     selectMenu.add(selectAllSequenceMenuItem);
1977     selectMenu.add(deselectAllSequenceMenuItem);
1978     selectMenu.add(invertSequenceMenuItem);
1979     selectMenu.add(invertColSel);
1980     selectMenu.add(createGroup);
1981     selectMenu.add(unGroup);
1982     selectMenu.add(grpsFromSelection);
1983     selectMenu.add(deleteGroups);
1984     calculateMenu.add(expandAlignment);
1985     // TODO - determine if the listenToViewSelections button is needed : see bug
1986     // JAL-574
1987     // selectMenu.addSeparator();
1988     // selectMenu.add(listenToViewSelections);
1989   }
1990
1991   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
1992   {
1993     // TODO Auto-generated method stub
1994
1995   }
1996
1997   protected void listenToViewSelections_actionPerformed(ActionEvent e)
1998   {
1999     // TODO Auto-generated method stub
2000
2001   }
2002
2003   protected void showAllhidden_actionPerformed(ActionEvent e)
2004   {
2005     // TODO Auto-generated method stub
2006
2007   }
2008
2009   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2010   {
2011     // TODO Auto-generated method stub
2012
2013   }
2014
2015   protected void hideAllSelection_actionPerformed(ActionEvent e)
2016   {
2017     // TODO Auto-generated method stub
2018
2019   }
2020
2021   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2022   {
2023     // TODO Auto-generated method stub
2024
2025   }
2026
2027   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2028   {
2029     // TODO Auto-generated method stub
2030
2031   }
2032
2033   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2034   {
2035     // TODO Auto-generated method stub
2036
2037   }
2038
2039   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2040   {
2041     // TODO Auto-generated method stub
2042
2043   }
2044
2045   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2046   {
2047     // TODO Auto-generated method stub
2048
2049   }
2050
2051   protected void showGroupConservation_actionPerformed(ActionEvent e)
2052   {
2053     // TODO Auto-generated method stub
2054
2055   }
2056
2057   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2058   {
2059     // TODO Auto-generated method stub
2060
2061   }
2062
2063   protected void showSeqFeaturesHeight_actionPerformed(
2064           ActionEvent actionEvent)
2065   {
2066     // TODO Auto-generated method stub
2067
2068   }
2069
2070   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2071   {
2072     // TODO Auto-generated method stub
2073
2074   }
2075
2076   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2077   {
2078     // TODO Auto-generated method stub
2079
2080   }
2081
2082   protected void followHighlight_actionPerformed()
2083   {
2084     // TODO Auto-generated method stub
2085
2086   }
2087
2088   protected void showNpFeats_actionPerformed(ActionEvent e)
2089   {
2090     // TODO Auto-generated method stub
2091
2092   }
2093
2094   protected void showDbRefs_actionPerformed(ActionEvent e)
2095   {
2096     // TODO Auto-generated method stub
2097
2098   }
2099
2100   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2101   {
2102   }
2103
2104   protected void showProducts_actionPerformed(ActionEvent e)
2105   {
2106   }
2107
2108   protected void buildSortByAnnotationScoresMenu()
2109   {
2110   }
2111
2112   protected void extractScores_actionPerformed(ActionEvent e)
2113   {
2114   }
2115
2116   protected void outputText_actionPerformed(ActionEvent e)
2117   {
2118   }
2119
2120   public void addFromFile_actionPerformed(ActionEvent e)
2121   {
2122
2123   }
2124
2125   public void addFromText_actionPerformed(ActionEvent e)
2126   {
2127
2128   }
2129
2130   public void addFromURL_actionPerformed(ActionEvent e)
2131   {
2132
2133   }
2134
2135   public void exportFeatures_actionPerformed(ActionEvent e)
2136   {
2137
2138   }
2139
2140   public void exportAnnotations_actionPerformed(ActionEvent e)
2141   {
2142
2143   }
2144
2145   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2146   {
2147   }
2148
2149   protected void closeMenuItem_actionPerformed(boolean b)
2150   {
2151   }
2152
2153   protected void redoMenuItem_actionPerformed(ActionEvent e)
2154   {
2155   }
2156
2157   protected void undoMenuItem_actionPerformed(ActionEvent e)
2158   {
2159   }
2160
2161   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2162   {
2163   }
2164
2165   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2166   {
2167   }
2168
2169   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2170   {
2171   }
2172
2173   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2174   {
2175   }
2176
2177   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2178   {
2179   }
2180
2181   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2182   {
2183   }
2184
2185   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2186   {
2187   }
2188
2189   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2190   {
2191   }
2192
2193   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2194   {
2195   }
2196
2197   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2198   {
2199   }
2200
2201   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2202   {
2203   }
2204
2205   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2206   {
2207   }
2208
2209   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2210   {
2211   }
2212
2213   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2214   {
2215   }
2216
2217   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2218   {
2219   }
2220
2221   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2222   {
2223   }
2224
2225   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2226   {
2227   }
2228
2229   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2230   {
2231   }
2232
2233   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2234   {
2235   }
2236
2237   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2238   {
2239   }
2240
2241   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2242   {
2243   }
2244
2245   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2246   {
2247   }
2248
2249   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2250   {
2251   }
2252
2253   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2254   {
2255   }
2256
2257   protected void clustalColour_actionPerformed(ActionEvent e)
2258   {
2259   }
2260
2261   protected void zappoColour_actionPerformed(ActionEvent e)
2262   {
2263   }
2264
2265   protected void taylorColour_actionPerformed(ActionEvent e)
2266   {
2267   }
2268
2269   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2270   {
2271   }
2272
2273   protected void helixColour_actionPerformed(ActionEvent e)
2274   {
2275   }
2276
2277   protected void strandColour_actionPerformed(ActionEvent e)
2278   {
2279   }
2280
2281   protected void turnColour_actionPerformed(ActionEvent e)
2282   {
2283   }
2284
2285   protected void buriedColour_actionPerformed(ActionEvent e)
2286   {
2287   }
2288
2289   protected void userDefinedColour_actionPerformed(ActionEvent e)
2290   {
2291   }
2292
2293   protected void PIDColour_actionPerformed(ActionEvent e)
2294   {
2295   }
2296
2297   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2298   {
2299   }
2300
2301   protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2302   {
2303   }
2304
2305   /*
2306    * protected void covariationColour_actionPerformed(ActionEvent e) { }
2307    */
2308
2309   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2310   {
2311   }
2312
2313   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2314   {
2315   }
2316
2317   protected void printMenuItem_actionPerformed(ActionEvent e)
2318   {
2319   }
2320
2321   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2322   {
2323   }
2324
2325   protected void findMenuItem_actionPerformed(ActionEvent e)
2326   {
2327   }
2328
2329   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2330   {
2331   }
2332
2333   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2334   {
2335   }
2336
2337   protected void nucleotideColour_actionPerformed(ActionEvent e)
2338   {
2339   }
2340
2341   protected void deleteGroups_actionPerformed(ActionEvent e)
2342   {
2343   }
2344
2345   protected void createGroup_actionPerformed(ActionEvent e)
2346   {
2347   }
2348
2349   protected void unGroup_actionPerformed(ActionEvent e)
2350   {
2351   }
2352
2353   protected void copy_actionPerformed(ActionEvent e)
2354   {
2355   }
2356
2357   protected void cut_actionPerformed(ActionEvent e)
2358   {
2359   }
2360
2361   protected void delete_actionPerformed(ActionEvent e)
2362   {
2363   }
2364
2365   protected void pasteNew_actionPerformed(ActionEvent e)
2366   {
2367   }
2368
2369   protected void pasteThis_actionPerformed(ActionEvent e)
2370   {
2371   }
2372
2373   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2374   {
2375   }
2376
2377   public void createPNG(java.io.File f)
2378   {
2379   }
2380
2381   protected void font_actionPerformed(ActionEvent e)
2382   {
2383   }
2384
2385   protected void seqLimit_actionPerformed(ActionEvent e)
2386   {
2387   }
2388
2389   public void seqDBRef_actionPerformed(ActionEvent e)
2390   {
2391
2392   }
2393
2394   public void createEPS(java.io.File f)
2395   {
2396   }
2397
2398   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2399   {
2400
2401   }
2402
2403   /**
2404    * Template method to handle the 'load T-Coffee scores' menu event.
2405    * <p>
2406    * Subclasses override this method to provide a custom action.
2407    *
2408    * @param event
2409    *          The raised event
2410    */
2411   protected void loadScores_actionPerformed(ActionEvent event)
2412   {
2413
2414   }
2415
2416   /**
2417    * Template method to handle the 'Color T-Coffee scores' menu event.
2418    * <p>
2419    * Subclasses override this method to provide a custom action.
2420    *
2421    * @param event
2422    *          The raised event
2423    */
2424   protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2425   {
2426
2427   }
2428
2429   protected void jpred_actionPerformed(ActionEvent e)
2430   {
2431   }
2432
2433   protected void scaleAbove_actionPerformed(ActionEvent e)
2434   {
2435   }
2436
2437   protected void scaleLeft_actionPerformed(ActionEvent e)
2438   {
2439   }
2440
2441   protected void scaleRight_actionPerformed(ActionEvent e)
2442   {
2443   }
2444
2445   protected void modifyPID_actionPerformed(ActionEvent e)
2446   {
2447   }
2448
2449   protected void modifyConservation_actionPerformed(ActionEvent e)
2450   {
2451   }
2452
2453   protected void saveAs_actionPerformed(ActionEvent e)
2454   {
2455   }
2456
2457   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2458   {
2459   }
2460
2461   public void vamsasStore_actionPerformed(ActionEvent e)
2462   {
2463
2464   }
2465
2466   public void vamsasLoad_actionPerformed(ActionEvent e)
2467   {
2468
2469   }
2470
2471   public void showTranslation_actionPerformed(ActionEvent e)
2472   {
2473
2474   }
2475
2476   public void featureSettings_actionPerformed(ActionEvent e)
2477   {
2478
2479   }
2480
2481   public void fetchSequence_actionPerformed(ActionEvent e)
2482   {
2483
2484   }
2485
2486   public void smoothFont_actionPerformed(ActionEvent e)
2487   {
2488
2489   }
2490
2491   public void annotationColour_actionPerformed(ActionEvent e)
2492   {
2493
2494   }
2495
2496   public void rnahelicesColour_actionPerformed(ActionEvent e)
2497   {
2498
2499   }
2500
2501   public void associatedData_actionPerformed(ActionEvent e)
2502   {
2503
2504   }
2505
2506   public void autoCalculate_actionPerformed(ActionEvent e)
2507   {
2508
2509   }
2510
2511   public void sortByTreeOption_actionPerformed(ActionEvent e)
2512   {
2513
2514   }
2515
2516   public void showAllSeqs_actionPerformed(ActionEvent e)
2517   {
2518
2519   }
2520
2521   public void showAllColumns_actionPerformed(ActionEvent e)
2522   {
2523
2524   }
2525
2526   public void hideSelSequences_actionPerformed(ActionEvent e)
2527   {
2528
2529   }
2530
2531   public void hideSelColumns_actionPerformed(ActionEvent e)
2532   {
2533
2534   }
2535
2536   public void hiddenMarkers_actionPerformed(ActionEvent e)
2537   {
2538
2539   }
2540
2541   public void findPdbId_actionPerformed(ActionEvent e)
2542   {
2543
2544   }
2545
2546   public void enterPdbId_actionPerformed(ActionEvent e)
2547   {
2548
2549   }
2550
2551   public void pdbFile_actionPerformed(ActionEvent e)
2552   {
2553
2554   }
2555
2556   public void invertColSel_actionPerformed(ActionEvent e)
2557   {
2558
2559   }
2560
2561   public void tabSelectionChanged(int sel)
2562   {
2563
2564   }
2565
2566   public void tabbedPane_mousePressed(MouseEvent e)
2567   {
2568
2569   }
2570
2571   public void tabbedPane_focusGained(FocusEvent e)
2572   {
2573     requestFocus();
2574   }
2575
2576   public void save_actionPerformed(ActionEvent e)
2577   {
2578
2579   }
2580
2581   public void reload_actionPerformed(ActionEvent e)
2582   {
2583
2584   }
2585
2586   public void newView_actionPerformed(ActionEvent e)
2587   {
2588
2589   }
2590
2591   public void textColour_actionPerformed(ActionEvent e)
2592   {
2593
2594   }
2595
2596   public void idRightAlign_actionPerformed(ActionEvent e)
2597   {
2598
2599   }
2600
2601   public void expandViews_actionPerformed(ActionEvent e)
2602   {
2603
2604   }
2605
2606   public void gatherViews_actionPerformed(ActionEvent e)
2607   {
2608
2609   }
2610
2611   public void buildTreeMenu()
2612   {
2613
2614   }
2615
2616   public void pageSetup_actionPerformed(ActionEvent e)
2617   {
2618
2619   }
2620
2621   public void alignmentProperties()
2622   {
2623
2624   }
2625
2626   protected void expand_newalign(ActionEvent e)
2627   {
2628     // TODO Auto-generated method stub
2629
2630   }
2631 }