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