src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   3  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   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  */
  18 package jalview.jbgui;
  19
  20 import jalview.schemes.ColourSchemeProperty;
  21 import jalview.util.MessageManager;
  22
  23 import java.awt.BorderLayout;
  24 import java.awt.Color;
  25 import java.awt.GridLayout;
  26 import java.awt.Toolkit;
  27 import java.awt.event.ActionEvent;
  28 import java.awt.event.ActionListener;
  29 import java.awt.event.FocusAdapter;
  30 import java.awt.event.FocusEvent;
  31 import java.awt.event.MouseAdapter;
  32 import java.awt.event.MouseEvent;
  33
  34 import javax.swing.BorderFactory;
  35 import javax.swing.ButtonGroup;
  36 import javax.swing.JCheckBoxMenuItem;
  37 import javax.swing.JInternalFrame;
  38 import javax.swing.JLabel;
  39 import javax.swing.JMenu;
  40 import javax.swing.JMenuBar;
  41 import javax.swing.JMenuItem;
  42 import javax.swing.JOptionPane;
  43 import javax.swing.JPanel;
  44 import javax.swing.JRadioButtonMenuItem;
  45 import javax.swing.JTabbedPane;
  46 import javax.swing.SwingUtilities;
  47 import javax.swing.event.ChangeEvent;
  48 import javax.swing.event.MenuEvent;
  49 import javax.swing.event.MenuListener;
  50
  51 public class GAlignFrame extends JInternalFrame
  52 {
  53   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  54
  55   protected JMenu fileMenu = new JMenu();
  56
  57   protected JMenuItem closeMenuItem = new JMenuItem();
  58
  59   protected JMenu editMenu = new JMenu();
  60
  61   protected JMenu viewMenu = new JMenu();
  62
  63   protected JMenu colourMenu = new JMenu();
  64
  65   protected JMenu calculateMenu = new JMenu();
  66
  67   protected JMenu webService = new JMenu();
  68
  69   protected JMenuItem webServiceNoServices;
  70
  71   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  72
  73   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  74
  75   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  76
  77   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  78
  79   protected JMenuItem remove2RightMenuItem = new JMenuItem();
  80
  81   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  82
  83   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  84
  85   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  86
  87   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  88
  89   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  90
  91   protected JMenuItem sortIDMenuItem = new JMenuItem();
  92
  93   protected JMenuItem sortLengthMenuItem = new JMenuItem();
  94
  95   protected JMenuItem sortGroupMenuItem = new JMenuItem();
  96
  97   protected JMenu sortByAnnotScore = new JMenu();
  98
  99   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
 100
 101   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
 102
 103   protected JMenuItem PCAMenuItem = new JMenuItem();
 104
 105   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
 106
 107   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
 108
 109   BorderLayout borderLayout1 = new BorderLayout();
 110
 111   public JLabel statusBar = new JLabel();
 112
 113   protected JMenuItem saveAs = new JMenuItem();
 114
 115   protected JMenu outputTextboxMenu = new JMenu();
 116
 117   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
 118
 119   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
 120
 121   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
 122
 123   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
 124
 125   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
 126
 127   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
 128
 129   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
 130
 131   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 132
 133   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
 134
 135   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
 136
 137   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 138
 139   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
 140
 141   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
 142
 143   protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
 144
 145   // protected JRadioButtonMenuItem covariationColour = new
 146   // JRadioButtonMenuItem();
 147
 148   protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
 149
 150   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 151
 152   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
 153
 154   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 155
 156   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 157
 158   public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
 159
 160   JMenuItem htmlMenuItem = new JMenuItem();
 161
 162   JMenuItem overviewMenuItem = new JMenuItem();
 163
 164   protected JMenuItem undoMenuItem = new JMenuItem();
 165
 166   protected JMenuItem redoMenuItem = new JMenuItem();
 167
 168   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 169
 170   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 171
 172   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 173
 174   JMenuItem printMenuItem = new JMenuItem();
 175
 176   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 177
 178   JMenuItem findMenuItem = new JMenuItem();
 179
 180   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 181
 182   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 183
 184   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 185
 186   JMenuItem deleteGroups = new JMenuItem();
 187
 188   JMenuItem createGroup = new JMenuItem();
 189   JMenuItem unGroup = new JMenuItem();
 190
 191   JMenuItem delete = new JMenuItem();
 192
 193   JMenuItem copy = new JMenuItem();
 194
 195   JMenuItem cut = new JMenuItem();
 196
 197   JMenu pasteMenu = new JMenu();
 198
 199   JMenuItem pasteNew = new JMenuItem();
 200
 201   JMenuItem pasteThis = new JMenuItem();
 202
 203   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
 204
 205   JMenuItem createPNG = new JMenuItem();
 206
 207   protected JMenuItem font = new JMenuItem();
 208
 209   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 210
 211   JMenuItem epsFile = new JMenuItem();
 212
 213   JMenuItem LoadtreeMenuItem = new JMenuItem();
 214
 215   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 216
 217   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 218
 219   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 220
 221   protected JMenuItem modifyPID = new JMenuItem();
 222
 223   protected JMenuItem modifyConservation = new JMenuItem();
 224
 225   protected JMenu sortByTreeMenu = new JMenu();
 226
 227   protected JMenu sort = new JMenu();
 228
 229   protected JMenu calculateTree = new JMenu();
 230
 231   JMenu jMenu2 = new JMenu();
 232
 233   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 234
 235   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 236
 237   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 238
 239   protected ButtonGroup colours = new ButtonGroup();
 240
 241   JMenuItem vamsasStore = new JMenuItem();
 242
 243   protected JMenuItem showTranslation = new JMenuItem();
 244
 245   protected JMenuItem extractScores = new JMenuItem();
 246
 247   protected JMenu showProducts = new JMenu();
 248
 249   public JMenuItem openFeatureSettings = new JMenuItem();
 250
 251   JMenuItem fetchSequence = new JMenuItem();
 252
 253   JMenuItem annotationColour = new JMenuItem();
 254
 255   protected JMenuItem rnahelicesColour = new JMenuItem();
 256
 257   JMenuItem associatedData = new JMenuItem();
 258
 259   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 260
 261   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 262
 263   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 264
 265   JMenu addSequenceMenu = new JMenu();
 266
 267   JMenuItem addFromFile = new JMenuItem();
 268
 269   JMenuItem addFromText = new JMenuItem();
 270
 271   JMenuItem addFromURL = new JMenuItem();
 272
 273   JMenuItem exportAnnotations = new JMenuItem();
 274
 275   JMenuItem exportFeatures = new JMenuItem();
 276
 277   protected JPanel statusPanel = new JPanel();
 278
 279   GridLayout gridLayout1 = new GridLayout();
 280
 281   JMenu jMenu3 = new JMenu();
 282
 283   JMenuItem showAllSeqs = new JMenuItem();
 284
 285   JMenuItem showAllColumns = new JMenuItem();
 286
 287   JMenu hideMenu = new JMenu();
 288
 289   JMenuItem hideSelSequences = new JMenuItem();
 290
 291   JMenuItem hideSelColumns = new JMenuItem();
 292
 293   JMenuItem hideAllButSelection = new JMenuItem();
 294
 295   JMenuItem hideAllSelection = new JMenuItem();
 296
 297   JMenuItem showAllhidden = new JMenuItem();
 298
 299   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 300
 301   JMenuItem invertColSel = new JMenuItem();
 302
 303   protected JTabbedPane tabbedPane = new JTabbedPane();
 304
 305   JMenuItem save = new JMenuItem();
 306
 307   protected JMenuItem reload = new JMenuItem();
 308
 309   JMenuItem newView = new JMenuItem();
 310
 311   JMenuItem textColour = new JMenuItem();
 312
 313   JMenu formatMenu = new JMenu();
 314
 315   JMenu selectMenu = new JMenu();
 316
 317   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 318
 319   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 320
 321   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 322
 323   protected JMenuItem gatherViews = new JMenuItem();
 324
 325   protected JMenuItem expandViews = new JMenuItem();
 326
 327   JMenuItem pageSetup = new JMenuItem();
 328
 329   JMenuItem alignmentProperties = new JMenuItem();
 330
 331   JMenu tooltipSettingsMenu = new JMenu();
 332
 333   private JMenuItem justifyLeftMenuItem = new JMenuItem();
 334
 335   private JMenuItem justifyRightMenuItem = new JMenuItem();
 336
 337   JMenu autoAnnMenu = new JMenu();
 338
 339   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 340
 341   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 342
 343   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 344
 345   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 346
 347   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 348
 349   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 350
 351   private JMenuItem grpsFromSelection = new JMenuItem();
 352
 353   public GAlignFrame()
 354   {
 355     try
 356     {
 357       jbInit();
 358       setJMenuBar(alignFrameMenuBar);
 359
 360       // dynamically fill save as menu with available formats
 361       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 362       {
 363         JMenuItem item = new JMenuItem(
 364                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 365
 366         item.addActionListener(new java.awt.event.ActionListener()
 367         {
 368           public void actionPerformed(ActionEvent e)
 369           {
 370             outputText_actionPerformed(e);
 371           }
 372         });
 373
 374         outputTextboxMenu.add(item);
 375       }
 376     } catch (Exception e)
 377     {
 378     }
 379
 380     if (!new jalview.util.Platform().isAMac())
 381     {
 382       closeMenuItem.setMnemonic('C');
 383       outputTextboxMenu.setMnemonic('T');
 384       undoMenuItem.setMnemonic('Z');
 385       redoMenuItem.setMnemonic('0');
 386       copy.setMnemonic('C');
 387       cut.setMnemonic('U');
 388       pasteMenu.setMnemonic('P');
 389       reload.setMnemonic('R');
 390     }
 391
 392     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 393     {
 394       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 395               .getUserColourSchemes().keys();
 396
 397       while (userColours.hasMoreElements())
 398       {
 399         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 400                 userColours.nextElement().toString());
 401         radioItem.setName("USER_DEFINED");
 402         radioItem.addMouseListener(new MouseAdapter()
 403         {
 404           public void mousePressed(MouseEvent evt)
 405           {
 406             if (evt.isControlDown()
 407                     || SwingUtilities.isRightMouseButton(evt))
 408             {
 409               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 410
 411               int option = JOptionPane.showInternalConfirmDialog(
 412                       jalview.gui.Desktop.desktop,
 413                       MessageManager.getString("label.remove_from_default_list"),
 414                       MessageManager.getString("label.remove_user_defined_colour"),
 415                       JOptionPane.YES_NO_OPTION);
 416               if (option == JOptionPane.YES_OPTION)
 417               {
 418                 jalview.gui.UserDefinedColours
 419                         .removeColourFromDefaults(radioItem.getText());
 420                 colourMenu.remove(radioItem);
 421               }
 422               else
 423               {
 424                 radioItem.addActionListener(new ActionListener()
 425                 {
 426                   public void actionPerformed(ActionEvent evt)
 427                   {
 428                     userDefinedColour_actionPerformed(evt);
 429                   }
 430                 });
 431               }
 432             }
 433           }
 434         });
 435         radioItem.addActionListener(new ActionListener()
 436         {
 437           public void actionPerformed(ActionEvent evt)
 438           {
 439             userDefinedColour_actionPerformed(evt);
 440           }
 441         });
 442         colourMenu.insert(radioItem, 15);
 443         colours.add(radioItem);
 444       }
 445     }
 446     colours.add(noColourmenuItem);
 447     colours.add(clustalColour);
 448     colours.add(zappoColour);
 449     colours.add(taylorColour);
 450     colours.add(hydrophobicityColour);
 451     colours.add(helixColour);
 452     colours.add(strandColour);
 453     colours.add(turnColour);
 454     colours.add(buriedColour);
 455     colours.add(userDefinedColour);
 456     colours.add(PIDColour);
 457     colours.add(BLOSUM62Colour);
 458     colours.add(nucleotideColour);
 459     colours.add(purinePyrimidineColour);
 460     // colours.add(covariationColour);
 461     colours.add(tcoffeeColour);
 462     colours.add(RNAInteractionColour);
 463     setColourSelected(jalview.bin.Cache
 464             .getDefault("DEFAULT_COLOUR", "None"));
 465
 466   }
 467
 468   public void setColourSelected(String defaultColour)
 469   {
 470
 471     if (defaultColour != null)
 472     {
 473       int index = ColourSchemeProperty
 474               .getColourIndexFromName(defaultColour);
 475
 476       switch (index)
 477       {
 478       case ColourSchemeProperty.CLUSTAL:
 479         clustalColour.setSelected(true);
 480
 481         break;
 482
 483       case ColourSchemeProperty.BLOSUM:
 484         BLOSUM62Colour.setSelected(true);
 485
 486         break;
 487
 488       case ColourSchemeProperty.PID:
 489         PIDColour.setSelected(true);
 490
 491         break;
 492
 493       case ColourSchemeProperty.ZAPPO:
 494         zappoColour.setSelected(true);
 495
 496         break;
 497
 498       case ColourSchemeProperty.TAYLOR:
 499         taylorColour.setSelected(true);
 500         break;
 501
 502       case ColourSchemeProperty.HYDROPHOBIC:
 503         hydrophobicityColour.setSelected(true);
 504
 505         break;
 506
 507       case ColourSchemeProperty.HELIX:
 508         helixColour.setSelected(true);
 509
 510         break;
 511
 512       case ColourSchemeProperty.STRAND:
 513         strandColour.setSelected(true);
 514
 515         break;
 516
 517       case ColourSchemeProperty.TURN:
 518         turnColour.setSelected(true);
 519
 520         break;
 521
 522       case ColourSchemeProperty.BURIED:
 523         buriedColour.setSelected(true);
 524
 525         break;
 526
 527       case ColourSchemeProperty.NUCLEOTIDE:
 528         nucleotideColour.setSelected(true);
 529
 530         break;
 531
 532       case ColourSchemeProperty.TCOFFEE:
 533         tcoffeeColour.setSelected(true);
 534         break;
 535
 536       case ColourSchemeProperty.PURINEPYRIMIDINE:
 537         purinePyrimidineColour.setSelected(true);
 538
 539         break;
 540
 541       case ColourSchemeProperty.RNAINTERACTION:
 542           RNAInteractionColour.setSelected(true);
 543
 544           break;
 545       /*
 546        * case ColourSchemeProperty.COVARIATION:
 547        * covariationColour.setSelected(true);
 548        *
 549        * break;
 550        */
 551       case ColourSchemeProperty.USER_DEFINED:
 552         userDefinedColour.setSelected(true);
 553
 554         break;
 555       case ColourSchemeProperty.NONE:
 556       default:
 557         noColourmenuItem.setSelected(true);
 558         break;
 559
 560       }
 561     }
 562
 563   }
 564
 565   private void jbInit() throws Exception
 566   {
 567     fileMenu.setText("File");
 568     saveAs.setText("Save As...");
 569     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 570             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
 571                     .getMenuShortcutKeyMask()
 572                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 573     saveAs.addActionListener(new ActionListener()
 574     {
 575       public void actionPerformed(ActionEvent e)
 576       {
 577         saveAs_actionPerformed(e);
 578       }
 579     });
 580     closeMenuItem.setText("Close");
 581     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 582             java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
 583                     .getMenuShortcutKeyMask(), false));
 584     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 585     {
 586       public void actionPerformed(ActionEvent e)
 587       {
 588         closeMenuItem_actionPerformed(false);
 589       }
 590     });
 591     editMenu.setText("Edit");
 592     viewMenu.setText("View");
 593     colourMenu.setText("Colour");
 594     calculateMenu.setText("Calculate");
 595     webService.setText("Web Service");
 596     selectAllSequenceMenuItem.setText("Select All");
 597     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 598             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
 599                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 600     selectAllSequenceMenuItem
 601             .addActionListener(new java.awt.event.ActionListener()
 602             {
 603               public void actionPerformed(ActionEvent e)
 604               {
 605                 selectAllSequenceMenuItem_actionPerformed(e);
 606               }
 607             });
 608     deselectAllSequenceMenuItem.setText("Deselect All");
 609     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 610             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 611     deselectAllSequenceMenuItem
 612             .addActionListener(new java.awt.event.ActionListener()
 613             {
 614               public void actionPerformed(ActionEvent e)
 615               {
 616                 deselectAllSequenceMenuItem_actionPerformed(e);
 617               }
 618             });
 619     invertSequenceMenuItem.setText("Invert Sequence Selection");
 620     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 621             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
 622                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 623     invertSequenceMenuItem
 624             .addActionListener(new java.awt.event.ActionListener()
 625             {
 626               public void actionPerformed(ActionEvent e)
 627               {
 628                 invertSequenceMenuItem_actionPerformed(e);
 629               }
 630             });
 631     grpsFromSelection.setText("Make Groups For Selection");
 632     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
 633     {
 634       public void actionPerformed(ActionEvent e)
 635       {
 636         makeGrpsFromSelection_actionPerformed(e);
 637       }
 638     });
 639
 640     remove2LeftMenuItem.setText("Remove Left");
 641     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 642             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
 643                     .getMenuShortcutKeyMask(), false));
 644     remove2LeftMenuItem
 645             .addActionListener(new java.awt.event.ActionListener()
 646             {
 647               public void actionPerformed(ActionEvent e)
 648               {
 649                 remove2LeftMenuItem_actionPerformed(e);
 650               }
 651             });
 652     remove2RightMenuItem.setText("Remove Right");
 653     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 654             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
 655                     .getMenuShortcutKeyMask(), false));
 656     remove2RightMenuItem
 657             .addActionListener(new java.awt.event.ActionListener()
 658             {
 659               public void actionPerformed(ActionEvent e)
 660               {
 661                 remove2RightMenuItem_actionPerformed(e);
 662               }
 663             });
 664     removeGappedColumnMenuItem.setText("Remove Empty Columns");
 665     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
 666             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 667                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 668     removeGappedColumnMenuItem
 669             .addActionListener(new java.awt.event.ActionListener()
 670             {
 671               public void actionPerformed(ActionEvent e)
 672               {
 673                 removeGappedColumnMenuItem_actionPerformed(e);
 674               }
 675             });
 676     removeAllGapsMenuItem.setText("Remove All Gaps");
 677     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
 678             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 679                     .getDefaultToolkit().getMenuShortcutKeyMask()
 680                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 681     removeAllGapsMenuItem
 682             .addActionListener(new java.awt.event.ActionListener()
 683             {
 684               public void actionPerformed(ActionEvent e)
 685               {
 686                 removeAllGapsMenuItem_actionPerformed(e);
 687               }
 688             });
 689     justifyLeftMenuItem.setText("Left Justify Alignment");
 690     justifyLeftMenuItem
 691             .addActionListener(new java.awt.event.ActionListener()
 692             {
 693               public void actionPerformed(ActionEvent e)
 694               {
 695                 justifyLeftMenuItem_actionPerformed(e);
 696               }
 697             });
 698     justifyRightMenuItem.setText("Right Justify Alignment");
 699     justifyRightMenuItem
 700             .addActionListener(new java.awt.event.ActionListener()
 701             {
 702               public void actionPerformed(ActionEvent e)
 703               {
 704                 justifyRightMenuItem_actionPerformed(e);
 705               }
 706             });
 707     viewBoxesMenuItem.setText("Boxes");
 708     viewBoxesMenuItem.setState(true);
 709     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 710     {
 711       public void actionPerformed(ActionEvent e)
 712       {
 713         viewBoxesMenuItem_actionPerformed(e);
 714       }
 715     });
 716     viewTextMenuItem.setText("Text");
 717     viewTextMenuItem.setState(true);
 718     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 719     {
 720       public void actionPerformed(ActionEvent e)
 721       {
 722         viewTextMenuItem_actionPerformed(e);
 723       }
 724     });
 725     showNonconservedMenuItem.setText("Show nonconserved");
 726     showNonconservedMenuItem.setState(false);
 727     showNonconservedMenuItem
 728             .addActionListener(new java.awt.event.ActionListener()
 729             {
 730               public void actionPerformed(ActionEvent e)
 731               {
 732                 showUnconservedMenuItem_actionPerformed(e);
 733               }
 734             });
 735     sortPairwiseMenuItem.setText("by Pairwise Identity");
 736     sortPairwiseMenuItem
 737             .addActionListener(new java.awt.event.ActionListener()
 738             {
 739               public void actionPerformed(ActionEvent e)
 740               {
 741                 sortPairwiseMenuItem_actionPerformed(e);
 742               }
 743             });
 744     sortIDMenuItem.setText("by ID");
 745     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 746     {
 747       public void actionPerformed(ActionEvent e)
 748       {
 749         sortIDMenuItem_actionPerformed(e);
 750       }
 751     });
 752     sortLengthMenuItem.setText("By Length");
 753     sortLengthMenuItem
 754             .addActionListener(new java.awt.event.ActionListener()
 755             {
 756               public void actionPerformed(ActionEvent e)
 757               {
 758                 sortLengthMenuItem_actionPerformed(e);
 759               }
 760             });
 761     sortGroupMenuItem.setText("by Group");
 762     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 763     {
 764       public void actionPerformed(ActionEvent e)
 765       {
 766         sortGroupMenuItem_actionPerformed(e);
 767       }
 768     });
 769     removeRedundancyMenuItem.setText("Remove Redundancy...");
 770     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
 771             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
 772                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 773     removeRedundancyMenuItem
 774             .addActionListener(new java.awt.event.ActionListener()
 775             {
 776               public void actionPerformed(ActionEvent e)
 777               {
 778                 removeRedundancyMenuItem_actionPerformed(e);
 779               }
 780             });
 781     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
 782     pairwiseAlignmentMenuItem
 783             .addActionListener(new java.awt.event.ActionListener()
 784             {
 785               public void actionPerformed(ActionEvent e)
 786               {
 787                 pairwiseAlignmentMenuItem_actionPerformed(e);
 788               }
 789             });
 790     PCAMenuItem.setText("Principal Component Analysis");
 791     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 792     {
 793       public void actionPerformed(ActionEvent e)
 794       {
 795         PCAMenuItem_actionPerformed(e);
 796       }
 797     });
 798     averageDistanceTreeMenuItem
 799             .setText("Average Distance Using % Identity");
 800     averageDistanceTreeMenuItem
 801             .addActionListener(new java.awt.event.ActionListener()
 802             {
 803               public void actionPerformed(ActionEvent e)
 804               {
 805                 averageDistanceTreeMenuItem_actionPerformed(e);
 806               }
 807             });
 808     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
 809     neighbourTreeMenuItem
 810             .addActionListener(new java.awt.event.ActionListener()
 811             {
 812               public void actionPerformed(ActionEvent e)
 813               {
 814                 neighbourTreeMenuItem_actionPerformed(e);
 815               }
 816             });
 817     this.getContentPane().setLayout(borderLayout1);
 818     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 819     statusBar.setBackground(Color.white);
 820     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 821     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 822     statusBar.setText("Status bar");
 823     outputTextboxMenu.setText("Output to Textbox");
 824     clustalColour.setText("Clustalx");
 825
 826     clustalColour.addActionListener(new java.awt.event.ActionListener()
 827     {
 828       public void actionPerformed(ActionEvent e)
 829       {
 830         clustalColour_actionPerformed(e);
 831       }
 832     });
 833     zappoColour.setText("Zappo");
 834     zappoColour.addActionListener(new java.awt.event.ActionListener()
 835     {
 836       public void actionPerformed(ActionEvent e)
 837       {
 838         zappoColour_actionPerformed(e);
 839       }
 840     });
 841     taylorColour.setText("Taylor");
 842     taylorColour.addActionListener(new java.awt.event.ActionListener()
 843     {
 844       public void actionPerformed(ActionEvent e)
 845       {
 846         taylorColour_actionPerformed(e);
 847       }
 848     });
 849     hydrophobicityColour.setText("Hydrophobicity");
 850     hydrophobicityColour
 851             .addActionListener(new java.awt.event.ActionListener()
 852             {
 853               public void actionPerformed(ActionEvent e)
 854               {
 855                 hydrophobicityColour_actionPerformed(e);
 856               }
 857             });
 858     helixColour.setText("Helix Propensity");
 859     helixColour.addActionListener(new java.awt.event.ActionListener()
 860     {
 861       public void actionPerformed(ActionEvent e)
 862       {
 863         helixColour_actionPerformed(e);
 864       }
 865     });
 866     strandColour.setText("Strand Propensity");
 867     strandColour.addActionListener(new java.awt.event.ActionListener()
 868     {
 869       public void actionPerformed(ActionEvent e)
 870       {
 871         strandColour_actionPerformed(e);
 872       }
 873     });
 874     turnColour.setText("Turn Propensity");
 875     turnColour.addActionListener(new java.awt.event.ActionListener()
 876     {
 877       public void actionPerformed(ActionEvent e)
 878       {
 879         turnColour_actionPerformed(e);
 880       }
 881     });
 882     buriedColour.setText("Buried Index");
 883     buriedColour.addActionListener(new java.awt.event.ActionListener()
 884     {
 885       public void actionPerformed(ActionEvent e)
 886       {
 887         buriedColour_actionPerformed(e);
 888       }
 889     });
 890     userDefinedColour.setText("User Defined...");
 891     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 892     {
 893       public void actionPerformed(ActionEvent e)
 894       {
 895         userDefinedColour_actionPerformed(e);
 896       }
 897     });
 898     PIDColour.setText("Percentage Identity");
 899     PIDColour.addActionListener(new java.awt.event.ActionListener()
 900     {
 901       public void actionPerformed(ActionEvent e)
 902       {
 903         PIDColour_actionPerformed(e);
 904       }
 905     });
 906     BLOSUM62Colour.setText("BLOSUM62 Score");
 907     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 908     {
 909       public void actionPerformed(ActionEvent e)
 910       {
 911         BLOSUM62Colour_actionPerformed(e);
 912       }
 913     });
 914     nucleotideColour.setText("Nucleotide");
 915     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
 916     {
 917       public void actionPerformed(ActionEvent e)
 918       {
 919         nucleotideColour_actionPerformed(e);
 920       }
 921     });
 922
 923     purinePyrimidineColour.setText("Purine/Pyrimidine");
 924     purinePyrimidineColour.addActionListener(new java.awt.event.ActionListener()
 925             {
 926               public void actionPerformed(ActionEvent e)
 927               {
 928                 purinePyrimidineColour_actionPerformed(e);
 929               }
 930             });
 931
 932     RNAInteractionColour.setText("RNA Interaction type");
 933     RNAInteractionColour.addActionListener(new java.awt.event.ActionListener()
 934             {
 935               public void actionPerformed(ActionEvent e)
 936               {
 937                   RNAInteractionColour_actionPerformed(e);
 938               }
 939             });
 940     /*
 941      * covariationColour.setText("Covariation");
 942      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
 943      * public void actionPerformed(ActionEvent e) {
 944      * covariationColour_actionPerformed(e); } });
 945      */
 946
 947     avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
 948     avDistanceTreeBlosumMenuItem
 949             .addActionListener(new java.awt.event.ActionListener()
 950             {
 951               public void actionPerformed(ActionEvent e)
 952               {
 953                 avTreeBlosumMenuItem_actionPerformed(e);
 954               }
 955             });
 956     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
 957     njTreeBlosumMenuItem
 958             .addActionListener(new java.awt.event.ActionListener()
 959             {
 960               public void actionPerformed(ActionEvent e)
 961               {
 962                 njTreeBlosumMenuItem_actionPerformed(e);
 963               }
 964             });
 965     annotationPanelMenuItem.setActionCommand("");
 966     annotationPanelMenuItem.setText("Show Annotations");
 967     annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
 968             "SHOW_ANNOTATIONS", true));
 969     annotationPanelMenuItem
 970             .addActionListener(new java.awt.event.ActionListener()
 971             {
 972               public void actionPerformed(ActionEvent e)
 973               {
 974                 annotationPanelMenuItem_actionPerformed(e);
 975               }
 976             });
 977     colourTextMenuItem.setText("Colour Text");
 978     colourTextMenuItem
 979             .addActionListener(new java.awt.event.ActionListener()
 980             {
 981               public void actionPerformed(ActionEvent e)
 982               {
 983                 colourTextMenuItem_actionPerformed(e);
 984               }
 985             });
 986     htmlMenuItem.setText("HTML");
 987     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
 988     {
 989       public void actionPerformed(ActionEvent e)
 990       {
 991         htmlMenuItem_actionPerformed(e);
 992       }
 993     });
 994     overviewMenuItem.setText("Overview Window");
 995     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
 996     {
 997       public void actionPerformed(ActionEvent e)
 998       {
 999         overviewMenuItem_actionPerformed(e);
1000       }
1001     });
1002     undoMenuItem.setEnabled(false);
1003     undoMenuItem.setText("Undo");
1004     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1005             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1006                     .getMenuShortcutKeyMask(), false));
1007     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1008     {
1009       public void actionPerformed(ActionEvent e)
1010       {
1011         undoMenuItem_actionPerformed(e);
1012       }
1013     });
1014     redoMenuItem.setEnabled(false);
1015     redoMenuItem.setText("Redo");
1016     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1017             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1018                     .getMenuShortcutKeyMask(), false));
1019     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1020     {
1021       public void actionPerformed(ActionEvent e)
1022       {
1023         redoMenuItem_actionPerformed(e);
1024       }
1025     });
1026     conservationMenuItem.setText("By Conservation");
1027     conservationMenuItem
1028             .addActionListener(new java.awt.event.ActionListener()
1029             {
1030               public void actionPerformed(ActionEvent e)
1031               {
1032                 conservationMenuItem_actionPerformed(e);
1033               }
1034             });
1035     noColourmenuItem.setText("None");
1036     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1037     {
1038       public void actionPerformed(ActionEvent e)
1039       {
1040         noColourmenuItem_actionPerformed(e);
1041       }
1042     });
1043     wrapMenuItem.setText("Wrap");
1044     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1045     {
1046       public void actionPerformed(ActionEvent e)
1047       {
1048         wrapMenuItem_actionPerformed(e);
1049       }
1050     });
1051     printMenuItem.setText("Print ...");
1052     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1053             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1054                     .getMenuShortcutKeyMask(), false));
1055     printMenuItem.addActionListener(new java.awt.event.ActionListener()
1056     {
1057       public void actionPerformed(ActionEvent e)
1058       {
1059         printMenuItem_actionPerformed(e);
1060       }
1061     });
1062     renderGapsMenuItem.setText("Show Gaps");
1063     renderGapsMenuItem.setState(true);
1064     renderGapsMenuItem
1065             .addActionListener(new java.awt.event.ActionListener()
1066             {
1067               public void actionPerformed(ActionEvent e)
1068               {
1069                 renderGapsMenuItem_actionPerformed(e);
1070               }
1071             });
1072     findMenuItem.setText("Find...");
1073     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1074             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1075                     .getMenuShortcutKeyMask(), false));
1076     findMenuItem.addActionListener(new java.awt.event.ActionListener()
1077     {
1078       public void actionPerformed(ActionEvent e)
1079       {
1080         findMenuItem_actionPerformed(e);
1081       }
1082     });
1083     abovePIDThreshold.setText("Above Identity Threshold");
1084     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1085     {
1086       public void actionPerformed(ActionEvent e)
1087       {
1088         abovePIDThreshold_actionPerformed(e);
1089       }
1090     });
1091     showSeqFeatures.setText("Show Sequence Features");
1092     showSeqFeatures.addActionListener(new ActionListener()
1093     {
1094       public void actionPerformed(ActionEvent actionEvent)
1095       {
1096         showSeqFeatures_actionPerformed(actionEvent);
1097       }
1098     });
1099     /*
1100      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1101      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1102      * void actionPerformed(ActionEvent actionEvent) {
1103      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1104      */
1105     showDbRefsMenuitem.setText("Show Database Refs");
1106     showDbRefsMenuitem.addActionListener(new ActionListener()
1107     {
1108
1109       public void actionPerformed(ActionEvent e)
1110       {
1111         showDbRefs_actionPerformed(e);
1112       }
1113
1114     });
1115     showNpFeatsMenuitem.setText("Show Non-Positional Features");
1116     showNpFeatsMenuitem.addActionListener(new ActionListener()
1117     {
1118
1119       public void actionPerformed(ActionEvent e)
1120       {
1121         showNpFeats_actionPerformed(e);
1122       }
1123
1124     });
1125     showGroupConservation.setText("Group Conservation");
1126     showGroupConservation.addActionListener(new ActionListener()
1127     {
1128
1129       public void actionPerformed(ActionEvent e)
1130       {
1131         showGroupConservation_actionPerformed(e);
1132       }
1133
1134     });
1135
1136     showGroupConsensus.setText("Group Consensus");
1137     showGroupConsensus.addActionListener(new ActionListener()
1138     {
1139
1140       public void actionPerformed(ActionEvent e)
1141       {
1142         showGroupConsensus_actionPerformed(e);
1143       }
1144
1145     });
1146     showConsensusHistogram.setText("Show Consensus Histogram");
1147     showConsensusHistogram.addActionListener(new ActionListener()
1148     {
1149
1150       public void actionPerformed(ActionEvent e)
1151       {
1152         showConsensusHistogram_actionPerformed(e);
1153       }
1154
1155     });
1156     showSequenceLogo.setText("Show Consensus Logo");
1157     showSequenceLogo.addActionListener(new ActionListener()
1158     {
1159
1160       public void actionPerformed(ActionEvent e)
1161       {
1162         showSequenceLogo_actionPerformed(e);
1163       }
1164
1165     });
1166     normaliseSequenceLogo.setText("Normalise Consensus Logo");
1167     normaliseSequenceLogo.addActionListener(new ActionListener()
1168     {
1169
1170       public void actionPerformed(ActionEvent e)
1171       {
1172         normaliseSequenceLogo_actionPerformed(e);
1173       }
1174
1175     });
1176     applyAutoAnnotationSettings.setText("Apply to all groups");
1177     applyAutoAnnotationSettings.setState(false);
1178     applyAutoAnnotationSettings.setVisible(true);
1179     applyAutoAnnotationSettings.addActionListener(new ActionListener()
1180     {
1181
1182       public void actionPerformed(ActionEvent e)
1183       {
1184         applyAutoAnnotationSettings_actionPerformed(e);
1185       }
1186
1187     });
1188
1189     nucleotideColour.setText("Nucleotide");
1190     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1191     {
1192       public void actionPerformed(ActionEvent e)
1193       {
1194         nucleotideColour_actionPerformed(e);
1195       }
1196     });
1197
1198     tcoffeeColour.setText("T-Coffee scores");
1199     tcoffeeColour.setEnabled(false);
1200     tcoffeeColour.addActionListener(new ActionListener()
1201     {
1202
1203       @Override
1204       public void actionPerformed(ActionEvent e)
1205       {
1206         tcoffeeColorScheme_actionPerformed(e);
1207       }
1208     });
1209
1210     deleteGroups.setText("Undefine groups");
1211     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1212             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1213                     .getMenuShortcutKeyMask(), false));
1214     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1215     {
1216       public void actionPerformed(ActionEvent e)
1217       {
1218         deleteGroups_actionPerformed(e);
1219       }
1220     });
1221     createGroup.setText("Create group");
1222     createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1223             java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1224                     .getMenuShortcutKeyMask(), false));
1225     createGroup.addActionListener(new java.awt.event.ActionListener()
1226     {
1227       public void actionPerformed(ActionEvent e)
1228       {
1229         createGroup_actionPerformed(e);
1230       }
1231     });
1232     unGroup.setText("Remove Group");
1233     unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1234             java.awt.event.KeyEvent.VK_G,Toolkit.getDefaultToolkit()
1235                     .getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));
1236     unGroup.addActionListener(new java.awt.event.ActionListener()
1237     {
1238       public void actionPerformed(ActionEvent e)
1239       {
1240         unGroup_actionPerformed(e);
1241       }
1242     });
1243     copy.setText("Copy");
1244     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1245             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1246                     .getMenuShortcutKeyMask(), false));
1247
1248     copy.addActionListener(new java.awt.event.ActionListener()
1249     {
1250       public void actionPerformed(ActionEvent e)
1251       {
1252         copy_actionPerformed(e);
1253       }
1254     });
1255     cut.setText("Cut");
1256     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1257             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1258                     .getMenuShortcutKeyMask(), false));
1259     cut.addActionListener(new java.awt.event.ActionListener()
1260     {
1261       public void actionPerformed(ActionEvent e)
1262       {
1263         cut_actionPerformed(e);
1264       }
1265     });
1266     delete.setText("Delete");
1267     delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1268             java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1269     delete.addActionListener(new java.awt.event.ActionListener()
1270     {
1271       public void actionPerformed(ActionEvent e)
1272       {
1273         delete_actionPerformed(e);
1274       }
1275     });
1276     pasteMenu.setText("Paste");
1277     pasteNew.setText("To New Alignment");
1278     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1279             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1280                     .getMenuShortcutKeyMask()
1281                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1282     pasteNew.addActionListener(new java.awt.event.ActionListener()
1283     {
1284       public void actionPerformed(ActionEvent e)
1285       {
1286         pasteNew_actionPerformed(e);
1287       }
1288     });
1289     pasteThis.setText("Add To This Alignment");
1290     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1291             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1292                     .getMenuShortcutKeyMask(), false));
1293     pasteThis.addActionListener(new java.awt.event.ActionListener()
1294     {
1295       public void actionPerformed(ActionEvent e)
1296       {
1297         pasteThis_actionPerformed(e);
1298       }
1299     });
1300     applyToAllGroups.setText("Apply Colour To All Groups");
1301     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1302     {
1303       public void actionPerformed(ActionEvent e)
1304       {
1305         applyToAllGroups_actionPerformed(e);
1306       }
1307     });
1308     createPNG.addActionListener(new java.awt.event.ActionListener()
1309     {
1310       public void actionPerformed(ActionEvent e)
1311       {
1312         createPNG(null);
1313       }
1314     });
1315     createPNG.setActionCommand("Save As PNG Image");
1316     createPNG.setText("PNG");
1317     font.setText("Font...");
1318     font.addActionListener(new java.awt.event.ActionListener()
1319     {
1320       public void actionPerformed(ActionEvent e)
1321       {
1322         font_actionPerformed(e);
1323       }
1324     });
1325
1326     seqLimits.setText("Show Sequence Limits");
1327     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1328     seqLimits.addActionListener(new java.awt.event.ActionListener()
1329     {
1330       public void actionPerformed(ActionEvent e)
1331       {
1332         seqLimit_actionPerformed(e);
1333       }
1334     });
1335     epsFile.setText("EPS");
1336     epsFile.addActionListener(new java.awt.event.ActionListener()
1337     {
1338       public void actionPerformed(ActionEvent e)
1339       {
1340         createEPS(null);
1341       }
1342     });
1343     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1344     LoadtreeMenuItem.setText("Load Associated Tree");
1345     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1346     {
1347       public void actionPerformed(ActionEvent e)
1348       {
1349         LoadtreeMenuItem_actionPerformed(e);
1350       }
1351     });
1352
1353     scaleAbove.setVisible(false);
1354     scaleAbove.setText("Scale Above");
1355     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1356     {
1357       public void actionPerformed(ActionEvent e)
1358       {
1359         scaleAbove_actionPerformed(e);
1360       }
1361     });
1362     scaleLeft.setVisible(false);
1363     scaleLeft.setSelected(true);
1364     scaleLeft.setText("Scale Left");
1365     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1366     {
1367       public void actionPerformed(ActionEvent e)
1368       {
1369         scaleLeft_actionPerformed(e);
1370       }
1371     });
1372     scaleRight.setVisible(false);
1373     scaleRight.setSelected(true);
1374     scaleRight.setText("Scale Right");
1375     scaleRight.addActionListener(new java.awt.event.ActionListener()
1376     {
1377       public void actionPerformed(ActionEvent e)
1378       {
1379         scaleRight_actionPerformed(e);
1380       }
1381     });
1382     centreColumnLabelsMenuItem.setVisible(true);
1383     centreColumnLabelsMenuItem.setState(false);
1384     centreColumnLabelsMenuItem.setText("Centre Column Labels");
1385     centreColumnLabelsMenuItem
1386             .addActionListener(new java.awt.event.ActionListener()
1387             {
1388               public void actionPerformed(ActionEvent e)
1389               {
1390                 centreColumnLabels_actionPerformed(e);
1391               }
1392             });
1393     followHighlightMenuItem.setVisible(true);
1394     followHighlightMenuItem.setState(true);
1395     followHighlightMenuItem.setText("Automatic Scrolling");
1396     followHighlightMenuItem.addActionListener(new ActionListener()
1397     {
1398
1399       public void actionPerformed(ActionEvent e)
1400       {
1401         followHighlight_actionPerformed();
1402       }
1403
1404     });
1405
1406     modifyPID.setText("Modify Identity Threshold...");
1407     modifyPID.addActionListener(new java.awt.event.ActionListener()
1408     {
1409       public void actionPerformed(ActionEvent e)
1410       {
1411         modifyPID_actionPerformed(e);
1412       }
1413     });
1414     modifyConservation.setText("Modify Conservation Threshold...");
1415     modifyConservation
1416             .addActionListener(new java.awt.event.ActionListener()
1417             {
1418               public void actionPerformed(ActionEvent e)
1419               {
1420                 modifyConservation_actionPerformed(e);
1421               }
1422             });
1423     sortByTreeMenu.setText("By Tree Order");
1424     sort.setText("Sort");
1425     sort.addMenuListener(new MenuListener()
1426     {
1427       public void menuSelected(MenuEvent e)
1428       {
1429         buildTreeMenu();
1430       }
1431
1432       public void menuDeselected(MenuEvent e)
1433       {
1434       }
1435
1436       public void menuCanceled(MenuEvent e)
1437       {
1438       }
1439     });
1440     sortByAnnotScore.setText("by Score");
1441     sort.add(sortByAnnotScore);
1442     sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1443     {
1444
1445       public void menuCanceled(MenuEvent e)
1446       {
1447       }
1448
1449       public void menuDeselected(MenuEvent e)
1450       {
1451       }
1452
1453       public void menuSelected(MenuEvent e)
1454       {
1455         buildSortByAnnotationScoresMenu();
1456       }
1457     });
1458     sortByAnnotScore.setVisible(false);
1459
1460     calculateTree.setText("Calculate Tree");
1461
1462     jMenu2.setText("Export Image");
1463     padGapsMenuitem.setText("Pad Gaps");
1464     padGapsMenuitem.setState(jalview.bin.Cache
1465             .getDefault("PAD_GAPS", false));
1466     padGapsMenuitem.addActionListener(new ActionListener()
1467     {
1468       public void actionPerformed(ActionEvent e)
1469       {
1470         padGapsMenuitem_actionPerformed(e);
1471       }
1472     });
1473     vamsasStore.setVisible(false);
1474     vamsasStore.setText("VAMSAS store");
1475     vamsasStore.addActionListener(new ActionListener()
1476     {
1477       public void actionPerformed(ActionEvent e)
1478       {
1479         vamsasStore_actionPerformed(e);
1480       }
1481     });
1482     showTranslation.setText("Translate cDNA");
1483     showTranslation.addActionListener(new ActionListener()
1484     {
1485       public void actionPerformed(ActionEvent e)
1486       {
1487         showTranslation_actionPerformed(e);
1488       }
1489     });
1490     extractScores.setText("Extract Scores...");
1491     extractScores.addActionListener(new ActionListener()
1492     {
1493       public void actionPerformed(ActionEvent e)
1494       {
1495         extractScores_actionPerformed(e);
1496       }
1497     });
1498     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1499     // score extraction
1500     showProducts.setText("Get Cross References");
1501     /*
1502      * showProducts.addActionListener(new ActionListener() {
1503      *
1504      * public void actionPerformed(ActionEvent e) {
1505      * showProducts_actionPerformed(e); } });
1506      */
1507     openFeatureSettings.setText("Feature Settings...");
1508     openFeatureSettings.addActionListener(new ActionListener()
1509     {
1510       public void actionPerformed(ActionEvent e)
1511       {
1512         featureSettings_actionPerformed(e);
1513       }
1514     });
1515     fetchSequence.setText("Fetch Sequence(s)...");
1516     fetchSequence.addActionListener(new ActionListener()
1517     {
1518       public void actionPerformed(ActionEvent e)
1519       {
1520         fetchSequence_actionPerformed(e);
1521       }
1522     });
1523
1524     annotationColour.setText("By Annotation...");
1525     annotationColour.addActionListener(new ActionListener()
1526     {
1527       public void actionPerformed(ActionEvent e)
1528       {
1529         annotationColour_actionPerformed(e);
1530       }
1531     });
1532
1533     rnahelicesColour.setText("By RNA helices");
1534     rnahelicesColour.addActionListener(new ActionListener()
1535     {
1536       public void actionPerformed(ActionEvent e)
1537       {
1538         rnahelicesColour_actionPerformed(e);
1539       }
1540     });
1541
1542     associatedData.setText("Load Features / Annotations");
1543     associatedData.addActionListener(new ActionListener()
1544     {
1545       public void actionPerformed(ActionEvent e)
1546       {
1547         associatedData_actionPerformed(e);
1548       }
1549     });
1550     autoCalculate.setText("Autocalculate Consensus");
1551     autoCalculate.setState(jalview.bin.Cache.getDefault(
1552             "AUTO_CALC_CONSENSUS", true));
1553     autoCalculate.addActionListener(new ActionListener()
1554     {
1555       public void actionPerformed(ActionEvent e)
1556       {
1557         autoCalculate_actionPerformed(e);
1558       }
1559     });
1560     sortByTree.setText("Sort Alignment With New Tree");
1561     sortByTree
1562             .setToolTipText("<html>Enable this to automatically sort<br>the alignment when you open<br> a new tree.");
1563     sortByTree
1564             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1565     sortByTree.addActionListener(new ActionListener()
1566     {
1567       public void actionPerformed(ActionEvent e)
1568       {
1569         sortByTreeOption_actionPerformed(e);
1570       }
1571     });
1572
1573     listenToViewSelections.setText("Listen for selections");
1574     listenToViewSelections
1575             .setToolTipText("<html>When selected, selections in this view will mirror<br>selections made on the same sequences in other views.");
1576     listenToViewSelections.setState(false);
1577     listenToViewSelections.addActionListener(new ActionListener()
1578     {
1579       public void actionPerformed(ActionEvent e)
1580       {
1581         listenToViewSelections_actionPerformed(e);
1582       }
1583     });
1584
1585     addSequenceMenu.setText("Add Sequences");
1586     addFromFile.setText("From File");
1587     addFromFile.addActionListener(new ActionListener()
1588     {
1589       public void actionPerformed(ActionEvent e)
1590       {
1591         addFromFile_actionPerformed(e);
1592       }
1593     });
1594     addFromText.setText("From Textbox");
1595     addFromText.addActionListener(new ActionListener()
1596     {
1597       public void actionPerformed(ActionEvent e)
1598       {
1599         addFromText_actionPerformed(e);
1600       }
1601     });
1602     addFromURL.setText("From URL");
1603     addFromURL.addActionListener(new ActionListener()
1604     {
1605       public void actionPerformed(ActionEvent e)
1606       {
1607         addFromURL_actionPerformed(e);
1608       }
1609     });
1610     exportFeatures.setText("Export Features...");
1611     exportFeatures.addActionListener(new ActionListener()
1612     {
1613       public void actionPerformed(ActionEvent e)
1614       {
1615         exportFeatures_actionPerformed(e);
1616       }
1617     });
1618     exportAnnotations.setText("Export Annotations...");
1619     exportAnnotations.addActionListener(new ActionListener()
1620     {
1621       public void actionPerformed(ActionEvent e)
1622       {
1623         exportAnnotations_actionPerformed(e);
1624       }
1625     });
1626     statusPanel.setLayout(gridLayout1);
1627     jMenu3.setText("Show");
1628     showAllSeqs.setText("All Sequences");
1629     showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1630     showAllSeqs.addActionListener(new ActionListener()
1631     {
1632       public void actionPerformed(ActionEvent e)
1633       {
1634         showAllSeqs_actionPerformed(e);
1635       }
1636     });
1637     showAllColumns.setText("All Columns");
1638     showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1639     showAllColumns.addActionListener(new ActionListener()
1640     {
1641       public void actionPerformed(ActionEvent e)
1642       {
1643         showAllColumns_actionPerformed(e);
1644       }
1645     });
1646     hideMenu.setText("Hide");
1647     hideSelSequences.setText("Selected Sequences");
1648     hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1649     hideSelSequences.addActionListener(new ActionListener()
1650     {
1651       public void actionPerformed(ActionEvent e)
1652       {
1653         hideSelSequences_actionPerformed(e);
1654       }
1655     });
1656     hideSelColumns.setText("Selected Columns");
1657     hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1658     hideSelColumns.addActionListener(new ActionListener()
1659     {
1660       public void actionPerformed(ActionEvent e)
1661       {
1662         hideSelColumns_actionPerformed(e);
1663       }
1664     });
1665     hideAllSelection.setText("Selected Region");
1666     hideAllSelection.addActionListener(new ActionListener()
1667     {
1668       public void actionPerformed(ActionEvent e)
1669       {
1670         hideAllSelection_actionPerformed(e);
1671       }
1672     });
1673     // TODO: should be hidden if no selection exists.
1674     hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
1675     hideAllButSelection.addActionListener(new ActionListener()
1676     {
1677       public void actionPerformed(ActionEvent e)
1678       {
1679         hideAllButSelection_actionPerformed(e);
1680       }
1681     });
1682     showAllhidden.setText("All Sequences and Columns");
1683     showAllhidden
1684             .setToolTipText("H toggles visibility of hidden or selected regions.");
1685     showAllhidden.addActionListener(new ActionListener()
1686     {
1687       public void actionPerformed(ActionEvent e)
1688       {
1689         showAllhidden_actionPerformed(e);
1690       }
1691     });
1692
1693     hiddenMarkers.setText("Show Hidden Markers");
1694     hiddenMarkers.addActionListener(new ActionListener()
1695     {
1696       public void actionPerformed(ActionEvent e)
1697       {
1698         hiddenMarkers_actionPerformed(e);
1699       }
1700     });
1701     invertColSel.setText("Invert Column Selection");
1702     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1703             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1704                     .getMenuShortcutKeyMask()
1705                     | java.awt.event.KeyEvent.ALT_MASK, false));
1706     invertColSel.addActionListener(new ActionListener()
1707     {
1708       public void actionPerformed(ActionEvent e)
1709       {
1710         invertColSel_actionPerformed(e);
1711       }
1712     });
1713     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1714     {
1715       public void stateChanged(ChangeEvent evt)
1716       {
1717         JTabbedPane pane = (JTabbedPane) evt.getSource();
1718         int sel = pane.getSelectedIndex();
1719         tabSelectionChanged(sel);
1720       }
1721     });
1722     tabbedPane.addMouseListener(new MouseAdapter()
1723     {
1724       public void mousePressed(MouseEvent e)
1725       {
1726         tabbedPane_mousePressed(e);
1727       }
1728     });
1729     tabbedPane.addFocusListener(new FocusAdapter()
1730     {
1731       public void focusGained(FocusEvent e)
1732       {
1733         tabbedPane_focusGained(e);
1734       }
1735     });
1736     save.setText("Save");
1737     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1738             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1739                     .getMenuShortcutKeyMask(), false));
1740     save.addActionListener(new ActionListener()
1741     {
1742       public void actionPerformed(ActionEvent e)
1743       {
1744         save_actionPerformed(e);
1745       }
1746     });
1747     reload.setEnabled(false);
1748     reload.setText("Reload");
1749     reload.addActionListener(new ActionListener()
1750     {
1751       public void actionPerformed(ActionEvent e)
1752       {
1753         reload_actionPerformed(e);
1754       }
1755     });
1756     newView.setText("New View");
1757     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1758             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1759                     .getMenuShortcutKeyMask(), false));
1760     newView.addActionListener(new ActionListener()
1761     {
1762       public void actionPerformed(ActionEvent e)
1763       {
1764         newView_actionPerformed(e);
1765       }
1766     });
1767     tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1768             + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1769     textColour.setText("Colour Text ...");
1770     textColour.addActionListener(new ActionListener()
1771     {
1772       public void actionPerformed(ActionEvent e)
1773       {
1774         textColour_actionPerformed(e);
1775       }
1776     });
1777     formatMenu.setText("Format");
1778     selectMenu.setText("Select");
1779     idRightAlign.setText("Right Align Sequence Id");
1780     idRightAlign.addActionListener(new ActionListener()
1781     {
1782       public void actionPerformed(ActionEvent e)
1783       {
1784         idRightAlign_actionPerformed(e);
1785       }
1786     });
1787     gatherViews.setEnabled(false);
1788     gatherViews.setText("Gather Views");
1789     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1790             java.awt.event.KeyEvent.VK_G, 0, false));
1791     gatherViews.addActionListener(new ActionListener()
1792     {
1793       public void actionPerformed(ActionEvent e)
1794       {
1795         gatherViews_actionPerformed(e);
1796       }
1797     });
1798     expandViews.setEnabled(false);
1799     expandViews.setText("Expand Views");
1800     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1801             java.awt.event.KeyEvent.VK_X, 0, false));
1802     expandViews.addActionListener(new ActionListener()
1803     {
1804       public void actionPerformed(ActionEvent e)
1805       {
1806         expandViews_actionPerformed(e);
1807       }
1808     });
1809     pageSetup.setText("Page Setup ...");
1810     pageSetup.addActionListener(new ActionListener()
1811     {
1812       public void actionPerformed(ActionEvent e)
1813       {
1814         pageSetup_actionPerformed(e);
1815       }
1816     });
1817     alignmentProperties.setText("Alignment Properties...");
1818     alignmentProperties.addActionListener(new ActionListener()
1819     {
1820       public void actionPerformed(ActionEvent actionEvent)
1821       {
1822         alignmentProperties();
1823       }
1824     });
1825     tooltipSettingsMenu.setText("Sequence ID Tooltip");
1826     autoAnnMenu.setText("Autocalculated Annotation");
1827     alignFrameMenuBar.add(fileMenu);
1828     alignFrameMenuBar.add(editMenu);
1829     alignFrameMenuBar.add(selectMenu);
1830     alignFrameMenuBar.add(viewMenu);
1831     alignFrameMenuBar.add(formatMenu);
1832     alignFrameMenuBar.add(colourMenu);
1833     alignFrameMenuBar.add(calculateMenu);
1834     alignFrameMenuBar.add(webService);
1835     fileMenu.add(fetchSequence);
1836     fileMenu.add(addSequenceMenu);
1837     fileMenu.add(reload);
1838     fileMenu.addSeparator();
1839     fileMenu.add(vamsasStore);
1840     fileMenu.add(save);
1841     fileMenu.add(saveAs);
1842     fileMenu.add(outputTextboxMenu);
1843     fileMenu.add(pageSetup);
1844     fileMenu.add(printMenuItem);
1845     fileMenu.addSeparator();
1846     fileMenu.add(jMenu2);
1847     fileMenu.add(exportFeatures);
1848     fileMenu.add(exportAnnotations);
1849     fileMenu.add(LoadtreeMenuItem);
1850     fileMenu.add(associatedData);
1851     fileMenu.addSeparator();
1852     fileMenu.add(closeMenuItem);
1853     editMenu.add(undoMenuItem);
1854     editMenu.add(redoMenuItem);
1855     editMenu.add(cut);
1856     editMenu.add(copy);
1857     editMenu.add(pasteMenu);
1858     editMenu.add(delete);
1859     editMenu.addSeparator();
1860     editMenu.add(remove2LeftMenuItem);
1861     editMenu.add(remove2RightMenuItem);
1862     editMenu.add(removeGappedColumnMenuItem);
1863     editMenu.add(removeAllGapsMenuItem);
1864     editMenu.add(removeRedundancyMenuItem);
1865     editMenu.addSeparator();
1866     // dont add these yet in the CVS build - they cannot be undone!
1867     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1868     // editMenu.add(justifyLeftMenuItem);
1869     // editMenu.add(justifyRightMenuItem);
1870     // editMenu.addSeparator();
1871     editMenu.add(padGapsMenuitem);
1872     viewMenu.add(newView);
1873     viewMenu.add(expandViews);
1874     viewMenu.add(gatherViews);
1875     viewMenu.addSeparator();
1876     viewMenu.add(jMenu3);
1877     viewMenu.add(hideMenu);
1878     viewMenu.addSeparator();
1879     viewMenu.add(followHighlightMenuItem);
1880     viewMenu.add(annotationPanelMenuItem);
1881     autoAnnMenu.add(applyAutoAnnotationSettings);
1882     autoAnnMenu.add(showConsensusHistogram);
1883     autoAnnMenu.add(showSequenceLogo);
1884     autoAnnMenu.add(normaliseSequenceLogo);
1885     autoAnnMenu.addSeparator();
1886     autoAnnMenu.add(showGroupConservation);
1887     autoAnnMenu.add(showGroupConsensus);
1888     viewMenu.add(autoAnnMenu);
1889     viewMenu.addSeparator();
1890     viewMenu.add(showSeqFeatures);
1891     // viewMenu.add(showSeqFeaturesHeight);
1892
1893     viewMenu.add(openFeatureSettings);
1894     tooltipSettingsMenu.add(showDbRefsMenuitem);
1895     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1896     viewMenu.add(tooltipSettingsMenu);
1897     viewMenu.addSeparator();
1898     viewMenu.add(alignmentProperties);
1899     viewMenu.addSeparator();
1900     viewMenu.add(overviewMenuItem);
1901     colourMenu.add(applyToAllGroups);
1902     colourMenu.add(textColour);
1903     colourMenu.addSeparator();
1904     colourMenu.add(noColourmenuItem);
1905     colourMenu.add(clustalColour);
1906     colourMenu.add(BLOSUM62Colour);
1907     colourMenu.add(PIDColour);
1908     colourMenu.add(zappoColour);
1909     colourMenu.add(taylorColour);
1910     colourMenu.add(hydrophobicityColour);
1911     colourMenu.add(helixColour);
1912     colourMenu.add(strandColour);
1913     colourMenu.add(turnColour);
1914     colourMenu.add(buriedColour);
1915     colourMenu.add(nucleotideColour);
1916     colourMenu.add(purinePyrimidineColour);
1917     colourMenu.add(RNAInteractionColour);
1918     // colourMenu.add(covariationColour);
1919     colourMenu.add(tcoffeeColour);
1920     colourMenu.add(userDefinedColour);
1921     colourMenu.addSeparator();
1922     colourMenu.add(conservationMenuItem);
1923     colourMenu.add(modifyConservation);
1924     colourMenu.add(abovePIDThreshold);
1925     colourMenu.add(modifyPID);
1926     colourMenu.add(annotationColour);
1927     colourMenu.add(rnahelicesColour);
1928     calculateMenu.add(sort);
1929     calculateMenu.add(calculateTree);
1930     calculateMenu.addSeparator();
1931     calculateMenu.add(pairwiseAlignmentMenuItem);
1932     calculateMenu.add(PCAMenuItem);
1933     calculateMenu.addSeparator();
1934     calculateMenu.add(showTranslation);
1935     calculateMenu.add(showProducts);
1936     calculateMenu.add(autoCalculate);
1937     calculateMenu.add(sortByTree);
1938     calculateMenu.addSeparator();
1939     calculateMenu.add(extractScores);
1940     webServiceNoServices = new JMenuItem("<No Services>");
1941     webService.add(webServiceNoServices);
1942     pasteMenu.add(pasteNew);
1943     pasteMenu.add(pasteThis);
1944     sort.add(sortIDMenuItem);
1945     sort.add(sortLengthMenuItem);
1946     sort.add(sortGroupMenuItem);
1947     sort.add(sortPairwiseMenuItem);
1948     sort.add(sortByTreeMenu);
1949     calculateTree.add(averageDistanceTreeMenuItem);
1950     calculateTree.add(neighbourTreeMenuItem);
1951     calculateTree.add(avDistanceTreeBlosumMenuItem);
1952     calculateTree.add(njTreeBlosumMenuItem);
1953     jMenu2.add(htmlMenuItem);
1954     jMenu2.add(epsFile);
1955     jMenu2.add(createPNG);
1956     addSequenceMenu.add(addFromFile);
1957     addSequenceMenu.add(addFromText);
1958     addSequenceMenu.add(addFromURL);
1959     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1960     statusPanel.add(statusBar, null);
1961     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1962     jMenu3.add(showAllColumns);
1963     jMenu3.add(showAllSeqs);
1964     jMenu3.add(showAllhidden);
1965     hideMenu.add(hideSelColumns);
1966     hideMenu.add(hideSelSequences);
1967     hideMenu.add(hideAllSelection);
1968     hideMenu.add(hideAllButSelection);
1969
1970     formatMenu.add(font);
1971     formatMenu.addSeparator();
1972     formatMenu.add(wrapMenuItem);
1973     formatMenu.add(scaleAbove);
1974     formatMenu.add(scaleLeft);
1975     formatMenu.add(scaleRight);
1976     formatMenu.add(seqLimits);
1977     formatMenu.add(idRightAlign);
1978     formatMenu.add(hiddenMarkers);
1979     formatMenu.add(viewBoxesMenuItem);
1980     formatMenu.add(viewTextMenuItem);
1981     formatMenu.add(colourTextMenuItem);
1982     formatMenu.add(renderGapsMenuItem);
1983     formatMenu.add(centreColumnLabelsMenuItem);
1984     formatMenu.add(showNonconservedMenuItem);
1985     selectMenu.add(findMenuItem);
1986     selectMenu.addSeparator();
1987     selectMenu.add(selectAllSequenceMenuItem);
1988     selectMenu.add(deselectAllSequenceMenuItem);
1989     selectMenu.add(invertSequenceMenuItem);
1990     selectMenu.add(invertColSel);
1991     selectMenu.add(createGroup);
1992     selectMenu.add(unGroup);
1993     selectMenu.add(grpsFromSelection);
1994     selectMenu.add(deleteGroups);
1995     // TODO - determine if the listenToViewSelections button is needed : see bug
1996     // JAL-574
1997     // selectMenu.addSeparator();
1998     // selectMenu.add(listenToViewSelections);
1999   }
2000
2001   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2002   {
2003     // TODO Auto-generated method stub
2004
2005   }
2006
2007   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2008   {
2009     // TODO Auto-generated method stub
2010
2011   }
2012
2013   protected void showAllhidden_actionPerformed(ActionEvent e)
2014   {
2015     // TODO Auto-generated method stub
2016
2017   }
2018
2019   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2020   {
2021     // TODO Auto-generated method stub
2022
2023   }
2024
2025   protected void hideAllSelection_actionPerformed(ActionEvent e)
2026   {
2027     // TODO Auto-generated method stub
2028
2029   }
2030
2031   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2032   {
2033     // TODO Auto-generated method stub
2034
2035   }
2036
2037   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2038   {
2039     // TODO Auto-generated method stub
2040
2041   }
2042
2043   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2044   {
2045     // TODO Auto-generated method stub
2046
2047   }
2048
2049   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2050   {
2051     // TODO Auto-generated method stub
2052
2053   }
2054
2055   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2056   {
2057     // TODO Auto-generated method stub
2058
2059   }
2060
2061   protected void showGroupConservation_actionPerformed(ActionEvent e)
2062   {
2063     // TODO Auto-generated method stub
2064
2065   }
2066
2067   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2068   {
2069     // TODO Auto-generated method stub
2070
2071   }
2072
2073   protected void showSeqFeaturesHeight_actionPerformed(
2074           ActionEvent actionEvent)
2075   {
2076     // TODO Auto-generated method stub
2077
2078   }
2079
2080   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2081   {
2082     // TODO Auto-generated method stub
2083
2084   }
2085
2086   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2087   {
2088     // TODO Auto-generated method stub
2089
2090   }
2091
2092   protected void followHighlight_actionPerformed()
2093   {
2094     // TODO Auto-generated method stub
2095
2096   }
2097
2098   protected void showNpFeats_actionPerformed(ActionEvent e)
2099   {
2100     // TODO Auto-generated method stub
2101
2102   }
2103
2104   protected void showDbRefs_actionPerformed(ActionEvent e)
2105   {
2106     // TODO Auto-generated method stub
2107
2108   }
2109
2110   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2111   {
2112   }
2113
2114   protected void showProducts_actionPerformed(ActionEvent e)
2115   {
2116   }
2117
2118   protected void buildSortByAnnotationScoresMenu()
2119   {
2120   }
2121
2122   protected void extractScores_actionPerformed(ActionEvent e)
2123   {
2124   }
2125
2126   protected void outputText_actionPerformed(ActionEvent e)
2127   {
2128   }
2129
2130   public void addFromFile_actionPerformed(ActionEvent e)
2131   {
2132
2133   }
2134
2135   public void addFromText_actionPerformed(ActionEvent e)
2136   {
2137
2138   }
2139
2140   public void addFromURL_actionPerformed(ActionEvent e)
2141   {
2142
2143   }
2144
2145   public void exportFeatures_actionPerformed(ActionEvent e)
2146   {
2147
2148   }
2149
2150   public void exportAnnotations_actionPerformed(ActionEvent e)
2151   {
2152
2153   }
2154
2155   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2156   {
2157   }
2158
2159   protected void closeMenuItem_actionPerformed(boolean b)
2160   {
2161   }
2162
2163   protected void redoMenuItem_actionPerformed(ActionEvent e)
2164   {
2165   }
2166
2167   protected void undoMenuItem_actionPerformed(ActionEvent e)
2168   {
2169   }
2170
2171   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2172   {
2173   }
2174
2175   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2176   {
2177   }
2178
2179   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2180   {
2181   }
2182
2183   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2184   {
2185   }
2186
2187   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2188   {
2189   }
2190
2191   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2192   {
2193   }
2194
2195   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2196   {
2197   }
2198
2199   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2200   {
2201   }
2202
2203   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2204   {
2205   }
2206
2207   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2208   {
2209   }
2210
2211   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2212   {
2213   }
2214
2215   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2216   {
2217   }
2218
2219   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2220   {
2221   }
2222
2223   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2224   {
2225   }
2226
2227   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2228   {
2229   }
2230
2231   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2232   {
2233   }
2234
2235   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2236   {
2237   }
2238
2239   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2240   {
2241   }
2242
2243   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2244   {
2245   }
2246
2247   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2248   {
2249   }
2250
2251   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2252   {
2253   }
2254
2255   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2256   {
2257   }
2258
2259   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2260   {
2261   }
2262
2263   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2264   {
2265   }
2266
2267   protected void clustalColour_actionPerformed(ActionEvent e)
2268   {
2269   }
2270
2271   protected void zappoColour_actionPerformed(ActionEvent e)
2272   {
2273   }
2274
2275   protected void taylorColour_actionPerformed(ActionEvent e)
2276   {
2277   }
2278
2279   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2280   {
2281   }
2282
2283   protected void helixColour_actionPerformed(ActionEvent e)
2284   {
2285   }
2286
2287   protected void strandColour_actionPerformed(ActionEvent e)
2288   {
2289   }
2290
2291   protected void turnColour_actionPerformed(ActionEvent e)
2292   {
2293   }
2294
2295   protected void buriedColour_actionPerformed(ActionEvent e)
2296   {
2297   }
2298
2299   protected void userDefinedColour_actionPerformed(ActionEvent e)
2300   {
2301   }
2302
2303   protected void PIDColour_actionPerformed(ActionEvent e)
2304   {
2305   }
2306
2307   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2308   {
2309   }
2310
2311   protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2312   {
2313   }
2314
2315   protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2316   {
2317   }
2318
2319
2320   /*
2321    * protected void covariationColour_actionPerformed(ActionEvent e) { }
2322    */
2323
2324   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2325   {
2326   }
2327
2328   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2329   {
2330   }
2331
2332   protected void printMenuItem_actionPerformed(ActionEvent e)
2333   {
2334   }
2335
2336   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2337   {
2338   }
2339
2340   protected void findMenuItem_actionPerformed(ActionEvent e)
2341   {
2342   }
2343
2344   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2345   {
2346   }
2347
2348   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2349   {
2350   }
2351
2352   protected void nucleotideColour_actionPerformed(ActionEvent e)
2353   {
2354   }
2355
2356   protected void deleteGroups_actionPerformed(ActionEvent e)
2357   {
2358   }
2359
2360   protected void createGroup_actionPerformed(ActionEvent e)
2361   {
2362   }
2363
2364   protected void unGroup_actionPerformed(ActionEvent e)
2365   {
2366   }
2367
2368   protected void copy_actionPerformed(ActionEvent e)
2369   {
2370   }
2371
2372   protected void cut_actionPerformed(ActionEvent e)
2373   {
2374   }
2375
2376   protected void delete_actionPerformed(ActionEvent e)
2377   {
2378   }
2379
2380   protected void pasteNew_actionPerformed(ActionEvent e)
2381   {
2382   }
2383
2384   protected void pasteThis_actionPerformed(ActionEvent e)
2385   {
2386   }
2387
2388   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2389   {
2390   }
2391
2392   public void createPNG(java.io.File f)
2393   {
2394   }
2395
2396   protected void font_actionPerformed(ActionEvent e)
2397   {
2398   }
2399
2400   protected void seqLimit_actionPerformed(ActionEvent e)
2401   {
2402   }
2403
2404   public void seqDBRef_actionPerformed(ActionEvent e)
2405   {
2406
2407   }
2408
2409   public void createEPS(java.io.File f)
2410   {
2411   }
2412
2413   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2414   {
2415
2416   }
2417
2418   /**
2419    * Template method to handle the 'load T-Coffee scores' menu event.
2420    * <p>
2421    * Subclasses override this method to provide a custom action.
2422    *
2423    * @param event
2424    *          The raised event
2425    */
2426   protected void loadScores_actionPerformed(ActionEvent event)
2427   {
2428
2429   }
2430
2431   /**
2432    * Template method to handle the 'Color T-Coffee scores' menu event.
2433    * <p>
2434    * Subclasses override this method to provide a custom action.
2435    *
2436    * @param event
2437    *          The raised event
2438    */
2439   protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2440   {
2441
2442   }
2443
2444   protected void jpred_actionPerformed(ActionEvent e)
2445   {
2446   }
2447
2448   protected void scaleAbove_actionPerformed(ActionEvent e)
2449   {
2450   }
2451
2452   protected void scaleLeft_actionPerformed(ActionEvent e)
2453   {
2454   }
2455
2456   protected void scaleRight_actionPerformed(ActionEvent e)
2457   {
2458   }
2459
2460   protected void modifyPID_actionPerformed(ActionEvent e)
2461   {
2462   }
2463
2464   protected void modifyConservation_actionPerformed(ActionEvent e)
2465   {
2466   }
2467
2468   protected void saveAs_actionPerformed(ActionEvent e)
2469   {
2470   }
2471
2472   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2473   {
2474   }
2475
2476   public void vamsasStore_actionPerformed(ActionEvent e)
2477   {
2478
2479   }
2480
2481   public void vamsasLoad_actionPerformed(ActionEvent e)
2482   {
2483
2484   }
2485
2486   public void showTranslation_actionPerformed(ActionEvent e)
2487   {
2488
2489   }
2490
2491   public void featureSettings_actionPerformed(ActionEvent e)
2492   {
2493
2494   }
2495
2496   public void fetchSequence_actionPerformed(ActionEvent e)
2497   {
2498
2499   }
2500
2501   public void smoothFont_actionPerformed(ActionEvent e)
2502   {
2503
2504   }
2505
2506   public void annotationColour_actionPerformed(ActionEvent e)
2507   {
2508
2509   }
2510
2511   public void rnahelicesColour_actionPerformed(ActionEvent e)
2512   {
2513
2514   }
2515
2516   public void associatedData_actionPerformed(ActionEvent e)
2517   {
2518
2519   }
2520
2521   public void autoCalculate_actionPerformed(ActionEvent e)
2522   {
2523
2524   }
2525
2526   public void sortByTreeOption_actionPerformed(ActionEvent e)
2527   {
2528
2529   }
2530
2531   public void showAllSeqs_actionPerformed(ActionEvent e)
2532   {
2533
2534   }
2535
2536   public void showAllColumns_actionPerformed(ActionEvent e)
2537   {
2538
2539   }
2540
2541   public void hideSelSequences_actionPerformed(ActionEvent e)
2542   {
2543
2544   }
2545
2546   public void hideSelColumns_actionPerformed(ActionEvent e)
2547   {
2548
2549   }
2550
2551   public void hiddenMarkers_actionPerformed(ActionEvent e)
2552   {
2553
2554   }
2555
2556   public void findPdbId_actionPerformed(ActionEvent e)
2557   {
2558
2559   }
2560
2561   public void enterPdbId_actionPerformed(ActionEvent e)
2562   {
2563
2564   }
2565
2566   public void pdbFile_actionPerformed(ActionEvent e)
2567   {
2568
2569   }
2570
2571   public void invertColSel_actionPerformed(ActionEvent e)
2572   {
2573
2574   }
2575
2576   public void tabSelectionChanged(int sel)
2577   {
2578
2579   }
2580
2581   public void tabbedPane_mousePressed(MouseEvent e)
2582   {
2583
2584   }
2585
2586   public void tabbedPane_focusGained(FocusEvent e)
2587   {
2588     requestFocus();
2589   }
2590
2591   public void save_actionPerformed(ActionEvent e)
2592   {
2593
2594   }
2595
2596   public void reload_actionPerformed(ActionEvent e)
2597   {
2598
2599   }
2600
2601   public void newView_actionPerformed(ActionEvent e)
2602   {
2603
2604   }
2605
2606   public void textColour_actionPerformed(ActionEvent e)
2607   {
2608
2609   }
2610
2611   public void idRightAlign_actionPerformed(ActionEvent e)
2612   {
2613
2614   }
2615
2616   public void expandViews_actionPerformed(ActionEvent e)
2617   {
2618
2619   }
2620
2621   public void gatherViews_actionPerformed(ActionEvent e)
2622   {
2623
2624   }
2625
2626   public void buildTreeMenu()
2627   {
2628
2629   }
2630
2631   public void pageSetup_actionPerformed(ActionEvent e)
2632   {
2633
2634   }
2635
2636   public void alignmentProperties()
2637   {
2638
2639   }
2640 }