src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
   3  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 java.awt.*;
  21 import java.awt.event.*;
  22
  23 import javax.swing.*;
  24 import javax.swing.event.*;
  25
  26 import jalview.schemes.*;
  27
  28 public class GAlignFrame extends JInternalFrame
  29 {
  30   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  31
  32   protected JMenu fileMenu = new JMenu();
  33
  34   protected JMenuItem closeMenuItem = new JMenuItem();
  35
  36   protected JMenu editMenu = new JMenu();
  37
  38   protected JMenu viewMenu = new JMenu();
  39
  40   protected JMenu colourMenu = new JMenu();
  41
  42   protected JMenu calculateMenu = new JMenu();
  43
  44   protected JMenu webService = new JMenu();
  45
  46   protected JMenuItem webServiceNoServices;
  47
  48   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  49
  50   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  51
  52   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  53
  54   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  55
  56   protected JMenuItem remove2RightMenuItem = new JMenuItem();
  57
  58   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  59
  60   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  61
  62   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  63
  64   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  65
  66   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  67
  68   protected JMenuItem sortIDMenuItem = new JMenuItem();
  69
  70   protected JMenuItem sortLengthMenuItem = new JMenuItem();
  71
  72   protected JMenuItem sortGroupMenuItem = new JMenuItem();
  73
  74   protected JMenu sortByAnnotScore = new JMenu();
  75
  76   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
  77
  78   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
  79
  80   protected JMenuItem PCAMenuItem = new JMenuItem();
  81
  82   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
  83
  84   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
  85
  86   BorderLayout borderLayout1 = new BorderLayout();
  87
  88   public JLabel statusBar = new JLabel();
  89
  90   protected JMenuItem saveAs = new JMenuItem();
  91
  92   protected JMenu outputTextboxMenu = new JMenu();
  93
  94   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  95
  96   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  97
  98   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  99
 100   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
 101
 102   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
 103
 104   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
 105
 106   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
 107
 108   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 109
 110   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
 111
 112   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
 113
 114   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 115
 116   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
 117
 118   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
 119
 120   // protected JRadioButtonMenuItem covariationColour = new
 121   // JRadioButtonMenuItem();
 122
 123   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 124
 125   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
 126
 127   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 128
 129   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 130
 131   public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
 132
 133   JMenuItem htmlMenuItem = new JMenuItem();
 134
 135   JMenuItem overviewMenuItem = new JMenuItem();
 136
 137   protected JMenuItem undoMenuItem = new JMenuItem();
 138
 139   protected JMenuItem redoMenuItem = new JMenuItem();
 140
 141   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 142
 143   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 144
 145   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 146
 147   JMenuItem printMenuItem = new JMenuItem();
 148
 149   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 150
 151   JMenuItem findMenuItem = new JMenuItem();
 152
 153   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 154
 155   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 156
 157   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 158
 159   JMenuItem deleteGroups = new JMenuItem();
 160
 161   JMenuItem delete = new JMenuItem();
 162
 163   JMenuItem copy = new JMenuItem();
 164
 165   JMenuItem cut = new JMenuItem();
 166
 167   JMenu pasteMenu = new JMenu();
 168
 169   JMenuItem pasteNew = new JMenuItem();
 170
 171   JMenuItem pasteThis = new JMenuItem();
 172
 173   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
 174
 175   JMenuItem createPNG = new JMenuItem();
 176
 177   protected JMenuItem font = new JMenuItem();
 178
 179   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 180
 181   JMenuItem epsFile = new JMenuItem();
 182
 183   JMenuItem LoadtreeMenuItem = new JMenuItem();
 184
 185   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 186
 187   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 188
 189   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 190
 191   protected JMenuItem modifyPID = new JMenuItem();
 192
 193   protected JMenuItem modifyConservation = new JMenuItem();
 194
 195   protected JMenu sortByTreeMenu = new JMenu();
 196
 197   protected JMenu sort = new JMenu();
 198
 199   protected JMenu calculateTree = new JMenu();
 200
 201   JMenu jMenu2 = new JMenu();
 202
 203   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 204
 205   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 206
 207   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 208
 209   protected ButtonGroup colours = new ButtonGroup();
 210
 211   JMenuItem vamsasStore = new JMenuItem();
 212
 213   protected JMenuItem showTranslation = new JMenuItem();
 214
 215   protected JMenuItem extractScores = new JMenuItem();
 216
 217   protected JMenu showProducts = new JMenu();
 218
 219   public JMenuItem openFeatureSettings = new JMenuItem();
 220
 221   JMenuItem fetchSequence = new JMenuItem();
 222
 223   JMenuItem annotationColour = new JMenuItem();
 224
 225   protected JMenuItem rnahelicesColour = new JMenuItem();
 226
 227   JMenuItem associatedData = new JMenuItem();
 228
 229   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 230
 231   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 232
 233   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 234
 235   JMenu addSequenceMenu = new JMenu();
 236
 237   JMenuItem addFromFile = new JMenuItem();
 238
 239   JMenuItem addFromText = new JMenuItem();
 240
 241   JMenuItem addFromURL = new JMenuItem();
 242
 243   JMenuItem exportAnnotations = new JMenuItem();
 244
 245   JMenuItem exportFeatures = new JMenuItem();
 246
 247   protected JPanel statusPanel = new JPanel();
 248
 249   GridLayout gridLayout1 = new GridLayout();
 250
 251   JMenu jMenu3 = new JMenu();
 252
 253   JMenuItem showAllSeqs = new JMenuItem();
 254
 255   JMenuItem showAllColumns = new JMenuItem();
 256
 257   JMenu hideMenu = new JMenu();
 258
 259   JMenuItem hideSelSequences = new JMenuItem();
 260
 261   JMenuItem hideSelColumns = new JMenuItem();
 262
 263   JMenuItem hideAllButSelection = new JMenuItem();
 264
 265   JMenuItem hideAllSelection = new JMenuItem();
 266
 267   JMenuItem showAllhidden = new JMenuItem();
 268
 269   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 270
 271   JMenuItem invertColSel = new JMenuItem();
 272
 273   protected JTabbedPane tabbedPane = new JTabbedPane();
 274
 275   JMenuItem save = new JMenuItem();
 276
 277   protected JMenuItem reload = new JMenuItem();
 278
 279   JMenuItem newView = new JMenuItem();
 280
 281   JMenuItem textColour = new JMenuItem();
 282
 283   JMenu formatMenu = new JMenu();
 284
 285   JMenu selectMenu = new JMenu();
 286
 287   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 288
 289   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 290
 291   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 292
 293   protected JMenuItem gatherViews = new JMenuItem();
 294
 295   protected JMenuItem expandViews = new JMenuItem();
 296
 297   JMenuItem pageSetup = new JMenuItem();
 298
 299   JMenuItem alignmentProperties = new JMenuItem();
 300
 301   JMenu tooltipSettingsMenu = new JMenu();
 302
 303   private JMenuItem justifyLeftMenuItem = new JMenuItem();
 304
 305   private JMenuItem justifyRightMenuItem = new JMenuItem();
 306
 307   JMenu autoAnnMenu = new JMenu();
 308
 309   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 310
 311   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 312
 313   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 314
 315   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 316
 317   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 318
 319   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 320
 321   private JMenuItem grpsFromSelection = new JMenuItem();
 322
 323   public GAlignFrame()
 324   {
 325     try
 326     {
 327       jbInit();
 328       setJMenuBar(alignFrameMenuBar);
 329
 330       // dynamically fill save as menu with available formats
 331       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 332       {
 333         JMenuItem item = new JMenuItem(
 334                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 335
 336         item.addActionListener(new java.awt.event.ActionListener()
 337         {
 338           public void actionPerformed(ActionEvent e)
 339           {
 340             outputText_actionPerformed(e);
 341           }
 342         });
 343
 344         outputTextboxMenu.add(item);
 345       }
 346     } catch (Exception e)
 347     {
 348     }
 349
 350     if (!new jalview.util.Platform().isAMac())
 351     {
 352       closeMenuItem.setMnemonic('C');
 353       outputTextboxMenu.setMnemonic('T');
 354       undoMenuItem.setMnemonic('Z');
 355       redoMenuItem.setMnemonic('0');
 356       copy.setMnemonic('C');
 357       cut.setMnemonic('U');
 358       pasteMenu.setMnemonic('P');
 359       reload.setMnemonic('R');
 360     }
 361
 362     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 363     {
 364       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 365               .getUserColourSchemes().keys();
 366
 367       while (userColours.hasMoreElements())
 368       {
 369         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 370                 userColours.nextElement().toString());
 371         radioItem.setName("USER_DEFINED");
 372         radioItem.addMouseListener(new MouseAdapter()
 373         {
 374           public void mousePressed(MouseEvent evt)
 375           {
 376             if (evt.isControlDown()
 377                     || SwingUtilities.isRightMouseButton(evt))
 378             {
 379               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 380
 381               int option = JOptionPane.showInternalConfirmDialog(
 382                       jalview.gui.Desktop.desktop,
 383                       "Remove from default list?",
 384                       "Remove user defined colour",
 385                       JOptionPane.YES_NO_OPTION);
 386               if (option == JOptionPane.YES_OPTION)
 387               {
 388                 jalview.gui.UserDefinedColours
 389                         .removeColourFromDefaults(radioItem.getText());
 390                 colourMenu.remove(radioItem);
 391               }
 392               else
 393               {
 394                 radioItem.addActionListener(new ActionListener()
 395                 {
 396                   public void actionPerformed(ActionEvent evt)
 397                   {
 398                     userDefinedColour_actionPerformed(evt);
 399                   }
 400                 });
 401               }
 402             }
 403           }
 404         });
 405         radioItem.addActionListener(new ActionListener()
 406         {
 407           public void actionPerformed(ActionEvent evt)
 408           {
 409             userDefinedColour_actionPerformed(evt);
 410           }
 411         });
 412         colourMenu.insert(radioItem, 15);
 413         colours.add(radioItem);
 414       }
 415     }
 416     colours.add(noColourmenuItem);
 417     colours.add(clustalColour);
 418     colours.add(zappoColour);
 419     colours.add(taylorColour);
 420     colours.add(hydrophobicityColour);
 421     colours.add(helixColour);
 422     colours.add(strandColour);
 423     colours.add(turnColour);
 424     colours.add(buriedColour);
 425     colours.add(userDefinedColour);
 426     colours.add(PIDColour);
 427     colours.add(BLOSUM62Colour);
 428     colours.add(nucleotideColour);
 429     colours.add(purinePyrimidineColour);
 430     // colours.add(covariationColour);
 431
 432     setColourSelected(jalview.bin.Cache
 433             .getDefault("DEFAULT_COLOUR", "None"));
 434
 435   }
 436
 437   public void setColourSelected(String defaultColour)
 438   {
 439
 440     if (defaultColour != null)
 441     {
 442       int index = ColourSchemeProperty
 443               .getColourIndexFromName(defaultColour);
 444
 445       switch (index)
 446       {
 447       case ColourSchemeProperty.CLUSTAL:
 448         clustalColour.setSelected(true);
 449
 450         break;
 451
 452       case ColourSchemeProperty.BLOSUM:
 453         BLOSUM62Colour.setSelected(true);
 454
 455         break;
 456
 457       case ColourSchemeProperty.PID:
 458         PIDColour.setSelected(true);
 459
 460         break;
 461
 462       case ColourSchemeProperty.ZAPPO:
 463         zappoColour.setSelected(true);
 464
 465         break;
 466
 467       case ColourSchemeProperty.TAYLOR:
 468         taylorColour.setSelected(true);
 469         break;
 470
 471       case ColourSchemeProperty.HYDROPHOBIC:
 472         hydrophobicityColour.setSelected(true);
 473
 474         break;
 475
 476       case ColourSchemeProperty.HELIX:
 477         helixColour.setSelected(true);
 478
 479         break;
 480
 481       case ColourSchemeProperty.STRAND:
 482         strandColour.setSelected(true);
 483
 484         break;
 485
 486       case ColourSchemeProperty.TURN:
 487         turnColour.setSelected(true);
 488
 489         break;
 490
 491       case ColourSchemeProperty.BURIED:
 492         buriedColour.setSelected(true);
 493
 494         break;
 495
 496       case ColourSchemeProperty.NUCLEOTIDE:
 497         nucleotideColour.setSelected(true);
 498
 499         break;
 500
 501       case ColourSchemeProperty.PURINEPYRIMIDINE:
 502         purinePyrimidineColour.setSelected(true);
 503
 504         break;
 505       /*
 506        * case ColourSchemeProperty.COVARIATION:
 507        * covariationColour.setSelected(true);
 508        *
 509        * break;
 510        */
 511       case ColourSchemeProperty.USER_DEFINED:
 512         userDefinedColour.setSelected(true);
 513
 514         break;
 515       case ColourSchemeProperty.NONE:
 516       default:
 517         noColourmenuItem.setSelected(true);
 518         break;
 519
 520       }
 521     }
 522
 523   }
 524
 525   private void jbInit() throws Exception
 526   {
 527     fileMenu.setText("File");
 528     saveAs.setText("Save As...");
 529     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 530             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
 531                     .getMenuShortcutKeyMask()
 532                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 533     saveAs.addActionListener(new ActionListener()
 534     {
 535       public void actionPerformed(ActionEvent e)
 536       {
 537         saveAs_actionPerformed(e);
 538       }
 539     });
 540     closeMenuItem.setText("Close");
 541     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 542             java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
 543                     .getMenuShortcutKeyMask(), false));
 544     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 545     {
 546       public void actionPerformed(ActionEvent e)
 547       {
 548         closeMenuItem_actionPerformed(false);
 549       }
 550     });
 551     editMenu.setText("Edit");
 552     viewMenu.setText("View");
 553     colourMenu.setText("Colour");
 554     calculateMenu.setText("Calculate");
 555     webService.setText("Web Service");
 556     selectAllSequenceMenuItem.setText("Select All");
 557     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 558             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
 559                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 560     selectAllSequenceMenuItem
 561             .addActionListener(new java.awt.event.ActionListener()
 562             {
 563               public void actionPerformed(ActionEvent e)
 564               {
 565                 selectAllSequenceMenuItem_actionPerformed(e);
 566               }
 567             });
 568     deselectAllSequenceMenuItem.setText("Deselect All");
 569     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 570             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 571     deselectAllSequenceMenuItem
 572             .addActionListener(new java.awt.event.ActionListener()
 573             {
 574               public void actionPerformed(ActionEvent e)
 575               {
 576                 deselectAllSequenceMenuItem_actionPerformed(e);
 577               }
 578             });
 579     invertSequenceMenuItem.setText("Invert Sequence Selection");
 580     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 581             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
 582                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 583     invertSequenceMenuItem
 584             .addActionListener(new java.awt.event.ActionListener()
 585             {
 586               public void actionPerformed(ActionEvent e)
 587               {
 588                 invertSequenceMenuItem_actionPerformed(e);
 589               }
 590             });
 591     grpsFromSelection.setText("Make Groups for selection");
 592     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
 593     {
 594       public void actionPerformed(ActionEvent e)
 595       {
 596         makeGrpsFromSelection_actionPerformed(e);
 597       }
 598     });
 599
 600     remove2LeftMenuItem.setText("Remove Left");
 601     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 602             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
 603                     .getMenuShortcutKeyMask(), false));
 604     remove2LeftMenuItem
 605             .addActionListener(new java.awt.event.ActionListener()
 606             {
 607               public void actionPerformed(ActionEvent e)
 608               {
 609                 remove2LeftMenuItem_actionPerformed(e);
 610               }
 611             });
 612     remove2RightMenuItem.setText("Remove Right");
 613     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 614             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
 615                     .getMenuShortcutKeyMask(), false));
 616     remove2RightMenuItem
 617             .addActionListener(new java.awt.event.ActionListener()
 618             {
 619               public void actionPerformed(ActionEvent e)
 620               {
 621                 remove2RightMenuItem_actionPerformed(e);
 622               }
 623             });
 624     removeGappedColumnMenuItem.setText("Remove Empty Columns");
 625     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
 626             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 627                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 628     removeGappedColumnMenuItem
 629             .addActionListener(new java.awt.event.ActionListener()
 630             {
 631               public void actionPerformed(ActionEvent e)
 632               {
 633                 removeGappedColumnMenuItem_actionPerformed(e);
 634               }
 635             });
 636     removeAllGapsMenuItem.setText("Remove All Gaps");
 637     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
 638             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 639                     .getDefaultToolkit().getMenuShortcutKeyMask()
 640                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 641     removeAllGapsMenuItem
 642             .addActionListener(new java.awt.event.ActionListener()
 643             {
 644               public void actionPerformed(ActionEvent e)
 645               {
 646                 removeAllGapsMenuItem_actionPerformed(e);
 647               }
 648             });
 649     justifyLeftMenuItem.setText("Left Justify Alignment");
 650     justifyLeftMenuItem
 651             .addActionListener(new java.awt.event.ActionListener()
 652             {
 653               public void actionPerformed(ActionEvent e)
 654               {
 655                 justifyLeftMenuItem_actionPerformed(e);
 656               }
 657             });
 658     justifyRightMenuItem.setText("Right Justify Alignment");
 659     justifyRightMenuItem
 660             .addActionListener(new java.awt.event.ActionListener()
 661             {
 662               public void actionPerformed(ActionEvent e)
 663               {
 664                 justifyRightMenuItem_actionPerformed(e);
 665               }
 666             });
 667     viewBoxesMenuItem.setText("Boxes");
 668     viewBoxesMenuItem.setState(true);
 669     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 670     {
 671       public void actionPerformed(ActionEvent e)
 672       {
 673         viewBoxesMenuItem_actionPerformed(e);
 674       }
 675     });
 676     viewTextMenuItem.setText("Text");
 677     viewTextMenuItem.setState(true);
 678     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 679     {
 680       public void actionPerformed(ActionEvent e)
 681       {
 682         viewTextMenuItem_actionPerformed(e);
 683       }
 684     });
 685     showNonconservedMenuItem.setText("Show nonconserved");
 686     showNonconservedMenuItem.setState(false);
 687     showNonconservedMenuItem
 688             .addActionListener(new java.awt.event.ActionListener()
 689             {
 690               public void actionPerformed(ActionEvent e)
 691               {
 692                 showUnconservedMenuItem_actionPerformed(e);
 693               }
 694             });
 695     sortPairwiseMenuItem.setText("by Pairwise Identity");
 696     sortPairwiseMenuItem
 697             .addActionListener(new java.awt.event.ActionListener()
 698             {
 699               public void actionPerformed(ActionEvent e)
 700               {
 701                 sortPairwiseMenuItem_actionPerformed(e);
 702               }
 703             });
 704     sortIDMenuItem.setText("by ID");
 705     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 706     {
 707       public void actionPerformed(ActionEvent e)
 708       {
 709         sortIDMenuItem_actionPerformed(e);
 710       }
 711     });
 712     sortLengthMenuItem.setText("By Length");
 713     sortLengthMenuItem
 714             .addActionListener(new java.awt.event.ActionListener()
 715             {
 716               public void actionPerformed(ActionEvent e)
 717               {
 718                 sortLengthMenuItem_actionPerformed(e);
 719               }
 720             });
 721     sortGroupMenuItem.setText("by Group");
 722     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 723     {
 724       public void actionPerformed(ActionEvent e)
 725       {
 726         sortGroupMenuItem_actionPerformed(e);
 727       }
 728     });
 729     removeRedundancyMenuItem.setText("Remove Redundancy...");
 730     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
 731             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
 732                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 733     removeRedundancyMenuItem
 734             .addActionListener(new java.awt.event.ActionListener()
 735             {
 736               public void actionPerformed(ActionEvent e)
 737               {
 738                 removeRedundancyMenuItem_actionPerformed(e);
 739               }
 740             });
 741     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
 742     pairwiseAlignmentMenuItem
 743             .addActionListener(new java.awt.event.ActionListener()
 744             {
 745               public void actionPerformed(ActionEvent e)
 746               {
 747                 pairwiseAlignmentMenuItem_actionPerformed(e);
 748               }
 749             });
 750     PCAMenuItem.setText("Principal Component Analysis");
 751     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 752     {
 753       public void actionPerformed(ActionEvent e)
 754       {
 755         PCAMenuItem_actionPerformed(e);
 756       }
 757     });
 758     averageDistanceTreeMenuItem
 759             .setText("Average Distance Using % Identity");
 760     averageDistanceTreeMenuItem
 761             .addActionListener(new java.awt.event.ActionListener()
 762             {
 763               public void actionPerformed(ActionEvent e)
 764               {
 765                 averageDistanceTreeMenuItem_actionPerformed(e);
 766               }
 767             });
 768     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
 769     neighbourTreeMenuItem
 770             .addActionListener(new java.awt.event.ActionListener()
 771             {
 772               public void actionPerformed(ActionEvent e)
 773               {
 774                 neighbourTreeMenuItem_actionPerformed(e);
 775               }
 776             });
 777     this.getContentPane().setLayout(borderLayout1);
 778     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 779     statusBar.setBackground(Color.white);
 780     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 781     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 782     statusBar.setText("Status bar");
 783     outputTextboxMenu.setText("Output to Textbox");
 784     clustalColour.setText("Clustalx");
 785
 786     clustalColour.addActionListener(new java.awt.event.ActionListener()
 787     {
 788       public void actionPerformed(ActionEvent e)
 789       {
 790         clustalColour_actionPerformed(e);
 791       }
 792     });
 793     zappoColour.setText("Zappo");
 794     zappoColour.addActionListener(new java.awt.event.ActionListener()
 795     {
 796       public void actionPerformed(ActionEvent e)
 797       {
 798         zappoColour_actionPerformed(e);
 799       }
 800     });
 801     taylorColour.setText("Taylor");
 802     taylorColour.addActionListener(new java.awt.event.ActionListener()
 803     {
 804       public void actionPerformed(ActionEvent e)
 805       {
 806         taylorColour_actionPerformed(e);
 807       }
 808     });
 809     hydrophobicityColour.setText("Hydrophobicity");
 810     hydrophobicityColour
 811             .addActionListener(new java.awt.event.ActionListener()
 812             {
 813               public void actionPerformed(ActionEvent e)
 814               {
 815                 hydrophobicityColour_actionPerformed(e);
 816               }
 817             });
 818     helixColour.setText("Helix Propensity");
 819     helixColour.addActionListener(new java.awt.event.ActionListener()
 820     {
 821       public void actionPerformed(ActionEvent e)
 822       {
 823         helixColour_actionPerformed(e);
 824       }
 825     });
 826     strandColour.setText("Strand Propensity");
 827     strandColour.addActionListener(new java.awt.event.ActionListener()
 828     {
 829       public void actionPerformed(ActionEvent e)
 830       {
 831         strandColour_actionPerformed(e);
 832       }
 833     });
 834     turnColour.setText("Turn Propensity");
 835     turnColour.addActionListener(new java.awt.event.ActionListener()
 836     {
 837       public void actionPerformed(ActionEvent e)
 838       {
 839         turnColour_actionPerformed(e);
 840       }
 841     });
 842     buriedColour.setText("Buried Index");
 843     buriedColour.addActionListener(new java.awt.event.ActionListener()
 844     {
 845       public void actionPerformed(ActionEvent e)
 846       {
 847         buriedColour_actionPerformed(e);
 848       }
 849     });
 850     userDefinedColour.setText("User Defined...");
 851     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 852     {
 853       public void actionPerformed(ActionEvent e)
 854       {
 855         userDefinedColour_actionPerformed(e);
 856       }
 857     });
 858     PIDColour.setText("Percentage Identity");
 859     PIDColour.addActionListener(new java.awt.event.ActionListener()
 860     {
 861       public void actionPerformed(ActionEvent e)
 862       {
 863         PIDColour_actionPerformed(e);
 864       }
 865     });
 866     BLOSUM62Colour.setText("BLOSUM62 Score");
 867     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 868     {
 869       public void actionPerformed(ActionEvent e)
 870       {
 871         BLOSUM62Colour_actionPerformed(e);
 872       }
 873     });
 874     nucleotideColour.setText("Nucleotide");
 875     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
 876     {
 877       public void actionPerformed(ActionEvent e)
 878       {
 879         nucleotideColour_actionPerformed(e);
 880       }
 881     });
 882
 883     purinePyrimidineColour.setText("Purine/Pyrimidine");
 884     purinePyrimidineColour
 885             .addActionListener(new java.awt.event.ActionListener()
 886             {
 887               public void actionPerformed(ActionEvent e)
 888               {
 889                 purinePyrimidineColour_actionPerformed(e);
 890               }
 891             });
 892     /*
 893      * covariationColour.setText("Covariation");
 894      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
 895      * public void actionPerformed(ActionEvent e) {
 896      * covariationColour_actionPerformed(e); } });
 897      */
 898
 899     avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
 900     avDistanceTreeBlosumMenuItem
 901             .addActionListener(new java.awt.event.ActionListener()
 902             {
 903               public void actionPerformed(ActionEvent e)
 904               {
 905                 avTreeBlosumMenuItem_actionPerformed(e);
 906               }
 907             });
 908     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
 909     njTreeBlosumMenuItem
 910             .addActionListener(new java.awt.event.ActionListener()
 911             {
 912               public void actionPerformed(ActionEvent e)
 913               {
 914                 njTreeBlosumMenuItem_actionPerformed(e);
 915               }
 916             });
 917     annotationPanelMenuItem.setActionCommand("");
 918     annotationPanelMenuItem.setText("Show Annotations");
 919     annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
 920             "SHOW_ANNOTATIONS", true));
 921     annotationPanelMenuItem
 922             .addActionListener(new java.awt.event.ActionListener()
 923             {
 924               public void actionPerformed(ActionEvent e)
 925               {
 926                 annotationPanelMenuItem_actionPerformed(e);
 927               }
 928             });
 929     colourTextMenuItem.setText("Colour Text");
 930     colourTextMenuItem
 931             .addActionListener(new java.awt.event.ActionListener()
 932             {
 933               public void actionPerformed(ActionEvent e)
 934               {
 935                 colourTextMenuItem_actionPerformed(e);
 936               }
 937             });
 938     htmlMenuItem.setText("HTML");
 939     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
 940     {
 941       public void actionPerformed(ActionEvent e)
 942       {
 943         htmlMenuItem_actionPerformed(e);
 944       }
 945     });
 946     overviewMenuItem.setText("Overview Window");
 947     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
 948     {
 949       public void actionPerformed(ActionEvent e)
 950       {
 951         overviewMenuItem_actionPerformed(e);
 952       }
 953     });
 954     undoMenuItem.setEnabled(false);
 955     undoMenuItem.setText("Undo");
 956     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 957             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
 958                     .getMenuShortcutKeyMask(), false));
 959     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
 960     {
 961       public void actionPerformed(ActionEvent e)
 962       {
 963         undoMenuItem_actionPerformed(e);
 964       }
 965     });
 966     redoMenuItem.setEnabled(false);
 967     redoMenuItem.setText("Redo");
 968     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 969             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
 970                     .getMenuShortcutKeyMask(), false));
 971     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
 972     {
 973       public void actionPerformed(ActionEvent e)
 974       {
 975         redoMenuItem_actionPerformed(e);
 976       }
 977     });
 978     conservationMenuItem.setText("By Conservation");
 979     conservationMenuItem
 980             .addActionListener(new java.awt.event.ActionListener()
 981             {
 982               public void actionPerformed(ActionEvent e)
 983               {
 984                 conservationMenuItem_actionPerformed(e);
 985               }
 986             });
 987     noColourmenuItem.setText("None");
 988     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 989     {
 990       public void actionPerformed(ActionEvent e)
 991       {
 992         noColourmenuItem_actionPerformed(e);
 993       }
 994     });
 995     wrapMenuItem.setText("Wrap");
 996     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
 997     {
 998       public void actionPerformed(ActionEvent e)
 999       {
1000         wrapMenuItem_actionPerformed(e);
1001       }
1002     });
1003     printMenuItem.setText("Print ...");
1004     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1005             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1006                     .getMenuShortcutKeyMask(), false));
1007     printMenuItem.addActionListener(new java.awt.event.ActionListener()
1008     {
1009       public void actionPerformed(ActionEvent e)
1010       {
1011         printMenuItem_actionPerformed(e);
1012       }
1013     });
1014     renderGapsMenuItem.setText("Show Gaps");
1015     renderGapsMenuItem.setState(true);
1016     renderGapsMenuItem
1017             .addActionListener(new java.awt.event.ActionListener()
1018             {
1019               public void actionPerformed(ActionEvent e)
1020               {
1021                 renderGapsMenuItem_actionPerformed(e);
1022               }
1023             });
1024     findMenuItem.setText("Find...");
1025     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1026             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1027                     .getMenuShortcutKeyMask(), false));
1028     findMenuItem.addActionListener(new java.awt.event.ActionListener()
1029     {
1030       public void actionPerformed(ActionEvent e)
1031       {
1032         findMenuItem_actionPerformed(e);
1033       }
1034     });
1035     abovePIDThreshold.setText("Above Identity Threshold");
1036     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1037     {
1038       public void actionPerformed(ActionEvent e)
1039       {
1040         abovePIDThreshold_actionPerformed(e);
1041       }
1042     });
1043     showSeqFeatures.setText("Show Sequence Features");
1044     showSeqFeatures.addActionListener(new ActionListener()
1045     {
1046       public void actionPerformed(ActionEvent actionEvent)
1047       {
1048         showSeqFeatures_actionPerformed(actionEvent);
1049       }
1050     });
1051     /*
1052      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1053      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1054      * void actionPerformed(ActionEvent actionEvent) {
1055      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1056      */
1057     showDbRefsMenuitem.setText("Show Database Refs");
1058     showDbRefsMenuitem.addActionListener(new ActionListener()
1059     {
1060
1061       public void actionPerformed(ActionEvent e)
1062       {
1063         showDbRefs_actionPerformed(e);
1064       }
1065
1066     });
1067     showNpFeatsMenuitem.setText("Show Non-Positional Features");
1068     showNpFeatsMenuitem.addActionListener(new ActionListener()
1069     {
1070
1071       public void actionPerformed(ActionEvent e)
1072       {
1073         showNpFeats_actionPerformed(e);
1074       }
1075
1076     });
1077     showGroupConservation.setText("Group Conservation");
1078     showGroupConservation.addActionListener(new ActionListener()
1079     {
1080
1081       public void actionPerformed(ActionEvent e)
1082       {
1083         showGroupConservation_actionPerformed(e);
1084       }
1085
1086     });
1087
1088     showGroupConsensus.setText("Group Consensus");
1089     showGroupConsensus.addActionListener(new ActionListener()
1090     {
1091
1092       public void actionPerformed(ActionEvent e)
1093       {
1094         showGroupConsensus_actionPerformed(e);
1095       }
1096
1097     });
1098     showConsensusHistogram.setText("Show Consensus Histogram");
1099     showConsensusHistogram.addActionListener(new ActionListener()
1100     {
1101
1102       public void actionPerformed(ActionEvent e)
1103       {
1104         showConsensusHistogram_actionPerformed(e);
1105       }
1106
1107     });
1108     showSequenceLogo.setText("Show Consensus Logo");
1109     showSequenceLogo.addActionListener(new ActionListener()
1110     {
1111
1112       public void actionPerformed(ActionEvent e)
1113       {
1114         showSequenceLogo_actionPerformed(e);
1115       }
1116
1117     });
1118     normaliseSequenceLogo.setText("Normalise Consensus Logo");
1119     normaliseSequenceLogo.addActionListener(new ActionListener()
1120     {
1121
1122       public void actionPerformed(ActionEvent e)
1123       {
1124         normaliseSequenceLogo_actionPerformed(e);
1125       }
1126
1127     });
1128     applyAutoAnnotationSettings.setText("Apply to all groups");
1129     applyAutoAnnotationSettings.setState(false);
1130     applyAutoAnnotationSettings.setVisible(true);
1131     applyAutoAnnotationSettings.addActionListener(new ActionListener()
1132     {
1133
1134       public void actionPerformed(ActionEvent e)
1135       {
1136         applyAutoAnnotationSettings_actionPerformed(e);
1137       }
1138
1139     });
1140
1141     nucleotideColour.setText("Nucleotide");
1142     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1143     {
1144       public void actionPerformed(ActionEvent e)
1145       {
1146         nucleotideColour_actionPerformed(e);
1147       }
1148     });
1149     deleteGroups.setText("Undefine groups");
1150     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1151             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1152                     .getMenuShortcutKeyMask(), false));
1153     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1154     {
1155       public void actionPerformed(ActionEvent e)
1156       {
1157         deleteGroups_actionPerformed(e);
1158       }
1159     });
1160     copy.setText("Copy");
1161     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1162             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1163                     .getMenuShortcutKeyMask(), false));
1164
1165     copy.addActionListener(new java.awt.event.ActionListener()
1166     {
1167       public void actionPerformed(ActionEvent e)
1168       {
1169         copy_actionPerformed(e);
1170       }
1171     });
1172     cut.setText("Cut");
1173     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1174             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1175                     .getMenuShortcutKeyMask(), false));
1176     cut.addActionListener(new java.awt.event.ActionListener()
1177     {
1178       public void actionPerformed(ActionEvent e)
1179       {
1180         cut_actionPerformed(e);
1181       }
1182     });
1183     delete.setText("Delete");
1184     delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1185             java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1186     delete.addActionListener(new java.awt.event.ActionListener()
1187     {
1188       public void actionPerformed(ActionEvent e)
1189       {
1190         delete_actionPerformed(e);
1191       }
1192     });
1193     pasteMenu.setText("Paste");
1194     pasteNew.setText("To New Alignment");
1195     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1196             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1197                     .getMenuShortcutKeyMask()
1198                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1199     pasteNew.addActionListener(new java.awt.event.ActionListener()
1200     {
1201       public void actionPerformed(ActionEvent e)
1202       {
1203         pasteNew_actionPerformed(e);
1204       }
1205     });
1206     pasteThis.setText("Add To This Alignment");
1207     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1208             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1209                     .getMenuShortcutKeyMask(), false));
1210     pasteThis.addActionListener(new java.awt.event.ActionListener()
1211     {
1212       public void actionPerformed(ActionEvent e)
1213       {
1214         pasteThis_actionPerformed(e);
1215       }
1216     });
1217     applyToAllGroups.setText("Apply Colour To All Groups");
1218     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1219     {
1220       public void actionPerformed(ActionEvent e)
1221       {
1222         applyToAllGroups_actionPerformed(e);
1223       }
1224     });
1225     createPNG.addActionListener(new java.awt.event.ActionListener()
1226     {
1227       public void actionPerformed(ActionEvent e)
1228       {
1229         createPNG(null);
1230       }
1231     });
1232     createPNG.setActionCommand("Save As PNG Image");
1233     createPNG.setText("PNG");
1234     font.setText("Font...");
1235     font.addActionListener(new java.awt.event.ActionListener()
1236     {
1237       public void actionPerformed(ActionEvent e)
1238       {
1239         font_actionPerformed(e);
1240       }
1241     });
1242
1243     seqLimits.setText("Show Sequence Limits");
1244     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1245     seqLimits.addActionListener(new java.awt.event.ActionListener()
1246     {
1247       public void actionPerformed(ActionEvent e)
1248       {
1249         seqLimit_actionPerformed(e);
1250       }
1251     });
1252     epsFile.setText("EPS");
1253     epsFile.addActionListener(new java.awt.event.ActionListener()
1254     {
1255       public void actionPerformed(ActionEvent e)
1256       {
1257         createEPS(null);
1258       }
1259     });
1260     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1261     LoadtreeMenuItem.setText("Load Associated Tree");
1262     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1263     {
1264       public void actionPerformed(ActionEvent e)
1265       {
1266         LoadtreeMenuItem_actionPerformed(e);
1267       }
1268     });
1269     scaleAbove.setVisible(false);
1270     scaleAbove.setText("Scale Above");
1271     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1272     {
1273       public void actionPerformed(ActionEvent e)
1274       {
1275         scaleAbove_actionPerformed(e);
1276       }
1277     });
1278     scaleLeft.setVisible(false);
1279     scaleLeft.setSelected(true);
1280     scaleLeft.setText("Scale Left");
1281     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1282     {
1283       public void actionPerformed(ActionEvent e)
1284       {
1285         scaleLeft_actionPerformed(e);
1286       }
1287     });
1288     scaleRight.setVisible(false);
1289     scaleRight.setSelected(true);
1290     scaleRight.setText("Scale Right");
1291     scaleRight.addActionListener(new java.awt.event.ActionListener()
1292     {
1293       public void actionPerformed(ActionEvent e)
1294       {
1295         scaleRight_actionPerformed(e);
1296       }
1297     });
1298     centreColumnLabelsMenuItem.setVisible(true);
1299     centreColumnLabelsMenuItem.setState(false);
1300     centreColumnLabelsMenuItem.setText("Centre Column Labels");
1301     centreColumnLabelsMenuItem
1302             .addActionListener(new java.awt.event.ActionListener()
1303             {
1304               public void actionPerformed(ActionEvent e)
1305               {
1306                 centreColumnLabels_actionPerformed(e);
1307               }
1308             });
1309     followHighlightMenuItem.setVisible(true);
1310     followHighlightMenuItem.setState(true);
1311     followHighlightMenuItem.setText("Automatic Scrolling");
1312     followHighlightMenuItem.addActionListener(new ActionListener()
1313     {
1314
1315       public void actionPerformed(ActionEvent e)
1316       {
1317         followHighlight_actionPerformed();
1318       }
1319
1320     });
1321
1322     modifyPID.setText("Modify Identity Threshold...");
1323     modifyPID.addActionListener(new java.awt.event.ActionListener()
1324     {
1325       public void actionPerformed(ActionEvent e)
1326       {
1327         modifyPID_actionPerformed(e);
1328       }
1329     });
1330     modifyConservation.setText("Modify Conservation Threshold...");
1331     modifyConservation
1332             .addActionListener(new java.awt.event.ActionListener()
1333             {
1334               public void actionPerformed(ActionEvent e)
1335               {
1336                 modifyConservation_actionPerformed(e);
1337               }
1338             });
1339     sortByTreeMenu.setText("By Tree Order");
1340     sort.setText("Sort");
1341     sort.addMenuListener(new MenuListener()
1342     {
1343       public void menuSelected(MenuEvent e)
1344       {
1345         buildTreeMenu();
1346       }
1347
1348       public void menuDeselected(MenuEvent e)
1349       {
1350       }
1351
1352       public void menuCanceled(MenuEvent e)
1353       {
1354       }
1355     });
1356     sortByAnnotScore.setText("by Score");
1357     sort.add(sortByAnnotScore);
1358     sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1359     {
1360
1361       public void menuCanceled(MenuEvent e)
1362       {
1363       }
1364
1365       public void menuDeselected(MenuEvent e)
1366       {
1367       }
1368
1369       public void menuSelected(MenuEvent e)
1370       {
1371         buildSortByAnnotationScoresMenu();
1372       }
1373     });
1374     sortByAnnotScore.setVisible(false);
1375
1376     calculateTree.setText("Calculate Tree");
1377
1378     jMenu2.setText("Export Image");
1379     padGapsMenuitem.setText("Pad Gaps");
1380     padGapsMenuitem.setState(jalview.bin.Cache
1381             .getDefault("PAD_GAPS", false));
1382     padGapsMenuitem.addActionListener(new ActionListener()
1383     {
1384       public void actionPerformed(ActionEvent e)
1385       {
1386         padGapsMenuitem_actionPerformed(e);
1387       }
1388     });
1389     vamsasStore.setVisible(false);
1390     vamsasStore.setText("VAMSAS store");
1391     vamsasStore.addActionListener(new ActionListener()
1392     {
1393       public void actionPerformed(ActionEvent e)
1394       {
1395         vamsasStore_actionPerformed(e);
1396       }
1397     });
1398     showTranslation.setText("Translate cDNA");
1399     showTranslation.addActionListener(new ActionListener()
1400     {
1401       public void actionPerformed(ActionEvent e)
1402       {
1403         showTranslation_actionPerformed(e);
1404       }
1405     });
1406     extractScores.setText("Extract Scores...");
1407     extractScores.addActionListener(new ActionListener()
1408     {
1409       public void actionPerformed(ActionEvent e)
1410       {
1411         extractScores_actionPerformed(e);
1412       }
1413     });
1414     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1415     // score extraction
1416     showProducts.setText("Get Cross References");
1417     /*
1418      * showProducts.addActionListener(new ActionListener() {
1419      *
1420      * public void actionPerformed(ActionEvent e) {
1421      * showProducts_actionPerformed(e); } });
1422      */
1423     openFeatureSettings.setText("Feature Settings...");
1424     openFeatureSettings.addActionListener(new ActionListener()
1425     {
1426       public void actionPerformed(ActionEvent e)
1427       {
1428         featureSettings_actionPerformed(e);
1429       }
1430     });
1431     fetchSequence.setText("Fetch Sequence(s)...");
1432     fetchSequence.addActionListener(new ActionListener()
1433     {
1434       public void actionPerformed(ActionEvent e)
1435       {
1436         fetchSequence_actionPerformed(e);
1437       }
1438     });
1439
1440     annotationColour.setText("By Annotation...");
1441     annotationColour.addActionListener(new ActionListener()
1442     {
1443       public void actionPerformed(ActionEvent e)
1444       {
1445         annotationColour_actionPerformed(e);
1446       }
1447     });
1448
1449     rnahelicesColour.setText("By RNA helices");
1450     rnahelicesColour.addActionListener(new ActionListener()
1451     {
1452       public void actionPerformed(ActionEvent e)
1453       {
1454         rnahelicesColour_actionPerformed(e);
1455       }
1456     });
1457
1458     associatedData.setText("Load Features / Annotations");
1459     associatedData.addActionListener(new ActionListener()
1460     {
1461       public void actionPerformed(ActionEvent e)
1462       {
1463         associatedData_actionPerformed(e);
1464       }
1465     });
1466     autoCalculate.setText("Autocalculate Consensus");
1467     autoCalculate.setState(jalview.bin.Cache.getDefault(
1468             "AUTO_CALC_CONSENSUS", true));
1469     autoCalculate.addActionListener(new ActionListener()
1470     {
1471       public void actionPerformed(ActionEvent e)
1472       {
1473         autoCalculate_actionPerformed(e);
1474       }
1475     });
1476     sortByTree.setText("Sort Alignment With New Tree");
1477     sortByTree.setToolTipText("<html>Enable this to automatically sort<br>the alignment when you open<br> a new tree.");
1478     sortByTree.setState(jalview.bin.Cache.getDefault(
1479             "SORT_BY_TREE", false));
1480     sortByTree.addActionListener(new ActionListener()
1481     {
1482       public void actionPerformed(ActionEvent e)
1483       {
1484         sortByTreeOption_actionPerformed(e);
1485       }
1486     });
1487
1488     listenToViewSelections.setText("Listen for selections");
1489     listenToViewSelections.setToolTipText("<html>When selected, selections in this view will mirror<br>selections made on the same sequences in other views.");
1490     listenToViewSelections.setState(false);
1491     listenToViewSelections.addActionListener(new ActionListener()
1492     {
1493       public void actionPerformed(ActionEvent e)
1494       {
1495         listenToViewSelections_actionPerformed(e);
1496       }
1497     });
1498
1499     addSequenceMenu.setText("Add Sequences");
1500     addFromFile.setText("From File");
1501     addFromFile.addActionListener(new ActionListener()
1502     {
1503       public void actionPerformed(ActionEvent e)
1504       {
1505         addFromFile_actionPerformed(e);
1506       }
1507     });
1508     addFromText.setText("From Textbox");
1509     addFromText.addActionListener(new ActionListener()
1510     {
1511       public void actionPerformed(ActionEvent e)
1512       {
1513         addFromText_actionPerformed(e);
1514       }
1515     });
1516     addFromURL.setText("From URL");
1517     addFromURL.addActionListener(new ActionListener()
1518     {
1519       public void actionPerformed(ActionEvent e)
1520       {
1521         addFromURL_actionPerformed(e);
1522       }
1523     });
1524     exportFeatures.setText("Export Features...");
1525     exportFeatures.addActionListener(new ActionListener()
1526     {
1527       public void actionPerformed(ActionEvent e)
1528       {
1529         exportFeatures_actionPerformed(e);
1530       }
1531     });
1532     exportAnnotations.setText("Export Annotations...");
1533     exportAnnotations.addActionListener(new ActionListener()
1534     {
1535       public void actionPerformed(ActionEvent e)
1536       {
1537         exportAnnotations_actionPerformed(e);
1538       }
1539     });
1540     statusPanel.setLayout(gridLayout1);
1541     jMenu3.setText("Show");
1542     showAllSeqs.setText("All Sequences");
1543     showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1544     showAllSeqs.addActionListener(new ActionListener()
1545     {
1546       public void actionPerformed(ActionEvent e)
1547       {
1548         showAllSeqs_actionPerformed(e);
1549       }
1550     });
1551     showAllColumns.setText("All Columns");
1552     showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1553     showAllColumns.addActionListener(new ActionListener()
1554     {
1555       public void actionPerformed(ActionEvent e)
1556       {
1557         showAllColumns_actionPerformed(e);
1558       }
1559     });
1560     hideMenu.setText("Hide");
1561     hideSelSequences.setText("Selected Sequences");
1562     hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1563     hideSelSequences.addActionListener(new ActionListener()
1564     {
1565       public void actionPerformed(ActionEvent e)
1566       {
1567         hideSelSequences_actionPerformed(e);
1568       }
1569     });
1570     hideSelColumns.setText("Selected Columns");
1571     hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1572     hideSelColumns.addActionListener(new ActionListener()
1573     {
1574       public void actionPerformed(ActionEvent e)
1575       {
1576         hideSelColumns_actionPerformed(e);
1577       }
1578     });
1579     hideAllSelection.setText("Selected Region");
1580     hideAllSelection.addActionListener(new ActionListener()
1581     {
1582       public void actionPerformed(ActionEvent e)
1583       {
1584         hideAllSelection_actionPerformed(e);
1585       }
1586     });
1587     // TODO: should be hidden if no selection exists.
1588     hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
1589     hideAllButSelection.addActionListener(new ActionListener()
1590     {
1591       public void actionPerformed(ActionEvent e)
1592       {
1593         hideAllButSelection_actionPerformed(e);
1594       }
1595     });
1596     showAllhidden.setText("All Sequences and Columns");
1597     showAllhidden
1598             .setToolTipText("H toggles visibility of hidden or selected regions.");
1599     showAllhidden.addActionListener(new ActionListener()
1600     {
1601       public void actionPerformed(ActionEvent e)
1602       {
1603         showAllhidden_actionPerformed(e);
1604       }
1605     });
1606
1607     hiddenMarkers.setText("Show Hidden Markers");
1608     hiddenMarkers.addActionListener(new ActionListener()
1609     {
1610       public void actionPerformed(ActionEvent e)
1611       {
1612         hiddenMarkers_actionPerformed(e);
1613       }
1614     });
1615     invertColSel.setText("Invert Column Selection");
1616     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1617             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1618                     .getMenuShortcutKeyMask()
1619                     | java.awt.event.KeyEvent.ALT_MASK, false));
1620     invertColSel.addActionListener(new ActionListener()
1621     {
1622       public void actionPerformed(ActionEvent e)
1623       {
1624         invertColSel_actionPerformed(e);
1625       }
1626     });
1627     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1628     {
1629       public void stateChanged(ChangeEvent evt)
1630       {
1631         JTabbedPane pane = (JTabbedPane) evt.getSource();
1632         int sel = pane.getSelectedIndex();
1633         tabSelectionChanged(sel);
1634       }
1635     });
1636     tabbedPane.addMouseListener(new MouseAdapter()
1637     {
1638       public void mousePressed(MouseEvent e)
1639       {
1640         tabbedPane_mousePressed(e);
1641       }
1642     });
1643     tabbedPane.addFocusListener(new FocusAdapter()
1644     {
1645       public void focusGained(FocusEvent e)
1646       {
1647         tabbedPane_focusGained(e);
1648       }
1649     });
1650     save.setText("Save");
1651     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1652             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1653                     .getMenuShortcutKeyMask(), false));
1654     save.addActionListener(new ActionListener()
1655     {
1656       public void actionPerformed(ActionEvent e)
1657       {
1658         save_actionPerformed(e);
1659       }
1660     });
1661     reload.setEnabled(false);
1662     reload.setText("Reload");
1663     reload.addActionListener(new ActionListener()
1664     {
1665       public void actionPerformed(ActionEvent e)
1666       {
1667         reload_actionPerformed(e);
1668       }
1669     });
1670     newView.setText("New View");
1671     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1672             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1673                     .getMenuShortcutKeyMask(), false));
1674     newView.addActionListener(new ActionListener()
1675     {
1676       public void actionPerformed(ActionEvent e)
1677       {
1678         newView_actionPerformed(e);
1679       }
1680     });
1681     tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1682             + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1683     textColour.setText("Colour Text ...");
1684     textColour.addActionListener(new ActionListener()
1685     {
1686       public void actionPerformed(ActionEvent e)
1687       {
1688         textColour_actionPerformed(e);
1689       }
1690     });
1691     formatMenu.setText("Format");
1692     selectMenu.setText("Select");
1693     idRightAlign.setText("Right Align Sequence Id");
1694     idRightAlign.addActionListener(new ActionListener()
1695     {
1696       public void actionPerformed(ActionEvent e)
1697       {
1698         idRightAlign_actionPerformed(e);
1699       }
1700     });
1701     gatherViews.setEnabled(false);
1702     gatherViews.setText("Gather Views");
1703     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1704             java.awt.event.KeyEvent.VK_G, 0, false));
1705     gatherViews.addActionListener(new ActionListener()
1706     {
1707       public void actionPerformed(ActionEvent e)
1708       {
1709         gatherViews_actionPerformed(e);
1710       }
1711     });
1712     expandViews.setEnabled(false);
1713     expandViews.setText("Expand Views");
1714     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1715             java.awt.event.KeyEvent.VK_X, 0, false));
1716     expandViews.addActionListener(new ActionListener()
1717     {
1718       public void actionPerformed(ActionEvent e)
1719       {
1720         expandViews_actionPerformed(e);
1721       }
1722     });
1723     pageSetup.setText("Page Setup ...");
1724     pageSetup.addActionListener(new ActionListener()
1725     {
1726       public void actionPerformed(ActionEvent e)
1727       {
1728         pageSetup_actionPerformed(e);
1729       }
1730     });
1731     alignmentProperties.setText("Alignment Properties...");
1732     alignmentProperties.addActionListener(new ActionListener()
1733     {
1734       public void actionPerformed(ActionEvent actionEvent)
1735       {
1736         alignmentProperties();
1737       }
1738     });
1739     tooltipSettingsMenu.setText("Sequence ID Tooltip");
1740     autoAnnMenu.setText("Autocalculated Annotation");
1741     alignFrameMenuBar.add(fileMenu);
1742     alignFrameMenuBar.add(editMenu);
1743     alignFrameMenuBar.add(selectMenu);
1744     alignFrameMenuBar.add(viewMenu);
1745     alignFrameMenuBar.add(formatMenu);
1746     alignFrameMenuBar.add(colourMenu);
1747     alignFrameMenuBar.add(calculateMenu);
1748     alignFrameMenuBar.add(webService);
1749     fileMenu.add(fetchSequence);
1750     fileMenu.add(addSequenceMenu);
1751     fileMenu.add(reload);
1752     fileMenu.addSeparator();
1753     fileMenu.add(vamsasStore);
1754     fileMenu.add(save);
1755     fileMenu.add(saveAs);
1756     fileMenu.add(outputTextboxMenu);
1757     fileMenu.add(pageSetup);
1758     fileMenu.add(printMenuItem);
1759     fileMenu.addSeparator();
1760     fileMenu.add(jMenu2);
1761     fileMenu.add(exportFeatures);
1762     fileMenu.add(exportAnnotations);
1763     fileMenu.add(LoadtreeMenuItem);
1764     fileMenu.add(associatedData);
1765     fileMenu.addSeparator();
1766     fileMenu.add(closeMenuItem);
1767     editMenu.add(undoMenuItem);
1768     editMenu.add(redoMenuItem);
1769     editMenu.add(cut);
1770     editMenu.add(copy);
1771     editMenu.add(pasteMenu);
1772     editMenu.add(delete);
1773     editMenu.addSeparator();
1774     editMenu.add(remove2LeftMenuItem);
1775     editMenu.add(remove2RightMenuItem);
1776     editMenu.add(removeGappedColumnMenuItem);
1777     editMenu.add(removeAllGapsMenuItem);
1778     editMenu.add(removeRedundancyMenuItem);
1779     editMenu.addSeparator();
1780     // dont add these yet in the CVS build - they cannot be undone!
1781     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1782     // editMenu.add(justifyLeftMenuItem);
1783     // editMenu.add(justifyRightMenuItem);
1784     // editMenu.addSeparator();
1785     editMenu.add(padGapsMenuitem);
1786     viewMenu.add(newView);
1787     viewMenu.add(expandViews);
1788     viewMenu.add(gatherViews);
1789     viewMenu.addSeparator();
1790     viewMenu.add(jMenu3);
1791     viewMenu.add(hideMenu);
1792     viewMenu.addSeparator();
1793     viewMenu.add(followHighlightMenuItem);
1794     viewMenu.add(annotationPanelMenuItem);
1795     autoAnnMenu.add(applyAutoAnnotationSettings);
1796     autoAnnMenu.add(showConsensusHistogram);
1797     autoAnnMenu.add(showSequenceLogo);
1798     autoAnnMenu.add(normaliseSequenceLogo);
1799     autoAnnMenu.addSeparator();
1800     autoAnnMenu.add(showGroupConservation);
1801     autoAnnMenu.add(showGroupConsensus);
1802     viewMenu.add(autoAnnMenu);
1803     viewMenu.addSeparator();
1804     viewMenu.add(showSeqFeatures);
1805     // viewMenu.add(showSeqFeaturesHeight);
1806
1807     viewMenu.add(openFeatureSettings);
1808     tooltipSettingsMenu.add(showDbRefsMenuitem);
1809     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1810     viewMenu.add(tooltipSettingsMenu);
1811     viewMenu.addSeparator();
1812     viewMenu.add(alignmentProperties);
1813     viewMenu.addSeparator();
1814     viewMenu.add(overviewMenuItem);
1815     colourMenu.add(applyToAllGroups);
1816     colourMenu.add(textColour);
1817     colourMenu.addSeparator();
1818     colourMenu.add(noColourmenuItem);
1819     colourMenu.add(clustalColour);
1820     colourMenu.add(BLOSUM62Colour);
1821     colourMenu.add(PIDColour);
1822     colourMenu.add(zappoColour);
1823     colourMenu.add(taylorColour);
1824     colourMenu.add(hydrophobicityColour);
1825     colourMenu.add(helixColour);
1826     colourMenu.add(strandColour);
1827     colourMenu.add(turnColour);
1828     colourMenu.add(buriedColour);
1829     colourMenu.add(nucleotideColour);
1830     colourMenu.add(purinePyrimidineColour);
1831     // colourMenu.add(covariationColour);
1832     colourMenu.add(userDefinedColour);
1833     colourMenu.addSeparator();
1834     colourMenu.add(conservationMenuItem);
1835     colourMenu.add(modifyConservation);
1836     colourMenu.add(abovePIDThreshold);
1837     colourMenu.add(modifyPID);
1838     colourMenu.add(annotationColour);
1839     colourMenu.add(rnahelicesColour);
1840     calculateMenu.add(sort);
1841     calculateMenu.add(calculateTree);
1842     calculateMenu.addSeparator();
1843     calculateMenu.add(pairwiseAlignmentMenuItem);
1844     calculateMenu.add(PCAMenuItem);
1845     calculateMenu.addSeparator();
1846     calculateMenu.add(showTranslation);
1847     calculateMenu.add(showProducts);
1848     calculateMenu.add(autoCalculate);
1849     calculateMenu.add(sortByTree);
1850     calculateMenu.addSeparator();
1851     calculateMenu.add(extractScores);
1852     webServiceNoServices = new JMenuItem("<No Services>");
1853     webService.add(webServiceNoServices);
1854     pasteMenu.add(pasteNew);
1855     pasteMenu.add(pasteThis);
1856     sort.add(sortIDMenuItem);
1857     sort.add(sortLengthMenuItem);
1858     sort.add(sortGroupMenuItem);
1859     sort.add(sortPairwiseMenuItem);
1860     sort.add(sortByTreeMenu);
1861     calculateTree.add(averageDistanceTreeMenuItem);
1862     calculateTree.add(neighbourTreeMenuItem);
1863     calculateTree.add(avDistanceTreeBlosumMenuItem);
1864     calculateTree.add(njTreeBlosumMenuItem);
1865     jMenu2.add(htmlMenuItem);
1866     jMenu2.add(epsFile);
1867     jMenu2.add(createPNG);
1868     addSequenceMenu.add(addFromFile);
1869     addSequenceMenu.add(addFromText);
1870     addSequenceMenu.add(addFromURL);
1871     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1872     statusPanel.add(statusBar, null);
1873     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1874     jMenu3.add(showAllColumns);
1875     jMenu3.add(showAllSeqs);
1876     jMenu3.add(showAllhidden);
1877     hideMenu.add(hideSelColumns);
1878     hideMenu.add(hideSelSequences);
1879     hideMenu.add(hideAllSelection);
1880     hideMenu.add(hideAllButSelection);
1881
1882     formatMenu.add(font);
1883     formatMenu.addSeparator();
1884     formatMenu.add(wrapMenuItem);
1885     formatMenu.add(scaleAbove);
1886     formatMenu.add(scaleLeft);
1887     formatMenu.add(scaleRight);
1888     formatMenu.add(seqLimits);
1889     formatMenu.add(idRightAlign);
1890     formatMenu.add(hiddenMarkers);
1891     formatMenu.add(viewBoxesMenuItem);
1892     formatMenu.add(viewTextMenuItem);
1893     formatMenu.add(colourTextMenuItem);
1894     formatMenu.add(renderGapsMenuItem);
1895     formatMenu.add(centreColumnLabelsMenuItem);
1896     formatMenu.add(showNonconservedMenuItem);
1897     selectMenu.add(findMenuItem);
1898     selectMenu.addSeparator();
1899     selectMenu.add(selectAllSequenceMenuItem);
1900     selectMenu.add(deselectAllSequenceMenuItem);
1901     selectMenu.add(invertSequenceMenuItem);
1902     selectMenu.add(invertColSel);
1903     selectMenu.add(deleteGroups);
1904     selectMenu.add(grpsFromSelection);
1905     // TODO - determine if the listenToViewSelections button is needed : see bug JAL-574
1906     //selectMenu.addSeparator();
1907     //selectMenu.add(listenToViewSelections);
1908   }
1909
1910   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
1911   {
1912     // TODO Auto-generated method stub
1913
1914   }
1915
1916   protected void listenToViewSelections_actionPerformed(ActionEvent e)
1917   {
1918     // TODO Auto-generated method stub
1919
1920   }
1921
1922   protected void showAllhidden_actionPerformed(ActionEvent e)
1923   {
1924     // TODO Auto-generated method stub
1925
1926   }
1927
1928   protected void hideAllButSelection_actionPerformed(ActionEvent e)
1929   {
1930     // TODO Auto-generated method stub
1931
1932   }
1933
1934   protected void hideAllSelection_actionPerformed(ActionEvent e)
1935   {
1936     // TODO Auto-generated method stub
1937
1938   }
1939
1940   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
1941   {
1942     // TODO Auto-generated method stub
1943
1944   }
1945
1946   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
1947   {
1948     // TODO Auto-generated method stub
1949
1950   }
1951
1952   protected void showSequenceLogo_actionPerformed(ActionEvent e)
1953   {
1954     // TODO Auto-generated method stub
1955
1956   }
1957
1958   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
1959   {
1960     // TODO Auto-generated method stub
1961
1962   }
1963
1964   protected void showGroupConsensus_actionPerformed(ActionEvent e)
1965   {
1966     // TODO Auto-generated method stub
1967
1968   }
1969
1970   protected void showGroupConservation_actionPerformed(ActionEvent e)
1971   {
1972     // TODO Auto-generated method stub
1973
1974   }
1975
1976   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
1977   {
1978     // TODO Auto-generated method stub
1979
1980   }
1981
1982   protected void showSeqFeaturesHeight_actionPerformed(
1983           ActionEvent actionEvent)
1984   {
1985     // TODO Auto-generated method stub
1986
1987   }
1988
1989   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
1990   {
1991     // TODO Auto-generated method stub
1992
1993   }
1994
1995   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
1996   {
1997     // TODO Auto-generated method stub
1998
1999   }
2000
2001   protected void followHighlight_actionPerformed()
2002   {
2003     // TODO Auto-generated method stub
2004
2005   }
2006
2007   protected void showNpFeats_actionPerformed(ActionEvent e)
2008   {
2009     // TODO Auto-generated method stub
2010
2011   }
2012
2013   protected void showDbRefs_actionPerformed(ActionEvent e)
2014   {
2015     // TODO Auto-generated method stub
2016
2017   }
2018
2019   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2020   {
2021   }
2022
2023   protected void showProducts_actionPerformed(ActionEvent e)
2024   {
2025   }
2026
2027   protected void buildSortByAnnotationScoresMenu()
2028   {
2029   }
2030
2031   protected void extractScores_actionPerformed(ActionEvent e)
2032   {
2033   }
2034
2035   protected void outputText_actionPerformed(ActionEvent e)
2036   {
2037   }
2038
2039   public void addFromFile_actionPerformed(ActionEvent e)
2040   {
2041
2042   }
2043
2044   public void addFromText_actionPerformed(ActionEvent e)
2045   {
2046
2047   }
2048
2049   public void addFromURL_actionPerformed(ActionEvent e)
2050   {
2051
2052   }
2053
2054   public void exportFeatures_actionPerformed(ActionEvent e)
2055   {
2056
2057   }
2058
2059   public void exportAnnotations_actionPerformed(ActionEvent e)
2060   {
2061
2062   }
2063
2064   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2065   {
2066   }
2067
2068   protected void closeMenuItem_actionPerformed(boolean b)
2069   {
2070   }
2071
2072   protected void redoMenuItem_actionPerformed(ActionEvent e)
2073   {
2074   }
2075
2076   protected void undoMenuItem_actionPerformed(ActionEvent e)
2077   {
2078   }
2079
2080   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2081   {
2082   }
2083
2084   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2085   {
2086   }
2087
2088   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2089   {
2090   }
2091
2092   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2093   {
2094   }
2095
2096   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2097   {
2098   }
2099
2100   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2101   {
2102   }
2103
2104   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2105   {
2106   }
2107
2108   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2109   {
2110   }
2111
2112   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2113   {
2114   }
2115
2116   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2117   {
2118   }
2119
2120   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2121   {
2122   }
2123
2124   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2125   {
2126   }
2127
2128   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2129   {
2130   }
2131
2132   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2133   {
2134   }
2135
2136   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2137   {
2138   }
2139
2140   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2141   {
2142   }
2143
2144   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2145   {
2146   }
2147
2148   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2149   {
2150   }
2151
2152   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2153   {
2154   }
2155
2156   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2157   {
2158   }
2159
2160   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2161   {
2162   }
2163
2164   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2165   {
2166   }
2167
2168   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2169   {
2170   }
2171
2172   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2173   {
2174   }
2175
2176   protected void clustalColour_actionPerformed(ActionEvent e)
2177   {
2178   }
2179
2180   protected void zappoColour_actionPerformed(ActionEvent e)
2181   {
2182   }
2183
2184   protected void taylorColour_actionPerformed(ActionEvent e)
2185   {
2186   }
2187
2188   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2189   {
2190   }
2191
2192   protected void helixColour_actionPerformed(ActionEvent e)
2193   {
2194   }
2195
2196   protected void strandColour_actionPerformed(ActionEvent e)
2197   {
2198   }
2199
2200   protected void turnColour_actionPerformed(ActionEvent e)
2201   {
2202   }
2203
2204   protected void buriedColour_actionPerformed(ActionEvent e)
2205   {
2206   }
2207
2208   protected void userDefinedColour_actionPerformed(ActionEvent e)
2209   {
2210   }
2211
2212   protected void PIDColour_actionPerformed(ActionEvent e)
2213   {
2214   }
2215
2216   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2217   {
2218   }
2219
2220   protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2221   {
2222   }
2223
2224   /*
2225    * protected void covariationColour_actionPerformed(ActionEvent e) { }
2226    */
2227
2228   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2229   {
2230   }
2231
2232   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2233   {
2234   }
2235
2236   protected void printMenuItem_actionPerformed(ActionEvent e)
2237   {
2238   }
2239
2240   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2241   {
2242   }
2243
2244   protected void findMenuItem_actionPerformed(ActionEvent e)
2245   {
2246   }
2247
2248   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2249   {
2250   }
2251
2252   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2253   {
2254   }
2255
2256   protected void nucleotideColour_actionPerformed(ActionEvent e)
2257   {
2258   }
2259
2260   protected void deleteGroups_actionPerformed(ActionEvent e)
2261   {
2262   }
2263
2264   protected void copy_actionPerformed(ActionEvent e)
2265   {
2266   }
2267
2268   protected void cut_actionPerformed(ActionEvent e)
2269   {
2270   }
2271
2272   protected void delete_actionPerformed(ActionEvent e)
2273   {
2274   }
2275
2276   protected void pasteNew_actionPerformed(ActionEvent e)
2277   {
2278   }
2279
2280   protected void pasteThis_actionPerformed(ActionEvent e)
2281   {
2282   }
2283
2284   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2285   {
2286   }
2287
2288   public void createPNG(java.io.File f)
2289   {
2290   }
2291
2292   protected void font_actionPerformed(ActionEvent e)
2293   {
2294   }
2295
2296   protected void seqLimit_actionPerformed(ActionEvent e)
2297   {
2298   }
2299
2300   public void seqDBRef_actionPerformed(ActionEvent e)
2301   {
2302
2303   }
2304
2305   public void createEPS(java.io.File f)
2306   {
2307   }
2308
2309   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2310   {
2311   }
2312
2313   protected void jpred_actionPerformed(ActionEvent e)
2314   {
2315   }
2316
2317   protected void scaleAbove_actionPerformed(ActionEvent e)
2318   {
2319   }
2320
2321   protected void scaleLeft_actionPerformed(ActionEvent e)
2322   {
2323   }
2324
2325   protected void scaleRight_actionPerformed(ActionEvent e)
2326   {
2327   }
2328
2329   protected void modifyPID_actionPerformed(ActionEvent e)
2330   {
2331   }
2332
2333   protected void modifyConservation_actionPerformed(ActionEvent e)
2334   {
2335   }
2336
2337   protected void saveAs_actionPerformed(ActionEvent e)
2338   {
2339   }
2340
2341   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2342   {
2343   }
2344
2345   public void vamsasStore_actionPerformed(ActionEvent e)
2346   {
2347
2348   }
2349
2350   public void vamsasLoad_actionPerformed(ActionEvent e)
2351   {
2352
2353   }
2354
2355   public void showTranslation_actionPerformed(ActionEvent e)
2356   {
2357
2358   }
2359
2360   public void featureSettings_actionPerformed(ActionEvent e)
2361   {
2362
2363   }
2364
2365   public void fetchSequence_actionPerformed(ActionEvent e)
2366   {
2367
2368   }
2369
2370   public void smoothFont_actionPerformed(ActionEvent e)
2371   {
2372
2373   }
2374
2375   public void annotationColour_actionPerformed(ActionEvent e)
2376   {
2377
2378   }
2379
2380   public void rnahelicesColour_actionPerformed(ActionEvent e)
2381   {
2382
2383   }
2384
2385   public void associatedData_actionPerformed(ActionEvent e)
2386   {
2387
2388   }
2389
2390   public void autoCalculate_actionPerformed(ActionEvent e)
2391   {
2392
2393   }
2394
2395   public void sortByTreeOption_actionPerformed(ActionEvent e)
2396   {
2397
2398   }
2399
2400   public void showAllSeqs_actionPerformed(ActionEvent e)
2401   {
2402
2403   }
2404
2405   public void showAllColumns_actionPerformed(ActionEvent e)
2406   {
2407
2408   }
2409
2410   public void hideSelSequences_actionPerformed(ActionEvent e)
2411   {
2412
2413   }
2414
2415   public void hideSelColumns_actionPerformed(ActionEvent e)
2416   {
2417
2418   }
2419
2420   public void hiddenMarkers_actionPerformed(ActionEvent e)
2421   {
2422
2423   }
2424
2425   public void findPdbId_actionPerformed(ActionEvent e)
2426   {
2427
2428   }
2429
2430   public void enterPdbId_actionPerformed(ActionEvent e)
2431   {
2432
2433   }
2434
2435   public void pdbFile_actionPerformed(ActionEvent e)
2436   {
2437
2438   }
2439
2440   public void invertColSel_actionPerformed(ActionEvent e)
2441   {
2442
2443   }
2444
2445   public void tabSelectionChanged(int sel)
2446   {
2447
2448   }
2449
2450   public void tabbedPane_mousePressed(MouseEvent e)
2451   {
2452
2453   }
2454
2455   public void tabbedPane_focusGained(FocusEvent e)
2456   {
2457     requestFocus();
2458   }
2459
2460   public void save_actionPerformed(ActionEvent e)
2461   {
2462
2463   }
2464
2465   public void reload_actionPerformed(ActionEvent e)
2466   {
2467
2468   }
2469
2470   public void newView_actionPerformed(ActionEvent e)
2471   {
2472
2473   }
2474
2475   public void textColour_actionPerformed(ActionEvent e)
2476   {
2477
2478   }
2479
2480   public void idRightAlign_actionPerformed(ActionEvent e)
2481   {
2482
2483   }
2484
2485   public void expandViews_actionPerformed(ActionEvent e)
2486   {
2487
2488   }
2489
2490   public void gatherViews_actionPerformed(ActionEvent e)
2491   {
2492
2493   }
2494
2495   public void buildTreeMenu()
2496   {
2497
2498   }
2499
2500   public void pageSetup_actionPerformed(ActionEvent e)
2501   {
2502
2503   }
2504
2505   public void alignmentProperties()
2506   {
2507
2508   }
2509 }