src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
   3  * Copyright (C) 2010 J Procter, AM Waterhouse, 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   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 117
 118   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
 119
 120   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 121
 122   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 123
 124   public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
 125
 126   JMenuItem htmlMenuItem = new JMenuItem();
 127
 128   JMenuItem overviewMenuItem = new JMenuItem();
 129
 130   protected JMenuItem undoMenuItem = new JMenuItem();
 131
 132   protected JMenuItem redoMenuItem = new JMenuItem();
 133
 134   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 135
 136   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 137
 138   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 139
 140   JMenuItem printMenuItem = new JMenuItem();
 141
 142   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 143
 144   JMenuItem findMenuItem = new JMenuItem();
 145
 146   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 147
 148   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 149
 150   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 151
 152   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
 153
 154   JMenuItem deleteGroups = new JMenuItem();
 155
 156   JMenuItem delete = new JMenuItem();
 157
 158   JMenuItem copy = new JMenuItem();
 159
 160   JMenuItem cut = new JMenuItem();
 161
 162   JMenu pasteMenu = new JMenu();
 163
 164   JMenuItem pasteNew = new JMenuItem();
 165
 166   JMenuItem pasteThis = new JMenuItem();
 167
 168   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
 169
 170   JMenuItem createPNG = new JMenuItem();
 171
 172   protected JMenuItem font = new JMenuItem();
 173
 174   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 175
 176   JMenuItem epsFile = new JMenuItem();
 177
 178   JMenuItem LoadtreeMenuItem = new JMenuItem();
 179
 180   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 181
 182   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 183
 184   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 185
 186   protected JMenuItem modifyPID = new JMenuItem();
 187
 188   protected JMenuItem modifyConservation = new JMenuItem();
 189
 190   protected JMenu sortByTreeMenu = new JMenu();
 191
 192   protected JMenu sort = new JMenu();
 193
 194   protected JMenu calculateTree = new JMenu();
 195
 196   JMenu jMenu2 = new JMenu();
 197
 198   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 199
 200   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 201
 202   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 203
 204   protected ButtonGroup colours = new ButtonGroup();
 205
 206   JMenuItem vamsasStore = new JMenuItem();
 207
 208   protected JMenuItem showTranslation = new JMenuItem();
 209
 210   protected JMenuItem extractScores = new JMenuItem();
 211
 212   protected JMenu showProducts = new JMenu();
 213
 214   public JMenuItem featureSettings = new JMenuItem();
 215
 216   JMenuItem fetchSequence = new JMenuItem();
 217
 218   JMenuItem annotationColour = new JMenuItem();
 219
 220   JMenuItem associatedData = new JMenuItem();
 221
 222   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 223
 224   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 225
 226   JMenu addSequenceMenu = new JMenu();
 227
 228   JMenuItem addFromFile = new JMenuItem();
 229
 230   JMenuItem addFromText = new JMenuItem();
 231
 232   JMenuItem addFromURL = new JMenuItem();
 233
 234   JMenuItem exportAnnotations = new JMenuItem();
 235
 236   JMenuItem exportFeatures = new JMenuItem();
 237
 238   protected JPanel statusPanel = new JPanel();
 239
 240   GridLayout gridLayout1 = new GridLayout();
 241
 242   JMenu jMenu3 = new JMenu();
 243
 244   JMenuItem showAllSeqs = new JMenuItem();
 245
 246   JMenuItem showAllColumns = new JMenuItem();
 247
 248   JMenu hideMenu = new JMenu();
 249
 250   JMenuItem hideSelSequences = new JMenuItem();
 251
 252   JMenuItem hideSelColumns = new JMenuItem();
 253
 254   JMenuItem hideAllButSelection = new JMenuItem();
 255
 256   JMenuItem hideAllSelection = new JMenuItem();
 257
 258   JMenuItem showAllhidden = new JMenuItem();
 259
 260   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 261
 262   JMenuItem invertColSel = new JMenuItem();
 263
 264   protected JTabbedPane tabbedPane = new JTabbedPane();
 265
 266   JMenuItem save = new JMenuItem();
 267
 268   protected JMenuItem reload = new JMenuItem();
 269
 270   JMenuItem newView = new JMenuItem();
 271
 272   JMenuItem textColour = new JMenuItem();
 273
 274   JMenu formatMenu = new JMenu();
 275
 276   JMenu selectMenu = new JMenu();
 277
 278   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 279
 280   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 281
 282   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 283
 284   protected JMenuItem gatherViews = new JMenuItem();
 285
 286   protected JMenuItem expandViews = new JMenuItem();
 287
 288   JMenuItem pageSetup = new JMenuItem();
 289
 290   JMenuItem alignmentProperties = new JMenuItem();
 291
 292   JMenu tooltipSettingsMenu = new JMenu();
 293
 294   private JMenuItem justifyLeftMenuItem = new JMenuItem();
 295
 296   private JMenuItem justifyRightMenuItem = new JMenuItem();
 297
 298   JMenu autoAnnMenu = new JMenu();
 299
 300   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 301
 302   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 303
 304   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 305
 306   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 307
 308   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 309
 310   private JMenuItem grpsFromSelection = new JMenuItem();
 311
 312   public GAlignFrame()
 313   {
 314     try
 315     {
 316       jbInit();
 317       setJMenuBar(alignFrameMenuBar);
 318
 319       // dynamically fill save as menu with available formats
 320       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 321       {
 322         JMenuItem item = new JMenuItem(
 323                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 324
 325         item.addActionListener(new java.awt.event.ActionListener()
 326         {
 327           public void actionPerformed(ActionEvent e)
 328           {
 329             outputText_actionPerformed(e);
 330           }
 331         });
 332
 333         outputTextboxMenu.add(item);
 334       }
 335     } catch (Exception e)
 336     {
 337     }
 338
 339     if (!new jalview.util.Platform().isAMac())
 340     {
 341       closeMenuItem.setMnemonic('C');
 342       outputTextboxMenu.setMnemonic('T');
 343       undoMenuItem.setMnemonic('Z');
 344       redoMenuItem.setMnemonic('0');
 345       copy.setMnemonic('C');
 346       cut.setMnemonic('U');
 347       pasteMenu.setMnemonic('P');
 348       reload.setMnemonic('R');
 349     }
 350
 351     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 352     {
 353       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 354               .getUserColourSchemes().keys();
 355
 356       while (userColours.hasMoreElements())
 357       {
 358         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 359                 userColours.nextElement().toString());
 360         radioItem.setName("USER_DEFINED");
 361         radioItem.addMouseListener(new MouseAdapter()
 362         {
 363           public void mousePressed(MouseEvent evt)
 364           {
 365             if (evt.isControlDown()
 366                     || SwingUtilities.isRightMouseButton(evt))
 367             {
 368               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 369
 370               int option = JOptionPane.showInternalConfirmDialog(
 371                       jalview.gui.Desktop.desktop,
 372                       "Remove from default list?",
 373                       "Remove user defined colour",
 374                       JOptionPane.YES_NO_OPTION);
 375               if (option == JOptionPane.YES_OPTION)
 376               {
 377                 jalview.gui.UserDefinedColours
 378                         .removeColourFromDefaults(radioItem.getText());
 379                 colourMenu.remove(radioItem);
 380               }
 381               else
 382               {
 383                 radioItem.addActionListener(new ActionListener()
 384                 {
 385                   public void actionPerformed(ActionEvent evt)
 386                   {
 387                     userDefinedColour_actionPerformed(evt);
 388                   }
 389                 });
 390               }
 391             }
 392           }
 393         });
 394         radioItem.addActionListener(new ActionListener()
 395         {
 396           public void actionPerformed(ActionEvent evt)
 397           {
 398             userDefinedColour_actionPerformed(evt);
 399           }
 400         });
 401         colourMenu.insert(radioItem, 15);
 402         colours.add(radioItem);
 403       }
 404     }
 405     colours.add(noColourmenuItem);
 406     colours.add(clustalColour);
 407     colours.add(zappoColour);
 408     colours.add(taylorColour);
 409     colours.add(hydrophobicityColour);
 410     colours.add(helixColour);
 411     colours.add(strandColour);
 412     colours.add(turnColour);
 413     colours.add(buriedColour);
 414     colours.add(userDefinedColour);
 415     colours.add(PIDColour);
 416     colours.add(BLOSUM62Colour);
 417     colours.add(nucleotideColour);
 418
 419     setColourSelected(jalview.bin.Cache
 420             .getDefault("DEFAULT_COLOUR", "None"));
 421
 422   }
 423
 424   public void setColourSelected(String defaultColour)
 425   {
 426
 427     if (defaultColour != null)
 428     {
 429       int index = ColourSchemeProperty
 430               .getColourIndexFromName(defaultColour);
 431
 432       switch (index)
 433       {
 434       case ColourSchemeProperty.CLUSTAL:
 435         clustalColour.setSelected(true);
 436
 437         break;
 438
 439       case ColourSchemeProperty.BLOSUM:
 440         BLOSUM62Colour.setSelected(true);
 441
 442         break;
 443
 444       case ColourSchemeProperty.PID:
 445         PIDColour.setSelected(true);
 446
 447         break;
 448
 449       case ColourSchemeProperty.ZAPPO:
 450         zappoColour.setSelected(true);
 451
 452         break;
 453
 454       case ColourSchemeProperty.TAYLOR:
 455         taylorColour.setSelected(true);
 456         break;
 457
 458       case ColourSchemeProperty.HYDROPHOBIC:
 459         hydrophobicityColour.setSelected(true);
 460
 461         break;
 462
 463       case ColourSchemeProperty.HELIX:
 464         helixColour.setSelected(true);
 465
 466         break;
 467
 468       case ColourSchemeProperty.STRAND:
 469         strandColour.setSelected(true);
 470
 471         break;
 472
 473       case ColourSchemeProperty.TURN:
 474         turnColour.setSelected(true);
 475
 476         break;
 477
 478       case ColourSchemeProperty.BURIED:
 479         buriedColour.setSelected(true);
 480
 481         break;
 482
 483       case ColourSchemeProperty.NUCLEOTIDE:
 484         nucleotideColour.setSelected(true);
 485
 486         break;
 487
 488       case ColourSchemeProperty.USER_DEFINED:
 489         userDefinedColour.setSelected(true);
 490
 491         break;
 492       case ColourSchemeProperty.NONE:
 493       default:
 494         noColourmenuItem.setSelected(true);
 495         break;
 496
 497       }
 498     }
 499
 500   }
 501
 502   private void jbInit() throws Exception
 503   {
 504     fileMenu.setText("File");
 505     saveAs.setText("Save As...");
 506     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 507             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
 508                     .getMenuShortcutKeyMask()
 509                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 510     saveAs.addActionListener(new ActionListener()
 511     {
 512       public void actionPerformed(ActionEvent e)
 513       {
 514         saveAs_actionPerformed(e);
 515       }
 516     });
 517     closeMenuItem.setText("Close");
 518     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 519             java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
 520                     .getMenuShortcutKeyMask(), false));
 521     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 522     {
 523       public void actionPerformed(ActionEvent e)
 524       {
 525         closeMenuItem_actionPerformed(false);
 526       }
 527     });
 528     editMenu.setText("Edit");
 529     viewMenu.setText("View");
 530     colourMenu.setText("Colour");
 531     calculateMenu.setText("Calculate");
 532     webService.setText("Web Service");
 533     selectAllSequenceMenuItem.setText("Select All");
 534     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 535             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
 536                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 537     selectAllSequenceMenuItem
 538             .addActionListener(new java.awt.event.ActionListener()
 539             {
 540               public void actionPerformed(ActionEvent e)
 541               {
 542                 selectAllSequenceMenuItem_actionPerformed(e);
 543               }
 544             });
 545     deselectAllSequenceMenuItem.setText("Deselect All");
 546     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 547             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 548     deselectAllSequenceMenuItem
 549             .addActionListener(new java.awt.event.ActionListener()
 550             {
 551               public void actionPerformed(ActionEvent e)
 552               {
 553                 deselectAllSequenceMenuItem_actionPerformed(e);
 554               }
 555             });
 556     invertSequenceMenuItem.setText("Invert Sequence Selection");
 557     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 558             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
 559                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 560     invertSequenceMenuItem
 561             .addActionListener(new java.awt.event.ActionListener()
 562             {
 563               public void actionPerformed(ActionEvent e)
 564               {
 565                 invertSequenceMenuItem_actionPerformed(e);
 566               }
 567             });
 568     grpsFromSelection.setText("Make Groups for selection");
 569     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
 570     {
 571       public void actionPerformed(ActionEvent e)
 572       {
 573         makeGrpsFromSelection_actionPerformed(e);
 574       }
 575     });
 576
 577     remove2LeftMenuItem.setText("Remove Left");
 578     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 579             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
 580                     .getMenuShortcutKeyMask(), false));
 581     remove2LeftMenuItem
 582             .addActionListener(new java.awt.event.ActionListener()
 583             {
 584               public void actionPerformed(ActionEvent e)
 585               {
 586                 remove2LeftMenuItem_actionPerformed(e);
 587               }
 588             });
 589     remove2RightMenuItem.setText("Remove Right");
 590     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 591             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
 592                     .getMenuShortcutKeyMask(), false));
 593     remove2RightMenuItem
 594             .addActionListener(new java.awt.event.ActionListener()
 595             {
 596               public void actionPerformed(ActionEvent e)
 597               {
 598                 remove2RightMenuItem_actionPerformed(e);
 599               }
 600             });
 601     removeGappedColumnMenuItem.setText("Remove Empty Columns");
 602     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
 603             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 604                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 605     removeGappedColumnMenuItem
 606             .addActionListener(new java.awt.event.ActionListener()
 607             {
 608               public void actionPerformed(ActionEvent e)
 609               {
 610                 removeGappedColumnMenuItem_actionPerformed(e);
 611               }
 612             });
 613     removeAllGapsMenuItem.setText("Remove All Gaps");
 614     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
 615             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 616                     .getDefaultToolkit().getMenuShortcutKeyMask()
 617                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 618     removeAllGapsMenuItem
 619             .addActionListener(new java.awt.event.ActionListener()
 620             {
 621               public void actionPerformed(ActionEvent e)
 622               {
 623                 removeAllGapsMenuItem_actionPerformed(e);
 624               }
 625             });
 626     justifyLeftMenuItem.setText("Left Justify Alignment");
 627     justifyLeftMenuItem
 628             .addActionListener(new java.awt.event.ActionListener()
 629             {
 630               public void actionPerformed(ActionEvent e)
 631               {
 632                 justifyLeftMenuItem_actionPerformed(e);
 633               }
 634             });
 635     justifyRightMenuItem.setText("Right Justify Alignment");
 636     justifyRightMenuItem
 637             .addActionListener(new java.awt.event.ActionListener()
 638             {
 639               public void actionPerformed(ActionEvent e)
 640               {
 641                 justifyRightMenuItem_actionPerformed(e);
 642               }
 643             });
 644     viewBoxesMenuItem.setText("Boxes");
 645     viewBoxesMenuItem.setState(true);
 646     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 647     {
 648       public void actionPerformed(ActionEvent e)
 649       {
 650         viewBoxesMenuItem_actionPerformed(e);
 651       }
 652     });
 653     viewTextMenuItem.setText("Text");
 654     viewTextMenuItem.setState(true);
 655     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 656     {
 657       public void actionPerformed(ActionEvent e)
 658       {
 659         viewTextMenuItem_actionPerformed(e);
 660       }
 661     });
 662     showNonconservedMenuItem.setText("Show nonconserved");
 663     showNonconservedMenuItem.setState(false);
 664     showNonconservedMenuItem
 665             .addActionListener(new java.awt.event.ActionListener()
 666             {
 667               public void actionPerformed(ActionEvent e)
 668               {
 669                 showUnconservedMenuItem_actionPerformed(e);
 670               }
 671             });
 672     sortPairwiseMenuItem.setText("by Pairwise Identity");
 673     sortPairwiseMenuItem
 674             .addActionListener(new java.awt.event.ActionListener()
 675             {
 676               public void actionPerformed(ActionEvent e)
 677               {
 678                 sortPairwiseMenuItem_actionPerformed(e);
 679               }
 680             });
 681     sortIDMenuItem.setText("by ID");
 682     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 683     {
 684       public void actionPerformed(ActionEvent e)
 685       {
 686         sortIDMenuItem_actionPerformed(e);
 687       }
 688     });
 689     sortLengthMenuItem.setText("By Length");
 690     sortLengthMenuItem
 691             .addActionListener(new java.awt.event.ActionListener()
 692             {
 693               public void actionPerformed(ActionEvent e)
 694               {
 695                 sortLengthMenuItem_actionPerformed(e);
 696               }
 697             });
 698     sortGroupMenuItem.setText("by Group");
 699     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 700     {
 701       public void actionPerformed(ActionEvent e)
 702       {
 703         sortGroupMenuItem_actionPerformed(e);
 704       }
 705     });
 706     removeRedundancyMenuItem.setText("Remove Redundancy...");
 707     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
 708             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
 709                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 710     removeRedundancyMenuItem
 711             .addActionListener(new java.awt.event.ActionListener()
 712             {
 713               public void actionPerformed(ActionEvent e)
 714               {
 715                 removeRedundancyMenuItem_actionPerformed(e);
 716               }
 717             });
 718     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
 719     pairwiseAlignmentMenuItem
 720             .addActionListener(new java.awt.event.ActionListener()
 721             {
 722               public void actionPerformed(ActionEvent e)
 723               {
 724                 pairwiseAlignmentMenuItem_actionPerformed(e);
 725               }
 726             });
 727     PCAMenuItem.setText("Principal Component Analysis");
 728     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 729     {
 730       public void actionPerformed(ActionEvent e)
 731       {
 732         PCAMenuItem_actionPerformed(e);
 733       }
 734     });
 735     averageDistanceTreeMenuItem
 736             .setText("Average Distance Using % Identity");
 737     averageDistanceTreeMenuItem
 738             .addActionListener(new java.awt.event.ActionListener()
 739             {
 740               public void actionPerformed(ActionEvent e)
 741               {
 742                 averageDistanceTreeMenuItem_actionPerformed(e);
 743               }
 744             });
 745     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
 746     neighbourTreeMenuItem
 747             .addActionListener(new java.awt.event.ActionListener()
 748             {
 749               public void actionPerformed(ActionEvent e)
 750               {
 751                 neighbourTreeMenuItem_actionPerformed(e);
 752               }
 753             });
 754     this.getContentPane().setLayout(borderLayout1);
 755     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 756     statusBar.setBackground(Color.white);
 757     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 758     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 759     statusBar.setText("Status bar");
 760     outputTextboxMenu.setText("Output to Textbox");
 761     clustalColour.setText("Clustalx");
 762
 763     clustalColour.addActionListener(new java.awt.event.ActionListener()
 764     {
 765       public void actionPerformed(ActionEvent e)
 766       {
 767         clustalColour_actionPerformed(e);
 768       }
 769     });
 770     zappoColour.setText("Zappo");
 771     zappoColour.addActionListener(new java.awt.event.ActionListener()
 772     {
 773       public void actionPerformed(ActionEvent e)
 774       {
 775         zappoColour_actionPerformed(e);
 776       }
 777     });
 778     taylorColour.setText("Taylor");
 779     taylorColour.addActionListener(new java.awt.event.ActionListener()
 780     {
 781       public void actionPerformed(ActionEvent e)
 782       {
 783         taylorColour_actionPerformed(e);
 784       }
 785     });
 786     hydrophobicityColour.setText("Hydrophobicity");
 787     hydrophobicityColour
 788             .addActionListener(new java.awt.event.ActionListener()
 789             {
 790               public void actionPerformed(ActionEvent e)
 791               {
 792                 hydrophobicityColour_actionPerformed(e);
 793               }
 794             });
 795     helixColour.setText("Helix Propensity");
 796     helixColour.addActionListener(new java.awt.event.ActionListener()
 797     {
 798       public void actionPerformed(ActionEvent e)
 799       {
 800         helixColour_actionPerformed(e);
 801       }
 802     });
 803     strandColour.setText("Strand Propensity");
 804     strandColour.addActionListener(new java.awt.event.ActionListener()
 805     {
 806       public void actionPerformed(ActionEvent e)
 807       {
 808         strandColour_actionPerformed(e);
 809       }
 810     });
 811     turnColour.setText("Turn Propensity");
 812     turnColour.addActionListener(new java.awt.event.ActionListener()
 813     {
 814       public void actionPerformed(ActionEvent e)
 815       {
 816         turnColour_actionPerformed(e);
 817       }
 818     });
 819     buriedColour.setText("Buried Index");
 820     buriedColour.addActionListener(new java.awt.event.ActionListener()
 821     {
 822       public void actionPerformed(ActionEvent e)
 823       {
 824         buriedColour_actionPerformed(e);
 825       }
 826     });
 827     userDefinedColour.setText("User Defined...");
 828     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 829     {
 830       public void actionPerformed(ActionEvent e)
 831       {
 832         userDefinedColour_actionPerformed(e);
 833       }
 834     });
 835     PIDColour.setText("Percentage Identity");
 836     PIDColour.addActionListener(new java.awt.event.ActionListener()
 837     {
 838       public void actionPerformed(ActionEvent e)
 839       {
 840         PIDColour_actionPerformed(e);
 841       }
 842     });
 843     BLOSUM62Colour.setText("BLOSUM62 Score");
 844     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 845     {
 846       public void actionPerformed(ActionEvent e)
 847       {
 848         BLOSUM62Colour_actionPerformed(e);
 849       }
 850     });
 851     avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
 852     avDistanceTreeBlosumMenuItem
 853             .addActionListener(new java.awt.event.ActionListener()
 854             {
 855               public void actionPerformed(ActionEvent e)
 856               {
 857                 avTreeBlosumMenuItem_actionPerformed(e);
 858               }
 859             });
 860     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
 861     njTreeBlosumMenuItem
 862             .addActionListener(new java.awt.event.ActionListener()
 863             {
 864               public void actionPerformed(ActionEvent e)
 865               {
 866                 njTreeBlosumMenuItem_actionPerformed(e);
 867               }
 868             });
 869     annotationPanelMenuItem.setActionCommand("");
 870     annotationPanelMenuItem.setText("Show Annotations");
 871     annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
 872             "SHOW_ANNOTATIONS", true));
 873     annotationPanelMenuItem
 874             .addActionListener(new java.awt.event.ActionListener()
 875             {
 876               public void actionPerformed(ActionEvent e)
 877               {
 878                 annotationPanelMenuItem_actionPerformed(e);
 879               }
 880             });
 881     colourTextMenuItem.setText("Colour Text");
 882     colourTextMenuItem
 883             .addActionListener(new java.awt.event.ActionListener()
 884             {
 885               public void actionPerformed(ActionEvent e)
 886               {
 887                 colourTextMenuItem_actionPerformed(e);
 888               }
 889             });
 890     htmlMenuItem.setText("HTML");
 891     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
 892     {
 893       public void actionPerformed(ActionEvent e)
 894       {
 895         htmlMenuItem_actionPerformed(e);
 896       }
 897     });
 898     overviewMenuItem.setText("Overview Window");
 899     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
 900     {
 901       public void actionPerformed(ActionEvent e)
 902       {
 903         overviewMenuItem_actionPerformed(e);
 904       }
 905     });
 906     undoMenuItem.setEnabled(false);
 907     undoMenuItem.setText("Undo");
 908     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 909             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
 910                     .getMenuShortcutKeyMask(), false));
 911     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
 912     {
 913       public void actionPerformed(ActionEvent e)
 914       {
 915         undoMenuItem_actionPerformed(e);
 916       }
 917     });
 918     redoMenuItem.setEnabled(false);
 919     redoMenuItem.setText("Redo");
 920     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 921             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
 922                     .getMenuShortcutKeyMask(), false));
 923     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
 924     {
 925       public void actionPerformed(ActionEvent e)
 926       {
 927         redoMenuItem_actionPerformed(e);
 928       }
 929     });
 930     conservationMenuItem.setText("By Conservation");
 931     conservationMenuItem
 932             .addActionListener(new java.awt.event.ActionListener()
 933             {
 934               public void actionPerformed(ActionEvent e)
 935               {
 936                 conservationMenuItem_actionPerformed(e);
 937               }
 938             });
 939     noColourmenuItem.setText("None");
 940     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 941     {
 942       public void actionPerformed(ActionEvent e)
 943       {
 944         noColourmenuItem_actionPerformed(e);
 945       }
 946     });
 947     wrapMenuItem.setText("Wrap");
 948     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
 949     {
 950       public void actionPerformed(ActionEvent e)
 951       {
 952         wrapMenuItem_actionPerformed(e);
 953       }
 954     });
 955     printMenuItem.setText("Print ...");
 956     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 957             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
 958                     .getMenuShortcutKeyMask(), false));
 959     printMenuItem.addActionListener(new java.awt.event.ActionListener()
 960     {
 961       public void actionPerformed(ActionEvent e)
 962       {
 963         printMenuItem_actionPerformed(e);
 964       }
 965     });
 966     renderGapsMenuItem.setText("Show Gaps");
 967     renderGapsMenuItem.setState(true);
 968     renderGapsMenuItem
 969             .addActionListener(new java.awt.event.ActionListener()
 970             {
 971               public void actionPerformed(ActionEvent e)
 972               {
 973                 renderGapsMenuItem_actionPerformed(e);
 974               }
 975             });
 976     findMenuItem.setText("Find...");
 977     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 978             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
 979                     .getMenuShortcutKeyMask(), false));
 980     findMenuItem.addActionListener(new java.awt.event.ActionListener()
 981     {
 982       public void actionPerformed(ActionEvent e)
 983       {
 984         findMenuItem_actionPerformed(e);
 985       }
 986     });
 987     abovePIDThreshold.setText("Above Identity Threshold");
 988     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
 989     {
 990       public void actionPerformed(ActionEvent e)
 991       {
 992         abovePIDThreshold_actionPerformed(e);
 993       }
 994     });
 995     showSeqFeatures.setText("Show Sequence Features");
 996     showSeqFeatures.addActionListener(new ActionListener()
 997     {
 998       public void actionPerformed(ActionEvent actionEvent)
 999       {
1000         showSeqFeatures_actionPerformed(actionEvent);
1001       }
1002     });
1003     /*
1004      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1005      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1006      * void actionPerformed(ActionEvent actionEvent) {
1007      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1008      */
1009     showDbRefsMenuitem.setText("Show Database Refs");
1010     showDbRefsMenuitem.addActionListener(new ActionListener()
1011     {
1012
1013       public void actionPerformed(ActionEvent e)
1014       {
1015         showDbRefs_actionPerformed(e);
1016       }
1017
1018     });
1019     showNpFeatsMenuitem.setText("Show Non-Positional Features");
1020     showNpFeatsMenuitem.addActionListener(new ActionListener()
1021     {
1022
1023       public void actionPerformed(ActionEvent e)
1024       {
1025         showNpFeats_actionPerformed(e);
1026       }
1027
1028     });
1029     showGroupConservation.setText("Group Conservation");
1030     showGroupConservation.addActionListener(new ActionListener()
1031     {
1032
1033       public void actionPerformed(ActionEvent e)
1034       {
1035         showGroupConservation_actionPerformed(e);
1036       }
1037
1038     });
1039
1040     showGroupConsensus.setText("Group Consensus");
1041     showGroupConsensus.addActionListener(new ActionListener()
1042     {
1043
1044       public void actionPerformed(ActionEvent e)
1045       {
1046         showGroupConsensus_actionPerformed(e);
1047       }
1048
1049     });
1050     showConsensusHistogram.setText("Show Consensus Histogram");
1051     showConsensusHistogram.addActionListener(new ActionListener()
1052     {
1053
1054       public void actionPerformed(ActionEvent e)
1055       {
1056         showConsensusHistogram_actionPerformed(e);
1057       }
1058
1059     });
1060     showSequenceLogo.setText("Show Consensus Logo");
1061     showSequenceLogo.addActionListener(new ActionListener()
1062     {
1063
1064       public void actionPerformed(ActionEvent e)
1065       {
1066         showSequenceLogo_actionPerformed(e);
1067       }
1068
1069     });
1070     applyAutoAnnotationSettings.setText("Apply to all groups");
1071     applyAutoAnnotationSettings.setState(false);
1072     applyAutoAnnotationSettings.setVisible(true);
1073     applyAutoAnnotationSettings.addActionListener(new ActionListener()
1074     {
1075
1076       public void actionPerformed(ActionEvent e)
1077       {
1078         applyAutoAnnotationSettings_actionPerformed(e);
1079       }
1080
1081     });
1082
1083     nucleotideColour.setText("Nucleotide");
1084     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1085     {
1086       public void actionPerformed(ActionEvent e)
1087       {
1088         nucleotideColour_actionPerformed(e);
1089       }
1090     });
1091     deleteGroups.setText("Undefine groups");
1092     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1093             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1094                     .getMenuShortcutKeyMask(), false));
1095     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1096     {
1097       public void actionPerformed(ActionEvent e)
1098       {
1099         deleteGroups_actionPerformed(e);
1100       }
1101     });
1102     copy.setText("Copy");
1103     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1104             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1105                     .getMenuShortcutKeyMask(), false));
1106
1107     copy.addActionListener(new java.awt.event.ActionListener()
1108     {
1109       public void actionPerformed(ActionEvent e)
1110       {
1111         copy_actionPerformed(e);
1112       }
1113     });
1114     cut.setText("Cut");
1115     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1116             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1117                     .getMenuShortcutKeyMask(), false));
1118     cut.addActionListener(new java.awt.event.ActionListener()
1119     {
1120       public void actionPerformed(ActionEvent e)
1121       {
1122         cut_actionPerformed(e);
1123       }
1124     });
1125     delete.setText("Delete");
1126     delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1127             java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1128     delete.addActionListener(new java.awt.event.ActionListener()
1129     {
1130       public void actionPerformed(ActionEvent e)
1131       {
1132         delete_actionPerformed(e);
1133       }
1134     });
1135     pasteMenu.setText("Paste");
1136     pasteNew.setText("To New Alignment");
1137     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1138             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1139                     .getMenuShortcutKeyMask()
1140                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1141     pasteNew.addActionListener(new java.awt.event.ActionListener()
1142     {
1143       public void actionPerformed(ActionEvent e)
1144       {
1145         pasteNew_actionPerformed(e);
1146       }
1147     });
1148     pasteThis.setText("Add To This Alignment");
1149     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1150             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1151                     .getMenuShortcutKeyMask(), false));
1152     pasteThis.addActionListener(new java.awt.event.ActionListener()
1153     {
1154       public void actionPerformed(ActionEvent e)
1155       {
1156         pasteThis_actionPerformed(e);
1157       }
1158     });
1159     applyToAllGroups.setText("Apply Colour To All Groups");
1160     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1161     {
1162       public void actionPerformed(ActionEvent e)
1163       {
1164         applyToAllGroups_actionPerformed(e);
1165       }
1166     });
1167     createPNG.addActionListener(new java.awt.event.ActionListener()
1168     {
1169       public void actionPerformed(ActionEvent e)
1170       {
1171         createPNG(null);
1172       }
1173     });
1174     createPNG.setActionCommand("Save As PNG Image");
1175     createPNG.setText("PNG");
1176     font.setText("Font...");
1177     font.addActionListener(new java.awt.event.ActionListener()
1178     {
1179       public void actionPerformed(ActionEvent e)
1180       {
1181         font_actionPerformed(e);
1182       }
1183     });
1184
1185     seqLimits.setText("Show Sequence Limits");
1186     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1187     seqLimits.addActionListener(new java.awt.event.ActionListener()
1188     {
1189       public void actionPerformed(ActionEvent e)
1190       {
1191         seqLimit_actionPerformed(e);
1192       }
1193     });
1194     epsFile.setText("EPS");
1195     epsFile.addActionListener(new java.awt.event.ActionListener()
1196     {
1197       public void actionPerformed(ActionEvent e)
1198       {
1199         createEPS(null);
1200       }
1201     });
1202     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1203     LoadtreeMenuItem.setText("Load Associated Tree");
1204     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1205     {
1206       public void actionPerformed(ActionEvent e)
1207       {
1208         LoadtreeMenuItem_actionPerformed(e);
1209       }
1210     });
1211     scaleAbove.setVisible(false);
1212     scaleAbove.setText("Scale Above");
1213     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1214     {
1215       public void actionPerformed(ActionEvent e)
1216       {
1217         scaleAbove_actionPerformed(e);
1218       }
1219     });
1220     scaleLeft.setVisible(false);
1221     scaleLeft.setSelected(true);
1222     scaleLeft.setText("Scale Left");
1223     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1224     {
1225       public void actionPerformed(ActionEvent e)
1226       {
1227         scaleLeft_actionPerformed(e);
1228       }
1229     });
1230     scaleRight.setVisible(false);
1231     scaleRight.setSelected(true);
1232     scaleRight.setText("Scale Right");
1233     scaleRight.addActionListener(new java.awt.event.ActionListener()
1234     {
1235       public void actionPerformed(ActionEvent e)
1236       {
1237         scaleRight_actionPerformed(e);
1238       }
1239     });
1240     centreColumnLabelsMenuItem.setVisible(true);
1241     centreColumnLabelsMenuItem.setState(false);
1242     centreColumnLabelsMenuItem.setText("Centre Column Labels");
1243     centreColumnLabelsMenuItem
1244             .addActionListener(new java.awt.event.ActionListener()
1245             {
1246               public void actionPerformed(ActionEvent e)
1247               {
1248                 centreColumnLabels_actionPerformed(e);
1249               }
1250             });
1251     followHighlightMenuItem.setVisible(true);
1252     followHighlightMenuItem.setState(true);
1253     followHighlightMenuItem.setText("Automatic Scrolling");
1254     followHighlightMenuItem.addActionListener(new ActionListener()
1255     {
1256
1257       public void actionPerformed(ActionEvent e)
1258       {
1259         followHighlight_actionPerformed();
1260       }
1261
1262     });
1263
1264     modifyPID.setText("Modify Identity Threshold...");
1265     modifyPID.addActionListener(new java.awt.event.ActionListener()
1266     {
1267       public void actionPerformed(ActionEvent e)
1268       {
1269         modifyPID_actionPerformed(e);
1270       }
1271     });
1272     modifyConservation.setText("Modify Conservation Threshold...");
1273     modifyConservation
1274             .addActionListener(new java.awt.event.ActionListener()
1275             {
1276               public void actionPerformed(ActionEvent e)
1277               {
1278                 modifyConservation_actionPerformed(e);
1279               }
1280             });
1281     sortByTreeMenu.setText("By Tree Order");
1282     sort.setText("Sort");
1283     sort.addMenuListener(new MenuListener()
1284     {
1285       public void menuSelected(MenuEvent e)
1286       {
1287         buildTreeMenu();
1288       }
1289
1290       public void menuDeselected(MenuEvent e)
1291       {
1292       }
1293
1294       public void menuCanceled(MenuEvent e)
1295       {
1296       }
1297     });
1298     sortByAnnotScore.setText("by Score");
1299     sort.add(sortByAnnotScore);
1300     sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1301     {
1302
1303       public void menuCanceled(MenuEvent e)
1304       {
1305       }
1306
1307       public void menuDeselected(MenuEvent e)
1308       {
1309       }
1310
1311       public void menuSelected(MenuEvent e)
1312       {
1313         buildSortByAnnotationScoresMenu();
1314       }
1315     });
1316     sortByAnnotScore.setVisible(false);
1317
1318     calculateTree.setText("Calculate Tree");
1319
1320     jMenu2.setText("Export Image");
1321     padGapsMenuitem.setText("Pad Gaps");
1322     padGapsMenuitem.setState(jalview.bin.Cache
1323             .getDefault("PAD_GAPS", false));
1324     padGapsMenuitem.addActionListener(new ActionListener()
1325     {
1326       public void actionPerformed(ActionEvent e)
1327       {
1328         padGapsMenuitem_actionPerformed(e);
1329       }
1330     });
1331     vamsasStore.setVisible(false);
1332     vamsasStore.setText("VAMSAS store");
1333     vamsasStore.addActionListener(new ActionListener()
1334     {
1335       public void actionPerformed(ActionEvent e)
1336       {
1337         vamsasStore_actionPerformed(e);
1338       }
1339     });
1340     showTranslation.setText("Translate cDNA");
1341     showTranslation.addActionListener(new ActionListener()
1342     {
1343       public void actionPerformed(ActionEvent e)
1344       {
1345         showTranslation_actionPerformed(e);
1346       }
1347     });
1348     extractScores.setText("Extract Scores...");
1349     extractScores.addActionListener(new ActionListener()
1350     {
1351       public void actionPerformed(ActionEvent e)
1352       {
1353         extractScores_actionPerformed(e);
1354       }
1355     });
1356     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1357     // score extraction
1358     showProducts.setText("Get Cross References");
1359     /*
1360      * showProducts.addActionListener(new ActionListener() {
1361      *
1362      * public void actionPerformed(ActionEvent e) {
1363      * showProducts_actionPerformed(e); } });
1364      */
1365     featureSettings.setText("Feature Settings...");
1366     featureSettings.addActionListener(new ActionListener()
1367     {
1368       public void actionPerformed(ActionEvent e)
1369       {
1370         featureSettings_actionPerformed(e);
1371       }
1372     });
1373     fetchSequence.setText("Fetch Sequence(s)...");
1374     fetchSequence.addActionListener(new ActionListener()
1375     {
1376       public void actionPerformed(ActionEvent e)
1377       {
1378         fetchSequence_actionPerformed(e);
1379       }
1380     });
1381
1382     annotationColour.setText("By Annotation...");
1383     annotationColour.addActionListener(new ActionListener()
1384     {
1385       public void actionPerformed(ActionEvent e)
1386       {
1387         annotationColour_actionPerformed(e);
1388       }
1389     });
1390     associatedData.setText("Load Features / Annotations");
1391     associatedData.addActionListener(new ActionListener()
1392     {
1393       public void actionPerformed(ActionEvent e)
1394       {
1395         associatedData_actionPerformed(e);
1396       }
1397     });
1398     autoCalculate.setText("Autocalculate Consensus");
1399     autoCalculate.setState(jalview.bin.Cache.getDefault(
1400             "AUTO_CALC_CONSENSUS", true));
1401     autoCalculate.addActionListener(new ActionListener()
1402     {
1403       public void actionPerformed(ActionEvent e)
1404       {
1405         autoCalculate_actionPerformed(e);
1406       }
1407     });
1408     sortByTree.setText("Sort Alignment With New Tree");
1409     sortByTree.setToolTipText("<html>Enable this to automatically sort<br>the alignment when you open<br> a new tree.");
1410     sortByTree.setState(jalview.bin.Cache.getDefault(
1411             "SORT_BY_TREE", false));
1412     sortByTree.addActionListener(new ActionListener()
1413     {
1414       public void actionPerformed(ActionEvent e)
1415       {
1416         sortByTreeOption_actionPerformed(e);
1417       }
1418     });
1419
1420     addSequenceMenu.setText("Add Sequences");
1421     addFromFile.setText("From File");
1422     addFromFile.addActionListener(new ActionListener()
1423     {
1424       public void actionPerformed(ActionEvent e)
1425       {
1426         addFromFile_actionPerformed(e);
1427       }
1428     });
1429     addFromText.setText("From Textbox");
1430     addFromText.addActionListener(new ActionListener()
1431     {
1432       public void actionPerformed(ActionEvent e)
1433       {
1434         addFromText_actionPerformed(e);
1435       }
1436     });
1437     addFromURL.setText("From URL");
1438     addFromURL.addActionListener(new ActionListener()
1439     {
1440       public void actionPerformed(ActionEvent e)
1441       {
1442         addFromURL_actionPerformed(e);
1443       }
1444     });
1445     exportFeatures.setText("Export Features...");
1446     exportFeatures.addActionListener(new ActionListener()
1447     {
1448       public void actionPerformed(ActionEvent e)
1449       {
1450         exportFeatures_actionPerformed(e);
1451       }
1452     });
1453     exportAnnotations.setText("Export Annotations...");
1454     exportAnnotations.addActionListener(new ActionListener()
1455     {
1456       public void actionPerformed(ActionEvent e)
1457       {
1458         exportAnnotations_actionPerformed(e);
1459       }
1460     });
1461     statusPanel.setLayout(gridLayout1);
1462     jMenu3.setText("Show");
1463     showAllSeqs.setText("All Sequences");
1464     showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1465     showAllSeqs.addActionListener(new ActionListener()
1466     {
1467       public void actionPerformed(ActionEvent e)
1468       {
1469         showAllSeqs_actionPerformed(e);
1470       }
1471     });
1472     showAllColumns.setText("All Columns");
1473     showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1474     showAllColumns.addActionListener(new ActionListener()
1475     {
1476       public void actionPerformed(ActionEvent e)
1477       {
1478         showAllColumns_actionPerformed(e);
1479       }
1480     });
1481     hideMenu.setText("Hide");
1482     hideSelSequences.setText("Selected Sequences");
1483     hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1484     hideSelSequences.addActionListener(new ActionListener()
1485     {
1486       public void actionPerformed(ActionEvent e)
1487       {
1488         hideSelSequences_actionPerformed(e);
1489       }
1490     });
1491     hideSelColumns.setText("Selected Columns");
1492     hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1493     hideSelColumns.addActionListener(new ActionListener()
1494     {
1495       public void actionPerformed(ActionEvent e)
1496       {
1497         hideSelColumns_actionPerformed(e);
1498       }
1499     });
1500     hideAllSelection.setText("Selected Region");
1501     hideAllSelection.addActionListener(new ActionListener()
1502     {
1503       public void actionPerformed(ActionEvent e)
1504       {
1505         hideAllSelection_actionPerformed(e);
1506       }
1507     });
1508     // TODO: should be hidden if no selection exists.
1509     hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
1510     hideAllButSelection.addActionListener(new ActionListener()
1511     {
1512       public void actionPerformed(ActionEvent e)
1513       {
1514         hideAllButSelection_actionPerformed(e);
1515       }
1516     });
1517     showAllhidden.setText("All Sequences and Columns");
1518     showAllhidden
1519             .setToolTipText("H toggles visibility of hidden or selected regions.");
1520     showAllhidden.addActionListener(new ActionListener()
1521     {
1522       public void actionPerformed(ActionEvent e)
1523       {
1524         showAllhidden_actionPerformed(e);
1525       }
1526     });
1527
1528     hiddenMarkers.setText("Show Hidden Markers");
1529     hiddenMarkers.addActionListener(new ActionListener()
1530     {
1531       public void actionPerformed(ActionEvent e)
1532       {
1533         hiddenMarkers_actionPerformed(e);
1534       }
1535     });
1536     invertColSel.setText("Invert Column Selection");
1537     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1538             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1539                     .getMenuShortcutKeyMask()
1540                     | java.awt.event.KeyEvent.ALT_MASK, false));
1541     invertColSel.addActionListener(new ActionListener()
1542     {
1543       public void actionPerformed(ActionEvent e)
1544       {
1545         invertColSel_actionPerformed(e);
1546       }
1547     });
1548     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1549     {
1550       public void stateChanged(ChangeEvent evt)
1551       {
1552         JTabbedPane pane = (JTabbedPane) evt.getSource();
1553         int sel = pane.getSelectedIndex();
1554         tabSelectionChanged(sel);
1555       }
1556     });
1557     tabbedPane.addMouseListener(new MouseAdapter()
1558     {
1559       public void mousePressed(MouseEvent e)
1560       {
1561         tabbedPane_mousePressed(e);
1562       }
1563     });
1564     tabbedPane.addFocusListener(new FocusAdapter()
1565     {
1566       public void focusGained(FocusEvent e)
1567       {
1568         tabbedPane_focusGained(e);
1569       }
1570     });
1571     save.setText("Save");
1572     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1573             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1574                     .getMenuShortcutKeyMask(), false));
1575     save.addActionListener(new ActionListener()
1576     {
1577       public void actionPerformed(ActionEvent e)
1578       {
1579         save_actionPerformed(e);
1580       }
1581     });
1582     reload.setEnabled(false);
1583     reload.setText("Reload");
1584     reload.addActionListener(new ActionListener()
1585     {
1586       public void actionPerformed(ActionEvent e)
1587       {
1588         reload_actionPerformed(e);
1589       }
1590     });
1591     newView.setText("New View");
1592     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1593             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1594                     .getMenuShortcutKeyMask(), false));
1595     newView.addActionListener(new ActionListener()
1596     {
1597       public void actionPerformed(ActionEvent e)
1598       {
1599         newView_actionPerformed(e);
1600       }
1601     });
1602     tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1603             + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1604     textColour.setText("Colour Text ...");
1605     textColour.addActionListener(new ActionListener()
1606     {
1607       public void actionPerformed(ActionEvent e)
1608       {
1609         textColour_actionPerformed(e);
1610       }
1611     });
1612     formatMenu.setText("Format");
1613     selectMenu.setText("Select");
1614     idRightAlign.setText("Right Align Sequence Id");
1615     idRightAlign.addActionListener(new ActionListener()
1616     {
1617       public void actionPerformed(ActionEvent e)
1618       {
1619         idRightAlign_actionPerformed(e);
1620       }
1621     });
1622     gatherViews.setEnabled(false);
1623     gatherViews.setText("Gather Views");
1624     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1625             java.awt.event.KeyEvent.VK_G, 0, false));
1626     gatherViews.addActionListener(new ActionListener()
1627     {
1628       public void actionPerformed(ActionEvent e)
1629       {
1630         gatherViews_actionPerformed(e);
1631       }
1632     });
1633     expandViews.setEnabled(false);
1634     expandViews.setText("Expand Views");
1635     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1636             java.awt.event.KeyEvent.VK_X, 0, false));
1637     expandViews.addActionListener(new ActionListener()
1638     {
1639       public void actionPerformed(ActionEvent e)
1640       {
1641         expandViews_actionPerformed(e);
1642       }
1643     });
1644     pageSetup.setText("Page Setup ...");
1645     pageSetup.addActionListener(new ActionListener()
1646     {
1647       public void actionPerformed(ActionEvent e)
1648       {
1649         pageSetup_actionPerformed(e);
1650       }
1651     });
1652     alignmentProperties.setText("Alignment Properties...");
1653     alignmentProperties.addActionListener(new ActionListener()
1654     {
1655       public void actionPerformed(ActionEvent actionEvent)
1656       {
1657         alignmentProperties();
1658       }
1659     });
1660     tooltipSettingsMenu.setText("Sequence ID Tooltip");
1661     autoAnnMenu.setText("Autocalculated Annotation");
1662     alignFrameMenuBar.add(fileMenu);
1663     alignFrameMenuBar.add(editMenu);
1664     alignFrameMenuBar.add(selectMenu);
1665     alignFrameMenuBar.add(viewMenu);
1666     alignFrameMenuBar.add(formatMenu);
1667     alignFrameMenuBar.add(colourMenu);
1668     alignFrameMenuBar.add(calculateMenu);
1669     alignFrameMenuBar.add(webService);
1670     fileMenu.add(fetchSequence);
1671     fileMenu.add(addSequenceMenu);
1672     fileMenu.add(reload);
1673     fileMenu.addSeparator();
1674     fileMenu.add(vamsasStore);
1675     fileMenu.add(save);
1676     fileMenu.add(saveAs);
1677     fileMenu.add(outputTextboxMenu);
1678     fileMenu.add(pageSetup);
1679     fileMenu.add(printMenuItem);
1680     fileMenu.addSeparator();
1681     fileMenu.add(jMenu2);
1682     fileMenu.add(exportFeatures);
1683     fileMenu.add(exportAnnotations);
1684     fileMenu.add(LoadtreeMenuItem);
1685     fileMenu.add(associatedData);
1686     fileMenu.addSeparator();
1687     fileMenu.add(closeMenuItem);
1688     editMenu.add(undoMenuItem);
1689     editMenu.add(redoMenuItem);
1690     editMenu.add(cut);
1691     editMenu.add(copy);
1692     editMenu.add(pasteMenu);
1693     editMenu.add(delete);
1694     editMenu.addSeparator();
1695     editMenu.add(remove2LeftMenuItem);
1696     editMenu.add(remove2RightMenuItem);
1697     editMenu.add(removeGappedColumnMenuItem);
1698     editMenu.add(removeAllGapsMenuItem);
1699     editMenu.add(removeRedundancyMenuItem);
1700     editMenu.addSeparator();
1701     // dont add these yet in the CVS build - they cannot be undone!
1702     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1703     // editMenu.add(justifyLeftMenuItem);
1704     // editMenu.add(justifyRightMenuItem);
1705     // editMenu.addSeparator();
1706     editMenu.add(padGapsMenuitem);
1707     viewMenu.add(newView);
1708     viewMenu.add(expandViews);
1709     viewMenu.add(gatherViews);
1710     viewMenu.addSeparator();
1711     viewMenu.add(jMenu3);
1712     viewMenu.add(hideMenu);
1713     viewMenu.addSeparator();
1714     viewMenu.add(followHighlightMenuItem);
1715     viewMenu.add(annotationPanelMenuItem);
1716     autoAnnMenu.add(applyAutoAnnotationSettings);
1717     autoAnnMenu.add(showConsensusHistogram);
1718     autoAnnMenu.add(showSequenceLogo);
1719     autoAnnMenu.addSeparator();
1720     autoAnnMenu.add(showGroupConservation);
1721     autoAnnMenu.add(showGroupConsensus);
1722     viewMenu.add(autoAnnMenu);
1723     viewMenu.addSeparator();
1724     viewMenu.add(showSeqFeatures);
1725     // viewMenu.add(showSeqFeaturesHeight);
1726
1727     viewMenu.add(featureSettings);
1728     tooltipSettingsMenu.add(showDbRefsMenuitem);
1729     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1730     viewMenu.add(tooltipSettingsMenu);
1731     viewMenu.addSeparator();
1732     viewMenu.add(alignmentProperties);
1733     viewMenu.addSeparator();
1734     viewMenu.add(overviewMenuItem);
1735     colourMenu.add(applyToAllGroups);
1736     colourMenu.add(textColour);
1737     colourMenu.addSeparator();
1738     colourMenu.add(noColourmenuItem);
1739     colourMenu.add(clustalColour);
1740     colourMenu.add(BLOSUM62Colour);
1741     colourMenu.add(PIDColour);
1742     colourMenu.add(zappoColour);
1743     colourMenu.add(taylorColour);
1744     colourMenu.add(hydrophobicityColour);
1745     colourMenu.add(helixColour);
1746     colourMenu.add(strandColour);
1747     colourMenu.add(turnColour);
1748     colourMenu.add(buriedColour);
1749     colourMenu.add(nucleotideColour);
1750     colourMenu.add(userDefinedColour);
1751     colourMenu.addSeparator();
1752     colourMenu.add(conservationMenuItem);
1753     colourMenu.add(modifyConservation);
1754     colourMenu.add(abovePIDThreshold);
1755     colourMenu.add(modifyPID);
1756     colourMenu.add(annotationColour);
1757     calculateMenu.add(sort);
1758     calculateMenu.add(calculateTree);
1759     calculateMenu.addSeparator();
1760     calculateMenu.add(pairwiseAlignmentMenuItem);
1761     calculateMenu.add(PCAMenuItem);
1762     calculateMenu.addSeparator();
1763     calculateMenu.add(showTranslation);
1764     calculateMenu.add(showProducts);
1765     calculateMenu.add(autoCalculate);
1766     calculateMenu.add(sortByTree);
1767     calculateMenu.addSeparator();
1768     calculateMenu.add(extractScores);
1769     webServiceNoServices = new JMenuItem("<No Services>");
1770     webService.add(webServiceNoServices);
1771     pasteMenu.add(pasteNew);
1772     pasteMenu.add(pasteThis);
1773     sort.add(sortIDMenuItem);
1774     sort.add(sortLengthMenuItem);
1775     sort.add(sortGroupMenuItem);
1776     sort.add(sortPairwiseMenuItem);
1777     sort.add(sortByTreeMenu);
1778     calculateTree.add(averageDistanceTreeMenuItem);
1779     calculateTree.add(neighbourTreeMenuItem);
1780     calculateTree.add(avDistanceTreeBlosumMenuItem);
1781     calculateTree.add(njTreeBlosumMenuItem);
1782     jMenu2.add(htmlMenuItem);
1783     jMenu2.add(epsFile);
1784     jMenu2.add(createPNG);
1785     addSequenceMenu.add(addFromFile);
1786     addSequenceMenu.add(addFromText);
1787     addSequenceMenu.add(addFromURL);
1788     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1789     statusPanel.add(statusBar, null);
1790     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1791     jMenu3.add(showAllColumns);
1792     jMenu3.add(showAllSeqs);
1793     jMenu3.add(showAllhidden);
1794     hideMenu.add(hideSelColumns);
1795     hideMenu.add(hideSelSequences);
1796     hideMenu.add(hideAllSelection);
1797     hideMenu.add(hideAllButSelection);
1798
1799     formatMenu.add(font);
1800     formatMenu.addSeparator();
1801     formatMenu.add(wrapMenuItem);
1802     formatMenu.add(scaleAbove);
1803     formatMenu.add(scaleLeft);
1804     formatMenu.add(scaleRight);
1805     formatMenu.add(seqLimits);
1806     formatMenu.add(idRightAlign);
1807     formatMenu.add(hiddenMarkers);
1808     formatMenu.add(viewBoxesMenuItem);
1809     formatMenu.add(viewTextMenuItem);
1810     formatMenu.add(colourTextMenuItem);
1811     formatMenu.add(renderGapsMenuItem);
1812     formatMenu.add(centreColumnLabelsMenuItem);
1813     formatMenu.add(showNonconservedMenuItem);
1814     selectMenu.add(findMenuItem);
1815     selectMenu.addSeparator();
1816     selectMenu.add(selectAllSequenceMenuItem);
1817     selectMenu.add(deselectAllSequenceMenuItem);
1818     selectMenu.add(invertSequenceMenuItem);
1819     selectMenu.add(invertColSel);
1820     selectMenu.add(deleteGroups);
1821     selectMenu.add(grpsFromSelection);
1822   }
1823
1824   protected void showAllhidden_actionPerformed(ActionEvent e)
1825   {
1826     // TODO Auto-generated method stub
1827
1828   }
1829
1830   protected void hideAllButSelection_actionPerformed(ActionEvent e)
1831   {
1832     // TODO Auto-generated method stub
1833
1834   }
1835
1836   protected void hideAllSelection_actionPerformed(ActionEvent e)
1837   {
1838     // TODO Auto-generated method stub
1839
1840   }
1841
1842   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
1843   {
1844     // TODO Auto-generated method stub
1845
1846   }
1847
1848   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
1849   {
1850     // TODO Auto-generated method stub
1851
1852   }
1853
1854   protected void showSequenceLogo_actionPerformed(ActionEvent e)
1855   {
1856     // TODO Auto-generated method stub
1857
1858   }
1859
1860   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
1861   {
1862     // TODO Auto-generated method stub
1863
1864   }
1865
1866   protected void showGroupConsensus_actionPerformed(ActionEvent e)
1867   {
1868     // TODO Auto-generated method stub
1869
1870   }
1871
1872   protected void showGroupConservation_actionPerformed(ActionEvent e)
1873   {
1874     // TODO Auto-generated method stub
1875
1876   }
1877
1878   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
1879   {
1880     // TODO Auto-generated method stub
1881
1882   }
1883
1884   protected void showSeqFeaturesHeight_actionPerformed(
1885           ActionEvent actionEvent)
1886   {
1887     // TODO Auto-generated method stub
1888
1889   }
1890
1891   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
1892   {
1893     // TODO Auto-generated method stub
1894
1895   }
1896
1897   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
1898   {
1899     // TODO Auto-generated method stub
1900
1901   }
1902
1903   protected void followHighlight_actionPerformed()
1904   {
1905     // TODO Auto-generated method stub
1906
1907   }
1908
1909   protected void showNpFeats_actionPerformed(ActionEvent e)
1910   {
1911     // TODO Auto-generated method stub
1912
1913   }
1914
1915   protected void showDbRefs_actionPerformed(ActionEvent e)
1916   {
1917     // TODO Auto-generated method stub
1918
1919   }
1920
1921   protected void centreColumnLabels_actionPerformed(ActionEvent e)
1922   {
1923   }
1924
1925   protected void showProducts_actionPerformed(ActionEvent e)
1926   {
1927   }
1928
1929   protected void buildSortByAnnotationScoresMenu()
1930   {
1931   }
1932
1933   protected void extractScores_actionPerformed(ActionEvent e)
1934   {
1935   }
1936
1937   protected void outputText_actionPerformed(ActionEvent e)
1938   {
1939   }
1940
1941   public void addFromFile_actionPerformed(ActionEvent e)
1942   {
1943
1944   }
1945
1946   public void addFromText_actionPerformed(ActionEvent e)
1947   {
1948
1949   }
1950
1951   public void addFromURL_actionPerformed(ActionEvent e)
1952   {
1953
1954   }
1955
1956   public void exportFeatures_actionPerformed(ActionEvent e)
1957   {
1958
1959   }
1960
1961   public void exportAnnotations_actionPerformed(ActionEvent e)
1962   {
1963
1964   }
1965
1966   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1967   {
1968   }
1969
1970   protected void closeMenuItem_actionPerformed(boolean b)
1971   {
1972   }
1973
1974   protected void redoMenuItem_actionPerformed(ActionEvent e)
1975   {
1976   }
1977
1978   protected void undoMenuItem_actionPerformed(ActionEvent e)
1979   {
1980   }
1981
1982   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1983   {
1984   }
1985
1986   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1987   {
1988   }
1989
1990   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1991   {
1992   }
1993
1994   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1995   {
1996   }
1997
1998   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
1999   {
2000   }
2001
2002   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2003   {
2004   }
2005
2006   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2007   {
2008   }
2009
2010   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2011   {
2012   }
2013
2014   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2015   {
2016   }
2017
2018   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2019   {
2020   }
2021
2022   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2023   {
2024   }
2025
2026   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2027   {
2028   }
2029
2030   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2031   {
2032   }
2033
2034   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2035   {
2036   }
2037
2038   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2039   {
2040   }
2041
2042   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2043   {
2044   }
2045
2046   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2047   {
2048   }
2049
2050   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2051   {
2052   }
2053
2054   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2055   {
2056   }
2057
2058   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2059   {
2060   }
2061
2062   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2063   {
2064   }
2065
2066   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2067   {
2068   }
2069
2070   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2071   {
2072   }
2073
2074   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2075   {
2076   }
2077
2078   protected void clustalColour_actionPerformed(ActionEvent e)
2079   {
2080   }
2081
2082   protected void zappoColour_actionPerformed(ActionEvent e)
2083   {
2084   }
2085
2086   protected void taylorColour_actionPerformed(ActionEvent e)
2087   {
2088   }
2089
2090   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2091   {
2092   }
2093
2094   protected void helixColour_actionPerformed(ActionEvent e)
2095   {
2096   }
2097
2098   protected void strandColour_actionPerformed(ActionEvent e)
2099   {
2100   }
2101
2102   protected void turnColour_actionPerformed(ActionEvent e)
2103   {
2104   }
2105
2106   protected void buriedColour_actionPerformed(ActionEvent e)
2107   {
2108   }
2109
2110   protected void userDefinedColour_actionPerformed(ActionEvent e)
2111   {
2112   }
2113
2114   protected void PIDColour_actionPerformed(ActionEvent e)
2115   {
2116   }
2117
2118   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2119   {
2120   }
2121
2122   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2123   {
2124   }
2125
2126   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2127   {
2128   }
2129
2130   protected void printMenuItem_actionPerformed(ActionEvent e)
2131   {
2132   }
2133
2134   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2135   {
2136   }
2137
2138   protected void findMenuItem_actionPerformed(ActionEvent e)
2139   {
2140   }
2141
2142   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2143   {
2144   }
2145
2146   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2147   {
2148   }
2149
2150   protected void nucleotideColour_actionPerformed(ActionEvent e)
2151   {
2152   }
2153
2154   protected void deleteGroups_actionPerformed(ActionEvent e)
2155   {
2156   }
2157
2158   protected void copy_actionPerformed(ActionEvent e)
2159   {
2160   }
2161
2162   protected void cut_actionPerformed(ActionEvent e)
2163   {
2164   }
2165
2166   protected void delete_actionPerformed(ActionEvent e)
2167   {
2168   }
2169
2170   protected void pasteNew_actionPerformed(ActionEvent e)
2171   {
2172   }
2173
2174   protected void pasteThis_actionPerformed(ActionEvent e)
2175   {
2176   }
2177
2178   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2179   {
2180   }
2181
2182   public void createPNG(java.io.File f)
2183   {
2184   }
2185
2186   protected void font_actionPerformed(ActionEvent e)
2187   {
2188   }
2189
2190   protected void seqLimit_actionPerformed(ActionEvent e)
2191   {
2192   }
2193
2194   public void seqDBRef_actionPerformed(ActionEvent e)
2195   {
2196
2197   }
2198
2199   public void createEPS(java.io.File f)
2200   {
2201   }
2202
2203   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2204   {
2205   }
2206
2207   protected void jpred_actionPerformed(ActionEvent e)
2208   {
2209   }
2210
2211   protected void scaleAbove_actionPerformed(ActionEvent e)
2212   {
2213   }
2214
2215   protected void scaleLeft_actionPerformed(ActionEvent e)
2216   {
2217   }
2218
2219   protected void scaleRight_actionPerformed(ActionEvent e)
2220   {
2221   }
2222
2223   protected void modifyPID_actionPerformed(ActionEvent e)
2224   {
2225   }
2226
2227   protected void modifyConservation_actionPerformed(ActionEvent e)
2228   {
2229   }
2230
2231   protected void saveAs_actionPerformed(ActionEvent e)
2232   {
2233   }
2234
2235   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2236   {
2237   }
2238
2239   public void vamsasStore_actionPerformed(ActionEvent e)
2240   {
2241
2242   }
2243
2244   public void vamsasLoad_actionPerformed(ActionEvent e)
2245   {
2246
2247   }
2248
2249   public void showTranslation_actionPerformed(ActionEvent e)
2250   {
2251
2252   }
2253
2254   public void featureSettings_actionPerformed(ActionEvent e)
2255   {
2256
2257   }
2258
2259   public void fetchSequence_actionPerformed(ActionEvent e)
2260   {
2261
2262   }
2263
2264   public void smoothFont_actionPerformed(ActionEvent e)
2265   {
2266
2267   }
2268
2269   public void annotationColour_actionPerformed(ActionEvent e)
2270   {
2271
2272   }
2273
2274   public void associatedData_actionPerformed(ActionEvent e)
2275   {
2276
2277   }
2278
2279   public void autoCalculate_actionPerformed(ActionEvent e)
2280   {
2281
2282   }
2283
2284   public void sortByTreeOption_actionPerformed(ActionEvent e)
2285   {
2286
2287   }
2288
2289   public void showAllSeqs_actionPerformed(ActionEvent e)
2290   {
2291
2292   }
2293
2294   public void showAllColumns_actionPerformed(ActionEvent e)
2295   {
2296
2297   }
2298
2299   public void hideSelSequences_actionPerformed(ActionEvent e)
2300   {
2301
2302   }
2303
2304   public void hideSelColumns_actionPerformed(ActionEvent e)
2305   {
2306
2307   }
2308
2309   public void hiddenMarkers_actionPerformed(ActionEvent e)
2310   {
2311
2312   }
2313
2314   public void findPdbId_actionPerformed(ActionEvent e)
2315   {
2316
2317   }
2318
2319   public void enterPdbId_actionPerformed(ActionEvent e)
2320   {
2321
2322   }
2323
2324   public void pdbFile_actionPerformed(ActionEvent e)
2325   {
2326
2327   }
2328
2329   public void invertColSel_actionPerformed(ActionEvent e)
2330   {
2331
2332   }
2333
2334   public void tabSelectionChanged(int sel)
2335   {
2336
2337   }
2338
2339   public void tabbedPane_mousePressed(MouseEvent e)
2340   {
2341
2342   }
2343
2344   public void tabbedPane_focusGained(FocusEvent e)
2345   {
2346     requestFocus();
2347   }
2348
2349   public void save_actionPerformed(ActionEvent e)
2350   {
2351
2352   }
2353
2354   public void reload_actionPerformed(ActionEvent e)
2355   {
2356
2357   }
2358
2359   public void newView_actionPerformed(ActionEvent e)
2360   {
2361
2362   }
2363
2364   public void textColour_actionPerformed(ActionEvent e)
2365   {
2366
2367   }
2368
2369   public void idRightAlign_actionPerformed(ActionEvent e)
2370   {
2371
2372   }
2373
2374   public void expandViews_actionPerformed(ActionEvent e)
2375   {
2376
2377   }
2378
2379   public void gatherViews_actionPerformed(ActionEvent e)
2380   {
2381
2382   }
2383
2384   public void buildTreeMenu()
2385   {
2386
2387   }
2388
2389   public void pageSetup_actionPerformed(ActionEvent e)
2390   {
2391
2392   }
2393
2394   public void alignmentProperties()
2395   {
2396
2397   }
2398 }