src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
   3  * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.jbgui;
  20
  21 import java.awt.*;
  22 import java.awt.event.*;
  23
  24 import javax.swing.*;
  25 import javax.swing.event.*;
  26
  27 import jalview.schemes.*;
  28
  29 public class GAlignFrame extends JInternalFrame
  30 {
  31   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  32
  33   protected JMenu fileMenu = new JMenu();
  34
  35   protected JMenuItem closeMenuItem = new JMenuItem();
  36
  37   protected JMenu editMenu = new JMenu();
  38
  39   protected JMenu viewMenu = new JMenu();
  40
  41   protected JMenu colourMenu = new JMenu();
  42
  43   protected JMenu calculateMenu = new JMenu();
  44
  45   protected JMenu webService = new JMenu();
  46
  47   protected JMenuItem webServiceNoServices;
  48
  49   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  50
  51   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  52
  53   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  54
  55   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  56
  57   protected JMenuItem remove2RightMenuItem = new JMenuItem();
  58
  59   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  60
  61   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  62
  63   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  64
  65   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  66
  67   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  68
  69   protected JMenuItem sortIDMenuItem = new JMenuItem();
  70
  71   protected JMenuItem sortLengthMenuItem = new JMenuItem();
  72
  73   protected JMenuItem sortGroupMenuItem = new JMenuItem();
  74
  75   protected JMenu sortByAnnotScore = new JMenu();
  76
  77   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
  78
  79   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
  80
  81   protected JMenuItem PCAMenuItem = new JMenuItem();
  82
  83   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
  84
  85   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
  86
  87   BorderLayout borderLayout1 = new BorderLayout();
  88
  89   public JLabel statusBar = new JLabel();
  90
  91   protected JMenuItem saveAs = new JMenuItem();
  92
  93   protected JMenu outputTextboxMenu = new JMenu();
  94
  95   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  96
  97   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  98
  99   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
 100
 101   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
 102
 103   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
 104
 105   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
 106
 107   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
 108
 109   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 110
 111   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
 112
 113   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
 114
 115   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 116
 117   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 118
 119   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
 120
 121   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 122
 123   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 124
 125   public JCheckBoxMenuItem showUnconservedMenuItem = new JCheckBoxMenuItem();
 126
 127   JMenuItem htmlMenuItem = new JMenuItem();
 128
 129   JMenuItem overviewMenuItem = new JMenuItem();
 130
 131   protected JMenuItem undoMenuItem = new JMenuItem();
 132
 133   protected JMenuItem redoMenuItem = new JMenuItem();
 134
 135   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 136
 137   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 138
 139   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 140
 141   JMenuItem printMenuItem = new JMenuItem();
 142
 143   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 144
 145   JMenuItem findMenuItem = new JMenuItem();
 146
 147   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 148
 149   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 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   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 200   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 201
 202   protected ButtonGroup colours = new ButtonGroup();
 203
 204   JMenuItem vamsasStore = new JMenuItem();
 205
 206   protected JMenuItem showTranslation = new JMenuItem();
 207
 208   protected JMenuItem extractScores = new JMenuItem();
 209
 210   protected JMenu showProducts = new JMenu();
 211
 212   public JMenuItem featureSettings = new JMenuItem();
 213
 214   JMenuItem fetchSequence = new JMenuItem();
 215
 216   JMenuItem annotationColour = new JMenuItem();
 217
 218   JMenuItem associatedData = new JMenuItem();
 219
 220   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 221
 222   JMenu addSequenceMenu = new JMenu();
 223
 224   JMenuItem addFromFile = new JMenuItem();
 225
 226   JMenuItem addFromText = new JMenuItem();
 227
 228   JMenuItem addFromURL = new JMenuItem();
 229
 230   JMenuItem exportAnnotations = new JMenuItem();
 231
 232   JMenuItem exportFeatures = new JMenuItem();
 233
 234   protected JPanel statusPanel = new JPanel();
 235
 236   GridLayout gridLayout1 = new GridLayout();
 237
 238   JMenu jMenu3 = new JMenu();
 239
 240   JMenuItem showAllSeqs = new JMenuItem();
 241
 242   JMenuItem showAllColumns = new JMenuItem();
 243
 244   JMenu hideMenu = new JMenu();
 245
 246   JMenuItem hideSelSequences = new JMenuItem();
 247
 248   JMenuItem hideSelColumns = new JMenuItem();
 249
 250   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 251
 252   JMenuItem invertColSel = new JMenuItem();
 253
 254   protected JTabbedPane tabbedPane = new JTabbedPane();
 255
 256   JMenuItem save = new JMenuItem();
 257
 258   protected JMenuItem reload = new JMenuItem();
 259
 260   JMenuItem newView = new JMenuItem();
 261
 262   JMenuItem textColour = new JMenuItem();
 263
 264   JMenu formatMenu = new JMenu();
 265
 266   JMenu selectMenu = new JMenu();
 267
 268   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 269
 270   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 271
 272   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 273
 274   protected JMenuItem gatherViews = new JMenuItem();
 275
 276   protected JMenuItem expandViews = new JMenuItem();
 277
 278   JMenuItem pageSetup = new JMenuItem();
 279
 280   JMenuItem alignmentProperties = new JMenuItem();
 281
 282   JMenu tooltipSettingsMenu = new JMenu();
 283
 284   private JMenuItem justifyLeftMenuItem=new JMenuItem();
 285
 286   private JMenuItem justifyRightMenuItem=new JMenuItem();
 287
 288   JMenu autoAnnMenu = new JMenu();
 289   protected JCheckBoxMenuItem showGroupConsensus=new JCheckBoxMenuItem();
 290   protected JCheckBoxMenuItem showGroupConservation=new JCheckBoxMenuItem();
 291   protected JCheckBoxMenuItem showConsensusHistogram=new JCheckBoxMenuItem();
 292   protected JCheckBoxMenuItem showSequenceLogo=new JCheckBoxMenuItem();
 293   protected JCheckBoxMenuItem applyAutoAnnotationSettings=new JCheckBoxMenuItem();
 294
 295   private JMenuItem grpsFromSelection = new JMenuItem();
 296   public GAlignFrame()
 297   {
 298     try
 299     {
 300       jbInit();
 301       setJMenuBar(alignFrameMenuBar);
 302
 303       // dynamically fill save as menu with available formats
 304       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 305       {
 306         JMenuItem item = new JMenuItem(
 307                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 308
 309         item.addActionListener(new java.awt.event.ActionListener()
 310         {
 311           public void actionPerformed(ActionEvent e)
 312           {
 313             outputText_actionPerformed(e);
 314           }
 315         });
 316
 317         outputTextboxMenu.add(item);
 318       }
 319     } catch (Exception e)
 320     {
 321     }
 322
 323     if (!new jalview.util.Platform().isAMac())
 324     {
 325       closeMenuItem.setMnemonic('C');
 326       outputTextboxMenu.setMnemonic('T');
 327       undoMenuItem.setMnemonic('Z');
 328       redoMenuItem.setMnemonic('0');
 329       copy.setMnemonic('C');
 330       cut.setMnemonic('U');
 331       pasteMenu.setMnemonic('P');
 332       reload.setMnemonic('R');
 333     }
 334
 335     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 336     {
 337       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 338               .getUserColourSchemes().keys();
 339
 340       while (userColours.hasMoreElements())
 341       {
 342         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 343                 userColours.nextElement().toString());
 344         radioItem.setName("USER_DEFINED");
 345         radioItem.addMouseListener(new MouseAdapter()
 346         {
 347           public void mousePressed(MouseEvent evt)
 348           {
 349             if (evt.isControlDown()
 350                     || SwingUtilities.isRightMouseButton(evt))
 351             {
 352               radioItem
 353                       .removeActionListener(radioItem.getActionListeners()[0]);
 354
 355               int option = JOptionPane.showInternalConfirmDialog(
 356                       jalview.gui.Desktop.desktop,
 357                       "Remove from default list?",
 358                       "Remove user defined colour",
 359                       JOptionPane.YES_NO_OPTION);
 360               if (option == JOptionPane.YES_OPTION)
 361               {
 362                 jalview.gui.UserDefinedColours
 363                         .removeColourFromDefaults(radioItem.getText());
 364                 colourMenu.remove(radioItem);
 365               }
 366               else
 367               {
 368                 radioItem.addActionListener(new ActionListener()
 369                 {
 370                   public void actionPerformed(ActionEvent evt)
 371                   {
 372                     userDefinedColour_actionPerformed(evt);
 373                   }
 374                 });
 375               }
 376             }
 377           }
 378         });
 379         radioItem.addActionListener(new ActionListener()
 380         {
 381           public void actionPerformed(ActionEvent evt)
 382           {
 383             userDefinedColour_actionPerformed(evt);
 384           }
 385         });
 386         colourMenu.insert(radioItem, 15);
 387         colours.add(radioItem);
 388       }
 389     }
 390     colours.add(noColourmenuItem);
 391     colours.add(clustalColour);
 392     colours.add(zappoColour);
 393     colours.add(taylorColour);
 394     colours.add(hydrophobicityColour);
 395     colours.add(helixColour);
 396     colours.add(strandColour);
 397     colours.add(turnColour);
 398     colours.add(buriedColour);
 399     colours.add(userDefinedColour);
 400     colours.add(PIDColour);
 401     colours.add(BLOSUM62Colour);
 402     colours.add(nucleotideColour);
 403
 404     setColourSelected(jalview.bin.Cache
 405             .getDefault("DEFAULT_COLOUR", "None"));
 406
 407   }
 408
 409   public void setColourSelected(String defaultColour)
 410   {
 411
 412     if (defaultColour != null)
 413     {
 414       int index = ColourSchemeProperty
 415               .getColourIndexFromName(defaultColour);
 416
 417       switch (index)
 418       {
 419       case ColourSchemeProperty.NONE:
 420         noColourmenuItem.setSelected(true);
 421         break;
 422       case ColourSchemeProperty.CLUSTAL:
 423         clustalColour.setSelected(true);
 424
 425         break;
 426
 427       case ColourSchemeProperty.BLOSUM:
 428         BLOSUM62Colour.setSelected(true);
 429
 430         break;
 431
 432       case ColourSchemeProperty.PID:
 433         PIDColour.setSelected(true);
 434
 435         break;
 436
 437       case ColourSchemeProperty.ZAPPO:
 438         zappoColour.setSelected(true);
 439
 440         break;
 441
 442       case ColourSchemeProperty.TAYLOR:
 443         taylorColour.setSelected(true);
 444         break;
 445
 446       case ColourSchemeProperty.HYDROPHOBIC:
 447         hydrophobicityColour.setSelected(true);
 448
 449         break;
 450
 451       case ColourSchemeProperty.HELIX:
 452         helixColour.setSelected(true);
 453
 454         break;
 455
 456       case ColourSchemeProperty.STRAND:
 457         strandColour.setSelected(true);
 458
 459         break;
 460
 461       case ColourSchemeProperty.TURN:
 462         turnColour.setSelected(true);
 463
 464         break;
 465
 466       case ColourSchemeProperty.BURIED:
 467         buriedColour.setSelected(true);
 468
 469         break;
 470
 471       case ColourSchemeProperty.NUCLEOTIDE:
 472         nucleotideColour.setSelected(true);
 473
 474         break;
 475
 476       case ColourSchemeProperty.USER_DEFINED:
 477         userDefinedColour.setSelected(true);
 478
 479         break;
 480       }
 481     }
 482
 483   }
 484
 485   private void jbInit() throws Exception
 486   {
 487     fileMenu.setText("File");
 488     saveAs.setText("Save As...");
 489     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 490             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
 491                     .getMenuShortcutKeyMask()
 492                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 493     saveAs.addActionListener(new ActionListener()
 494     {
 495       public void actionPerformed(ActionEvent e)
 496       {
 497         saveAs_actionPerformed(e);
 498       }
 499     });
 500     closeMenuItem.setText("Close");
 501     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 502             java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
 503                     .getMenuShortcutKeyMask(), false));
 504     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 505     {
 506       public void actionPerformed(ActionEvent e)
 507       {
 508         closeMenuItem_actionPerformed(false);
 509       }
 510     });
 511     editMenu.setText("Edit");
 512     viewMenu.setText("View");
 513     colourMenu.setText("Colour");
 514     calculateMenu.setText("Calculate");
 515     webService.setText("Web Service");
 516     selectAllSequenceMenuItem.setText("Select All");
 517     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 518             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
 519                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 520     selectAllSequenceMenuItem
 521             .addActionListener(new java.awt.event.ActionListener()
 522             {
 523               public void actionPerformed(ActionEvent e)
 524               {
 525                 selectAllSequenceMenuItem_actionPerformed(e);
 526               }
 527             });
 528     deselectAllSequenceMenuItem.setText("Deselect All");
 529     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 530             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 531     deselectAllSequenceMenuItem
 532             .addActionListener(new java.awt.event.ActionListener()
 533             {
 534               public void actionPerformed(ActionEvent e)
 535               {
 536                 deselectAllSequenceMenuItem_actionPerformed(e);
 537               }
 538             });
 539     invertSequenceMenuItem.setText("Invert Sequence Selection");
 540     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 541             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
 542                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 543     invertSequenceMenuItem
 544             .addActionListener(new java.awt.event.ActionListener()
 545             {
 546               public void actionPerformed(ActionEvent e)
 547               {
 548                 invertSequenceMenuItem_actionPerformed(e);
 549               }
 550             });
 551     grpsFromSelection.setText("Make Groups for selection");
 552     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
 553     {
 554       public void actionPerformed(ActionEvent e)
 555       {
 556         makeGrpsFromSelection_actionPerformed(e);
 557       }
 558     });
 559
 560     remove2LeftMenuItem.setText("Remove Left");
 561     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 562             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
 563                     .getMenuShortcutKeyMask(), false));
 564     remove2LeftMenuItem
 565             .addActionListener(new java.awt.event.ActionListener()
 566             {
 567               public void actionPerformed(ActionEvent e)
 568               {
 569                 remove2LeftMenuItem_actionPerformed(e);
 570               }
 571             });
 572     remove2RightMenuItem.setText("Remove Right");
 573     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 574             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
 575                     .getMenuShortcutKeyMask(), false));
 576     remove2RightMenuItem
 577             .addActionListener(new java.awt.event.ActionListener()
 578             {
 579               public void actionPerformed(ActionEvent e)
 580               {
 581                 remove2RightMenuItem_actionPerformed(e);
 582               }
 583             });
 584     removeGappedColumnMenuItem.setText("Remove Empty Columns");
 585     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
 586             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 587                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 588     removeGappedColumnMenuItem
 589             .addActionListener(new java.awt.event.ActionListener()
 590             {
 591               public void actionPerformed(ActionEvent e)
 592               {
 593                 removeGappedColumnMenuItem_actionPerformed(e);
 594               }
 595             });
 596     removeAllGapsMenuItem.setText("Remove All Gaps");
 597     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
 598             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 599                     .getDefaultToolkit().getMenuShortcutKeyMask()
 600                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 601     removeAllGapsMenuItem
 602             .addActionListener(new java.awt.event.ActionListener()
 603             {
 604               public void actionPerformed(ActionEvent e)
 605               {
 606                 removeAllGapsMenuItem_actionPerformed(e);
 607               }
 608             });
 609     justifyLeftMenuItem.setText("Left Justify Alignment");
 610     justifyLeftMenuItem.addActionListener(new java.awt.event.ActionListener()
 611     {
 612         public void actionPerformed(ActionEvent e)
 613         {
 614           justifyLeftMenuItem_actionPerformed(e);
 615         }
 616     });
 617     justifyRightMenuItem.setText("Right Justify Alignment");
 618     justifyRightMenuItem.addActionListener(new java.awt.event.ActionListener()
 619     {
 620         public void actionPerformed(ActionEvent e)
 621         {
 622           justifyRightMenuItem_actionPerformed(e);
 623         }
 624     });
 625     viewBoxesMenuItem.setText("Boxes");
 626     viewBoxesMenuItem.setState(true);
 627     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 628     {
 629       public void actionPerformed(ActionEvent e)
 630       {
 631         viewBoxesMenuItem_actionPerformed(e);
 632       }
 633     });
 634     viewTextMenuItem.setText("Text");
 635     viewTextMenuItem.setState(true);
 636     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 637     {
 638       public void actionPerformed(ActionEvent e)
 639       {
 640         viewTextMenuItem_actionPerformed(e);
 641       }
 642     });
 643     showUnconservedMenuItem.setText("Show Unconserved");
 644     showUnconservedMenuItem.setState(false);
 645     showUnconservedMenuItem.addActionListener(new java.awt.event.ActionListener()
 646     {
 647       public void actionPerformed(ActionEvent e)
 648       {
 649         showUnconservedMenuItem_actionPerformed(e);
 650       }
 651     });
 652     sortPairwiseMenuItem.setText("by Pairwise Identity");
 653     sortPairwiseMenuItem
 654             .addActionListener(new java.awt.event.ActionListener()
 655             {
 656               public void actionPerformed(ActionEvent e)
 657               {
 658                 sortPairwiseMenuItem_actionPerformed(e);
 659               }
 660             });
 661     sortIDMenuItem.setText("by ID");
 662     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 663     {
 664       public void actionPerformed(ActionEvent e)
 665       {
 666         sortIDMenuItem_actionPerformed(e);
 667       }
 668     });
 669     sortLengthMenuItem.setText("By Length");
 670     sortLengthMenuItem.addActionListener(new java.awt.event.ActionListener()
 671     {
 672       public void actionPerformed(ActionEvent e)
 673       {
 674         sortLengthMenuItem_actionPerformed(e);
 675       }
 676     });
 677     sortGroupMenuItem.setText("by Group");
 678     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 679     {
 680       public void actionPerformed(ActionEvent e)
 681       {
 682         sortGroupMenuItem_actionPerformed(e);
 683       }
 684     });
 685     removeRedundancyMenuItem.setText("Remove Redundancy...");
 686     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
 687             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
 688                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 689     removeRedundancyMenuItem
 690             .addActionListener(new java.awt.event.ActionListener()
 691             {
 692               public void actionPerformed(ActionEvent e)
 693               {
 694                 removeRedundancyMenuItem_actionPerformed(e);
 695               }
 696             });
 697     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
 698     pairwiseAlignmentMenuItem
 699             .addActionListener(new java.awt.event.ActionListener()
 700             {
 701               public void actionPerformed(ActionEvent e)
 702               {
 703                 pairwiseAlignmentMenuItem_actionPerformed(e);
 704               }
 705             });
 706     PCAMenuItem.setText("Principal Component Analysis");
 707     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 708     {
 709       public void actionPerformed(ActionEvent e)
 710       {
 711         PCAMenuItem_actionPerformed(e);
 712       }
 713     });
 714     averageDistanceTreeMenuItem
 715             .setText("Average Distance Using % Identity");
 716     averageDistanceTreeMenuItem
 717             .addActionListener(new java.awt.event.ActionListener()
 718             {
 719               public void actionPerformed(ActionEvent e)
 720               {
 721                 averageDistanceTreeMenuItem_actionPerformed(e);
 722               }
 723             });
 724     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
 725     neighbourTreeMenuItem
 726             .addActionListener(new java.awt.event.ActionListener()
 727             {
 728               public void actionPerformed(ActionEvent e)
 729               {
 730                 neighbourTreeMenuItem_actionPerformed(e);
 731               }
 732             });
 733     this.getContentPane().setLayout(borderLayout1);
 734     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 735     statusBar.setBackground(Color.white);
 736     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 737     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 738     statusBar.setText("Status bar");
 739     outputTextboxMenu.setText("Output to Textbox");
 740     clustalColour.setText("Clustalx");
 741
 742     clustalColour.addActionListener(new java.awt.event.ActionListener()
 743     {
 744       public void actionPerformed(ActionEvent e)
 745       {
 746         clustalColour_actionPerformed(e);
 747       }
 748     });
 749     zappoColour.setText("Zappo");
 750     zappoColour.addActionListener(new java.awt.event.ActionListener()
 751     {
 752       public void actionPerformed(ActionEvent e)
 753       {
 754         zappoColour_actionPerformed(e);
 755       }
 756     });
 757     taylorColour.setText("Taylor");
 758     taylorColour.addActionListener(new java.awt.event.ActionListener()
 759     {
 760       public void actionPerformed(ActionEvent e)
 761       {
 762         taylorColour_actionPerformed(e);
 763       }
 764     });
 765     hydrophobicityColour.setText("Hydrophobicity");
 766     hydrophobicityColour
 767             .addActionListener(new java.awt.event.ActionListener()
 768             {
 769               public void actionPerformed(ActionEvent e)
 770               {
 771                 hydrophobicityColour_actionPerformed(e);
 772               }
 773             });
 774     helixColour.setText("Helix Propensity");
 775     helixColour.addActionListener(new java.awt.event.ActionListener()
 776     {
 777       public void actionPerformed(ActionEvent e)
 778       {
 779         helixColour_actionPerformed(e);
 780       }
 781     });
 782     strandColour.setText("Strand Propensity");
 783     strandColour.addActionListener(new java.awt.event.ActionListener()
 784     {
 785       public void actionPerformed(ActionEvent e)
 786       {
 787         strandColour_actionPerformed(e);
 788       }
 789     });
 790     turnColour.setText("Turn Propensity");
 791     turnColour.addActionListener(new java.awt.event.ActionListener()
 792     {
 793       public void actionPerformed(ActionEvent e)
 794       {
 795         turnColour_actionPerformed(e);
 796       }
 797     });
 798     buriedColour.setText("Buried Index");
 799     buriedColour.addActionListener(new java.awt.event.ActionListener()
 800     {
 801       public void actionPerformed(ActionEvent e)
 802       {
 803         buriedColour_actionPerformed(e);
 804       }
 805     });
 806     userDefinedColour.setText("User Defined...");
 807     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 808     {
 809       public void actionPerformed(ActionEvent e)
 810       {
 811         userDefinedColour_actionPerformed(e);
 812       }
 813     });
 814     PIDColour.setText("Percentage Identity");
 815     PIDColour.addActionListener(new java.awt.event.ActionListener()
 816     {
 817       public void actionPerformed(ActionEvent e)
 818       {
 819         PIDColour_actionPerformed(e);
 820       }
 821     });
 822     BLOSUM62Colour.setText("BLOSUM62 Score");
 823     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 824     {
 825       public void actionPerformed(ActionEvent e)
 826       {
 827         BLOSUM62Colour_actionPerformed(e);
 828       }
 829     });
 830     avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
 831     avDistanceTreeBlosumMenuItem
 832             .addActionListener(new java.awt.event.ActionListener()
 833             {
 834               public void actionPerformed(ActionEvent e)
 835               {
 836                 avTreeBlosumMenuItem_actionPerformed(e);
 837               }
 838             });
 839     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
 840     njTreeBlosumMenuItem
 841             .addActionListener(new java.awt.event.ActionListener()
 842             {
 843               public void actionPerformed(ActionEvent e)
 844               {
 845                 njTreeBlosumMenuItem_actionPerformed(e);
 846               }
 847             });
 848     annotationPanelMenuItem.setActionCommand("");
 849     annotationPanelMenuItem.setText("Show Annotations");
 850     annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
 851             "SHOW_ANNOTATIONS", true));
 852     annotationPanelMenuItem
 853             .addActionListener(new java.awt.event.ActionListener()
 854             {
 855               public void actionPerformed(ActionEvent e)
 856               {
 857                 annotationPanelMenuItem_actionPerformed(e);
 858               }
 859             });
 860     colourTextMenuItem.setText("Colour Text");
 861     colourTextMenuItem
 862             .addActionListener(new java.awt.event.ActionListener()
 863             {
 864               public void actionPerformed(ActionEvent e)
 865               {
 866                 colourTextMenuItem_actionPerformed(e);
 867               }
 868             });
 869     htmlMenuItem.setText("HTML");
 870     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
 871     {
 872       public void actionPerformed(ActionEvent e)
 873       {
 874         htmlMenuItem_actionPerformed(e);
 875       }
 876     });
 877     overviewMenuItem.setText("Overview Window");
 878     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
 879     {
 880       public void actionPerformed(ActionEvent e)
 881       {
 882         overviewMenuItem_actionPerformed(e);
 883       }
 884     });
 885     undoMenuItem.setEnabled(false);
 886     undoMenuItem.setText("Undo");
 887     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 888             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
 889                     .getMenuShortcutKeyMask(), false));
 890     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
 891     {
 892       public void actionPerformed(ActionEvent e)
 893       {
 894         undoMenuItem_actionPerformed(e);
 895       }
 896     });
 897     redoMenuItem.setEnabled(false);
 898     redoMenuItem.setText("Redo");
 899     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 900             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
 901                     .getMenuShortcutKeyMask(), false));
 902     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
 903     {
 904       public void actionPerformed(ActionEvent e)
 905       {
 906         redoMenuItem_actionPerformed(e);
 907       }
 908     });
 909     conservationMenuItem.setText("By Conservation");
 910     conservationMenuItem
 911             .addActionListener(new java.awt.event.ActionListener()
 912             {
 913               public void actionPerformed(ActionEvent e)
 914               {
 915                 conservationMenuItem_actionPerformed(e);
 916               }
 917             });
 918     noColourmenuItem.setText("None");
 919     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 920     {
 921       public void actionPerformed(ActionEvent e)
 922       {
 923         noColourmenuItem_actionPerformed(e);
 924       }
 925     });
 926     wrapMenuItem.setText("Wrap");
 927     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
 928     {
 929       public void actionPerformed(ActionEvent e)
 930       {
 931         wrapMenuItem_actionPerformed(e);
 932       }
 933     });
 934     printMenuItem.setText("Print ...");
 935     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 936             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
 937                     .getMenuShortcutKeyMask(), false));
 938     printMenuItem.addActionListener(new java.awt.event.ActionListener()
 939     {
 940       public void actionPerformed(ActionEvent e)
 941       {
 942         printMenuItem_actionPerformed(e);
 943       }
 944     });
 945     renderGapsMenuItem.setText("Show Gaps");
 946     renderGapsMenuItem.setState(true);
 947     renderGapsMenuItem
 948             .addActionListener(new java.awt.event.ActionListener()
 949             {
 950               public void actionPerformed(ActionEvent e)
 951               {
 952                 renderGapsMenuItem_actionPerformed(e);
 953               }
 954             });
 955     findMenuItem.setText("Find...");
 956     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 957             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
 958                     .getMenuShortcutKeyMask(), false));
 959     findMenuItem.addActionListener(new java.awt.event.ActionListener()
 960     {
 961       public void actionPerformed(ActionEvent e)
 962       {
 963         findMenuItem_actionPerformed(e);
 964       }
 965     });
 966     abovePIDThreshold.setText("Above Identity Threshold");
 967     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
 968     {
 969       public void actionPerformed(ActionEvent e)
 970       {
 971         abovePIDThreshold_actionPerformed(e);
 972       }
 973     });
 974     showSeqFeatures.setText("Show Sequence Features");
 975     showSeqFeatures.addActionListener(new ActionListener()
 976     {
 977       public void actionPerformed(ActionEvent actionEvent)
 978       {
 979         showSeqFeatures_actionPerformed(actionEvent);
 980       }
 981     });
 982 /*
 983  *     showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
 984     showSeqFeaturesHeight.addActionListener(new ActionListener()
 985     {
 986       public void actionPerformed(ActionEvent actionEvent)
 987       {
 988         showSeqFeaturesHeight_actionPerformed(actionEvent);
 989       }
 990     }); */
 991     showDbRefsMenuitem.setText("Show Database Refs");
 992     showDbRefsMenuitem.addActionListener(new ActionListener()
 993     {
 994
 995       public void actionPerformed(ActionEvent e)
 996       {
 997         showDbRefs_actionPerformed(e);
 998       }
 999
1000     });
1001     showNpFeatsMenuitem.setText("Show Non-Positional Features");
1002     showNpFeatsMenuitem.addActionListener(new ActionListener()
1003     {
1004
1005       public void actionPerformed(ActionEvent e)
1006       {
1007         showNpFeats_actionPerformed(e);
1008       }
1009
1010     });
1011     showGroupConservation.setText("Group Conservation");
1012     showGroupConservation.addActionListener(new ActionListener()
1013     {
1014
1015       public void actionPerformed(ActionEvent e)
1016       {
1017         showGroupConservation_actionPerformed(e);
1018       }
1019
1020     });
1021
1022     showGroupConsensus.setText("Group Consensus");
1023     showGroupConsensus.addActionListener(new ActionListener()
1024     {
1025
1026       public void actionPerformed(ActionEvent e)
1027       {
1028         showGroupConsensus_actionPerformed(e);
1029       }
1030
1031     });
1032     showConsensusHistogram.setText("Show Consensus Histogram");
1033     showConsensusHistogram.addActionListener(new ActionListener()
1034     {
1035
1036       public void actionPerformed(ActionEvent e)
1037       {
1038         showConsensusHistogram_actionPerformed(e);
1039       }
1040
1041     });
1042     showSequenceLogo.setText("Show Consensus Logo");
1043     showSequenceLogo.addActionListener(new ActionListener()
1044     {
1045
1046       public void actionPerformed(ActionEvent e)
1047       {
1048         showSequenceLogo_actionPerformed(e);
1049       }
1050
1051     });
1052     applyAutoAnnotationSettings.setText("Apply to all groups");
1053     applyAutoAnnotationSettings.setState(false);
1054     applyAutoAnnotationSettings.setVisible(true);
1055     applyAutoAnnotationSettings.addActionListener(new ActionListener()
1056     {
1057
1058       public void actionPerformed(ActionEvent e)
1059       {
1060         applyAutoAnnotationSettings_actionPerformed(e);
1061       }
1062
1063     });
1064
1065     nucleotideColour.setText("Nucleotide");
1066     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1067     {
1068       public void actionPerformed(ActionEvent e)
1069       {
1070         nucleotideColour_actionPerformed(e);
1071       }
1072     });
1073     deleteGroups.setText("Undefine groups");
1074     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1075             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1076                     .getMenuShortcutKeyMask(), false));
1077     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1078     {
1079       public void actionPerformed(ActionEvent e)
1080       {
1081         deleteGroups_actionPerformed(e);
1082       }
1083     });
1084     copy.setText("Copy");
1085     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1086             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1087                     .getMenuShortcutKeyMask(), false));
1088
1089     copy.addActionListener(new java.awt.event.ActionListener()
1090     {
1091       public void actionPerformed(ActionEvent e)
1092       {
1093         copy_actionPerformed(e);
1094       }
1095     });
1096     cut.setText("Cut");
1097     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1098             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1099                     .getMenuShortcutKeyMask(), false));
1100     cut.addActionListener(new java.awt.event.ActionListener()
1101     {
1102       public void actionPerformed(ActionEvent e)
1103       {
1104         cut_actionPerformed(e);
1105       }
1106     });
1107     delete.setText("Delete");
1108     delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1109             java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1110     delete.addActionListener(new java.awt.event.ActionListener()
1111     {
1112       public void actionPerformed(ActionEvent e)
1113       {
1114         delete_actionPerformed(e);
1115       }
1116     });
1117     pasteMenu.setText("Paste");
1118     pasteNew.setText("To New Alignment");
1119     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1120             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1121                     .getMenuShortcutKeyMask()
1122                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1123     pasteNew.addActionListener(new java.awt.event.ActionListener()
1124     {
1125       public void actionPerformed(ActionEvent e)
1126       {
1127         pasteNew_actionPerformed(e);
1128       }
1129     });
1130     pasteThis.setText("Add To This Alignment");
1131     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1132             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1133                     .getMenuShortcutKeyMask(), false));
1134     pasteThis.addActionListener(new java.awt.event.ActionListener()
1135     {
1136       public void actionPerformed(ActionEvent e)
1137       {
1138         pasteThis_actionPerformed(e);
1139       }
1140     });
1141     applyToAllGroups.setText("Apply Colour To All Groups");
1142     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1143     {
1144       public void actionPerformed(ActionEvent e)
1145       {
1146         applyToAllGroups_actionPerformed(e);
1147       }
1148     });
1149     createPNG.addActionListener(new java.awt.event.ActionListener()
1150     {
1151       public void actionPerformed(ActionEvent e)
1152       {
1153         createPNG(null);
1154       }
1155     });
1156     createPNG.setActionCommand("Save As PNG Image");
1157     createPNG.setText("PNG");
1158     font.setText("Font...");
1159     font.addActionListener(new java.awt.event.ActionListener()
1160     {
1161       public void actionPerformed(ActionEvent e)
1162       {
1163         font_actionPerformed(e);
1164       }
1165     });
1166
1167     seqLimits.setText("Show Sequence Limits");
1168     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1169     seqLimits.addActionListener(new java.awt.event.ActionListener()
1170     {
1171       public void actionPerformed(ActionEvent e)
1172       {
1173         seqLimit_actionPerformed(e);
1174       }
1175     });
1176     epsFile.setText("EPS");
1177     epsFile.addActionListener(new java.awt.event.ActionListener()
1178     {
1179       public void actionPerformed(ActionEvent e)
1180       {
1181         createEPS(null);
1182       }
1183     });
1184     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1185     LoadtreeMenuItem.setText("Load Associated Tree");
1186     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1187     {
1188       public void actionPerformed(ActionEvent e)
1189       {
1190         LoadtreeMenuItem_actionPerformed(e);
1191       }
1192     });
1193     scaleAbove.setVisible(false);
1194     scaleAbove.setText("Scale Above");
1195     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1196     {
1197       public void actionPerformed(ActionEvent e)
1198       {
1199         scaleAbove_actionPerformed(e);
1200       }
1201     });
1202     scaleLeft.setVisible(false);
1203     scaleLeft.setSelected(true);
1204     scaleLeft.setText("Scale Left");
1205     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1206     {
1207       public void actionPerformed(ActionEvent e)
1208       {
1209         scaleLeft_actionPerformed(e);
1210       }
1211     });
1212     scaleRight.setVisible(false);
1213     scaleRight.setSelected(true);
1214     scaleRight.setText("Scale Right");
1215     scaleRight.addActionListener(new java.awt.event.ActionListener()
1216     {
1217       public void actionPerformed(ActionEvent e)
1218       {
1219         scaleRight_actionPerformed(e);
1220       }
1221     });
1222     centreColumnLabelsMenuItem.setVisible(true);
1223     centreColumnLabelsMenuItem.setState(false);
1224     centreColumnLabelsMenuItem.setText("Centre Column Labels");
1225     centreColumnLabelsMenuItem
1226             .addActionListener(new java.awt.event.ActionListener()
1227             {
1228               public void actionPerformed(ActionEvent e)
1229               {
1230                 centreColumnLabels_actionPerformed(e);
1231               }
1232             });
1233     followHighlightMenuItem.setVisible(true);
1234     followHighlightMenuItem.setState(true);
1235     followHighlightMenuItem.setText("Automatic Scrolling");
1236     followHighlightMenuItem.addActionListener(new ActionListener()
1237     {
1238
1239       public void actionPerformed(ActionEvent e)
1240       {
1241         followHighlight_actionPerformed();
1242       }
1243
1244     });
1245
1246     modifyPID.setText("Modify Identity Threshold...");
1247     modifyPID.addActionListener(new java.awt.event.ActionListener()
1248     {
1249       public void actionPerformed(ActionEvent e)
1250       {
1251         modifyPID_actionPerformed(e);
1252       }
1253     });
1254     modifyConservation.setText("Modify Conservation Threshold...");
1255     modifyConservation
1256             .addActionListener(new java.awt.event.ActionListener()
1257             {
1258               public void actionPerformed(ActionEvent e)
1259               {
1260                 modifyConservation_actionPerformed(e);
1261               }
1262             });
1263     sortByTreeMenu.setText("By Tree Order");
1264     sort.setText("Sort");
1265     sort.addMenuListener(new MenuListener()
1266     {
1267       public void menuSelected(MenuEvent e)
1268       {
1269         buildTreeMenu();
1270       }
1271
1272       public void menuDeselected(MenuEvent e)
1273       {
1274       }
1275
1276       public void menuCanceled(MenuEvent e)
1277       {
1278       }
1279     });
1280     sortByAnnotScore.setText("by Score");
1281     sort.add(sortByAnnotScore);
1282     sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1283     {
1284
1285       public void menuCanceled(MenuEvent e)
1286       {
1287       }
1288
1289       public void menuDeselected(MenuEvent e)
1290       {
1291       }
1292
1293       public void menuSelected(MenuEvent e)
1294       {
1295         buildSortByAnnotationScoresMenu();
1296       }
1297     });
1298     sortByAnnotScore.setVisible(false);
1299
1300     calculateTree.setText("Calculate Tree");
1301
1302     jMenu2.setText("Export Image");
1303     padGapsMenuitem.setText("Pad Gaps");
1304     padGapsMenuitem.setState(jalview.bin.Cache
1305             .getDefault("PAD_GAPS", false));
1306     padGapsMenuitem.addActionListener(new ActionListener()
1307     {
1308       public void actionPerformed(ActionEvent e)
1309       {
1310         padGapsMenuitem_actionPerformed(e);
1311       }
1312     });
1313     vamsasStore.setVisible(false);
1314     vamsasStore.setText("VAMSAS store");
1315     vamsasStore.addActionListener(new ActionListener()
1316     {
1317       public void actionPerformed(ActionEvent e)
1318       {
1319         vamsasStore_actionPerformed(e);
1320       }
1321     });
1322     showTranslation.setText("Translate cDNA");
1323     showTranslation.addActionListener(new ActionListener()
1324     {
1325       public void actionPerformed(ActionEvent e)
1326       {
1327         showTranslation_actionPerformed(e);
1328       }
1329     });
1330     extractScores.setText("Extract Scores...");
1331     extractScores.addActionListener(new ActionListener()
1332     {
1333       public void actionPerformed(ActionEvent e)
1334       {
1335         extractScores_actionPerformed(e);
1336       }
1337     });
1338     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1339                                     // score extraction
1340     showProducts.setText("Get Cross References");
1341     /*
1342      * showProducts.addActionListener(new ActionListener() {
1343      *
1344      * public void actionPerformed(ActionEvent e) {
1345      * showProducts_actionPerformed(e); } });
1346      */
1347     featureSettings.setText("Feature Settings...");
1348     featureSettings.addActionListener(new ActionListener()
1349     {
1350       public void actionPerformed(ActionEvent e)
1351       {
1352         featureSettings_actionPerformed(e);
1353       }
1354     });
1355     fetchSequence.setText("Fetch Sequence(s)...");
1356     fetchSequence.addActionListener(new ActionListener()
1357     {
1358       public void actionPerformed(ActionEvent e)
1359       {
1360         fetchSequence_actionPerformed(e);
1361       }
1362     });
1363
1364     annotationColour.setText("By Annotation...");
1365     annotationColour.addActionListener(new ActionListener()
1366     {
1367       public void actionPerformed(ActionEvent e)
1368       {
1369         annotationColour_actionPerformed(e);
1370       }
1371     });
1372     associatedData.setText("Load Features / Annotations");
1373     associatedData.addActionListener(new ActionListener()
1374     {
1375       public void actionPerformed(ActionEvent e)
1376       {
1377         associatedData_actionPerformed(e);
1378       }
1379     });
1380     autoCalculate.setText("Autocalculate Consensus");
1381     autoCalculate.setState(jalview.bin.Cache.getDefault(
1382             "AUTO_CALC_CONSENSUS", true));
1383     autoCalculate.addActionListener(new ActionListener()
1384     {
1385       public void actionPerformed(ActionEvent e)
1386       {
1387         autoCalculate_actionPerformed(e);
1388       }
1389     });
1390     addSequenceMenu.setText("Add Sequences");
1391     addFromFile.setText("From File");
1392     addFromFile.addActionListener(new ActionListener()
1393     {
1394       public void actionPerformed(ActionEvent e)
1395       {
1396         addFromFile_actionPerformed(e);
1397       }
1398     });
1399     addFromText.setText("From Textbox");
1400     addFromText.addActionListener(new ActionListener()
1401     {
1402       public void actionPerformed(ActionEvent e)
1403       {
1404         addFromText_actionPerformed(e);
1405       }
1406     });
1407     addFromURL.setText("From URL");
1408     addFromURL.addActionListener(new ActionListener()
1409     {
1410       public void actionPerformed(ActionEvent e)
1411       {
1412         addFromURL_actionPerformed(e);
1413       }
1414     });
1415     exportFeatures.setText("Export Features...");
1416     exportFeatures.addActionListener(new ActionListener()
1417     {
1418       public void actionPerformed(ActionEvent e)
1419       {
1420         exportFeatures_actionPerformed(e);
1421       }
1422     });
1423     exportAnnotations.setText("Export Annotations...");
1424     exportAnnotations.addActionListener(new ActionListener()
1425     {
1426       public void actionPerformed(ActionEvent e)
1427       {
1428         exportAnnotations_actionPerformed(e);
1429       }
1430     });
1431     statusPanel.setLayout(gridLayout1);
1432     jMenu3.setText("Show");
1433     showAllSeqs.setText("All Sequences");
1434     showAllSeqs.addActionListener(new ActionListener()
1435     {
1436       public void actionPerformed(ActionEvent e)
1437       {
1438         showAllSeqs_actionPerformed(e);
1439       }
1440     });
1441     showAllColumns.setText("All Columns");
1442     showAllColumns.addActionListener(new ActionListener()
1443     {
1444       public void actionPerformed(ActionEvent e)
1445       {
1446         showAllColumns_actionPerformed(e);
1447       }
1448     });
1449     hideMenu.setText("Hide");
1450     hideSelSequences.setText("Selected Sequences");
1451     hideSelSequences.addActionListener(new ActionListener()
1452     {
1453       public void actionPerformed(ActionEvent e)
1454       {
1455         hideSelSequences_actionPerformed(e);
1456       }
1457     });
1458     hideSelColumns.setText("Selected Columns");
1459     hideSelColumns.addActionListener(new ActionListener()
1460     {
1461       public void actionPerformed(ActionEvent e)
1462       {
1463         hideSelColumns_actionPerformed(e);
1464       }
1465     });
1466     hiddenMarkers.setText("Show Hidden Markers");
1467     hiddenMarkers.addActionListener(new ActionListener()
1468     {
1469       public void actionPerformed(ActionEvent e)
1470       {
1471         hiddenMarkers_actionPerformed(e);
1472       }
1473     });
1474     invertColSel.setText("Invert Column Selection");
1475     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1476             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1477                     .getMenuShortcutKeyMask()
1478                     | java.awt.event.KeyEvent.ALT_MASK, false));
1479     invertColSel.addActionListener(new ActionListener()
1480     {
1481       public void actionPerformed(ActionEvent e)
1482       {
1483         invertColSel_actionPerformed(e);
1484       }
1485     });
1486     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1487     {
1488       public void stateChanged(ChangeEvent evt)
1489       {
1490         JTabbedPane pane = (JTabbedPane) evt.getSource();
1491         int sel = pane.getSelectedIndex();
1492         tabSelectionChanged(sel);
1493       }
1494     });
1495     tabbedPane.addMouseListener(new MouseAdapter()
1496     {
1497       public void mousePressed(MouseEvent e)
1498       {
1499         tabbedPane_mousePressed(e);
1500       }
1501     });
1502     tabbedPane.addFocusListener(new FocusAdapter()
1503     {
1504       public void focusGained(FocusEvent e)
1505       {
1506         tabbedPane_focusGained(e);
1507       }
1508     });
1509     save.setText("Save");
1510     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1511             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1512                     .getMenuShortcutKeyMask(), false));
1513     save.addActionListener(new ActionListener()
1514     {
1515       public void actionPerformed(ActionEvent e)
1516       {
1517         save_actionPerformed(e);
1518       }
1519     });
1520     reload.setEnabled(false);
1521     reload.setText("Reload");
1522     reload.addActionListener(new ActionListener()
1523     {
1524       public void actionPerformed(ActionEvent e)
1525       {
1526         reload_actionPerformed(e);
1527       }
1528     });
1529     newView.setText("New View");
1530     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1531             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1532                     .getMenuShortcutKeyMask(), false));
1533     newView.addActionListener(new ActionListener()
1534     {
1535       public void actionPerformed(ActionEvent e)
1536       {
1537         newView_actionPerformed(e);
1538       }
1539     });
1540     tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1541             + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1542     textColour.setText("Colour Text ...");
1543     textColour.addActionListener(new ActionListener()
1544     {
1545       public void actionPerformed(ActionEvent e)
1546       {
1547         textColour_actionPerformed(e);
1548       }
1549     });
1550     formatMenu.setText("Format");
1551     selectMenu.setText("Select");
1552     idRightAlign.setText("Right Align Sequence Id");
1553     idRightAlign.addActionListener(new ActionListener()
1554     {
1555       public void actionPerformed(ActionEvent e)
1556       {
1557         idRightAlign_actionPerformed(e);
1558       }
1559     });
1560     gatherViews.setEnabled(false);
1561     gatherViews.setText("Gather Views");
1562     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1563             java.awt.event.KeyEvent.VK_G, 0, false));
1564     gatherViews.addActionListener(new ActionListener()
1565     {
1566       public void actionPerformed(ActionEvent e)
1567       {
1568         gatherViews_actionPerformed(e);
1569       }
1570     });
1571     expandViews.setEnabled(false);
1572     expandViews.setText("Expand Views");
1573     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1574             java.awt.event.KeyEvent.VK_X, 0, false));
1575     expandViews.addActionListener(new ActionListener()
1576     {
1577       public void actionPerformed(ActionEvent e)
1578       {
1579         expandViews_actionPerformed(e);
1580       }
1581     });
1582     pageSetup.setText("Page Setup ...");
1583     pageSetup.addActionListener(new ActionListener()
1584     {
1585       public void actionPerformed(ActionEvent e)
1586       {
1587         pageSetup_actionPerformed(e);
1588       }
1589     });
1590     alignmentProperties.setText("Alignment Properties...");
1591     alignmentProperties.addActionListener(new ActionListener()
1592     {
1593       public void actionPerformed(ActionEvent actionEvent)
1594       {
1595         alignmentProperties();
1596       }
1597     });
1598     tooltipSettingsMenu.setText("Sequence ID Tooltip");
1599     autoAnnMenu.setText("Autocalculated Annotation");
1600     alignFrameMenuBar.add(fileMenu);
1601     alignFrameMenuBar.add(editMenu);
1602     alignFrameMenuBar.add(selectMenu);
1603     alignFrameMenuBar.add(viewMenu);
1604     alignFrameMenuBar.add(formatMenu);
1605     alignFrameMenuBar.add(colourMenu);
1606     alignFrameMenuBar.add(calculateMenu);
1607     alignFrameMenuBar.add(webService);
1608     fileMenu.add(fetchSequence);
1609     fileMenu.add(addSequenceMenu);
1610     fileMenu.add(reload);
1611     fileMenu.addSeparator();
1612     fileMenu.add(vamsasStore);
1613     fileMenu.add(save);
1614     fileMenu.add(saveAs);
1615     fileMenu.add(outputTextboxMenu);
1616     fileMenu.add(pageSetup);
1617     fileMenu.add(printMenuItem);
1618     fileMenu.addSeparator();
1619     fileMenu.add(jMenu2);
1620     fileMenu.add(exportFeatures);
1621     fileMenu.add(exportAnnotations);
1622     fileMenu.add(LoadtreeMenuItem);
1623     fileMenu.add(associatedData);
1624     fileMenu.addSeparator();
1625     fileMenu.add(closeMenuItem);
1626     editMenu.add(undoMenuItem);
1627     editMenu.add(redoMenuItem);
1628     editMenu.add(cut);
1629     editMenu.add(copy);
1630     editMenu.add(pasteMenu);
1631     editMenu.add(delete);
1632     editMenu.addSeparator();
1633     editMenu.add(remove2LeftMenuItem);
1634     editMenu.add(remove2RightMenuItem);
1635     editMenu.add(removeGappedColumnMenuItem);
1636     editMenu.add(removeAllGapsMenuItem);
1637     editMenu.add(removeRedundancyMenuItem);
1638     editMenu.addSeparator();
1639     // dont add these yet in the CVS build - they cannot be undone!
1640     editMenu.add(justifyLeftMenuItem);
1641     editMenu.add(justifyRightMenuItem);
1642     editMenu.addSeparator();
1643     editMenu.add(padGapsMenuitem);
1644     viewMenu.add(newView);
1645     viewMenu.add(expandViews);
1646     viewMenu.add(gatherViews);
1647     viewMenu.addSeparator();
1648     viewMenu.add(jMenu3);
1649     viewMenu.add(hideMenu);
1650     viewMenu.addSeparator();
1651     viewMenu.add(followHighlightMenuItem);
1652     viewMenu.add(annotationPanelMenuItem);
1653     autoAnnMenu.add(applyAutoAnnotationSettings);
1654     autoAnnMenu.add(showConsensusHistogram);
1655     autoAnnMenu.add(showSequenceLogo);
1656     autoAnnMenu.addSeparator();
1657     autoAnnMenu.add(showGroupConservation);
1658     autoAnnMenu.add(showGroupConsensus);
1659     viewMenu.add(autoAnnMenu);
1660     viewMenu.addSeparator();
1661     viewMenu.add(showSeqFeatures);
1662     //viewMenu.add(showSeqFeaturesHeight);
1663
1664     viewMenu.add(featureSettings);
1665     tooltipSettingsMenu.add(showDbRefsMenuitem);
1666     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1667     viewMenu.add(tooltipSettingsMenu);
1668     viewMenu.addSeparator();
1669     viewMenu.add(alignmentProperties);
1670     viewMenu.addSeparator();
1671     viewMenu.add(overviewMenuItem);
1672     colourMenu.add(applyToAllGroups);
1673     colourMenu.add(textColour);
1674     colourMenu.addSeparator();
1675     colourMenu.add(noColourmenuItem);
1676     colourMenu.add(clustalColour);
1677     colourMenu.add(BLOSUM62Colour);
1678     colourMenu.add(PIDColour);
1679     colourMenu.add(zappoColour);
1680     colourMenu.add(taylorColour);
1681     colourMenu.add(hydrophobicityColour);
1682     colourMenu.add(helixColour);
1683     colourMenu.add(strandColour);
1684     colourMenu.add(turnColour);
1685     colourMenu.add(buriedColour);
1686     colourMenu.add(nucleotideColour);
1687     colourMenu.add(userDefinedColour);
1688     colourMenu.addSeparator();
1689     colourMenu.add(conservationMenuItem);
1690     colourMenu.add(modifyConservation);
1691     colourMenu.add(abovePIDThreshold);
1692     colourMenu.add(modifyPID);
1693     colourMenu.add(annotationColour);
1694     calculateMenu.add(sort);
1695     calculateMenu.add(calculateTree);
1696     calculateMenu.addSeparator();
1697     calculateMenu.add(pairwiseAlignmentMenuItem);
1698     calculateMenu.add(PCAMenuItem);
1699     calculateMenu.addSeparator();
1700     calculateMenu.add(showTranslation);
1701     calculateMenu.add(showProducts);
1702     calculateMenu.add(autoCalculate);
1703     calculateMenu.addSeparator();
1704     calculateMenu.add(extractScores);
1705     webServiceNoServices = new JMenuItem("<No Services>");
1706     webService.add(webServiceNoServices);
1707     pasteMenu.add(pasteNew);
1708     pasteMenu.add(pasteThis);
1709     sort.add(sortIDMenuItem);
1710     sort.add(sortLengthMenuItem);
1711     sort.add(sortGroupMenuItem);
1712     sort.add(sortPairwiseMenuItem);
1713     sort.add(sortByTreeMenu);
1714     calculateTree.add(averageDistanceTreeMenuItem);
1715     calculateTree.add(neighbourTreeMenuItem);
1716     calculateTree.add(avDistanceTreeBlosumMenuItem);
1717     calculateTree.add(njTreeBlosumMenuItem);
1718     jMenu2.add(htmlMenuItem);
1719     jMenu2.add(epsFile);
1720     jMenu2.add(createPNG);
1721     addSequenceMenu.add(addFromFile);
1722     addSequenceMenu.add(addFromText);
1723     addSequenceMenu.add(addFromURL);
1724     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1725     statusPanel.add(statusBar, null);
1726     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1727     jMenu3.add(showAllColumns);
1728     jMenu3.add(showAllSeqs);
1729     hideMenu.add(hideSelColumns);
1730     hideMenu.add(hideSelSequences);
1731     formatMenu.add(font);
1732     formatMenu.addSeparator();
1733     formatMenu.add(wrapMenuItem);
1734     formatMenu.add(scaleAbove);
1735     formatMenu.add(scaleLeft);
1736     formatMenu.add(scaleRight);
1737     formatMenu.add(seqLimits);
1738     formatMenu.add(idRightAlign);
1739     formatMenu.add(hiddenMarkers);
1740     formatMenu.add(viewBoxesMenuItem);
1741     formatMenu.add(viewTextMenuItem);
1742     formatMenu.add(colourTextMenuItem);
1743     formatMenu.add(renderGapsMenuItem);
1744     formatMenu.add(centreColumnLabelsMenuItem);
1745     formatMenu.add(showUnconservedMenuItem);
1746     selectMenu.add(findMenuItem);
1747     selectMenu.addSeparator();
1748     selectMenu.add(selectAllSequenceMenuItem);
1749     selectMenu.add(deselectAllSequenceMenuItem);
1750     selectMenu.add(invertSequenceMenuItem);
1751     selectMenu.add(invertColSel);
1752     selectMenu.add(deleteGroups);
1753     selectMenu.add(grpsFromSelection);
1754   }
1755
1756   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
1757   {
1758     // TODO Auto-generated method stub
1759
1760   }
1761
1762   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
1763   {
1764     // TODO Auto-generated method stub
1765
1766   }
1767
1768   protected void showSequenceLogo_actionPerformed(ActionEvent e)
1769   {
1770     // TODO Auto-generated method stub
1771
1772   }
1773
1774   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
1775   {
1776     // TODO Auto-generated method stub
1777
1778   }
1779
1780   protected void showGroupConsensus_actionPerformed(ActionEvent e)
1781   {
1782     // TODO Auto-generated method stub
1783
1784   }
1785
1786   protected void showGroupConservation_actionPerformed(ActionEvent e)
1787   {
1788     // TODO Auto-generated method stub
1789
1790   }
1791
1792   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
1793   {
1794     // TODO Auto-generated method stub
1795
1796   }
1797
1798   protected void showSeqFeaturesHeight_actionPerformed(
1799           ActionEvent actionEvent)
1800   {
1801     // TODO Auto-generated method stub
1802
1803   }
1804
1805   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
1806   {
1807     // TODO Auto-generated method stub
1808
1809   }
1810
1811   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
1812   {
1813     // TODO Auto-generated method stub
1814
1815   }
1816
1817   protected void followHighlight_actionPerformed()
1818   {
1819     // TODO Auto-generated method stub
1820
1821   }
1822
1823   protected void showNpFeats_actionPerformed(ActionEvent e)
1824   {
1825     // TODO Auto-generated method stub
1826
1827   }
1828
1829   protected void showDbRefs_actionPerformed(ActionEvent e)
1830   {
1831     // TODO Auto-generated method stub
1832
1833   }
1834
1835   protected void centreColumnLabels_actionPerformed(ActionEvent e)
1836   {
1837   }
1838
1839   protected void showProducts_actionPerformed(ActionEvent e)
1840   {
1841   }
1842
1843   protected void buildSortByAnnotationScoresMenu()
1844   {
1845   }
1846
1847   protected void extractScores_actionPerformed(ActionEvent e)
1848   {
1849   }
1850
1851   protected void outputText_actionPerformed(ActionEvent e)
1852   {
1853   }
1854
1855   public void addFromFile_actionPerformed(ActionEvent e)
1856   {
1857
1858   }
1859
1860   public void addFromText_actionPerformed(ActionEvent e)
1861   {
1862
1863   }
1864
1865   public void addFromURL_actionPerformed(ActionEvent e)
1866   {
1867
1868   }
1869
1870   public void exportFeatures_actionPerformed(ActionEvent e)
1871   {
1872
1873   }
1874
1875   public void exportAnnotations_actionPerformed(ActionEvent e)
1876   {
1877
1878   }
1879
1880   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1881   {
1882   }
1883
1884   protected void closeMenuItem_actionPerformed(boolean b)
1885   {
1886   }
1887
1888   protected void redoMenuItem_actionPerformed(ActionEvent e)
1889   {
1890   }
1891
1892   protected void undoMenuItem_actionPerformed(ActionEvent e)
1893   {
1894   }
1895
1896   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1897   {
1898   }
1899
1900   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1901   {
1902   }
1903
1904   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1905   {
1906   }
1907
1908   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1909   {
1910   }
1911
1912   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
1913   {
1914   }
1915
1916   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1917   {
1918   }
1919
1920   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1921   {
1922   }
1923
1924   protected void wrapMenuItem_actionPerformed(ActionEvent e)
1925   {
1926   }
1927
1928   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1929   {
1930   }
1931
1932   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
1933   {
1934   }
1935
1936   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
1937   {
1938   }
1939
1940   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
1941   {
1942   }
1943
1944   protected void overviewMenuItem_actionPerformed(ActionEvent e)
1945   {
1946   }
1947
1948   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
1949   {
1950   }
1951
1952   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
1953   {
1954   }
1955
1956   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
1957   {
1958   }
1959
1960   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
1961   {
1962   }
1963
1964   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
1965   {
1966   }
1967
1968   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
1969   {
1970   }
1971
1972   protected void PCAMenuItem_actionPerformed(ActionEvent e)
1973   {
1974   }
1975
1976   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
1977   {
1978   }
1979
1980   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
1981   {
1982   }
1983
1984   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1985   {
1986   }
1987
1988   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1989   {
1990   }
1991
1992   protected void clustalColour_actionPerformed(ActionEvent e)
1993   {
1994   }
1995
1996   protected void zappoColour_actionPerformed(ActionEvent e)
1997   {
1998   }
1999
2000   protected void taylorColour_actionPerformed(ActionEvent e)
2001   {
2002   }
2003
2004   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2005   {
2006   }
2007
2008   protected void helixColour_actionPerformed(ActionEvent e)
2009   {
2010   }
2011
2012   protected void strandColour_actionPerformed(ActionEvent e)
2013   {
2014   }
2015
2016   protected void turnColour_actionPerformed(ActionEvent e)
2017   {
2018   }
2019
2020   protected void buriedColour_actionPerformed(ActionEvent e)
2021   {
2022   }
2023
2024   protected void userDefinedColour_actionPerformed(ActionEvent e)
2025   {
2026   }
2027
2028   protected void PIDColour_actionPerformed(ActionEvent e)
2029   {
2030   }
2031
2032   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2033   {
2034   }
2035
2036   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2037   {
2038   }
2039
2040   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2041   {
2042   }
2043
2044   protected void printMenuItem_actionPerformed(ActionEvent e)
2045   {
2046   }
2047
2048   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2049   {
2050   }
2051
2052   protected void findMenuItem_actionPerformed(ActionEvent e)
2053   {
2054   }
2055
2056   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2057   {
2058   }
2059
2060   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2061   {
2062   }
2063
2064   protected void nucleotideColour_actionPerformed(ActionEvent e)
2065   {
2066   }
2067
2068   protected void deleteGroups_actionPerformed(ActionEvent e)
2069   {
2070   }
2071
2072   protected void copy_actionPerformed(ActionEvent e)
2073   {
2074   }
2075
2076   protected void cut_actionPerformed(ActionEvent e)
2077   {
2078   }
2079
2080   protected void delete_actionPerformed(ActionEvent e)
2081   {
2082   }
2083
2084   protected void pasteNew_actionPerformed(ActionEvent e)
2085   {
2086   }
2087
2088   protected void pasteThis_actionPerformed(ActionEvent e)
2089   {
2090   }
2091
2092   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2093   {
2094   }
2095
2096   public void createPNG(java.io.File f)
2097   {
2098   }
2099
2100   protected void font_actionPerformed(ActionEvent e)
2101   {
2102   }
2103
2104   protected void seqLimit_actionPerformed(ActionEvent e)
2105   {
2106   }
2107
2108   public void seqDBRef_actionPerformed(ActionEvent e)
2109   {
2110
2111   }
2112
2113   public void createEPS(java.io.File f)
2114   {
2115   }
2116
2117   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2118   {
2119   }
2120
2121   protected void jpred_actionPerformed(ActionEvent e)
2122   {
2123   }
2124
2125   protected void scaleAbove_actionPerformed(ActionEvent e)
2126   {
2127   }
2128
2129   protected void scaleLeft_actionPerformed(ActionEvent e)
2130   {
2131   }
2132
2133   protected void scaleRight_actionPerformed(ActionEvent e)
2134   {
2135   }
2136
2137   protected void modifyPID_actionPerformed(ActionEvent e)
2138   {
2139   }
2140
2141   protected void modifyConservation_actionPerformed(ActionEvent e)
2142   {
2143   }
2144
2145   protected void saveAs_actionPerformed(ActionEvent e)
2146   {
2147   }
2148
2149   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2150   {
2151   }
2152
2153   public void vamsasStore_actionPerformed(ActionEvent e)
2154   {
2155
2156   }
2157
2158   public void vamsasLoad_actionPerformed(ActionEvent e)
2159   {
2160
2161   }
2162
2163   public void showTranslation_actionPerformed(ActionEvent e)
2164   {
2165
2166   }
2167
2168   public void featureSettings_actionPerformed(ActionEvent e)
2169   {
2170
2171   }
2172
2173   public void fetchSequence_actionPerformed(ActionEvent e)
2174   {
2175
2176   }
2177
2178   public void smoothFont_actionPerformed(ActionEvent e)
2179   {
2180
2181   }
2182
2183   public void annotationColour_actionPerformed(ActionEvent e)
2184   {
2185
2186   }
2187
2188   public void associatedData_actionPerformed(ActionEvent e)
2189   {
2190
2191   }
2192
2193   public void autoCalculate_actionPerformed(ActionEvent e)
2194   {
2195
2196   }
2197
2198   public void showAllSeqs_actionPerformed(ActionEvent e)
2199   {
2200
2201   }
2202
2203   public void showAllColumns_actionPerformed(ActionEvent e)
2204   {
2205
2206   }
2207
2208   public void hideSelSequences_actionPerformed(ActionEvent e)
2209   {
2210
2211   }
2212
2213   public void hideSelColumns_actionPerformed(ActionEvent e)
2214   {
2215
2216   }
2217
2218   public void hiddenMarkers_actionPerformed(ActionEvent e)
2219   {
2220
2221   }
2222
2223   public void findPdbId_actionPerformed(ActionEvent e)
2224   {
2225
2226   }
2227
2228   public void enterPdbId_actionPerformed(ActionEvent e)
2229   {
2230
2231   }
2232
2233   public void pdbFile_actionPerformed(ActionEvent e)
2234   {
2235
2236   }
2237
2238   public void invertColSel_actionPerformed(ActionEvent e)
2239   {
2240
2241   }
2242
2243   public void tabSelectionChanged(int sel)
2244   {
2245
2246   }
2247
2248   public void tabbedPane_mousePressed(MouseEvent e)
2249   {
2250
2251   }
2252
2253   public void tabbedPane_focusGained(FocusEvent e)
2254   {
2255     requestFocus();
2256   }
2257
2258   public void save_actionPerformed(ActionEvent e)
2259   {
2260
2261   }
2262
2263   public void reload_actionPerformed(ActionEvent e)
2264   {
2265
2266   }
2267
2268   public void newView_actionPerformed(ActionEvent e)
2269   {
2270
2271   }
2272
2273   public void textColour_actionPerformed(ActionEvent e)
2274   {
2275
2276   }
2277
2278   public void idRightAlign_actionPerformed(ActionEvent e)
2279   {
2280
2281   }
2282
2283   public void expandViews_actionPerformed(ActionEvent e)
2284   {
2285
2286   }
2287
2288   public void gatherViews_actionPerformed(ActionEvent e)
2289   {
2290
2291   }
2292
2293   public void buildTreeMenu()
2294   {
2295
2296   }
2297
2298   public void pageSetup_actionPerformed(ActionEvent e)
2299   {
2300
2301   }
2302
2303   public void alignmentProperties()
2304   {
2305
2306   }
2307 }