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