src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
   3  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.jbgui;
  19
  20 import java.awt.*;
  21 import java.awt.event.*;
  22
  23 import javax.swing.*;
  24 import javax.swing.event.*;
  25
  26 import jalview.schemes.*;
  27
  28 public class GAlignFrame extends JInternalFrame
  29 {
  30   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  31
  32   protected JMenu fileMenu = new JMenu();
  33
  34   protected JMenuItem closeMenuItem = new JMenuItem();
  35
  36   protected JMenu editMenu = new JMenu();
  37
  38   protected JMenu viewMenu = new JMenu();
  39
  40   protected JMenu colourMenu = new JMenu();
  41
  42   protected JMenu calculateMenu = new JMenu();
  43
  44   protected JMenu webService = new JMenu();
  45
  46   protected JMenuItem webServiceNoServices;
  47
  48   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  49
  50   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  51
  52   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  53
  54   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  55
  56   protected JMenuItem remove2RightMenuItem = new JMenuItem();
  57
  58   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  59
  60   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  61
  62   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  63
  64   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  65
  66   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  67
  68   protected JMenuItem sortIDMenuItem = new JMenuItem();
  69
  70   protected JMenuItem sortLengthMenuItem = new JMenuItem();
  71
  72   protected JMenuItem sortGroupMenuItem = new JMenuItem();
  73
  74   protected JMenu sortByAnnotScore = new JMenu();
  75
  76   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
  77
  78   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
  79
  80   protected JMenuItem PCAMenuItem = new JMenuItem();
  81
  82   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
  83
  84   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
  85
  86   BorderLayout borderLayout1 = new BorderLayout();
  87
  88   public JLabel statusBar = new JLabel();
  89
  90   protected JMenuItem saveAs = new JMenuItem();
  91
  92   protected JMenu outputTextboxMenu = new JMenu();
  93
  94   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  95
  96   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  97
  98   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  99
 100   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
 101
 102   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
 103
 104   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
 105
 106   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
 107
 108   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 109
 110   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
 111
 112   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
 113
 114   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 115
 116   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 117
 118   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
 119
 120   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 121
 122   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 123
 124   public JCheckBoxMenuItem showUnconservedMenuItem = new JCheckBoxMenuItem();
 125
 126   JMenuItem htmlMenuItem = new JMenuItem();
 127
 128   JMenuItem overviewMenuItem = new JMenuItem();
 129
 130   protected JMenuItem undoMenuItem = new JMenuItem();
 131
 132   protected JMenuItem redoMenuItem = new JMenuItem();
 133
 134   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 135
 136   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 137
 138   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 139
 140   JMenuItem printMenuItem = new JMenuItem();
 141
 142   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 143
 144   JMenuItem findMenuItem = new JMenuItem();
 145
 146   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 147
 148   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 149
 150   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 151
 152   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
 153
 154   JMenuItem deleteGroups = new JMenuItem();
 155
 156   JMenuItem delete = new JMenuItem();
 157
 158   JMenuItem copy = new JMenuItem();
 159
 160   JMenuItem cut = new JMenuItem();
 161
 162   JMenu pasteMenu = new JMenu();
 163
 164   JMenuItem pasteNew = new JMenuItem();
 165
 166   JMenuItem pasteThis = new JMenuItem();
 167
 168   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
 169
 170   JMenuItem createPNG = new JMenuItem();
 171
 172   protected JMenuItem font = new JMenuItem();
 173
 174   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 175
 176   JMenuItem epsFile = new JMenuItem();
 177
 178   JMenuItem LoadtreeMenuItem = new JMenuItem();
 179
 180   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 181
 182   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 183
 184   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 185
 186   protected JMenuItem modifyPID = new JMenuItem();
 187
 188   protected JMenuItem modifyConservation = new JMenuItem();
 189
 190   protected JMenu sortByTreeMenu = new JMenu();
 191
 192   protected JMenu sort = new JMenu();
 193
 194   protected JMenu calculateTree = new JMenu();
 195
 196   JMenu jMenu2 = new JMenu();
 197
 198   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 199
 200   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 201
 202   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 203
 204   protected ButtonGroup colours = new ButtonGroup();
 205
 206   JMenuItem vamsasStore = new JMenuItem();
 207
 208   protected JMenuItem showTranslation = new JMenuItem();
 209
 210   protected JMenuItem extractScores = new JMenuItem();
 211
 212   protected JMenu showProducts = new JMenu();
 213
 214   public JMenuItem featureSettings = new JMenuItem();
 215
 216   JMenuItem fetchSequence = new JMenuItem();
 217
 218   JMenuItem annotationColour = new JMenuItem();
 219
 220   JMenuItem associatedData = new JMenuItem();
 221
 222   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 223
 224   JMenu addSequenceMenu = new JMenu();
 225
 226   JMenuItem addFromFile = new JMenuItem();
 227
 228   JMenuItem addFromText = new JMenuItem();
 229
 230   JMenuItem addFromURL = new JMenuItem();
 231
 232   JMenuItem exportAnnotations = new JMenuItem();
 233
 234   JMenuItem exportFeatures = new JMenuItem();
 235
 236   protected JPanel statusPanel = new JPanel();
 237
 238   GridLayout gridLayout1 = new GridLayout();
 239
 240   JMenu jMenu3 = new JMenu();
 241
 242   JMenuItem showAllSeqs = new JMenuItem();
 243
 244   JMenuItem showAllColumns = new JMenuItem();
 245
 246   JMenu hideMenu = new JMenu();
 247
 248   JMenuItem hideSelSequences = new JMenuItem();
 249
 250   JMenuItem hideSelColumns = new JMenuItem();
 251
 252   JMenuItem hideAllButSelection = new JMenuItem();
 253
 254   JMenuItem hideAllSelection = new JMenuItem();
 255
 256   JMenuItem showAllhidden = new JMenuItem();
 257
 258   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 259
 260   JMenuItem invertColSel = new JMenuItem();
 261
 262   protected JTabbedPane tabbedPane = new JTabbedPane();
 263
 264   JMenuItem save = new JMenuItem();
 265
 266   protected JMenuItem reload = new JMenuItem();
 267
 268   JMenuItem newView = new JMenuItem();
 269
 270   JMenuItem textColour = new JMenuItem();
 271
 272   JMenu formatMenu = new JMenu();
 273
 274   JMenu selectMenu = new JMenu();
 275
 276   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 277
 278   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 279
 280   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 281
 282   protected JMenuItem gatherViews = new JMenuItem();
 283
 284   protected JMenuItem expandViews = new JMenuItem();
 285
 286   JMenuItem pageSetup = new JMenuItem();
 287
 288   JMenuItem alignmentProperties = new JMenuItem();
 289
 290   JMenu tooltipSettingsMenu = new JMenu();
 291
 292   private JMenuItem justifyLeftMenuItem = new JMenuItem();
 293
 294   private JMenuItem justifyRightMenuItem = new JMenuItem();
 295
 296   JMenu autoAnnMenu = new JMenu();
 297
 298   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 299
 300   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 301
 302   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 303
 304   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 305
 306   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 307
 308   private JMenuItem grpsFromSelection = new JMenuItem();
 309
 310   public GAlignFrame()
 311   {
 312     try
 313     {
 314       jbInit();
 315       setJMenuBar(alignFrameMenuBar);
 316
 317       // dynamically fill save as menu with available formats
 318       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 319       {
 320         JMenuItem item = new JMenuItem(
 321                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 322
 323         item.addActionListener(new java.awt.event.ActionListener()
 324         {
 325           public void actionPerformed(ActionEvent e)
 326           {
 327             outputText_actionPerformed(e);
 328           }
 329         });
 330
 331         outputTextboxMenu.add(item);
 332       }
 333     } catch (Exception e)
 334     {
 335     }
 336
 337     if (!new jalview.util.Platform().isAMac())
 338     {
 339       closeMenuItem.setMnemonic('C');
 340       outputTextboxMenu.setMnemonic('T');
 341       undoMenuItem.setMnemonic('Z');
 342       redoMenuItem.setMnemonic('0');
 343       copy.setMnemonic('C');
 344       cut.setMnemonic('U');
 345       pasteMenu.setMnemonic('P');
 346       reload.setMnemonic('R');
 347     }
 348
 349     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 350     {
 351       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 352               .getUserColourSchemes().keys();
 353
 354       while (userColours.hasMoreElements())
 355       {
 356         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 357                 userColours.nextElement().toString());
 358         radioItem.setName("USER_DEFINED");
 359         radioItem.addMouseListener(new MouseAdapter()
 360         {
 361           public void mousePressed(MouseEvent evt)
 362           {
 363             if (evt.isControlDown()
 364                     || SwingUtilities.isRightMouseButton(evt))
 365             {
 366               radioItem
 367                       .removeActionListener(radioItem.getActionListeners()[0]);
 368
 369               int option = JOptionPane.showInternalConfirmDialog(
 370                       jalview.gui.Desktop.desktop,
 371                       "Remove from default list?",
 372                       "Remove user defined colour",
 373                       JOptionPane.YES_NO_OPTION);
 374               if (option == JOptionPane.YES_OPTION)
 375               {
 376                 jalview.gui.UserDefinedColours
 377                         .removeColourFromDefaults(radioItem.getText());
 378                 colourMenu.remove(radioItem);
 379               }
 380               else
 381               {
 382                 radioItem.addActionListener(new ActionListener()
 383                 {
 384                   public void actionPerformed(ActionEvent evt)
 385                   {
 386                     userDefinedColour_actionPerformed(evt);
 387                   }
 388                 });
 389               }
 390             }
 391           }
 392         });
 393         radioItem.addActionListener(new ActionListener()
 394         {
 395           public void actionPerformed(ActionEvent evt)
 396           {
 397             userDefinedColour_actionPerformed(evt);
 398           }
 399         });
 400         colourMenu.insert(radioItem, 15);
 401         colours.add(radioItem);
 402       }
 403     }
 404     colours.add(noColourmenuItem);
 405     colours.add(clustalColour);
 406     colours.add(zappoColour);
 407     colours.add(taylorColour);
 408     colours.add(hydrophobicityColour);
 409     colours.add(helixColour);
 410     colours.add(strandColour);
 411     colours.add(turnColour);
 412     colours.add(buriedColour);
 413     colours.add(userDefinedColour);
 414     colours.add(PIDColour);
 415     colours.add(BLOSUM62Colour);
 416     colours.add(nucleotideColour);
 417
 418     setColourSelected(jalview.bin.Cache
 419             .getDefault("DEFAULT_COLOUR", "None"));
 420
 421   }
 422
 423   public void setColourSelected(String defaultColour)
 424   {
 425
 426     if (defaultColour != null)
 427     {
 428       int index = ColourSchemeProperty
 429               .getColourIndexFromName(defaultColour);
 430
 431       switch (index)
 432       {
 433       case ColourSchemeProperty.NONE:
 434         noColourmenuItem.setSelected(true);
 435         break;
 436       case ColourSchemeProperty.CLUSTAL:
 437         clustalColour.setSelected(true);
 438
 439         break;
 440
 441       case ColourSchemeProperty.BLOSUM:
 442         BLOSUM62Colour.setSelected(true);
 443
 444         break;
 445
 446       case ColourSchemeProperty.PID:
 447         PIDColour.setSelected(true);
 448
 449         break;
 450
 451       case ColourSchemeProperty.ZAPPO:
 452         zappoColour.setSelected(true);
 453
 454         break;
 455
 456       case ColourSchemeProperty.TAYLOR:
 457         taylorColour.setSelected(true);
 458         break;
 459
 460       case ColourSchemeProperty.HYDROPHOBIC:
 461         hydrophobicityColour.setSelected(true);
 462
 463         break;
 464
 465       case ColourSchemeProperty.HELIX:
 466         helixColour.setSelected(true);
 467
 468         break;
 469
 470       case ColourSchemeProperty.STRAND:
 471         strandColour.setSelected(true);
 472
 473         break;
 474
 475       case ColourSchemeProperty.TURN:
 476         turnColour.setSelected(true);
 477
 478         break;
 479
 480       case ColourSchemeProperty.BURIED:
 481         buriedColour.setSelected(true);
 482
 483         break;
 484
 485       case ColourSchemeProperty.NUCLEOTIDE:
 486         nucleotideColour.setSelected(true);
 487
 488         break;
 489
 490       case ColourSchemeProperty.USER_DEFINED:
 491         userDefinedColour.setSelected(true);
 492
 493         break;
 494       }
 495     }
 496
 497   }
 498
 499   private void jbInit() throws Exception
 500   {
 501     fileMenu.setText("File");
 502     saveAs.setText("Save As...");
 503     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 504             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
 505                     .getMenuShortcutKeyMask()
 506                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 507     saveAs.addActionListener(new ActionListener()
 508     {
 509       public void actionPerformed(ActionEvent e)
 510       {
 511         saveAs_actionPerformed(e);
 512       }
 513     });
 514     closeMenuItem.setText("Close");
 515     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 516             java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
 517                     .getMenuShortcutKeyMask(), false));
 518     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 519     {
 520       public void actionPerformed(ActionEvent e)
 521       {
 522         closeMenuItem_actionPerformed(false);
 523       }
 524     });
 525     editMenu.setText("Edit");
 526     viewMenu.setText("View");
 527     colourMenu.setText("Colour");
 528     calculateMenu.setText("Calculate");
 529     webService.setText("Web Service");
 530     selectAllSequenceMenuItem.setText("Select All");
 531     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 532             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
 533                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 534     selectAllSequenceMenuItem
 535             .addActionListener(new java.awt.event.ActionListener()
 536             {
 537               public void actionPerformed(ActionEvent e)
 538               {
 539                 selectAllSequenceMenuItem_actionPerformed(e);
 540               }
 541             });
 542     deselectAllSequenceMenuItem.setText("Deselect All");
 543     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 544             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 545     deselectAllSequenceMenuItem
 546             .addActionListener(new java.awt.event.ActionListener()
 547             {
 548               public void actionPerformed(ActionEvent e)
 549               {
 550                 deselectAllSequenceMenuItem_actionPerformed(e);
 551               }
 552             });
 553     invertSequenceMenuItem.setText("Invert Sequence Selection");
 554     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 555             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
 556                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 557     invertSequenceMenuItem
 558             .addActionListener(new java.awt.event.ActionListener()
 559             {
 560               public void actionPerformed(ActionEvent e)
 561               {
 562                 invertSequenceMenuItem_actionPerformed(e);
 563               }
 564             });
 565     grpsFromSelection.setText("Make Groups for selection");
 566     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
 567     {
 568       public void actionPerformed(ActionEvent e)
 569       {
 570         makeGrpsFromSelection_actionPerformed(e);
 571       }
 572     });
 573
 574     remove2LeftMenuItem.setText("Remove Left");
 575     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 576             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
 577                     .getMenuShortcutKeyMask(), false));
 578     remove2LeftMenuItem
 579             .addActionListener(new java.awt.event.ActionListener()
 580             {
 581               public void actionPerformed(ActionEvent e)
 582               {
 583                 remove2LeftMenuItem_actionPerformed(e);
 584               }
 585             });
 586     remove2RightMenuItem.setText("Remove Right");
 587     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 588             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
 589                     .getMenuShortcutKeyMask(), false));
 590     remove2RightMenuItem
 591             .addActionListener(new java.awt.event.ActionListener()
 592             {
 593               public void actionPerformed(ActionEvent e)
 594               {
 595                 remove2RightMenuItem_actionPerformed(e);
 596               }
 597             });
 598     removeGappedColumnMenuItem.setText("Remove Empty Columns");
 599     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
 600             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 601                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 602     removeGappedColumnMenuItem
 603             .addActionListener(new java.awt.event.ActionListener()
 604             {
 605               public void actionPerformed(ActionEvent e)
 606               {
 607                 removeGappedColumnMenuItem_actionPerformed(e);
 608               }
 609             });
 610     removeAllGapsMenuItem.setText("Remove All Gaps");
 611     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
 612             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 613                     .getDefaultToolkit().getMenuShortcutKeyMask()
 614                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 615     removeAllGapsMenuItem
 616             .addActionListener(new java.awt.event.ActionListener()
 617             {
 618               public void actionPerformed(ActionEvent e)
 619               {
 620                 removeAllGapsMenuItem_actionPerformed(e);
 621               }
 622             });
 623     justifyLeftMenuItem.setText("Left Justify Alignment");
 624     justifyLeftMenuItem
 625             .addActionListener(new java.awt.event.ActionListener()
 626             {
 627               public void actionPerformed(ActionEvent e)
 628               {
 629                 justifyLeftMenuItem_actionPerformed(e);
 630               }
 631             });
 632     justifyRightMenuItem.setText("Right Justify Alignment");
 633     justifyRightMenuItem
 634             .addActionListener(new java.awt.event.ActionListener()
 635             {
 636               public void actionPerformed(ActionEvent e)
 637               {
 638                 justifyRightMenuItem_actionPerformed(e);
 639               }
 640             });
 641     viewBoxesMenuItem.setText("Boxes");
 642     viewBoxesMenuItem.setState(true);
 643     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 644     {
 645       public void actionPerformed(ActionEvent e)
 646       {
 647         viewBoxesMenuItem_actionPerformed(e);
 648       }
 649     });
 650     viewTextMenuItem.setText("Text");
 651     viewTextMenuItem.setState(true);
 652     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 653     {
 654       public void actionPerformed(ActionEvent e)
 655       {
 656         viewTextMenuItem_actionPerformed(e);
 657       }
 658     });
 659     showUnconservedMenuItem.setText("Show Unconserved");
 660     showUnconservedMenuItem.setState(false);
 661     showUnconservedMenuItem
 662             .addActionListener(new java.awt.event.ActionListener()
 663             {
 664               public void actionPerformed(ActionEvent e)
 665               {
 666                 showUnconservedMenuItem_actionPerformed(e);
 667               }
 668             });
 669     sortPairwiseMenuItem.setText("by Pairwise Identity");
 670     sortPairwiseMenuItem
 671             .addActionListener(new java.awt.event.ActionListener()
 672             {
 673               public void actionPerformed(ActionEvent e)
 674               {
 675                 sortPairwiseMenuItem_actionPerformed(e);
 676               }
 677             });
 678     sortIDMenuItem.setText("by ID");
 679     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 680     {
 681       public void actionPerformed(ActionEvent e)
 682       {
 683         sortIDMenuItem_actionPerformed(e);
 684       }
 685     });
 686     sortLengthMenuItem.setText("By Length");
 687     sortLengthMenuItem
 688             .addActionListener(new java.awt.event.ActionListener()
 689             {
 690               public void actionPerformed(ActionEvent e)
 691               {
 692                 sortLengthMenuItem_actionPerformed(e);
 693               }
 694             });
 695     sortGroupMenuItem.setText("by Group");
 696     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 697     {
 698       public void actionPerformed(ActionEvent e)
 699       {
 700         sortGroupMenuItem_actionPerformed(e);
 701       }
 702     });
 703     removeRedundancyMenuItem.setText("Remove Redundancy...");
 704     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
 705             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
 706                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 707     removeRedundancyMenuItem
 708             .addActionListener(new java.awt.event.ActionListener()
 709             {
 710               public void actionPerformed(ActionEvent e)
 711               {
 712                 removeRedundancyMenuItem_actionPerformed(e);
 713               }
 714             });
 715     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
 716     pairwiseAlignmentMenuItem
 717             .addActionListener(new java.awt.event.ActionListener()
 718             {
 719               public void actionPerformed(ActionEvent e)
 720               {
 721                 pairwiseAlignmentMenuItem_actionPerformed(e);
 722               }
 723             });
 724     PCAMenuItem.setText("Principal Component Analysis");
 725     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 726     {
 727       public void actionPerformed(ActionEvent e)
 728       {
 729         PCAMenuItem_actionPerformed(e);
 730       }
 731     });
 732     averageDistanceTreeMenuItem
 733             .setText("Average Distance Using % Identity");
 734     averageDistanceTreeMenuItem
 735             .addActionListener(new java.awt.event.ActionListener()
 736             {
 737               public void actionPerformed(ActionEvent e)
 738               {
 739                 averageDistanceTreeMenuItem_actionPerformed(e);
 740               }
 741             });
 742     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
 743     neighbourTreeMenuItem
 744             .addActionListener(new java.awt.event.ActionListener()
 745             {
 746               public void actionPerformed(ActionEvent e)
 747               {
 748                 neighbourTreeMenuItem_actionPerformed(e);
 749               }
 750             });
 751     this.getContentPane().setLayout(borderLayout1);
 752     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 753     statusBar.setBackground(Color.white);
 754     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 755     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 756     statusBar.setText("Status bar");
 757     outputTextboxMenu.setText("Output to Textbox");
 758     clustalColour.setText("Clustalx");
 759
 760     clustalColour.addActionListener(new java.awt.event.ActionListener()
 761     {
 762       public void actionPerformed(ActionEvent e)
 763       {
 764         clustalColour_actionPerformed(e);
 765       }
 766     });
 767     zappoColour.setText("Zappo");
 768     zappoColour.addActionListener(new java.awt.event.ActionListener()
 769     {
 770       public void actionPerformed(ActionEvent e)
 771       {
 772         zappoColour_actionPerformed(e);
 773       }
 774     });
 775     taylorColour.setText("Taylor");
 776     taylorColour.addActionListener(new java.awt.event.ActionListener()
 777     {
 778       public void actionPerformed(ActionEvent e)
 779       {
 780         taylorColour_actionPerformed(e);
 781       }
 782     });
 783     hydrophobicityColour.setText("Hydrophobicity");
 784     hydrophobicityColour
 785             .addActionListener(new java.awt.event.ActionListener()
 786             {
 787               public void actionPerformed(ActionEvent e)
 788               {
 789                 hydrophobicityColour_actionPerformed(e);
 790               }
 791             });
 792     helixColour.setText("Helix Propensity");
 793     helixColour.addActionListener(new java.awt.event.ActionListener()
 794     {
 795       public void actionPerformed(ActionEvent e)
 796       {
 797         helixColour_actionPerformed(e);
 798       }
 799     });
 800     strandColour.setText("Strand Propensity");
 801     strandColour.addActionListener(new java.awt.event.ActionListener()
 802     {
 803       public void actionPerformed(ActionEvent e)
 804       {
 805         strandColour_actionPerformed(e);
 806       }
 807     });
 808     turnColour.setText("Turn Propensity");
 809     turnColour.addActionListener(new java.awt.event.ActionListener()
 810     {
 811       public void actionPerformed(ActionEvent e)
 812       {
 813         turnColour_actionPerformed(e);
 814       }
 815     });
 816     buriedColour.setText("Buried Index");
 817     buriedColour.addActionListener(new java.awt.event.ActionListener()
 818     {
 819       public void actionPerformed(ActionEvent e)
 820       {
 821         buriedColour_actionPerformed(e);
 822       }
 823     });
 824     userDefinedColour.setText("User Defined...");
 825     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 826     {
 827       public void actionPerformed(ActionEvent e)
 828       {
 829         userDefinedColour_actionPerformed(e);
 830       }
 831     });
 832     PIDColour.setText("Percentage Identity");
 833     PIDColour.addActionListener(new java.awt.event.ActionListener()
 834     {
 835       public void actionPerformed(ActionEvent e)
 836       {
 837         PIDColour_actionPerformed(e);
 838       }
 839     });
 840     BLOSUM62Colour.setText("BLOSUM62 Score");
 841     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 842     {
 843       public void actionPerformed(ActionEvent e)
 844       {
 845         BLOSUM62Colour_actionPerformed(e);
 846       }
 847     });
 848     avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
 849     avDistanceTreeBlosumMenuItem
 850             .addActionListener(new java.awt.event.ActionListener()
 851             {
 852               public void actionPerformed(ActionEvent e)
 853               {
 854                 avTreeBlosumMenuItem_actionPerformed(e);
 855               }
 856             });
 857     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
 858     njTreeBlosumMenuItem
 859             .addActionListener(new java.awt.event.ActionListener()
 860             {
 861               public void actionPerformed(ActionEvent e)
 862               {
 863                 njTreeBlosumMenuItem_actionPerformed(e);
 864               }
 865             });
 866     annotationPanelMenuItem.setActionCommand("");
 867     annotationPanelMenuItem.setText("Show Annotations");
 868     annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
 869             "SHOW_ANNOTATIONS", true));
 870     annotationPanelMenuItem
 871             .addActionListener(new java.awt.event.ActionListener()
 872             {
 873               public void actionPerformed(ActionEvent e)
 874               {
 875                 annotationPanelMenuItem_actionPerformed(e);
 876               }
 877             });
 878     colourTextMenuItem.setText("Colour Text");
 879     colourTextMenuItem
 880             .addActionListener(new java.awt.event.ActionListener()
 881             {
 882               public void actionPerformed(ActionEvent e)
 883               {
 884                 colourTextMenuItem_actionPerformed(e);
 885               }
 886             });
 887     htmlMenuItem.setText("HTML");
 888     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
 889     {
 890       public void actionPerformed(ActionEvent e)
 891       {
 892         htmlMenuItem_actionPerformed(e);
 893       }
 894     });
 895     overviewMenuItem.setText("Overview Window");
 896     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
 897     {
 898       public void actionPerformed(ActionEvent e)
 899       {
 900         overviewMenuItem_actionPerformed(e);
 901       }
 902     });
 903     undoMenuItem.setEnabled(false);
 904     undoMenuItem.setText("Undo");
 905     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 906             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
 907                     .getMenuShortcutKeyMask(), false));
 908     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
 909     {
 910       public void actionPerformed(ActionEvent e)
 911       {
 912         undoMenuItem_actionPerformed(e);
 913       }
 914     });
 915     redoMenuItem.setEnabled(false);
 916     redoMenuItem.setText("Redo");
 917     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 918             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
 919                     .getMenuShortcutKeyMask(), false));
 920     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
 921     {
 922       public void actionPerformed(ActionEvent e)
 923       {
 924         redoMenuItem_actionPerformed(e);
 925       }
 926     });
 927     conservationMenuItem.setText("By Conservation");
 928     conservationMenuItem
 929             .addActionListener(new java.awt.event.ActionListener()
 930             {
 931               public void actionPerformed(ActionEvent e)
 932               {
 933                 conservationMenuItem_actionPerformed(e);
 934               }
 935             });
 936     noColourmenuItem.setText("None");
 937     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 938     {
 939       public void actionPerformed(ActionEvent e)
 940       {
 941         noColourmenuItem_actionPerformed(e);
 942       }
 943     });
 944     wrapMenuItem.setText("Wrap");
 945     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
 946     {
 947       public void actionPerformed(ActionEvent e)
 948       {
 949         wrapMenuItem_actionPerformed(e);
 950       }
 951     });
 952     printMenuItem.setText("Print ...");
 953     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 954             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
 955                     .getMenuShortcutKeyMask(), false));
 956     printMenuItem.addActionListener(new java.awt.event.ActionListener()
 957     {
 958       public void actionPerformed(ActionEvent e)
 959       {
 960         printMenuItem_actionPerformed(e);
 961       }
 962     });
 963     renderGapsMenuItem.setText("Show Gaps");
 964     renderGapsMenuItem.setState(true);
 965     renderGapsMenuItem
 966             .addActionListener(new java.awt.event.ActionListener()
 967             {
 968               public void actionPerformed(ActionEvent e)
 969               {
 970                 renderGapsMenuItem_actionPerformed(e);
 971               }
 972             });
 973     findMenuItem.setText("Find...");
 974     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 975             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
 976                     .getMenuShortcutKeyMask(), false));
 977     findMenuItem.addActionListener(new java.awt.event.ActionListener()
 978     {
 979       public void actionPerformed(ActionEvent e)
 980       {
 981         findMenuItem_actionPerformed(e);
 982       }
 983     });
 984     abovePIDThreshold.setText("Above Identity Threshold");
 985     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
 986     {
 987       public void actionPerformed(ActionEvent e)
 988       {
 989         abovePIDThreshold_actionPerformed(e);
 990       }
 991     });
 992     showSeqFeatures.setText("Show Sequence Features");
 993     showSeqFeatures.addActionListener(new ActionListener()
 994     {
 995       public void actionPerformed(ActionEvent actionEvent)
 996       {
 997         showSeqFeatures_actionPerformed(actionEvent);
 998       }
 999     });
1000     /*
1001      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1002      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1003      * void actionPerformed(ActionEvent actionEvent) {
1004      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1005      */
1006     showDbRefsMenuitem.setText("Show Database Refs");
1007     showDbRefsMenuitem.addActionListener(new ActionListener()
1008     {
1009
1010       public void actionPerformed(ActionEvent e)
1011       {
1012         showDbRefs_actionPerformed(e);
1013       }
1014
1015     });
1016     showNpFeatsMenuitem.setText("Show Non-Positional Features");
1017     showNpFeatsMenuitem.addActionListener(new ActionListener()
1018     {
1019
1020       public void actionPerformed(ActionEvent e)
1021       {
1022         showNpFeats_actionPerformed(e);
1023       }
1024
1025     });
1026     showGroupConservation.setText("Group Conservation");
1027     showGroupConservation.addActionListener(new ActionListener()
1028     {
1029
1030       public void actionPerformed(ActionEvent e)
1031       {
1032         showGroupConservation_actionPerformed(e);
1033       }
1034
1035     });
1036
1037     showGroupConsensus.setText("Group Consensus");
1038     showGroupConsensus.addActionListener(new ActionListener()
1039     {
1040
1041       public void actionPerformed(ActionEvent e)
1042       {
1043         showGroupConsensus_actionPerformed(e);
1044       }
1045
1046     });
1047     showConsensusHistogram.setText("Show Consensus Histogram");
1048     showConsensusHistogram.addActionListener(new ActionListener()
1049     {
1050
1051       public void actionPerformed(ActionEvent e)
1052       {
1053         showConsensusHistogram_actionPerformed(e);
1054       }
1055
1056     });
1057     showSequenceLogo.setText("Show Consensus Logo");
1058     showSequenceLogo.addActionListener(new ActionListener()
1059     {
1060
1061       public void actionPerformed(ActionEvent e)
1062       {
1063         showSequenceLogo_actionPerformed(e);
1064       }
1065
1066     });
1067     applyAutoAnnotationSettings.setText("Apply to all groups");
1068     applyAutoAnnotationSettings.setState(false);
1069     applyAutoAnnotationSettings.setVisible(true);
1070     applyAutoAnnotationSettings.addActionListener(new ActionListener()
1071     {
1072
1073       public void actionPerformed(ActionEvent e)
1074       {
1075         applyAutoAnnotationSettings_actionPerformed(e);
1076       }
1077
1078     });
1079
1080     nucleotideColour.setText("Nucleotide");
1081     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1082     {
1083       public void actionPerformed(ActionEvent e)
1084       {
1085         nucleotideColour_actionPerformed(e);
1086       }
1087     });
1088     deleteGroups.setText("Undefine groups");
1089     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1090             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1091                     .getMenuShortcutKeyMask(), false));
1092     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1093     {
1094       public void actionPerformed(ActionEvent e)
1095       {
1096         deleteGroups_actionPerformed(e);
1097       }
1098     });
1099     copy.setText("Copy");
1100     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1101             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1102                     .getMenuShortcutKeyMask(), false));
1103
1104     copy.addActionListener(new java.awt.event.ActionListener()
1105     {
1106       public void actionPerformed(ActionEvent e)
1107       {
1108         copy_actionPerformed(e);
1109       }
1110     });
1111     cut.setText("Cut");
1112     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1113             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1114                     .getMenuShortcutKeyMask(), false));
1115     cut.addActionListener(new java.awt.event.ActionListener()
1116     {
1117       public void actionPerformed(ActionEvent e)
1118       {
1119         cut_actionPerformed(e);
1120       }
1121     });
1122     delete.setText("Delete");
1123     delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1124             java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1125     delete.addActionListener(new java.awt.event.ActionListener()
1126     {
1127       public void actionPerformed(ActionEvent e)
1128       {
1129         delete_actionPerformed(e);
1130       }
1131     });
1132     pasteMenu.setText("Paste");
1133     pasteNew.setText("To New Alignment");
1134     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1135             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1136                     .getMenuShortcutKeyMask()
1137                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1138     pasteNew.addActionListener(new java.awt.event.ActionListener()
1139     {
1140       public void actionPerformed(ActionEvent e)
1141       {
1142         pasteNew_actionPerformed(e);
1143       }
1144     });
1145     pasteThis.setText("Add To This Alignment");
1146     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1147             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1148                     .getMenuShortcutKeyMask(), false));
1149     pasteThis.addActionListener(new java.awt.event.ActionListener()
1150     {
1151       public void actionPerformed(ActionEvent e)
1152       {
1153         pasteThis_actionPerformed(e);
1154       }
1155     });
1156     applyToAllGroups.setText("Apply Colour To All Groups");
1157     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1158     {
1159       public void actionPerformed(ActionEvent e)
1160       {
1161         applyToAllGroups_actionPerformed(e);
1162       }
1163     });
1164     createPNG.addActionListener(new java.awt.event.ActionListener()
1165     {
1166       public void actionPerformed(ActionEvent e)
1167       {
1168         createPNG(null);
1169       }
1170     });
1171     createPNG.setActionCommand("Save As PNG Image");
1172     createPNG.setText("PNG");
1173     font.setText("Font...");
1174     font.addActionListener(new java.awt.event.ActionListener()
1175     {
1176       public void actionPerformed(ActionEvent e)
1177       {
1178         font_actionPerformed(e);
1179       }
1180     });
1181
1182     seqLimits.setText("Show Sequence Limits");
1183     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1184     seqLimits.addActionListener(new java.awt.event.ActionListener()
1185     {
1186       public void actionPerformed(ActionEvent e)
1187       {
1188         seqLimit_actionPerformed(e);
1189       }
1190     });
1191     epsFile.setText("EPS");
1192     epsFile.addActionListener(new java.awt.event.ActionListener()
1193     {
1194       public void actionPerformed(ActionEvent e)
1195       {
1196         createEPS(null);
1197       }
1198     });
1199     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1200     LoadtreeMenuItem.setText("Load Associated Tree");
1201     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1202     {
1203       public void actionPerformed(ActionEvent e)
1204       {
1205         LoadtreeMenuItem_actionPerformed(e);
1206       }
1207     });
1208     scaleAbove.setVisible(false);
1209     scaleAbove.setText("Scale Above");
1210     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1211     {
1212       public void actionPerformed(ActionEvent e)
1213       {
1214         scaleAbove_actionPerformed(e);
1215       }
1216     });
1217     scaleLeft.setVisible(false);
1218     scaleLeft.setSelected(true);
1219     scaleLeft.setText("Scale Left");
1220     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1221     {
1222       public void actionPerformed(ActionEvent e)
1223       {
1224         scaleLeft_actionPerformed(e);
1225       }
1226     });
1227     scaleRight.setVisible(false);
1228     scaleRight.setSelected(true);
1229     scaleRight.setText("Scale Right");
1230     scaleRight.addActionListener(new java.awt.event.ActionListener()
1231     {
1232       public void actionPerformed(ActionEvent e)
1233       {
1234         scaleRight_actionPerformed(e);
1235       }
1236     });
1237     centreColumnLabelsMenuItem.setVisible(true);
1238     centreColumnLabelsMenuItem.setState(false);
1239     centreColumnLabelsMenuItem.setText("Centre Column Labels");
1240     centreColumnLabelsMenuItem
1241             .addActionListener(new java.awt.event.ActionListener()
1242             {
1243               public void actionPerformed(ActionEvent e)
1244               {
1245                 centreColumnLabels_actionPerformed(e);
1246               }
1247             });
1248     followHighlightMenuItem.setVisible(true);
1249     followHighlightMenuItem.setState(true);
1250     followHighlightMenuItem.setText("Automatic Scrolling");
1251     followHighlightMenuItem.addActionListener(new ActionListener()
1252     {
1253
1254       public void actionPerformed(ActionEvent e)
1255       {
1256         followHighlight_actionPerformed();
1257       }
1258
1259     });
1260
1261     modifyPID.setText("Modify Identity Threshold...");
1262     modifyPID.addActionListener(new java.awt.event.ActionListener()
1263     {
1264       public void actionPerformed(ActionEvent e)
1265       {
1266         modifyPID_actionPerformed(e);
1267       }
1268     });
1269     modifyConservation.setText("Modify Conservation Threshold...");
1270     modifyConservation
1271             .addActionListener(new java.awt.event.ActionListener()
1272             {
1273               public void actionPerformed(ActionEvent e)
1274               {
1275                 modifyConservation_actionPerformed(e);
1276               }
1277             });
1278     sortByTreeMenu.setText("By Tree Order");
1279     sort.setText("Sort");
1280     sort.addMenuListener(new MenuListener()
1281     {
1282       public void menuSelected(MenuEvent e)
1283       {
1284         buildTreeMenu();
1285       }
1286
1287       public void menuDeselected(MenuEvent e)
1288       {
1289       }
1290
1291       public void menuCanceled(MenuEvent e)
1292       {
1293       }
1294     });
1295     sortByAnnotScore.setText("by Score");
1296     sort.add(sortByAnnotScore);
1297     sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1298     {
1299
1300       public void menuCanceled(MenuEvent e)
1301       {
1302       }
1303
1304       public void menuDeselected(MenuEvent e)
1305       {
1306       }
1307
1308       public void menuSelected(MenuEvent e)
1309       {
1310         buildSortByAnnotationScoresMenu();
1311       }
1312     });
1313     sortByAnnotScore.setVisible(false);
1314
1315     calculateTree.setText("Calculate Tree");
1316
1317     jMenu2.setText("Export Image");
1318     padGapsMenuitem.setText("Pad Gaps");
1319     padGapsMenuitem.setState(jalview.bin.Cache
1320             .getDefault("PAD_GAPS", false));
1321     padGapsMenuitem.addActionListener(new ActionListener()
1322     {
1323       public void actionPerformed(ActionEvent e)
1324       {
1325         padGapsMenuitem_actionPerformed(e);
1326       }
1327     });
1328     vamsasStore.setVisible(false);
1329     vamsasStore.setText("VAMSAS store");
1330     vamsasStore.addActionListener(new ActionListener()
1331     {
1332       public void actionPerformed(ActionEvent e)
1333       {
1334         vamsasStore_actionPerformed(e);
1335       }
1336     });
1337     showTranslation.setText("Translate cDNA");
1338     showTranslation.addActionListener(new ActionListener()
1339     {
1340       public void actionPerformed(ActionEvent e)
1341       {
1342         showTranslation_actionPerformed(e);
1343       }
1344     });
1345     extractScores.setText("Extract Scores...");
1346     extractScores.addActionListener(new ActionListener()
1347     {
1348       public void actionPerformed(ActionEvent e)
1349       {
1350         extractScores_actionPerformed(e);
1351       }
1352     });
1353     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1354     // score extraction
1355     showProducts.setText("Get Cross References");
1356     /*
1357      * showProducts.addActionListener(new ActionListener() {
1358      *
1359      * public void actionPerformed(ActionEvent e) {
1360      * showProducts_actionPerformed(e); } });
1361      */
1362     featureSettings.setText("Feature Settings...");
1363     featureSettings.addActionListener(new ActionListener()
1364     {
1365       public void actionPerformed(ActionEvent e)
1366       {
1367         featureSettings_actionPerformed(e);
1368       }
1369     });
1370     fetchSequence.setText("Fetch Sequence(s)...");
1371     fetchSequence.addActionListener(new ActionListener()
1372     {
1373       public void actionPerformed(ActionEvent e)
1374       {
1375         fetchSequence_actionPerformed(e);
1376       }
1377     });
1378
1379     annotationColour.setText("By Annotation...");
1380     annotationColour.addActionListener(new ActionListener()
1381     {
1382       public void actionPerformed(ActionEvent e)
1383       {
1384         annotationColour_actionPerformed(e);
1385       }
1386     });
1387     associatedData.setText("Load Features / Annotations");
1388     associatedData.addActionListener(new ActionListener()
1389     {
1390       public void actionPerformed(ActionEvent e)
1391       {
1392         associatedData_actionPerformed(e);
1393       }
1394     });
1395     autoCalculate.setText("Autocalculate Consensus");
1396     autoCalculate.setState(jalview.bin.Cache.getDefault(
1397             "AUTO_CALC_CONSENSUS", true));
1398     autoCalculate.addActionListener(new ActionListener()
1399     {
1400       public void actionPerformed(ActionEvent e)
1401       {
1402         autoCalculate_actionPerformed(e);
1403       }
1404     });
1405     addSequenceMenu.setText("Add Sequences");
1406     addFromFile.setText("From File");
1407     addFromFile.addActionListener(new ActionListener()
1408     {
1409       public void actionPerformed(ActionEvent e)
1410       {
1411         addFromFile_actionPerformed(e);
1412       }
1413     });
1414     addFromText.setText("From Textbox");
1415     addFromText.addActionListener(new ActionListener()
1416     {
1417       public void actionPerformed(ActionEvent e)
1418       {
1419         addFromText_actionPerformed(e);
1420       }
1421     });
1422     addFromURL.setText("From URL");
1423     addFromURL.addActionListener(new ActionListener()
1424     {
1425       public void actionPerformed(ActionEvent e)
1426       {
1427         addFromURL_actionPerformed(e);
1428       }
1429     });
1430     exportFeatures.setText("Export Features...");
1431     exportFeatures.addActionListener(new ActionListener()
1432     {
1433       public void actionPerformed(ActionEvent e)
1434       {
1435         exportFeatures_actionPerformed(e);
1436       }
1437     });
1438     exportAnnotations.setText("Export Annotations...");
1439     exportAnnotations.addActionListener(new ActionListener()
1440     {
1441       public void actionPerformed(ActionEvent e)
1442       {
1443         exportAnnotations_actionPerformed(e);
1444       }
1445     });
1446     statusPanel.setLayout(gridLayout1);
1447     jMenu3.setText("Show");
1448     showAllSeqs.setText("All Sequences");
1449     showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1450     showAllSeqs.addActionListener(new ActionListener()
1451     {
1452       public void actionPerformed(ActionEvent e)
1453       {
1454         showAllSeqs_actionPerformed(e);
1455       }
1456     });
1457     showAllColumns.setText("All Columns");
1458     showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1459     showAllColumns.addActionListener(new ActionListener()
1460     {
1461       public void actionPerformed(ActionEvent e)
1462       {
1463         showAllColumns_actionPerformed(e);
1464       }
1465     });
1466     hideMenu.setText("Hide");
1467     hideSelSequences.setText("Selected Sequences");
1468     hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1469     hideSelSequences.addActionListener(new ActionListener()
1470     {
1471       public void actionPerformed(ActionEvent e)
1472       {
1473         hideSelSequences_actionPerformed(e);
1474       }
1475     });
1476     hideSelColumns.setText("Selected Columns");
1477     hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1478     hideSelColumns.addActionListener(new ActionListener()
1479     {
1480       public void actionPerformed(ActionEvent e)
1481       {
1482         hideSelColumns_actionPerformed(e);
1483       }
1484     });
1485     hideAllSelection.setText("Selected Region");
1486     hideAllSelection.addActionListener(new ActionListener()
1487     {
1488       public void actionPerformed(ActionEvent e)
1489       {
1490         hideAllSelection_actionPerformed(e);
1491       }
1492     });
1493     // TODO: should be hidden if no selection exists.
1494     hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
1495     hideAllButSelection.addActionListener(new ActionListener()
1496     {
1497       public void actionPerformed(ActionEvent e)
1498       {
1499         hideAllButSelection_actionPerformed(e);
1500       }
1501     });
1502     showAllhidden.setText("All Sequences and Columns");
1503     showAllhidden
1504             .setToolTipText("H toggles visibility of hidden or selected regions.");
1505     showAllhidden.addActionListener(new ActionListener()
1506     {
1507       public void actionPerformed(ActionEvent e)
1508       {
1509         showAllhidden_actionPerformed(e);
1510       }
1511     });
1512
1513     hiddenMarkers.setText("Show Hidden Markers");
1514     hiddenMarkers.addActionListener(new ActionListener()
1515     {
1516       public void actionPerformed(ActionEvent e)
1517       {
1518         hiddenMarkers_actionPerformed(e);
1519       }
1520     });
1521     invertColSel.setText("Invert Column Selection");
1522     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1523             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1524                     .getMenuShortcutKeyMask()
1525                     | java.awt.event.KeyEvent.ALT_MASK, false));
1526     invertColSel.addActionListener(new ActionListener()
1527     {
1528       public void actionPerformed(ActionEvent e)
1529       {
1530         invertColSel_actionPerformed(e);
1531       }
1532     });
1533     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1534     {
1535       public void stateChanged(ChangeEvent evt)
1536       {
1537         JTabbedPane pane = (JTabbedPane) evt.getSource();
1538         int sel = pane.getSelectedIndex();
1539         tabSelectionChanged(sel);
1540       }
1541     });
1542     tabbedPane.addMouseListener(new MouseAdapter()
1543     {
1544       public void mousePressed(MouseEvent e)
1545       {
1546         tabbedPane_mousePressed(e);
1547       }
1548     });
1549     tabbedPane.addFocusListener(new FocusAdapter()
1550     {
1551       public void focusGained(FocusEvent e)
1552       {
1553         tabbedPane_focusGained(e);
1554       }
1555     });
1556     save.setText("Save");
1557     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1558             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1559                     .getMenuShortcutKeyMask(), false));
1560     save.addActionListener(new ActionListener()
1561     {
1562       public void actionPerformed(ActionEvent e)
1563       {
1564         save_actionPerformed(e);
1565       }
1566     });
1567     reload.setEnabled(false);
1568     reload.setText("Reload");
1569     reload.addActionListener(new ActionListener()
1570     {
1571       public void actionPerformed(ActionEvent e)
1572       {
1573         reload_actionPerformed(e);
1574       }
1575     });
1576     newView.setText("New View");
1577     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1578             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1579                     .getMenuShortcutKeyMask(), false));
1580     newView.addActionListener(new ActionListener()
1581     {
1582       public void actionPerformed(ActionEvent e)
1583       {
1584         newView_actionPerformed(e);
1585       }
1586     });
1587     tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1588             + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1589     textColour.setText("Colour Text ...");
1590     textColour.addActionListener(new ActionListener()
1591     {
1592       public void actionPerformed(ActionEvent e)
1593       {
1594         textColour_actionPerformed(e);
1595       }
1596     });
1597     formatMenu.setText("Format");
1598     selectMenu.setText("Select");
1599     idRightAlign.setText("Right Align Sequence Id");
1600     idRightAlign.addActionListener(new ActionListener()
1601     {
1602       public void actionPerformed(ActionEvent e)
1603       {
1604         idRightAlign_actionPerformed(e);
1605       }
1606     });
1607     gatherViews.setEnabled(false);
1608     gatherViews.setText("Gather Views");
1609     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1610             java.awt.event.KeyEvent.VK_G, 0, false));
1611     gatherViews.addActionListener(new ActionListener()
1612     {
1613       public void actionPerformed(ActionEvent e)
1614       {
1615         gatherViews_actionPerformed(e);
1616       }
1617     });
1618     expandViews.setEnabled(false);
1619     expandViews.setText("Expand Views");
1620     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1621             java.awt.event.KeyEvent.VK_X, 0, false));
1622     expandViews.addActionListener(new ActionListener()
1623     {
1624       public void actionPerformed(ActionEvent e)
1625       {
1626         expandViews_actionPerformed(e);
1627       }
1628     });
1629     pageSetup.setText("Page Setup ...");
1630     pageSetup.addActionListener(new ActionListener()
1631     {
1632       public void actionPerformed(ActionEvent e)
1633       {
1634         pageSetup_actionPerformed(e);
1635       }
1636     });
1637     alignmentProperties.setText("Alignment Properties...");
1638     alignmentProperties.addActionListener(new ActionListener()
1639     {
1640       public void actionPerformed(ActionEvent actionEvent)
1641       {
1642         alignmentProperties();
1643       }
1644     });
1645     tooltipSettingsMenu.setText("Sequence ID Tooltip");
1646     autoAnnMenu.setText("Autocalculated Annotation");
1647     alignFrameMenuBar.add(fileMenu);
1648     alignFrameMenuBar.add(editMenu);
1649     alignFrameMenuBar.add(selectMenu);
1650     alignFrameMenuBar.add(viewMenu);
1651     alignFrameMenuBar.add(formatMenu);
1652     alignFrameMenuBar.add(colourMenu);
1653     alignFrameMenuBar.add(calculateMenu);
1654     alignFrameMenuBar.add(webService);
1655     fileMenu.add(fetchSequence);
1656     fileMenu.add(addSequenceMenu);
1657     fileMenu.add(reload);
1658     fileMenu.addSeparator();
1659     fileMenu.add(vamsasStore);
1660     fileMenu.add(save);
1661     fileMenu.add(saveAs);
1662     fileMenu.add(outputTextboxMenu);
1663     fileMenu.add(pageSetup);
1664     fileMenu.add(printMenuItem);
1665     fileMenu.addSeparator();
1666     fileMenu.add(jMenu2);
1667     fileMenu.add(exportFeatures);
1668     fileMenu.add(exportAnnotations);
1669     fileMenu.add(LoadtreeMenuItem);
1670     fileMenu.add(associatedData);
1671     fileMenu.addSeparator();
1672     fileMenu.add(closeMenuItem);
1673     editMenu.add(undoMenuItem);
1674     editMenu.add(redoMenuItem);
1675     editMenu.add(cut);
1676     editMenu.add(copy);
1677     editMenu.add(pasteMenu);
1678     editMenu.add(delete);
1679     editMenu.addSeparator();
1680     editMenu.add(remove2LeftMenuItem);
1681     editMenu.add(remove2RightMenuItem);
1682     editMenu.add(removeGappedColumnMenuItem);
1683     editMenu.add(removeAllGapsMenuItem);
1684     editMenu.add(removeRedundancyMenuItem);
1685     editMenu.addSeparator();
1686     // dont add these yet in the CVS build - they cannot be undone!
1687     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1688     // editMenu.add(justifyLeftMenuItem);
1689     // editMenu.add(justifyRightMenuItem);
1690     // editMenu.addSeparator();
1691     editMenu.add(padGapsMenuitem);
1692     viewMenu.add(newView);
1693     viewMenu.add(expandViews);
1694     viewMenu.add(gatherViews);
1695     viewMenu.addSeparator();
1696     viewMenu.add(jMenu3);
1697     viewMenu.add(hideMenu);
1698     viewMenu.addSeparator();
1699     viewMenu.add(followHighlightMenuItem);
1700     viewMenu.add(annotationPanelMenuItem);
1701     autoAnnMenu.add(applyAutoAnnotationSettings);
1702     autoAnnMenu.add(showConsensusHistogram);
1703     autoAnnMenu.add(showSequenceLogo);
1704     autoAnnMenu.addSeparator();
1705     autoAnnMenu.add(showGroupConservation);
1706     autoAnnMenu.add(showGroupConsensus);
1707     viewMenu.add(autoAnnMenu);
1708     viewMenu.addSeparator();
1709     viewMenu.add(showSeqFeatures);
1710     // viewMenu.add(showSeqFeaturesHeight);
1711
1712     viewMenu.add(featureSettings);
1713     tooltipSettingsMenu.add(showDbRefsMenuitem);
1714     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1715     viewMenu.add(tooltipSettingsMenu);
1716     viewMenu.addSeparator();
1717     viewMenu.add(alignmentProperties);
1718     viewMenu.addSeparator();
1719     viewMenu.add(overviewMenuItem);
1720     colourMenu.add(applyToAllGroups);
1721     colourMenu.add(textColour);
1722     colourMenu.addSeparator();
1723     colourMenu.add(noColourmenuItem);
1724     colourMenu.add(clustalColour);
1725     colourMenu.add(BLOSUM62Colour);
1726     colourMenu.add(PIDColour);
1727     colourMenu.add(zappoColour);
1728     colourMenu.add(taylorColour);
1729     colourMenu.add(hydrophobicityColour);
1730     colourMenu.add(helixColour);
1731     colourMenu.add(strandColour);
1732     colourMenu.add(turnColour);
1733     colourMenu.add(buriedColour);
1734     colourMenu.add(nucleotideColour);
1735     colourMenu.add(userDefinedColour);
1736     colourMenu.addSeparator();
1737     colourMenu.add(conservationMenuItem);
1738     colourMenu.add(modifyConservation);
1739     colourMenu.add(abovePIDThreshold);
1740     colourMenu.add(modifyPID);
1741     colourMenu.add(annotationColour);
1742     calculateMenu.add(sort);
1743     calculateMenu.add(calculateTree);
1744     calculateMenu.addSeparator();
1745     calculateMenu.add(pairwiseAlignmentMenuItem);
1746     calculateMenu.add(PCAMenuItem);
1747     calculateMenu.addSeparator();
1748     calculateMenu.add(showTranslation);
1749     calculateMenu.add(showProducts);
1750     calculateMenu.add(autoCalculate);
1751     calculateMenu.addSeparator();
1752     calculateMenu.add(extractScores);
1753     webServiceNoServices = new JMenuItem("<No Services>");
1754     webService.add(webServiceNoServices);
1755     pasteMenu.add(pasteNew);
1756     pasteMenu.add(pasteThis);
1757     sort.add(sortIDMenuItem);
1758     sort.add(sortLengthMenuItem);
1759     sort.add(sortGroupMenuItem);
1760     sort.add(sortPairwiseMenuItem);
1761     sort.add(sortByTreeMenu);
1762     calculateTree.add(averageDistanceTreeMenuItem);
1763     calculateTree.add(neighbourTreeMenuItem);
1764     calculateTree.add(avDistanceTreeBlosumMenuItem);
1765     calculateTree.add(njTreeBlosumMenuItem);
1766     jMenu2.add(htmlMenuItem);
1767     jMenu2.add(epsFile);
1768     jMenu2.add(createPNG);
1769     addSequenceMenu.add(addFromFile);
1770     addSequenceMenu.add(addFromText);
1771     addSequenceMenu.add(addFromURL);
1772     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1773     statusPanel.add(statusBar, null);
1774     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1775     jMenu3.add(showAllColumns);
1776     jMenu3.add(showAllSeqs);
1777     jMenu3.add(showAllhidden);
1778     hideMenu.add(hideSelColumns);
1779     hideMenu.add(hideSelSequences);
1780     hideMenu.add(hideAllSelection);
1781     hideMenu.add(hideAllButSelection);
1782
1783     formatMenu.add(font);
1784     formatMenu.addSeparator();
1785     formatMenu.add(wrapMenuItem);
1786     formatMenu.add(scaleAbove);
1787     formatMenu.add(scaleLeft);
1788     formatMenu.add(scaleRight);
1789     formatMenu.add(seqLimits);
1790     formatMenu.add(idRightAlign);
1791     formatMenu.add(hiddenMarkers);
1792     formatMenu.add(viewBoxesMenuItem);
1793     formatMenu.add(viewTextMenuItem);
1794     formatMenu.add(colourTextMenuItem);
1795     formatMenu.add(renderGapsMenuItem);
1796     formatMenu.add(centreColumnLabelsMenuItem);
1797     formatMenu.add(showUnconservedMenuItem);
1798     selectMenu.add(findMenuItem);
1799     selectMenu.addSeparator();
1800     selectMenu.add(selectAllSequenceMenuItem);
1801     selectMenu.add(deselectAllSequenceMenuItem);
1802     selectMenu.add(invertSequenceMenuItem);
1803     selectMenu.add(invertColSel);
1804     selectMenu.add(deleteGroups);
1805     selectMenu.add(grpsFromSelection);
1806   }
1807
1808   protected void showAllhidden_actionPerformed(ActionEvent e)
1809   {
1810     // TODO Auto-generated method stub
1811
1812   }
1813
1814   protected void hideAllButSelection_actionPerformed(ActionEvent e)
1815   {
1816     // TODO Auto-generated method stub
1817
1818   }
1819
1820   protected void hideAllSelection_actionPerformed(ActionEvent e)
1821   {
1822     // TODO Auto-generated method stub
1823
1824   }
1825
1826   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
1827   {
1828     // TODO Auto-generated method stub
1829
1830   }
1831
1832   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
1833   {
1834     // TODO Auto-generated method stub
1835
1836   }
1837
1838   protected void showSequenceLogo_actionPerformed(ActionEvent e)
1839   {
1840     // TODO Auto-generated method stub
1841
1842   }
1843
1844   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
1845   {
1846     // TODO Auto-generated method stub
1847
1848   }
1849
1850   protected void showGroupConsensus_actionPerformed(ActionEvent e)
1851   {
1852     // TODO Auto-generated method stub
1853
1854   }
1855
1856   protected void showGroupConservation_actionPerformed(ActionEvent e)
1857   {
1858     // TODO Auto-generated method stub
1859
1860   }
1861
1862   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
1863   {
1864     // TODO Auto-generated method stub
1865
1866   }
1867
1868   protected void showSeqFeaturesHeight_actionPerformed(
1869           ActionEvent actionEvent)
1870   {
1871     // TODO Auto-generated method stub
1872
1873   }
1874
1875   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
1876   {
1877     // TODO Auto-generated method stub
1878
1879   }
1880
1881   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
1882   {
1883     // TODO Auto-generated method stub
1884
1885   }
1886
1887   protected void followHighlight_actionPerformed()
1888   {
1889     // TODO Auto-generated method stub
1890
1891   }
1892
1893   protected void showNpFeats_actionPerformed(ActionEvent e)
1894   {
1895     // TODO Auto-generated method stub
1896
1897   }
1898
1899   protected void showDbRefs_actionPerformed(ActionEvent e)
1900   {
1901     // TODO Auto-generated method stub
1902
1903   }
1904
1905   protected void centreColumnLabels_actionPerformed(ActionEvent e)
1906   {
1907   }
1908
1909   protected void showProducts_actionPerformed(ActionEvent e)
1910   {
1911   }
1912
1913   protected void buildSortByAnnotationScoresMenu()
1914   {
1915   }
1916
1917   protected void extractScores_actionPerformed(ActionEvent e)
1918   {
1919   }
1920
1921   protected void outputText_actionPerformed(ActionEvent e)
1922   {
1923   }
1924
1925   public void addFromFile_actionPerformed(ActionEvent e)
1926   {
1927
1928   }
1929
1930   public void addFromText_actionPerformed(ActionEvent e)
1931   {
1932
1933   }
1934
1935   public void addFromURL_actionPerformed(ActionEvent e)
1936   {
1937
1938   }
1939
1940   public void exportFeatures_actionPerformed(ActionEvent e)
1941   {
1942
1943   }
1944
1945   public void exportAnnotations_actionPerformed(ActionEvent e)
1946   {
1947
1948   }
1949
1950   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1951   {
1952   }
1953
1954   protected void closeMenuItem_actionPerformed(boolean b)
1955   {
1956   }
1957
1958   protected void redoMenuItem_actionPerformed(ActionEvent e)
1959   {
1960   }
1961
1962   protected void undoMenuItem_actionPerformed(ActionEvent e)
1963   {
1964   }
1965
1966   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1967   {
1968   }
1969
1970   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1971   {
1972   }
1973
1974   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1975   {
1976   }
1977
1978   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1979   {
1980   }
1981
1982   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
1983   {
1984   }
1985
1986   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1987   {
1988   }
1989
1990   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1991   {
1992   }
1993
1994   protected void wrapMenuItem_actionPerformed(ActionEvent e)
1995   {
1996   }
1997
1998   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1999   {
2000   }
2001
2002   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2003   {
2004   }
2005
2006   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2007   {
2008   }
2009
2010   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2011   {
2012   }
2013
2014   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2015   {
2016   }
2017
2018   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2019   {
2020   }
2021
2022   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2023   {
2024   }
2025
2026   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2027   {
2028   }
2029
2030   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2031   {
2032   }
2033
2034   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2035   {
2036   }
2037
2038   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2039   {
2040   }
2041
2042   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2043   {
2044   }
2045
2046   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2047   {
2048   }
2049
2050   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2051   {
2052   }
2053
2054   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2055   {
2056   }
2057
2058   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2059   {
2060   }
2061
2062   protected void clustalColour_actionPerformed(ActionEvent e)
2063   {
2064   }
2065
2066   protected void zappoColour_actionPerformed(ActionEvent e)
2067   {
2068   }
2069
2070   protected void taylorColour_actionPerformed(ActionEvent e)
2071   {
2072   }
2073
2074   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2075   {
2076   }
2077
2078   protected void helixColour_actionPerformed(ActionEvent e)
2079   {
2080   }
2081
2082   protected void strandColour_actionPerformed(ActionEvent e)
2083   {
2084   }
2085
2086   protected void turnColour_actionPerformed(ActionEvent e)
2087   {
2088   }
2089
2090   protected void buriedColour_actionPerformed(ActionEvent e)
2091   {
2092   }
2093
2094   protected void userDefinedColour_actionPerformed(ActionEvent e)
2095   {
2096   }
2097
2098   protected void PIDColour_actionPerformed(ActionEvent e)
2099   {
2100   }
2101
2102   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2103   {
2104   }
2105
2106   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2107   {
2108   }
2109
2110   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2111   {
2112   }
2113
2114   protected void printMenuItem_actionPerformed(ActionEvent e)
2115   {
2116   }
2117
2118   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2119   {
2120   }
2121
2122   protected void findMenuItem_actionPerformed(ActionEvent e)
2123   {
2124   }
2125
2126   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2127   {
2128   }
2129
2130   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2131   {
2132   }
2133
2134   protected void nucleotideColour_actionPerformed(ActionEvent e)
2135   {
2136   }
2137
2138   protected void deleteGroups_actionPerformed(ActionEvent e)
2139   {
2140   }
2141
2142   protected void copy_actionPerformed(ActionEvent e)
2143   {
2144   }
2145
2146   protected void cut_actionPerformed(ActionEvent e)
2147   {
2148   }
2149
2150   protected void delete_actionPerformed(ActionEvent e)
2151   {
2152   }
2153
2154   protected void pasteNew_actionPerformed(ActionEvent e)
2155   {
2156   }
2157
2158   protected void pasteThis_actionPerformed(ActionEvent e)
2159   {
2160   }
2161
2162   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2163   {
2164   }
2165
2166   public void createPNG(java.io.File f)
2167   {
2168   }
2169
2170   protected void font_actionPerformed(ActionEvent e)
2171   {
2172   }
2173
2174   protected void seqLimit_actionPerformed(ActionEvent e)
2175   {
2176   }
2177
2178   public void seqDBRef_actionPerformed(ActionEvent e)
2179   {
2180
2181   }
2182
2183   public void createEPS(java.io.File f)
2184   {
2185   }
2186
2187   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2188   {
2189   }
2190
2191   protected void jpred_actionPerformed(ActionEvent e)
2192   {
2193   }
2194
2195   protected void scaleAbove_actionPerformed(ActionEvent e)
2196   {
2197   }
2198
2199   protected void scaleLeft_actionPerformed(ActionEvent e)
2200   {
2201   }
2202
2203   protected void scaleRight_actionPerformed(ActionEvent e)
2204   {
2205   }
2206
2207   protected void modifyPID_actionPerformed(ActionEvent e)
2208   {
2209   }
2210
2211   protected void modifyConservation_actionPerformed(ActionEvent e)
2212   {
2213   }
2214
2215   protected void saveAs_actionPerformed(ActionEvent e)
2216   {
2217   }
2218
2219   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2220   {
2221   }
2222
2223   public void vamsasStore_actionPerformed(ActionEvent e)
2224   {
2225
2226   }
2227
2228   public void vamsasLoad_actionPerformed(ActionEvent e)
2229   {
2230
2231   }
2232
2233   public void showTranslation_actionPerformed(ActionEvent e)
2234   {
2235
2236   }
2237
2238   public void featureSettings_actionPerformed(ActionEvent e)
2239   {
2240
2241   }
2242
2243   public void fetchSequence_actionPerformed(ActionEvent e)
2244   {
2245
2246   }
2247
2248   public void smoothFont_actionPerformed(ActionEvent e)
2249   {
2250
2251   }
2252
2253   public void annotationColour_actionPerformed(ActionEvent e)
2254   {
2255
2256   }
2257
2258   public void associatedData_actionPerformed(ActionEvent e)
2259   {
2260
2261   }
2262
2263   public void autoCalculate_actionPerformed(ActionEvent e)
2264   {
2265
2266   }
2267
2268   public void showAllSeqs_actionPerformed(ActionEvent e)
2269   {
2270
2271   }
2272
2273   public void showAllColumns_actionPerformed(ActionEvent e)
2274   {
2275
2276   }
2277
2278   public void hideSelSequences_actionPerformed(ActionEvent e)
2279   {
2280
2281   }
2282
2283   public void hideSelColumns_actionPerformed(ActionEvent e)
2284   {
2285
2286   }
2287
2288   public void hiddenMarkers_actionPerformed(ActionEvent e)
2289   {
2290
2291   }
2292
2293   public void findPdbId_actionPerformed(ActionEvent e)
2294   {
2295
2296   }
2297
2298   public void enterPdbId_actionPerformed(ActionEvent e)
2299   {
2300
2301   }
2302
2303   public void pdbFile_actionPerformed(ActionEvent e)
2304   {
2305
2306   }
2307
2308   public void invertColSel_actionPerformed(ActionEvent e)
2309   {
2310
2311   }
2312
2313   public void tabSelectionChanged(int sel)
2314   {
2315
2316   }
2317
2318   public void tabbedPane_mousePressed(MouseEvent e)
2319   {
2320
2321   }
2322
2323   public void tabbedPane_focusGained(FocusEvent e)
2324   {
2325     requestFocus();
2326   }
2327
2328   public void save_actionPerformed(ActionEvent e)
2329   {
2330
2331   }
2332
2333   public void reload_actionPerformed(ActionEvent e)
2334   {
2335
2336   }
2337
2338   public void newView_actionPerformed(ActionEvent e)
2339   {
2340
2341   }
2342
2343   public void textColour_actionPerformed(ActionEvent e)
2344   {
2345
2346   }
2347
2348   public void idRightAlign_actionPerformed(ActionEvent e)
2349   {
2350
2351   }
2352
2353   public void expandViews_actionPerformed(ActionEvent e)
2354   {
2355
2356   }
2357
2358   public void gatherViews_actionPerformed(ActionEvent e)
2359   {
2360
2361   }
2362
2363   public void buildTreeMenu()
2364   {
2365
2366   }
2367
2368   public void pageSetup_actionPerformed(ActionEvent e)
2369   {
2370
2371   }
2372
2373   public void alignmentProperties()
2374   {
2375
2376   }
2377 }