src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
   3  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.jbgui;
  19
  20 import java.awt.*;
  21 import java.awt.event.*;
  22
  23 import javax.swing.*;
  24 import javax.swing.event.*;
  25
  26 import jalview.schemes.*;
  27
  28 public class GAlignFrame extends JInternalFrame
  29 {
  30   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  31
  32   protected JMenu fileMenu = new JMenu();
  33
  34   protected JMenuItem closeMenuItem = new JMenuItem();
  35
  36   protected JMenu editMenu = new JMenu();
  37
  38   protected JMenu viewMenu = new JMenu();
  39
  40   protected JMenu colourMenu = new JMenu();
  41
  42   protected JMenu calculateMenu = new JMenu();
  43
  44   protected JMenu webService = new JMenu();
  45
  46   protected JMenuItem webServiceNoServices;
  47
  48   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  49
  50   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  51
  52   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  53
  54   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  55
  56   protected JMenuItem remove2RightMenuItem = new JMenuItem();
  57
  58   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  59
  60   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  61
  62   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  63
  64   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  65
  66   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  67
  68   protected JMenuItem sortIDMenuItem = new JMenuItem();
  69
  70   protected JMenuItem sortLengthMenuItem = new JMenuItem();
  71
  72   protected JMenuItem sortGroupMenuItem = new JMenuItem();
  73
  74   protected JMenu sortByAnnotScore = new JMenu();
  75
  76   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
  77
  78   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
  79
  80   protected JMenuItem PCAMenuItem = new JMenuItem();
  81
  82   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
  83
  84   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
  85
  86   BorderLayout borderLayout1 = new BorderLayout();
  87
  88   public JLabel statusBar = new JLabel();
  89
  90   protected JMenuItem saveAs = new JMenuItem();
  91
  92   protected JMenu outputTextboxMenu = new JMenu();
  93
  94   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  95
  96   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  97
  98   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  99
 100   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
 101
 102   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
 103
 104   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
 105
 106   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
 107
 108   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 109
 110   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
 111
 112   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
 113
 114   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 115
 116   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 117
 118   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
 119
 120   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 121
 122   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 123
 124   public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
 125
 126   JMenuItem htmlMenuItem = new JMenuItem();
 127
 128   JMenuItem overviewMenuItem = new JMenuItem();
 129
 130   protected JMenuItem undoMenuItem = new JMenuItem();
 131
 132   protected JMenuItem redoMenuItem = new JMenuItem();
 133
 134   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 135
 136   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 137
 138   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 139
 140   JMenuItem printMenuItem = new JMenuItem();
 141
 142   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 143
 144   JMenuItem findMenuItem = new JMenuItem();
 145
 146   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 147
 148   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 149
 150   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 151
 152   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
 153
 154   JMenuItem deleteGroups = new JMenuItem();
 155
 156   JMenuItem delete = new JMenuItem();
 157
 158   JMenuItem copy = new JMenuItem();
 159
 160   JMenuItem cut = new JMenuItem();
 161
 162   JMenu pasteMenu = new JMenu();
 163
 164   JMenuItem pasteNew = new JMenuItem();
 165
 166   JMenuItem pasteThis = new JMenuItem();
 167
 168   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
 169
 170   JMenuItem createPNG = new JMenuItem();
 171
 172   protected JMenuItem font = new JMenuItem();
 173
 174   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 175
 176   JMenuItem epsFile = new JMenuItem();
 177
 178   JMenuItem LoadtreeMenuItem = new JMenuItem();
 179
 180   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 181
 182   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 183
 184   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 185
 186   protected JMenuItem modifyPID = new JMenuItem();
 187
 188   protected JMenuItem modifyConservation = new JMenuItem();
 189
 190   protected JMenu sortByTreeMenu = new JMenu();
 191
 192   protected JMenu sort = new JMenu();
 193
 194   protected JMenu calculateTree = new JMenu();
 195
 196   JMenu jMenu2 = new JMenu();
 197
 198   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 199
 200   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 201
 202   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 203
 204   protected ButtonGroup colours = new ButtonGroup();
 205
 206   JMenuItem vamsasStore = new JMenuItem();
 207
 208   protected JMenuItem showTranslation = new JMenuItem();
 209
 210   protected JMenuItem extractScores = new JMenuItem();
 211
 212   protected JMenu showProducts = new JMenu();
 213
 214   public JMenuItem featureSettings = new JMenuItem();
 215
 216   JMenuItem fetchSequence = new JMenuItem();
 217
 218   JMenuItem annotationColour = new JMenuItem();
 219
 220   JMenuItem associatedData = new JMenuItem();
 221
 222   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 223
 224   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.removeActionListener(radioItem.getActionListeners()[0]);
 367
 368               int option = JOptionPane.showInternalConfirmDialog(
 369                       jalview.gui.Desktop.desktop,
 370                       "Remove from default list?",
 371                       "Remove user defined colour",
 372                       JOptionPane.YES_NO_OPTION);
 373               if (option == JOptionPane.YES_OPTION)
 374               {
 375                 jalview.gui.UserDefinedColours
 376                         .removeColourFromDefaults(radioItem.getText());
 377                 colourMenu.remove(radioItem);
 378               }
 379               else
 380               {
 381                 radioItem.addActionListener(new ActionListener()
 382                 {
 383                   public void actionPerformed(ActionEvent evt)
 384                   {
 385                     userDefinedColour_actionPerformed(evt);
 386                   }
 387                 });
 388               }
 389             }
 390           }
 391         });
 392         radioItem.addActionListener(new ActionListener()
 393         {
 394           public void actionPerformed(ActionEvent evt)
 395           {
 396             userDefinedColour_actionPerformed(evt);
 397           }
 398         });
 399         colourMenu.insert(radioItem, 15);
 400         colours.add(radioItem);
 401       }
 402     }
 403     colours.add(noColourmenuItem);
 404     colours.add(clustalColour);
 405     colours.add(zappoColour);
 406     colours.add(taylorColour);
 407     colours.add(hydrophobicityColour);
 408     colours.add(helixColour);
 409     colours.add(strandColour);
 410     colours.add(turnColour);
 411     colours.add(buriedColour);
 412     colours.add(userDefinedColour);
 413     colours.add(PIDColour);
 414     colours.add(BLOSUM62Colour);
 415     colours.add(nucleotideColour);
 416
 417     setColourSelected(jalview.bin.Cache
 418             .getDefault("DEFAULT_COLOUR", "None"));
 419
 420   }
 421
 422   public void setColourSelected(String defaultColour)
 423   {
 424
 425     if (defaultColour != null)
 426     {
 427       int index = ColourSchemeProperty
 428               .getColourIndexFromName(defaultColour);
 429
 430       switch (index)
 431       {
 432       case ColourSchemeProperty.CLUSTAL:
 433         clustalColour.setSelected(true);
 434
 435         break;
 436
 437       case ColourSchemeProperty.BLOSUM:
 438         BLOSUM62Colour.setSelected(true);
 439
 440         break;
 441
 442       case ColourSchemeProperty.PID:
 443         PIDColour.setSelected(true);
 444
 445         break;
 446
 447       case ColourSchemeProperty.ZAPPO:
 448         zappoColour.setSelected(true);
 449
 450         break;
 451
 452       case ColourSchemeProperty.TAYLOR:
 453         taylorColour.setSelected(true);
 454         break;
 455
 456       case ColourSchemeProperty.HYDROPHOBIC:
 457         hydrophobicityColour.setSelected(true);
 458
 459         break;
 460
 461       case ColourSchemeProperty.HELIX:
 462         helixColour.setSelected(true);
 463
 464         break;
 465
 466       case ColourSchemeProperty.STRAND:
 467         strandColour.setSelected(true);
 468
 469         break;
 470
 471       case ColourSchemeProperty.TURN:
 472         turnColour.setSelected(true);
 473
 474         break;
 475
 476       case ColourSchemeProperty.BURIED:
 477         buriedColour.setSelected(true);
 478
 479         break;
 480
 481       case ColourSchemeProperty.NUCLEOTIDE:
 482         nucleotideColour.setSelected(true);
 483
 484         break;
 485
 486       case ColourSchemeProperty.USER_DEFINED:
 487         userDefinedColour.setSelected(true);
 488
 489         break;
 490       case ColourSchemeProperty.NONE:
 491       default:
 492         noColourmenuItem.setSelected(true);
 493         break;
 494
 495       }
 496     }
 497
 498   }
 499
 500   private void jbInit() throws Exception
 501   {
 502     fileMenu.setText("File");
 503     saveAs.setText("Save As...");
 504     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 505             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
 506                     .getMenuShortcutKeyMask()
 507                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 508     saveAs.addActionListener(new ActionListener()
 509     {
 510       public void actionPerformed(ActionEvent e)
 511       {
 512         saveAs_actionPerformed(e);
 513       }
 514     });
 515     closeMenuItem.setText("Close");
 516     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 517             java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
 518                     .getMenuShortcutKeyMask(), false));
 519     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 520     {
 521       public void actionPerformed(ActionEvent e)
 522       {
 523         closeMenuItem_actionPerformed(false);
 524       }
 525     });
 526     editMenu.setText("Edit");
 527     viewMenu.setText("View");
 528     colourMenu.setText("Colour");
 529     calculateMenu.setText("Calculate");
 530     webService.setText("Web Service");
 531     selectAllSequenceMenuItem.setText("Select All");
 532     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 533             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
 534                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 535     selectAllSequenceMenuItem
 536             .addActionListener(new java.awt.event.ActionListener()
 537             {
 538               public void actionPerformed(ActionEvent e)
 539               {
 540                 selectAllSequenceMenuItem_actionPerformed(e);
 541               }
 542             });
 543     deselectAllSequenceMenuItem.setText("Deselect All");
 544     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 545             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 546     deselectAllSequenceMenuItem
 547             .addActionListener(new java.awt.event.ActionListener()
 548             {
 549               public void actionPerformed(ActionEvent e)
 550               {
 551                 deselectAllSequenceMenuItem_actionPerformed(e);
 552               }
 553             });
 554     invertSequenceMenuItem.setText("Invert Sequence Selection");
 555     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 556             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
 557                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 558     invertSequenceMenuItem
 559             .addActionListener(new java.awt.event.ActionListener()
 560             {
 561               public void actionPerformed(ActionEvent e)
 562               {
 563                 invertSequenceMenuItem_actionPerformed(e);
 564               }
 565             });
 566     grpsFromSelection.setText("Make Groups for selection");
 567     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
 568     {
 569       public void actionPerformed(ActionEvent e)
 570       {
 571         makeGrpsFromSelection_actionPerformed(e);
 572       }
 573     });
 574
 575     remove2LeftMenuItem.setText("Remove Left");
 576     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 577             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
 578                     .getMenuShortcutKeyMask(), false));
 579     remove2LeftMenuItem
 580             .addActionListener(new java.awt.event.ActionListener()
 581             {
 582               public void actionPerformed(ActionEvent e)
 583               {
 584                 remove2LeftMenuItem_actionPerformed(e);
 585               }
 586             });
 587     remove2RightMenuItem.setText("Remove Right");
 588     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 589             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
 590                     .getMenuShortcutKeyMask(), false));
 591     remove2RightMenuItem
 592             .addActionListener(new java.awt.event.ActionListener()
 593             {
 594               public void actionPerformed(ActionEvent e)
 595               {
 596                 remove2RightMenuItem_actionPerformed(e);
 597               }
 598             });
 599     removeGappedColumnMenuItem.setText("Remove Empty Columns");
 600     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
 601             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 602                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 603     removeGappedColumnMenuItem
 604             .addActionListener(new java.awt.event.ActionListener()
 605             {
 606               public void actionPerformed(ActionEvent e)
 607               {
 608                 removeGappedColumnMenuItem_actionPerformed(e);
 609               }
 610             });
 611     removeAllGapsMenuItem.setText("Remove All Gaps");
 612     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
 613             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 614                     .getDefaultToolkit().getMenuShortcutKeyMask()
 615                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 616     removeAllGapsMenuItem
 617             .addActionListener(new java.awt.event.ActionListener()
 618             {
 619               public void actionPerformed(ActionEvent e)
 620               {
 621                 removeAllGapsMenuItem_actionPerformed(e);
 622               }
 623             });
 624     justifyLeftMenuItem.setText("Left Justify Alignment");
 625     justifyLeftMenuItem
 626             .addActionListener(new java.awt.event.ActionListener()
 627             {
 628               public void actionPerformed(ActionEvent e)
 629               {
 630                 justifyLeftMenuItem_actionPerformed(e);
 631               }
 632             });
 633     justifyRightMenuItem.setText("Right Justify Alignment");
 634     justifyRightMenuItem
 635             .addActionListener(new java.awt.event.ActionListener()
 636             {
 637               public void actionPerformed(ActionEvent e)
 638               {
 639                 justifyRightMenuItem_actionPerformed(e);
 640               }
 641             });
 642     viewBoxesMenuItem.setText("Boxes");
 643     viewBoxesMenuItem.setState(true);
 644     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 645     {
 646       public void actionPerformed(ActionEvent e)
 647       {
 648         viewBoxesMenuItem_actionPerformed(e);
 649       }
 650     });
 651     viewTextMenuItem.setText("Text");
 652     viewTextMenuItem.setState(true);
 653     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 654     {
 655       public void actionPerformed(ActionEvent e)
 656       {
 657         viewTextMenuItem_actionPerformed(e);
 658       }
 659     });
 660     showNonconservedMenuItem.setText("Show nonconserved");
 661     showNonconservedMenuItem.setState(false);
 662     showNonconservedMenuItem
 663             .addActionListener(new java.awt.event.ActionListener()
 664             {
 665               public void actionPerformed(ActionEvent e)
 666               {
 667                 showUnconservedMenuItem_actionPerformed(e);
 668               }
 669             });
 670     sortPairwiseMenuItem.setText("by Pairwise Identity");
 671     sortPairwiseMenuItem
 672             .addActionListener(new java.awt.event.ActionListener()
 673             {
 674               public void actionPerformed(ActionEvent e)
 675               {
 676                 sortPairwiseMenuItem_actionPerformed(e);
 677               }
 678             });
 679     sortIDMenuItem.setText("by ID");
 680     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 681     {
 682       public void actionPerformed(ActionEvent e)
 683       {
 684         sortIDMenuItem_actionPerformed(e);
 685       }
 686     });
 687     sortLengthMenuItem.setText("By Length");
 688     sortLengthMenuItem
 689             .addActionListener(new java.awt.event.ActionListener()
 690             {
 691               public void actionPerformed(ActionEvent e)
 692               {
 693                 sortLengthMenuItem_actionPerformed(e);
 694               }
 695             });
 696     sortGroupMenuItem.setText("by Group");
 697     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 698     {
 699       public void actionPerformed(ActionEvent e)
 700       {
 701         sortGroupMenuItem_actionPerformed(e);
 702       }
 703     });
 704     removeRedundancyMenuItem.setText("Remove Redundancy...");
 705     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
 706             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
 707                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 708     removeRedundancyMenuItem
 709             .addActionListener(new java.awt.event.ActionListener()
 710             {
 711               public void actionPerformed(ActionEvent e)
 712               {
 713                 removeRedundancyMenuItem_actionPerformed(e);
 714               }
 715             });
 716     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
 717     pairwiseAlignmentMenuItem
 718             .addActionListener(new java.awt.event.ActionListener()
 719             {
 720               public void actionPerformed(ActionEvent e)
 721               {
 722                 pairwiseAlignmentMenuItem_actionPerformed(e);
 723               }
 724             });
 725     PCAMenuItem.setText("Principal Component Analysis");
 726     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 727     {
 728       public void actionPerformed(ActionEvent e)
 729       {
 730         PCAMenuItem_actionPerformed(e);
 731       }
 732     });
 733     averageDistanceTreeMenuItem
 734             .setText("Average Distance Using % Identity");
 735     averageDistanceTreeMenuItem
 736             .addActionListener(new java.awt.event.ActionListener()
 737             {
 738               public void actionPerformed(ActionEvent e)
 739               {
 740                 averageDistanceTreeMenuItem_actionPerformed(e);
 741               }
 742             });
 743     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
 744     neighbourTreeMenuItem
 745             .addActionListener(new java.awt.event.ActionListener()
 746             {
 747               public void actionPerformed(ActionEvent e)
 748               {
 749                 neighbourTreeMenuItem_actionPerformed(e);
 750               }
 751             });
 752     this.getContentPane().setLayout(borderLayout1);
 753     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 754     statusBar.setBackground(Color.white);
 755     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 756     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 757     statusBar.setText("Status bar");
 758     outputTextboxMenu.setText("Output to Textbox");
 759     clustalColour.setText("Clustalx");
 760
 761     clustalColour.addActionListener(new java.awt.event.ActionListener()
 762     {
 763       public void actionPerformed(ActionEvent e)
 764       {
 765         clustalColour_actionPerformed(e);
 766       }
 767     });
 768     zappoColour.setText("Zappo");
 769     zappoColour.addActionListener(new java.awt.event.ActionListener()
 770     {
 771       public void actionPerformed(ActionEvent e)
 772       {
 773         zappoColour_actionPerformed(e);
 774       }
 775     });
 776     taylorColour.setText("Taylor");
 777     taylorColour.addActionListener(new java.awt.event.ActionListener()
 778     {
 779       public void actionPerformed(ActionEvent e)
 780       {
 781         taylorColour_actionPerformed(e);
 782       }
 783     });
 784     hydrophobicityColour.setText("Hydrophobicity");
 785     hydrophobicityColour
 786             .addActionListener(new java.awt.event.ActionListener()
 787             {
 788               public void actionPerformed(ActionEvent e)
 789               {
 790                 hydrophobicityColour_actionPerformed(e);
 791               }
 792             });
 793     helixColour.setText("Helix Propensity");
 794     helixColour.addActionListener(new java.awt.event.ActionListener()
 795     {
 796       public void actionPerformed(ActionEvent e)
 797       {
 798         helixColour_actionPerformed(e);
 799       }
 800     });
 801     strandColour.setText("Strand Propensity");
 802     strandColour.addActionListener(new java.awt.event.ActionListener()
 803     {
 804       public void actionPerformed(ActionEvent e)
 805       {
 806         strandColour_actionPerformed(e);
 807       }
 808     });
 809     turnColour.setText("Turn Propensity");
 810     turnColour.addActionListener(new java.awt.event.ActionListener()
 811     {
 812       public void actionPerformed(ActionEvent e)
 813       {
 814         turnColour_actionPerformed(e);
 815       }
 816     });
 817     buriedColour.setText("Buried Index");
 818     buriedColour.addActionListener(new java.awt.event.ActionListener()
 819     {
 820       public void actionPerformed(ActionEvent e)
 821       {
 822         buriedColour_actionPerformed(e);
 823       }
 824     });
 825     userDefinedColour.setText("User Defined...");
 826     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 827     {
 828       public void actionPerformed(ActionEvent e)
 829       {
 830         userDefinedColour_actionPerformed(e);
 831       }
 832     });
 833     PIDColour.setText("Percentage Identity");
 834     PIDColour.addActionListener(new java.awt.event.ActionListener()
 835     {
 836       public void actionPerformed(ActionEvent e)
 837       {
 838         PIDColour_actionPerformed(e);
 839       }
 840     });
 841     BLOSUM62Colour.setText("BLOSUM62 Score");
 842     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 843     {
 844       public void actionPerformed(ActionEvent e)
 845       {
 846         BLOSUM62Colour_actionPerformed(e);
 847       }
 848     });
 849     avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
 850     avDistanceTreeBlosumMenuItem
 851             .addActionListener(new java.awt.event.ActionListener()
 852             {
 853               public void actionPerformed(ActionEvent e)
 854               {
 855                 avTreeBlosumMenuItem_actionPerformed(e);
 856               }
 857             });
 858     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
 859     njTreeBlosumMenuItem
 860             .addActionListener(new java.awt.event.ActionListener()
 861             {
 862               public void actionPerformed(ActionEvent e)
 863               {
 864                 njTreeBlosumMenuItem_actionPerformed(e);
 865               }
 866             });
 867     annotationPanelMenuItem.setActionCommand("");
 868     annotationPanelMenuItem.setText("Show Annotations");
 869     annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
 870             "SHOW_ANNOTATIONS", true));
 871     annotationPanelMenuItem
 872             .addActionListener(new java.awt.event.ActionListener()
 873             {
 874               public void actionPerformed(ActionEvent e)
 875               {
 876                 annotationPanelMenuItem_actionPerformed(e);
 877               }
 878             });
 879     colourTextMenuItem.setText("Colour Text");
 880     colourTextMenuItem
 881             .addActionListener(new java.awt.event.ActionListener()
 882             {
 883               public void actionPerformed(ActionEvent e)
 884               {
 885                 colourTextMenuItem_actionPerformed(e);
 886               }
 887             });
 888     htmlMenuItem.setText("HTML");
 889     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
 890     {
 891       public void actionPerformed(ActionEvent e)
 892       {
 893         htmlMenuItem_actionPerformed(e);
 894       }
 895     });
 896     overviewMenuItem.setText("Overview Window");
 897     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
 898     {
 899       public void actionPerformed(ActionEvent e)
 900       {
 901         overviewMenuItem_actionPerformed(e);
 902       }
 903     });
 904     undoMenuItem.setEnabled(false);
 905     undoMenuItem.setText("Undo");
 906     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 907             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
 908                     .getMenuShortcutKeyMask(), false));
 909     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
 910     {
 911       public void actionPerformed(ActionEvent e)
 912       {
 913         undoMenuItem_actionPerformed(e);
 914       }
 915     });
 916     redoMenuItem.setEnabled(false);
 917     redoMenuItem.setText("Redo");
 918     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 919             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
 920                     .getMenuShortcutKeyMask(), false));
 921     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
 922     {
 923       public void actionPerformed(ActionEvent e)
 924       {
 925         redoMenuItem_actionPerformed(e);
 926       }
 927     });
 928     conservationMenuItem.setText("By Conservation");
 929     conservationMenuItem
 930             .addActionListener(new java.awt.event.ActionListener()
 931             {
 932               public void actionPerformed(ActionEvent e)
 933               {
 934                 conservationMenuItem_actionPerformed(e);
 935               }
 936             });
 937     noColourmenuItem.setText("None");
 938     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 939     {
 940       public void actionPerformed(ActionEvent e)
 941       {
 942         noColourmenuItem_actionPerformed(e);
 943       }
 944     });
 945     wrapMenuItem.setText("Wrap");
 946     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
 947     {
 948       public void actionPerformed(ActionEvent e)
 949       {
 950         wrapMenuItem_actionPerformed(e);
 951       }
 952     });
 953     printMenuItem.setText("Print ...");
 954     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 955             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
 956                     .getMenuShortcutKeyMask(), false));
 957     printMenuItem.addActionListener(new java.awt.event.ActionListener()
 958     {
 959       public void actionPerformed(ActionEvent e)
 960       {
 961         printMenuItem_actionPerformed(e);
 962       }
 963     });
 964     renderGapsMenuItem.setText("Show Gaps");
 965     renderGapsMenuItem.setState(true);
 966     renderGapsMenuItem
 967             .addActionListener(new java.awt.event.ActionListener()
 968             {
 969               public void actionPerformed(ActionEvent e)
 970               {
 971                 renderGapsMenuItem_actionPerformed(e);
 972               }
 973             });
 974     findMenuItem.setText("Find...");
 975     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 976             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
 977                     .getMenuShortcutKeyMask(), false));
 978     findMenuItem.addActionListener(new java.awt.event.ActionListener()
 979     {
 980       public void actionPerformed(ActionEvent e)
 981       {
 982         findMenuItem_actionPerformed(e);
 983       }
 984     });
 985     abovePIDThreshold.setText("Above Identity Threshold");
 986     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
 987     {
 988       public void actionPerformed(ActionEvent e)
 989       {
 990         abovePIDThreshold_actionPerformed(e);
 991       }
 992     });
 993     showSeqFeatures.setText("Show Sequence Features");
 994     showSeqFeatures.addActionListener(new ActionListener()
 995     {
 996       public void actionPerformed(ActionEvent actionEvent)
 997       {
 998         showSeqFeatures_actionPerformed(actionEvent);
 999       }
1000     });
1001     /*
1002      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1003      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1004      * void actionPerformed(ActionEvent actionEvent) {
1005      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1006      */
1007     showDbRefsMenuitem.setText("Show Database Refs");
1008     showDbRefsMenuitem.addActionListener(new ActionListener()
1009     {
1010
1011       public void actionPerformed(ActionEvent e)
1012       {
1013         showDbRefs_actionPerformed(e);
1014       }
1015
1016     });
1017     showNpFeatsMenuitem.setText("Show Non-Positional Features");
1018     showNpFeatsMenuitem.addActionListener(new ActionListener()
1019     {
1020
1021       public void actionPerformed(ActionEvent e)
1022       {
1023         showNpFeats_actionPerformed(e);
1024       }
1025
1026     });
1027     showGroupConservation.setText("Group Conservation");
1028     showGroupConservation.addActionListener(new ActionListener()
1029     {
1030
1031       public void actionPerformed(ActionEvent e)
1032       {
1033         showGroupConservation_actionPerformed(e);
1034       }
1035
1036     });
1037
1038     showGroupConsensus.setText("Group Consensus");
1039     showGroupConsensus.addActionListener(new ActionListener()
1040     {
1041
1042       public void actionPerformed(ActionEvent e)
1043       {
1044         showGroupConsensus_actionPerformed(e);
1045       }
1046
1047     });
1048     showConsensusHistogram.setText("Show Consensus Histogram");
1049     showConsensusHistogram.addActionListener(new ActionListener()
1050     {
1051
1052       public void actionPerformed(ActionEvent e)
1053       {
1054         showConsensusHistogram_actionPerformed(e);
1055       }
1056
1057     });
1058     showSequenceLogo.setText("Show Consensus Logo");
1059     showSequenceLogo.addActionListener(new ActionListener()
1060     {
1061
1062       public void actionPerformed(ActionEvent e)
1063       {
1064         showSequenceLogo_actionPerformed(e);
1065       }
1066
1067     });
1068     applyAutoAnnotationSettings.setText("Apply to all groups");
1069     applyAutoAnnotationSettings.setState(false);
1070     applyAutoAnnotationSettings.setVisible(true);
1071     applyAutoAnnotationSettings.addActionListener(new ActionListener()
1072     {
1073
1074       public void actionPerformed(ActionEvent e)
1075       {
1076         applyAutoAnnotationSettings_actionPerformed(e);
1077       }
1078
1079     });
1080
1081     nucleotideColour.setText("Nucleotide");
1082     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1083     {
1084       public void actionPerformed(ActionEvent e)
1085       {
1086         nucleotideColour_actionPerformed(e);
1087       }
1088     });
1089     deleteGroups.setText("Undefine groups");
1090     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1091             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1092                     .getMenuShortcutKeyMask(), false));
1093     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1094     {
1095       public void actionPerformed(ActionEvent e)
1096       {
1097         deleteGroups_actionPerformed(e);
1098       }
1099     });
1100     copy.setText("Copy");
1101     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1102             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1103                     .getMenuShortcutKeyMask(), false));
1104
1105     copy.addActionListener(new java.awt.event.ActionListener()
1106     {
1107       public void actionPerformed(ActionEvent e)
1108       {
1109         copy_actionPerformed(e);
1110       }
1111     });
1112     cut.setText("Cut");
1113     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1114             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1115                     .getMenuShortcutKeyMask(), false));
1116     cut.addActionListener(new java.awt.event.ActionListener()
1117     {
1118       public void actionPerformed(ActionEvent e)
1119       {
1120         cut_actionPerformed(e);
1121       }
1122     });
1123     delete.setText("Delete");
1124     delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1125             java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1126     delete.addActionListener(new java.awt.event.ActionListener()
1127     {
1128       public void actionPerformed(ActionEvent e)
1129       {
1130         delete_actionPerformed(e);
1131       }
1132     });
1133     pasteMenu.setText("Paste");
1134     pasteNew.setText("To New Alignment");
1135     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1136             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1137                     .getMenuShortcutKeyMask()
1138                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1139     pasteNew.addActionListener(new java.awt.event.ActionListener()
1140     {
1141       public void actionPerformed(ActionEvent e)
1142       {
1143         pasteNew_actionPerformed(e);
1144       }
1145     });
1146     pasteThis.setText("Add To This Alignment");
1147     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1148             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1149                     .getMenuShortcutKeyMask(), false));
1150     pasteThis.addActionListener(new java.awt.event.ActionListener()
1151     {
1152       public void actionPerformed(ActionEvent e)
1153       {
1154         pasteThis_actionPerformed(e);
1155       }
1156     });
1157     applyToAllGroups.setText("Apply Colour To All Groups");
1158     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1159     {
1160       public void actionPerformed(ActionEvent e)
1161       {
1162         applyToAllGroups_actionPerformed(e);
1163       }
1164     });
1165     createPNG.addActionListener(new java.awt.event.ActionListener()
1166     {
1167       public void actionPerformed(ActionEvent e)
1168       {
1169         createPNG(null);
1170       }
1171     });
1172     createPNG.setActionCommand("Save As PNG Image");
1173     createPNG.setText("PNG");
1174     font.setText("Font...");
1175     font.addActionListener(new java.awt.event.ActionListener()
1176     {
1177       public void actionPerformed(ActionEvent e)
1178       {
1179         font_actionPerformed(e);
1180       }
1181     });
1182
1183     seqLimits.setText("Show Sequence Limits");
1184     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1185     seqLimits.addActionListener(new java.awt.event.ActionListener()
1186     {
1187       public void actionPerformed(ActionEvent e)
1188       {
1189         seqLimit_actionPerformed(e);
1190       }
1191     });
1192     epsFile.setText("EPS");
1193     epsFile.addActionListener(new java.awt.event.ActionListener()
1194     {
1195       public void actionPerformed(ActionEvent e)
1196       {
1197         createEPS(null);
1198       }
1199     });
1200     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1201     LoadtreeMenuItem.setText("Load Associated Tree");
1202     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1203     {
1204       public void actionPerformed(ActionEvent e)
1205       {
1206         LoadtreeMenuItem_actionPerformed(e);
1207       }
1208     });
1209     scaleAbove.setVisible(false);
1210     scaleAbove.setText("Scale Above");
1211     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1212     {
1213       public void actionPerformed(ActionEvent e)
1214       {
1215         scaleAbove_actionPerformed(e);
1216       }
1217     });
1218     scaleLeft.setVisible(false);
1219     scaleLeft.setSelected(true);
1220     scaleLeft.setText("Scale Left");
1221     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1222     {
1223       public void actionPerformed(ActionEvent e)
1224       {
1225         scaleLeft_actionPerformed(e);
1226       }
1227     });
1228     scaleRight.setVisible(false);
1229     scaleRight.setSelected(true);
1230     scaleRight.setText("Scale Right");
1231     scaleRight.addActionListener(new java.awt.event.ActionListener()
1232     {
1233       public void actionPerformed(ActionEvent e)
1234       {
1235         scaleRight_actionPerformed(e);
1236       }
1237     });
1238     centreColumnLabelsMenuItem.setVisible(true);
1239     centreColumnLabelsMenuItem.setState(false);
1240     centreColumnLabelsMenuItem.setText("Centre Column Labels");
1241     centreColumnLabelsMenuItem
1242             .addActionListener(new java.awt.event.ActionListener()
1243             {
1244               public void actionPerformed(ActionEvent e)
1245               {
1246                 centreColumnLabels_actionPerformed(e);
1247               }
1248             });
1249     followHighlightMenuItem.setVisible(true);
1250     followHighlightMenuItem.setState(true);
1251     followHighlightMenuItem.setText("Automatic Scrolling");
1252     followHighlightMenuItem.addActionListener(new ActionListener()
1253     {
1254
1255       public void actionPerformed(ActionEvent e)
1256       {
1257         followHighlight_actionPerformed();
1258       }
1259
1260     });
1261
1262     modifyPID.setText("Modify Identity Threshold...");
1263     modifyPID.addActionListener(new java.awt.event.ActionListener()
1264     {
1265       public void actionPerformed(ActionEvent e)
1266       {
1267         modifyPID_actionPerformed(e);
1268       }
1269     });
1270     modifyConservation.setText("Modify Conservation Threshold...");
1271     modifyConservation
1272             .addActionListener(new java.awt.event.ActionListener()
1273             {
1274               public void actionPerformed(ActionEvent e)
1275               {
1276                 modifyConservation_actionPerformed(e);
1277               }
1278             });
1279     sortByTreeMenu.setText("By Tree Order");
1280     sort.setText("Sort");
1281     sort.addMenuListener(new MenuListener()
1282     {
1283       public void menuSelected(MenuEvent e)
1284       {
1285         buildTreeMenu();
1286       }
1287
1288       public void menuDeselected(MenuEvent e)
1289       {
1290       }
1291
1292       public void menuCanceled(MenuEvent e)
1293       {
1294       }
1295     });
1296     sortByAnnotScore.setText("by Score");
1297     sort.add(sortByAnnotScore);
1298     sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1299     {
1300
1301       public void menuCanceled(MenuEvent e)
1302       {
1303       }
1304
1305       public void menuDeselected(MenuEvent e)
1306       {
1307       }
1308
1309       public void menuSelected(MenuEvent e)
1310       {
1311         buildSortByAnnotationScoresMenu();
1312       }
1313     });
1314     sortByAnnotScore.setVisible(false);
1315
1316     calculateTree.setText("Calculate Tree");
1317
1318     jMenu2.setText("Export Image");
1319     padGapsMenuitem.setText("Pad Gaps");
1320     padGapsMenuitem.setState(jalview.bin.Cache
1321             .getDefault("PAD_GAPS", false));
1322     padGapsMenuitem.addActionListener(new ActionListener()
1323     {
1324       public void actionPerformed(ActionEvent e)
1325       {
1326         padGapsMenuitem_actionPerformed(e);
1327       }
1328     });
1329     vamsasStore.setVisible(false);
1330     vamsasStore.setText("VAMSAS store");
1331     vamsasStore.addActionListener(new ActionListener()
1332     {
1333       public void actionPerformed(ActionEvent e)
1334       {
1335         vamsasStore_actionPerformed(e);
1336       }
1337     });
1338     showTranslation.setText("Translate cDNA");
1339     showTranslation.addActionListener(new ActionListener()
1340     {
1341       public void actionPerformed(ActionEvent e)
1342       {
1343         showTranslation_actionPerformed(e);
1344       }
1345     });
1346     extractScores.setText("Extract Scores...");
1347     extractScores.addActionListener(new ActionListener()
1348     {
1349       public void actionPerformed(ActionEvent e)
1350       {
1351         extractScores_actionPerformed(e);
1352       }
1353     });
1354     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1355     // score extraction
1356     showProducts.setText("Get Cross References");
1357     /*
1358      * showProducts.addActionListener(new ActionListener() {
1359      *
1360      * public void actionPerformed(ActionEvent e) {
1361      * showProducts_actionPerformed(e); } });
1362      */
1363     featureSettings.setText("Feature Settings...");
1364     featureSettings.addActionListener(new ActionListener()
1365     {
1366       public void actionPerformed(ActionEvent e)
1367       {
1368         featureSettings_actionPerformed(e);
1369       }
1370     });
1371     fetchSequence.setText("Fetch Sequence(s)...");
1372     fetchSequence.addActionListener(new ActionListener()
1373     {
1374       public void actionPerformed(ActionEvent e)
1375       {
1376         fetchSequence_actionPerformed(e);
1377       }
1378     });
1379
1380     annotationColour.setText("By Annotation...");
1381     annotationColour.addActionListener(new ActionListener()
1382     {
1383       public void actionPerformed(ActionEvent e)
1384       {
1385         annotationColour_actionPerformed(e);
1386       }
1387     });
1388     associatedData.setText("Load Features / Annotations");
1389     associatedData.addActionListener(new ActionListener()
1390     {
1391       public void actionPerformed(ActionEvent e)
1392       {
1393         associatedData_actionPerformed(e);
1394       }
1395     });
1396     autoCalculate.setText("Autocalculate Consensus");
1397     autoCalculate.setState(jalview.bin.Cache.getDefault(
1398             "AUTO_CALC_CONSENSUS", true));
1399     autoCalculate.addActionListener(new ActionListener()
1400     {
1401       public void actionPerformed(ActionEvent e)
1402       {
1403         autoCalculate_actionPerformed(e);
1404       }
1405     });
1406     addSequenceMenu.setText("Add Sequences");
1407     addFromFile.setText("From File");
1408     addFromFile.addActionListener(new ActionListener()
1409     {
1410       public void actionPerformed(ActionEvent e)
1411       {
1412         addFromFile_actionPerformed(e);
1413       }
1414     });
1415     addFromText.setText("From Textbox");
1416     addFromText.addActionListener(new ActionListener()
1417     {
1418       public void actionPerformed(ActionEvent e)
1419       {
1420         addFromText_actionPerformed(e);
1421       }
1422     });
1423     addFromURL.setText("From URL");
1424     addFromURL.addActionListener(new ActionListener()
1425     {
1426       public void actionPerformed(ActionEvent e)
1427       {
1428         addFromURL_actionPerformed(e);
1429       }
1430     });
1431     exportFeatures.setText("Export Features...");
1432     exportFeatures.addActionListener(new ActionListener()
1433     {
1434       public void actionPerformed(ActionEvent e)
1435       {
1436         exportFeatures_actionPerformed(e);
1437       }
1438     });
1439     exportAnnotations.setText("Export Annotations...");
1440     exportAnnotations.addActionListener(new ActionListener()
1441     {
1442       public void actionPerformed(ActionEvent e)
1443       {
1444         exportAnnotations_actionPerformed(e);
1445       }
1446     });
1447     statusPanel.setLayout(gridLayout1);
1448     jMenu3.setText("Show");
1449     showAllSeqs.setText("All Sequences");
1450     showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1451     showAllSeqs.addActionListener(new ActionListener()
1452     {
1453       public void actionPerformed(ActionEvent e)
1454       {
1455         showAllSeqs_actionPerformed(e);
1456       }
1457     });
1458     showAllColumns.setText("All Columns");
1459     showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1460     showAllColumns.addActionListener(new ActionListener()
1461     {
1462       public void actionPerformed(ActionEvent e)
1463       {
1464         showAllColumns_actionPerformed(e);
1465       }
1466     });
1467     hideMenu.setText("Hide");
1468     hideSelSequences.setText("Selected Sequences");
1469     hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1470     hideSelSequences.addActionListener(new ActionListener()
1471     {
1472       public void actionPerformed(ActionEvent e)
1473       {
1474         hideSelSequences_actionPerformed(e);
1475       }
1476     });
1477     hideSelColumns.setText("Selected Columns");
1478     hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1479     hideSelColumns.addActionListener(new ActionListener()
1480     {
1481       public void actionPerformed(ActionEvent e)
1482       {
1483         hideSelColumns_actionPerformed(e);
1484       }
1485     });
1486     hideAllSelection.setText("Selected Region");
1487     hideAllSelection.addActionListener(new ActionListener()
1488     {
1489       public void actionPerformed(ActionEvent e)
1490       {
1491         hideAllSelection_actionPerformed(e);
1492       }
1493     });
1494     // TODO: should be hidden if no selection exists.
1495     hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
1496     hideAllButSelection.addActionListener(new ActionListener()
1497     {
1498       public void actionPerformed(ActionEvent e)
1499       {
1500         hideAllButSelection_actionPerformed(e);
1501       }
1502     });
1503     showAllhidden.setText("All Sequences and Columns");
1504     showAllhidden
1505             .setToolTipText("H toggles visibility of hidden or selected regions.");
1506     showAllhidden.addActionListener(new ActionListener()
1507     {
1508       public void actionPerformed(ActionEvent e)
1509       {
1510         showAllhidden_actionPerformed(e);
1511       }
1512     });
1513
1514     hiddenMarkers.setText("Show Hidden Markers");
1515     hiddenMarkers.addActionListener(new ActionListener()
1516     {
1517       public void actionPerformed(ActionEvent e)
1518       {
1519         hiddenMarkers_actionPerformed(e);
1520       }
1521     });
1522     invertColSel.setText("Invert Column Selection");
1523     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1524             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1525                     .getMenuShortcutKeyMask()
1526                     | java.awt.event.KeyEvent.ALT_MASK, false));
1527     invertColSel.addActionListener(new ActionListener()
1528     {
1529       public void actionPerformed(ActionEvent e)
1530       {
1531         invertColSel_actionPerformed(e);
1532       }
1533     });
1534     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1535     {
1536       public void stateChanged(ChangeEvent evt)
1537       {
1538         JTabbedPane pane = (JTabbedPane) evt.getSource();
1539         int sel = pane.getSelectedIndex();
1540         tabSelectionChanged(sel);
1541       }
1542     });
1543     tabbedPane.addMouseListener(new MouseAdapter()
1544     {
1545       public void mousePressed(MouseEvent e)
1546       {
1547         tabbedPane_mousePressed(e);
1548       }
1549     });
1550     tabbedPane.addFocusListener(new FocusAdapter()
1551     {
1552       public void focusGained(FocusEvent e)
1553       {
1554         tabbedPane_focusGained(e);
1555       }
1556     });
1557     save.setText("Save");
1558     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1559             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1560                     .getMenuShortcutKeyMask(), false));
1561     save.addActionListener(new ActionListener()
1562     {
1563       public void actionPerformed(ActionEvent e)
1564       {
1565         save_actionPerformed(e);
1566       }
1567     });
1568     reload.setEnabled(false);
1569     reload.setText("Reload");
1570     reload.addActionListener(new ActionListener()
1571     {
1572       public void actionPerformed(ActionEvent e)
1573       {
1574         reload_actionPerformed(e);
1575       }
1576     });
1577     newView.setText("New View");
1578     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1579             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1580                     .getMenuShortcutKeyMask(), false));
1581     newView.addActionListener(new ActionListener()
1582     {
1583       public void actionPerformed(ActionEvent e)
1584       {
1585         newView_actionPerformed(e);
1586       }
1587     });
1588     tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1589             + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1590     textColour.setText("Colour Text ...");
1591     textColour.addActionListener(new ActionListener()
1592     {
1593       public void actionPerformed(ActionEvent e)
1594       {
1595         textColour_actionPerformed(e);
1596       }
1597     });
1598     formatMenu.setText("Format");
1599     selectMenu.setText("Select");
1600     idRightAlign.setText("Right Align Sequence Id");
1601     idRightAlign.addActionListener(new ActionListener()
1602     {
1603       public void actionPerformed(ActionEvent e)
1604       {
1605         idRightAlign_actionPerformed(e);
1606       }
1607     });
1608     gatherViews.setEnabled(false);
1609     gatherViews.setText("Gather Views");
1610     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1611             java.awt.event.KeyEvent.VK_G, 0, false));
1612     gatherViews.addActionListener(new ActionListener()
1613     {
1614       public void actionPerformed(ActionEvent e)
1615       {
1616         gatherViews_actionPerformed(e);
1617       }
1618     });
1619     expandViews.setEnabled(false);
1620     expandViews.setText("Expand Views");
1621     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1622             java.awt.event.KeyEvent.VK_X, 0, false));
1623     expandViews.addActionListener(new ActionListener()
1624     {
1625       public void actionPerformed(ActionEvent e)
1626       {
1627         expandViews_actionPerformed(e);
1628       }
1629     });
1630     pageSetup.setText("Page Setup ...");
1631     pageSetup.addActionListener(new ActionListener()
1632     {
1633       public void actionPerformed(ActionEvent e)
1634       {
1635         pageSetup_actionPerformed(e);
1636       }
1637     });
1638     alignmentProperties.setText("Alignment Properties...");
1639     alignmentProperties.addActionListener(new ActionListener()
1640     {
1641       public void actionPerformed(ActionEvent actionEvent)
1642       {
1643         alignmentProperties();
1644       }
1645     });
1646     tooltipSettingsMenu.setText("Sequence ID Tooltip");
1647     autoAnnMenu.setText("Autocalculated Annotation");
1648     alignFrameMenuBar.add(fileMenu);
1649     alignFrameMenuBar.add(editMenu);
1650     alignFrameMenuBar.add(selectMenu);
1651     alignFrameMenuBar.add(viewMenu);
1652     alignFrameMenuBar.add(formatMenu);
1653     alignFrameMenuBar.add(colourMenu);
1654     alignFrameMenuBar.add(calculateMenu);
1655     alignFrameMenuBar.add(webService);
1656     fileMenu.add(fetchSequence);
1657     fileMenu.add(addSequenceMenu);
1658     fileMenu.add(reload);
1659     fileMenu.addSeparator();
1660     fileMenu.add(vamsasStore);
1661     fileMenu.add(save);
1662     fileMenu.add(saveAs);
1663     fileMenu.add(outputTextboxMenu);
1664     fileMenu.add(pageSetup);
1665     fileMenu.add(printMenuItem);
1666     fileMenu.addSeparator();
1667     fileMenu.add(jMenu2);
1668     fileMenu.add(exportFeatures);
1669     fileMenu.add(exportAnnotations);
1670     fileMenu.add(LoadtreeMenuItem);
1671     fileMenu.add(associatedData);
1672     fileMenu.addSeparator();
1673     fileMenu.add(closeMenuItem);
1674     editMenu.add(undoMenuItem);
1675     editMenu.add(redoMenuItem);
1676     editMenu.add(cut);
1677     editMenu.add(copy);
1678     editMenu.add(pasteMenu);
1679     editMenu.add(delete);
1680     editMenu.addSeparator();
1681     editMenu.add(remove2LeftMenuItem);
1682     editMenu.add(remove2RightMenuItem);
1683     editMenu.add(removeGappedColumnMenuItem);
1684     editMenu.add(removeAllGapsMenuItem);
1685     editMenu.add(removeRedundancyMenuItem);
1686     editMenu.addSeparator();
1687     // dont add these yet in the CVS build - they cannot be undone!
1688     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1689     // editMenu.add(justifyLeftMenuItem);
1690     // editMenu.add(justifyRightMenuItem);
1691     // editMenu.addSeparator();
1692     editMenu.add(padGapsMenuitem);
1693     viewMenu.add(newView);
1694     viewMenu.add(expandViews);
1695     viewMenu.add(gatherViews);
1696     viewMenu.addSeparator();
1697     viewMenu.add(jMenu3);
1698     viewMenu.add(hideMenu);
1699     viewMenu.addSeparator();
1700     viewMenu.add(followHighlightMenuItem);
1701     viewMenu.add(annotationPanelMenuItem);
1702     autoAnnMenu.add(applyAutoAnnotationSettings);
1703     autoAnnMenu.add(showConsensusHistogram);
1704     autoAnnMenu.add(showSequenceLogo);
1705     autoAnnMenu.addSeparator();
1706     autoAnnMenu.add(showGroupConservation);
1707     autoAnnMenu.add(showGroupConsensus);
1708     viewMenu.add(autoAnnMenu);
1709     viewMenu.addSeparator();
1710     viewMenu.add(showSeqFeatures);
1711     // viewMenu.add(showSeqFeaturesHeight);
1712
1713     viewMenu.add(featureSettings);
1714     tooltipSettingsMenu.add(showDbRefsMenuitem);
1715     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1716     viewMenu.add(tooltipSettingsMenu);
1717     viewMenu.addSeparator();
1718     viewMenu.add(alignmentProperties);
1719     viewMenu.addSeparator();
1720     viewMenu.add(overviewMenuItem);
1721     colourMenu.add(applyToAllGroups);
1722     colourMenu.add(textColour);
1723     colourMenu.addSeparator();
1724     colourMenu.add(noColourmenuItem);
1725     colourMenu.add(clustalColour);
1726     colourMenu.add(BLOSUM62Colour);
1727     colourMenu.add(PIDColour);
1728     colourMenu.add(zappoColour);
1729     colourMenu.add(taylorColour);
1730     colourMenu.add(hydrophobicityColour);
1731     colourMenu.add(helixColour);
1732     colourMenu.add(strandColour);
1733     colourMenu.add(turnColour);
1734     colourMenu.add(buriedColour);
1735     colourMenu.add(nucleotideColour);
1736     colourMenu.add(userDefinedColour);
1737     colourMenu.addSeparator();
1738     colourMenu.add(conservationMenuItem);
1739     colourMenu.add(modifyConservation);
1740     colourMenu.add(abovePIDThreshold);
1741     colourMenu.add(modifyPID);
1742     colourMenu.add(annotationColour);
1743     calculateMenu.add(sort);
1744     calculateMenu.add(calculateTree);
1745     calculateMenu.addSeparator();
1746     calculateMenu.add(pairwiseAlignmentMenuItem);
1747     calculateMenu.add(PCAMenuItem);
1748     calculateMenu.addSeparator();
1749     calculateMenu.add(showTranslation);
1750     calculateMenu.add(showProducts);
1751     calculateMenu.add(autoCalculate);
1752     calculateMenu.addSeparator();
1753     calculateMenu.add(extractScores);
1754     webServiceNoServices = new JMenuItem("<No Services>");
1755     webService.add(webServiceNoServices);
1756     pasteMenu.add(pasteNew);
1757     pasteMenu.add(pasteThis);
1758     sort.add(sortIDMenuItem);
1759     sort.add(sortLengthMenuItem);
1760     sort.add(sortGroupMenuItem);
1761     sort.add(sortPairwiseMenuItem);
1762     sort.add(sortByTreeMenu);
1763     calculateTree.add(averageDistanceTreeMenuItem);
1764     calculateTree.add(neighbourTreeMenuItem);
1765     calculateTree.add(avDistanceTreeBlosumMenuItem);
1766     calculateTree.add(njTreeBlosumMenuItem);
1767     jMenu2.add(htmlMenuItem);
1768     jMenu2.add(epsFile);
1769     jMenu2.add(createPNG);
1770     addSequenceMenu.add(addFromFile);
1771     addSequenceMenu.add(addFromText);
1772     addSequenceMenu.add(addFromURL);
1773     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1774     statusPanel.add(statusBar, null);
1775     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1776     jMenu3.add(showAllColumns);
1777     jMenu3.add(showAllSeqs);
1778     jMenu3.add(showAllhidden);
1779     hideMenu.add(hideSelColumns);
1780     hideMenu.add(hideSelSequences);
1781     hideMenu.add(hideAllSelection);
1782     hideMenu.add(hideAllButSelection);
1783
1784     formatMenu.add(font);
1785     formatMenu.addSeparator();
1786     formatMenu.add(wrapMenuItem);
1787     formatMenu.add(scaleAbove);
1788     formatMenu.add(scaleLeft);
1789     formatMenu.add(scaleRight);
1790     formatMenu.add(seqLimits);
1791     formatMenu.add(idRightAlign);
1792     formatMenu.add(hiddenMarkers);
1793     formatMenu.add(viewBoxesMenuItem);
1794     formatMenu.add(viewTextMenuItem);
1795     formatMenu.add(colourTextMenuItem);
1796     formatMenu.add(renderGapsMenuItem);
1797     formatMenu.add(centreColumnLabelsMenuItem);
1798     formatMenu.add(showNonconservedMenuItem);
1799     selectMenu.add(findMenuItem);
1800     selectMenu.addSeparator();
1801     selectMenu.add(selectAllSequenceMenuItem);
1802     selectMenu.add(deselectAllSequenceMenuItem);
1803     selectMenu.add(invertSequenceMenuItem);
1804     selectMenu.add(invertColSel);
1805     selectMenu.add(deleteGroups);
1806     selectMenu.add(grpsFromSelection);
1807   }
1808
1809   protected void showAllhidden_actionPerformed(ActionEvent e)
1810   {
1811     // TODO Auto-generated method stub
1812
1813   }
1814
1815   protected void hideAllButSelection_actionPerformed(ActionEvent e)
1816   {
1817     // TODO Auto-generated method stub
1818
1819   }
1820
1821   protected void hideAllSelection_actionPerformed(ActionEvent e)
1822   {
1823     // TODO Auto-generated method stub
1824
1825   }
1826
1827   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
1828   {
1829     // TODO Auto-generated method stub
1830
1831   }
1832
1833   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
1834   {
1835     // TODO Auto-generated method stub
1836
1837   }
1838
1839   protected void showSequenceLogo_actionPerformed(ActionEvent e)
1840   {
1841     // TODO Auto-generated method stub
1842
1843   }
1844
1845   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
1846   {
1847     // TODO Auto-generated method stub
1848
1849   }
1850
1851   protected void showGroupConsensus_actionPerformed(ActionEvent e)
1852   {
1853     // TODO Auto-generated method stub
1854
1855   }
1856
1857   protected void showGroupConservation_actionPerformed(ActionEvent e)
1858   {
1859     // TODO Auto-generated method stub
1860
1861   }
1862
1863   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
1864   {
1865     // TODO Auto-generated method stub
1866
1867   }
1868
1869   protected void showSeqFeaturesHeight_actionPerformed(
1870           ActionEvent actionEvent)
1871   {
1872     // TODO Auto-generated method stub
1873
1874   }
1875
1876   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
1877   {
1878     // TODO Auto-generated method stub
1879
1880   }
1881
1882   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
1883   {
1884     // TODO Auto-generated method stub
1885
1886   }
1887
1888   protected void followHighlight_actionPerformed()
1889   {
1890     // TODO Auto-generated method stub
1891
1892   }
1893
1894   protected void showNpFeats_actionPerformed(ActionEvent e)
1895   {
1896     // TODO Auto-generated method stub
1897
1898   }
1899
1900   protected void showDbRefs_actionPerformed(ActionEvent e)
1901   {
1902     // TODO Auto-generated method stub
1903
1904   }
1905
1906   protected void centreColumnLabels_actionPerformed(ActionEvent e)
1907   {
1908   }
1909
1910   protected void showProducts_actionPerformed(ActionEvent e)
1911   {
1912   }
1913
1914   protected void buildSortByAnnotationScoresMenu()
1915   {
1916   }
1917
1918   protected void extractScores_actionPerformed(ActionEvent e)
1919   {
1920   }
1921
1922   protected void outputText_actionPerformed(ActionEvent e)
1923   {
1924   }
1925
1926   public void addFromFile_actionPerformed(ActionEvent e)
1927   {
1928
1929   }
1930
1931   public void addFromText_actionPerformed(ActionEvent e)
1932   {
1933
1934   }
1935
1936   public void addFromURL_actionPerformed(ActionEvent e)
1937   {
1938
1939   }
1940
1941   public void exportFeatures_actionPerformed(ActionEvent e)
1942   {
1943
1944   }
1945
1946   public void exportAnnotations_actionPerformed(ActionEvent e)
1947   {
1948
1949   }
1950
1951   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1952   {
1953   }
1954
1955   protected void closeMenuItem_actionPerformed(boolean b)
1956   {
1957   }
1958
1959   protected void redoMenuItem_actionPerformed(ActionEvent e)
1960   {
1961   }
1962
1963   protected void undoMenuItem_actionPerformed(ActionEvent e)
1964   {
1965   }
1966
1967   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1968   {
1969   }
1970
1971   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1972   {
1973   }
1974
1975   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1976   {
1977   }
1978
1979   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1980   {
1981   }
1982
1983   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
1984   {
1985   }
1986
1987   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1988   {
1989   }
1990
1991   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1992   {
1993   }
1994
1995   protected void wrapMenuItem_actionPerformed(ActionEvent e)
1996   {
1997   }
1998
1999   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2000   {
2001   }
2002
2003   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2004   {
2005   }
2006
2007   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2008   {
2009   }
2010
2011   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2012   {
2013   }
2014
2015   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2016   {
2017   }
2018
2019   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2020   {
2021   }
2022
2023   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2024   {
2025   }
2026
2027   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2028   {
2029   }
2030
2031   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2032   {
2033   }
2034
2035   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2036   {
2037   }
2038
2039   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2040   {
2041   }
2042
2043   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2044   {
2045   }
2046
2047   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2048   {
2049   }
2050
2051   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2052   {
2053   }
2054
2055   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2056   {
2057   }
2058
2059   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2060   {
2061   }
2062
2063   protected void clustalColour_actionPerformed(ActionEvent e)
2064   {
2065   }
2066
2067   protected void zappoColour_actionPerformed(ActionEvent e)
2068   {
2069   }
2070
2071   protected void taylorColour_actionPerformed(ActionEvent e)
2072   {
2073   }
2074
2075   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2076   {
2077   }
2078
2079   protected void helixColour_actionPerformed(ActionEvent e)
2080   {
2081   }
2082
2083   protected void strandColour_actionPerformed(ActionEvent e)
2084   {
2085   }
2086
2087   protected void turnColour_actionPerformed(ActionEvent e)
2088   {
2089   }
2090
2091   protected void buriedColour_actionPerformed(ActionEvent e)
2092   {
2093   }
2094
2095   protected void userDefinedColour_actionPerformed(ActionEvent e)
2096   {
2097   }
2098
2099   protected void PIDColour_actionPerformed(ActionEvent e)
2100   {
2101   }
2102
2103   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2104   {
2105   }
2106
2107   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2108   {
2109   }
2110
2111   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2112   {
2113   }
2114
2115   protected void printMenuItem_actionPerformed(ActionEvent e)
2116   {
2117   }
2118
2119   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2120   {
2121   }
2122
2123   protected void findMenuItem_actionPerformed(ActionEvent e)
2124   {
2125   }
2126
2127   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2128   {
2129   }
2130
2131   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2132   {
2133   }
2134
2135   protected void nucleotideColour_actionPerformed(ActionEvent e)
2136   {
2137   }
2138
2139   protected void deleteGroups_actionPerformed(ActionEvent e)
2140   {
2141   }
2142
2143   protected void copy_actionPerformed(ActionEvent e)
2144   {
2145   }
2146
2147   protected void cut_actionPerformed(ActionEvent e)
2148   {
2149   }
2150
2151   protected void delete_actionPerformed(ActionEvent e)
2152   {
2153   }
2154
2155   protected void pasteNew_actionPerformed(ActionEvent e)
2156   {
2157   }
2158
2159   protected void pasteThis_actionPerformed(ActionEvent e)
2160   {
2161   }
2162
2163   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2164   {
2165   }
2166
2167   public void createPNG(java.io.File f)
2168   {
2169   }
2170
2171   protected void font_actionPerformed(ActionEvent e)
2172   {
2173   }
2174
2175   protected void seqLimit_actionPerformed(ActionEvent e)
2176   {
2177   }
2178
2179   public void seqDBRef_actionPerformed(ActionEvent e)
2180   {
2181
2182   }
2183
2184   public void createEPS(java.io.File f)
2185   {
2186   }
2187
2188   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2189   {
2190   }
2191
2192   protected void jpred_actionPerformed(ActionEvent e)
2193   {
2194   }
2195
2196   protected void scaleAbove_actionPerformed(ActionEvent e)
2197   {
2198   }
2199
2200   protected void scaleLeft_actionPerformed(ActionEvent e)
2201   {
2202   }
2203
2204   protected void scaleRight_actionPerformed(ActionEvent e)
2205   {
2206   }
2207
2208   protected void modifyPID_actionPerformed(ActionEvent e)
2209   {
2210   }
2211
2212   protected void modifyConservation_actionPerformed(ActionEvent e)
2213   {
2214   }
2215
2216   protected void saveAs_actionPerformed(ActionEvent e)
2217   {
2218   }
2219
2220   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2221   {
2222   }
2223
2224   public void vamsasStore_actionPerformed(ActionEvent e)
2225   {
2226
2227   }
2228
2229   public void vamsasLoad_actionPerformed(ActionEvent e)
2230   {
2231
2232   }
2233
2234   public void showTranslation_actionPerformed(ActionEvent e)
2235   {
2236
2237   }
2238
2239   public void featureSettings_actionPerformed(ActionEvent e)
2240   {
2241
2242   }
2243
2244   public void fetchSequence_actionPerformed(ActionEvent e)
2245   {
2246
2247   }
2248
2249   public void smoothFont_actionPerformed(ActionEvent e)
2250   {
2251
2252   }
2253
2254   public void annotationColour_actionPerformed(ActionEvent e)
2255   {
2256
2257   }
2258
2259   public void associatedData_actionPerformed(ActionEvent e)
2260   {
2261
2262   }
2263
2264   public void autoCalculate_actionPerformed(ActionEvent e)
2265   {
2266
2267   }
2268
2269   public void showAllSeqs_actionPerformed(ActionEvent e)
2270   {
2271
2272   }
2273
2274   public void showAllColumns_actionPerformed(ActionEvent e)
2275   {
2276
2277   }
2278
2279   public void hideSelSequences_actionPerformed(ActionEvent e)
2280   {
2281
2282   }
2283
2284   public void hideSelColumns_actionPerformed(ActionEvent e)
2285   {
2286
2287   }
2288
2289   public void hiddenMarkers_actionPerformed(ActionEvent e)
2290   {
2291
2292   }
2293
2294   public void findPdbId_actionPerformed(ActionEvent e)
2295   {
2296
2297   }
2298
2299   public void enterPdbId_actionPerformed(ActionEvent e)
2300   {
2301
2302   }
2303
2304   public void pdbFile_actionPerformed(ActionEvent e)
2305   {
2306
2307   }
2308
2309   public void invertColSel_actionPerformed(ActionEvent e)
2310   {
2311
2312   }
2313
2314   public void tabSelectionChanged(int sel)
2315   {
2316
2317   }
2318
2319   public void tabbedPane_mousePressed(MouseEvent e)
2320   {
2321
2322   }
2323
2324   public void tabbedPane_focusGained(FocusEvent e)
2325   {
2326     requestFocus();
2327   }
2328
2329   public void save_actionPerformed(ActionEvent e)
2330   {
2331
2332   }
2333
2334   public void reload_actionPerformed(ActionEvent e)
2335   {
2336
2337   }
2338
2339   public void newView_actionPerformed(ActionEvent e)
2340   {
2341
2342   }
2343
2344   public void textColour_actionPerformed(ActionEvent e)
2345   {
2346
2347   }
2348
2349   public void idRightAlign_actionPerformed(ActionEvent e)
2350   {
2351
2352   }
2353
2354   public void expandViews_actionPerformed(ActionEvent e)
2355   {
2356
2357   }
2358
2359   public void gatherViews_actionPerformed(ActionEvent e)
2360   {
2361
2362   }
2363
2364   public void buildTreeMenu()
2365   {
2366
2367   }
2368
2369   public void pageSetup_actionPerformed(ActionEvent e)
2370   {
2371
2372   }
2373
2374   public void alignmentProperties()
2375   {
2376
2377   }
2378 }