src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
   3  * Copyright (C) 2011 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 jalview.schemes.ColourSchemeProperty;
  21
  22 import java.awt.BorderLayout;
  23 import java.awt.Color;
  24 import java.awt.GridLayout;
  25 import java.awt.Toolkit;
  26 import java.awt.event.ActionEvent;
  27 import java.awt.event.ActionListener;
  28 import java.awt.event.FocusAdapter;
  29 import java.awt.event.FocusEvent;
  30 import java.awt.event.MouseAdapter;
  31 import java.awt.event.MouseEvent;
  32
  33 import javax.swing.BorderFactory;
  34 import javax.swing.ButtonGroup;
  35 import javax.swing.JCheckBoxMenuItem;
  36 import javax.swing.JInternalFrame;
  37 import javax.swing.JLabel;
  38 import javax.swing.JMenu;
  39 import javax.swing.JMenuBar;
  40 import javax.swing.JMenuItem;
  41 import javax.swing.JOptionPane;
  42 import javax.swing.JPanel;
  43 import javax.swing.JRadioButtonMenuItem;
  44 import javax.swing.JTabbedPane;
  45 import javax.swing.SwingUtilities;
  46 import javax.swing.event.ChangeEvent;
  47 import javax.swing.event.MenuEvent;
  48 import javax.swing.event.MenuListener;
  49
  50 public class GAlignFrame extends JInternalFrame
  51 {
  52   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  53
  54   protected JMenu fileMenu = new JMenu();
  55
  56   protected JMenuItem closeMenuItem = new JMenuItem();
  57
  58   protected JMenu editMenu = new JMenu();
  59
  60   protected JMenu viewMenu = new JMenu();
  61
  62   protected JMenu colourMenu = new JMenu();
  63
  64   protected JMenu calculateMenu = new JMenu();
  65
  66   protected JMenu webService = new JMenu();
  67
  68   protected JMenuItem webServiceNoServices;
  69
  70   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  71
  72   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  73
  74   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  75
  76   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  77
  78   protected JMenuItem remove2RightMenuItem = new JMenuItem();
  79
  80   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  81
  82   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  83
  84   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  85
  86   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  87
  88   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  89
  90   protected JMenuItem sortIDMenuItem = new JMenuItem();
  91
  92   protected JMenuItem sortLengthMenuItem = new JMenuItem();
  93
  94   protected JMenuItem sortGroupMenuItem = new JMenuItem();
  95
  96   protected JMenu sortByAnnotScore = new JMenu();
  97
  98   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
  99
 100   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
 101
 102   protected JMenuItem PCAMenuItem = new JMenuItem();
 103
 104   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
 105
 106   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
 107
 108   BorderLayout borderLayout1 = new BorderLayout();
 109
 110   public JLabel statusBar = new JLabel();
 111
 112   protected JMenuItem saveAs = new JMenuItem();
 113
 114   protected JMenu outputTextboxMenu = new JMenu();
 115
 116   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
 117
 118   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
 119
 120   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
 121
 122   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
 123
 124   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
 125
 126   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
 127
 128   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
 129
 130   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 131
 132   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
 133
 134   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
 135
 136   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 137
 138   protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
 139
 140
 141   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 142
 143   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
 144
 145   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 146
 147   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 148
 149   public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
 150
 151   JMenuItem htmlMenuItem = new JMenuItem();
 152
 153   JMenuItem overviewMenuItem = new JMenuItem();
 154
 155   protected JMenuItem undoMenuItem = new JMenuItem();
 156
 157   protected JMenuItem redoMenuItem = new JMenuItem();
 158
 159   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 160
 161   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 162
 163   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 164
 165   JMenuItem printMenuItem = new JMenuItem();
 166
 167   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 168
 169   JMenuItem findMenuItem = new JMenuItem();
 170
 171   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 172
 173   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 174
 175   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 176
 177   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
 178
 179   JMenuItem deleteGroups = new JMenuItem();
 180
 181   JMenuItem delete = new JMenuItem();
 182
 183   JMenuItem copy = new JMenuItem();
 184
 185   JMenuItem cut = new JMenuItem();
 186
 187   JMenu pasteMenu = new JMenu();
 188
 189   JMenuItem pasteNew = new JMenuItem();
 190
 191   JMenuItem pasteThis = new JMenuItem();
 192
 193   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
 194
 195   JMenuItem createPNG = new JMenuItem();
 196
 197   protected JMenuItem font = new JMenuItem();
 198
 199   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 200
 201   JMenuItem epsFile = new JMenuItem();
 202
 203   JMenuItem LoadtreeMenuItem = new JMenuItem();
 204
 205   JMenuItem loadScoresMenuItem = new JMenuItem();
 206
 207   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 208
 209   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 210
 211   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 212
 213   protected JMenuItem modifyPID = new JMenuItem();
 214
 215   protected JMenuItem modifyConservation = new JMenuItem();
 216
 217   protected JMenu sortByTreeMenu = new JMenu();
 218
 219   protected JMenu sort = new JMenu();
 220
 221   protected JMenu calculateTree = new JMenu();
 222
 223   JMenu jMenu2 = new JMenu();
 224
 225   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 226
 227   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 228
 229   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 230
 231   protected ButtonGroup colours = new ButtonGroup();
 232
 233   JMenuItem vamsasStore = new JMenuItem();
 234
 235   protected JMenuItem showTranslation = new JMenuItem();
 236
 237   protected JMenuItem extractScores = new JMenuItem();
 238
 239   protected JMenu showProducts = new JMenu();
 240
 241   public JMenuItem featureSettings = new JMenuItem();
 242
 243   JMenuItem fetchSequence = new JMenuItem();
 244
 245   JMenuItem annotationColour = new JMenuItem();
 246
 247   JMenuItem associatedData = new JMenuItem();
 248
 249   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 250
 251   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 252
 253   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 254
 255   JMenu addSequenceMenu = new JMenu();
 256
 257   JMenuItem addFromFile = new JMenuItem();
 258
 259   JMenuItem addFromText = new JMenuItem();
 260
 261   JMenuItem addFromURL = new JMenuItem();
 262
 263   JMenuItem exportAnnotations = new JMenuItem();
 264
 265   JMenuItem exportFeatures = new JMenuItem();
 266
 267   protected JPanel statusPanel = new JPanel();
 268
 269   GridLayout gridLayout1 = new GridLayout();
 270
 271   JMenu jMenu3 = new JMenu();
 272
 273   JMenuItem showAllSeqs = new JMenuItem();
 274
 275   JMenuItem showAllColumns = new JMenuItem();
 276
 277   JMenu hideMenu = new JMenu();
 278
 279   JMenuItem hideSelSequences = new JMenuItem();
 280
 281   JMenuItem hideSelColumns = new JMenuItem();
 282
 283   JMenuItem hideAllButSelection = new JMenuItem();
 284
 285   JMenuItem hideAllSelection = new JMenuItem();
 286
 287   JMenuItem showAllhidden = new JMenuItem();
 288
 289   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 290
 291   JMenuItem invertColSel = new JMenuItem();
 292
 293   protected JTabbedPane tabbedPane = new JTabbedPane();
 294
 295   JMenuItem save = new JMenuItem();
 296
 297   protected JMenuItem reload = new JMenuItem();
 298
 299   JMenuItem newView = new JMenuItem();
 300
 301   JMenuItem textColour = new JMenuItem();
 302
 303   JMenu formatMenu = new JMenu();
 304
 305   JMenu selectMenu = new JMenu();
 306
 307   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 308
 309   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 310
 311   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 312
 313   protected JMenuItem gatherViews = new JMenuItem();
 314
 315   protected JMenuItem expandViews = new JMenuItem();
 316
 317   JMenuItem pageSetup = new JMenuItem();
 318
 319   JMenuItem alignmentProperties = new JMenuItem();
 320
 321   JMenu tooltipSettingsMenu = new JMenu();
 322
 323   private JMenuItem justifyLeftMenuItem = new JMenuItem();
 324
 325   private JMenuItem justifyRightMenuItem = new JMenuItem();
 326
 327   JMenu autoAnnMenu = new JMenu();
 328
 329   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 330
 331   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 332
 333   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 334
 335   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 336
 337   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 338
 339   private JMenuItem grpsFromSelection = new JMenuItem();
 340
 341   public GAlignFrame()
 342   {
 343     try
 344     {
 345       jbInit();
 346       setJMenuBar(alignFrameMenuBar);
 347
 348       // dynamically fill save as menu with available formats
 349       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 350       {
 351         JMenuItem item = new JMenuItem(
 352                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 353
 354         item.addActionListener(new java.awt.event.ActionListener()
 355         {
 356           public void actionPerformed(ActionEvent e)
 357           {
 358             outputText_actionPerformed(e);
 359           }
 360         });
 361
 362         outputTextboxMenu.add(item);
 363       }
 364     } catch (Exception e)
 365     {
 366     }
 367
 368     if (!new jalview.util.Platform().isAMac())
 369     {
 370       closeMenuItem.setMnemonic('C');
 371       outputTextboxMenu.setMnemonic('T');
 372       undoMenuItem.setMnemonic('Z');
 373       redoMenuItem.setMnemonic('0');
 374       copy.setMnemonic('C');
 375       cut.setMnemonic('U');
 376       pasteMenu.setMnemonic('P');
 377       reload.setMnemonic('R');
 378     }
 379
 380     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 381     {
 382       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 383               .getUserColourSchemes().keys();
 384
 385       while (userColours.hasMoreElements())
 386       {
 387         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 388                 userColours.nextElement().toString());
 389         radioItem.setName("USER_DEFINED");
 390         radioItem.addMouseListener(new MouseAdapter()
 391         {
 392           public void mousePressed(MouseEvent evt)
 393           {
 394             if (evt.isControlDown()
 395                     || SwingUtilities.isRightMouseButton(evt))
 396             {
 397               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 398
 399               int option = JOptionPane.showInternalConfirmDialog(
 400                       jalview.gui.Desktop.desktop,
 401                       "Remove from default list?",
 402                       "Remove user defined colour",
 403                       JOptionPane.YES_NO_OPTION);
 404               if (option == JOptionPane.YES_OPTION)
 405               {
 406                 jalview.gui.UserDefinedColours
 407                         .removeColourFromDefaults(radioItem.getText());
 408                 colourMenu.remove(radioItem);
 409               }
 410               else
 411               {
 412                 radioItem.addActionListener(new ActionListener()
 413                 {
 414                   public void actionPerformed(ActionEvent evt)
 415                   {
 416                     userDefinedColour_actionPerformed(evt);
 417                   }
 418                 });
 419               }
 420             }
 421           }
 422         });
 423         radioItem.addActionListener(new ActionListener()
 424         {
 425           public void actionPerformed(ActionEvent evt)
 426           {
 427             userDefinedColour_actionPerformed(evt);
 428           }
 429         });
 430         colourMenu.insert(radioItem, 15);
 431         colours.add(radioItem);
 432       }
 433     }
 434     colours.add(noColourmenuItem);
 435     colours.add(clustalColour);
 436     colours.add(zappoColour);
 437     colours.add(taylorColour);
 438     colours.add(hydrophobicityColour);
 439     colours.add(helixColour);
 440     colours.add(strandColour);
 441     colours.add(turnColour);
 442     colours.add(buriedColour);
 443     colours.add(userDefinedColour);
 444     colours.add(PIDColour);
 445     colours.add(BLOSUM62Colour);
 446     colours.add(nucleotideColour);
 447     colours.add(tcoffeeColour);
 448
 449     setColourSelected(jalview.bin.Cache
 450             .getDefault("DEFAULT_COLOUR", "None"));
 451
 452   }
 453
 454   public void setColourSelected(String defaultColour)
 455   {
 456
 457     if (defaultColour != null)
 458     {
 459       int index = ColourSchemeProperty
 460               .getColourIndexFromName(defaultColour);
 461
 462       switch (index)
 463       {
 464       case ColourSchemeProperty.CLUSTAL:
 465         clustalColour.setSelected(true);
 466
 467         break;
 468
 469       case ColourSchemeProperty.BLOSUM:
 470         BLOSUM62Colour.setSelected(true);
 471
 472         break;
 473
 474       case ColourSchemeProperty.PID:
 475         PIDColour.setSelected(true);
 476
 477         break;
 478
 479       case ColourSchemeProperty.ZAPPO:
 480         zappoColour.setSelected(true);
 481
 482         break;
 483
 484       case ColourSchemeProperty.TAYLOR:
 485         taylorColour.setSelected(true);
 486         break;
 487
 488       case ColourSchemeProperty.HYDROPHOBIC:
 489         hydrophobicityColour.setSelected(true);
 490
 491         break;
 492
 493       case ColourSchemeProperty.HELIX:
 494         helixColour.setSelected(true);
 495
 496         break;
 497
 498       case ColourSchemeProperty.STRAND:
 499         strandColour.setSelected(true);
 500
 501         break;
 502
 503       case ColourSchemeProperty.TURN:
 504         turnColour.setSelected(true);
 505
 506         break;
 507
 508       case ColourSchemeProperty.BURIED:
 509         buriedColour.setSelected(true);
 510
 511         break;
 512
 513       case ColourSchemeProperty.NUCLEOTIDE:
 514         nucleotideColour.setSelected(true);
 515
 516         break;
 517
 518       case ColourSchemeProperty.TCOFFEE:
 519         tcoffeeColour.setSelected(true);
 520         break;
 521
 522       case ColourSchemeProperty.USER_DEFINED:
 523         userDefinedColour.setSelected(true);
 524
 525         break;
 526       case ColourSchemeProperty.NONE:
 527       default:
 528         noColourmenuItem.setSelected(true);
 529         break;
 530
 531       }
 532     }
 533
 534   }
 535
 536   private void jbInit() throws Exception
 537   {
 538     fileMenu.setText("File");
 539     saveAs.setText("Save As...");
 540     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 541             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
 542                     .getMenuShortcutKeyMask()
 543                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 544     saveAs.addActionListener(new ActionListener()
 545     {
 546       public void actionPerformed(ActionEvent e)
 547       {
 548         saveAs_actionPerformed(e);
 549       }
 550     });
 551     closeMenuItem.setText("Close");
 552     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 553             java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
 554                     .getMenuShortcutKeyMask(), false));
 555     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 556     {
 557       public void actionPerformed(ActionEvent e)
 558       {
 559         closeMenuItem_actionPerformed(false);
 560       }
 561     });
 562     editMenu.setText("Edit");
 563     viewMenu.setText("View");
 564     colourMenu.setText("Colour");
 565     calculateMenu.setText("Calculate");
 566     webService.setText("Web Service");
 567     selectAllSequenceMenuItem.setText("Select All");
 568     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 569             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
 570                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 571     selectAllSequenceMenuItem
 572             .addActionListener(new java.awt.event.ActionListener()
 573             {
 574               public void actionPerformed(ActionEvent e)
 575               {
 576                 selectAllSequenceMenuItem_actionPerformed(e);
 577               }
 578             });
 579     deselectAllSequenceMenuItem.setText("Deselect All");
 580     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 581             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 582     deselectAllSequenceMenuItem
 583             .addActionListener(new java.awt.event.ActionListener()
 584             {
 585               public void actionPerformed(ActionEvent e)
 586               {
 587                 deselectAllSequenceMenuItem_actionPerformed(e);
 588               }
 589             });
 590     invertSequenceMenuItem.setText("Invert Sequence Selection");
 591     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 592             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
 593                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 594     invertSequenceMenuItem
 595             .addActionListener(new java.awt.event.ActionListener()
 596             {
 597               public void actionPerformed(ActionEvent e)
 598               {
 599                 invertSequenceMenuItem_actionPerformed(e);
 600               }
 601             });
 602     grpsFromSelection.setText("Make Groups for selection");
 603     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
 604     {
 605       public void actionPerformed(ActionEvent e)
 606       {
 607         makeGrpsFromSelection_actionPerformed(e);
 608       }
 609     });
 610
 611     remove2LeftMenuItem.setText("Remove Left");
 612     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 613             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
 614                     .getMenuShortcutKeyMask(), false));
 615     remove2LeftMenuItem
 616             .addActionListener(new java.awt.event.ActionListener()
 617             {
 618               public void actionPerformed(ActionEvent e)
 619               {
 620                 remove2LeftMenuItem_actionPerformed(e);
 621               }
 622             });
 623     remove2RightMenuItem.setText("Remove Right");
 624     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 625             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
 626                     .getMenuShortcutKeyMask(), false));
 627     remove2RightMenuItem
 628             .addActionListener(new java.awt.event.ActionListener()
 629             {
 630               public void actionPerformed(ActionEvent e)
 631               {
 632                 remove2RightMenuItem_actionPerformed(e);
 633               }
 634             });
 635     removeGappedColumnMenuItem.setText("Remove Empty Columns");
 636     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
 637             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 638                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 639     removeGappedColumnMenuItem
 640             .addActionListener(new java.awt.event.ActionListener()
 641             {
 642               public void actionPerformed(ActionEvent e)
 643               {
 644                 removeGappedColumnMenuItem_actionPerformed(e);
 645               }
 646             });
 647     removeAllGapsMenuItem.setText("Remove All Gaps");
 648     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
 649             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 650                     .getDefaultToolkit().getMenuShortcutKeyMask()
 651                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 652     removeAllGapsMenuItem
 653             .addActionListener(new java.awt.event.ActionListener()
 654             {
 655               public void actionPerformed(ActionEvent e)
 656               {
 657                 removeAllGapsMenuItem_actionPerformed(e);
 658               }
 659             });
 660     justifyLeftMenuItem.setText("Left Justify Alignment");
 661     justifyLeftMenuItem
 662             .addActionListener(new java.awt.event.ActionListener()
 663             {
 664               public void actionPerformed(ActionEvent e)
 665               {
 666                 justifyLeftMenuItem_actionPerformed(e);
 667               }
 668             });
 669     justifyRightMenuItem.setText("Right Justify Alignment");
 670     justifyRightMenuItem
 671             .addActionListener(new java.awt.event.ActionListener()
 672             {
 673               public void actionPerformed(ActionEvent e)
 674               {
 675                 justifyRightMenuItem_actionPerformed(e);
 676               }
 677             });
 678     viewBoxesMenuItem.setText("Boxes");
 679     viewBoxesMenuItem.setState(true);
 680     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 681     {
 682       public void actionPerformed(ActionEvent e)
 683       {
 684         viewBoxesMenuItem_actionPerformed(e);
 685       }
 686     });
 687     viewTextMenuItem.setText("Text");
 688     viewTextMenuItem.setState(true);
 689     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 690     {
 691       public void actionPerformed(ActionEvent e)
 692       {
 693         viewTextMenuItem_actionPerformed(e);
 694       }
 695     });
 696     showNonconservedMenuItem.setText("Show nonconserved");
 697     showNonconservedMenuItem.setState(false);
 698     showNonconservedMenuItem
 699             .addActionListener(new java.awt.event.ActionListener()
 700             {
 701               public void actionPerformed(ActionEvent e)
 702               {
 703                 showUnconservedMenuItem_actionPerformed(e);
 704               }
 705             });
 706     sortPairwiseMenuItem.setText("by Pairwise Identity");
 707     sortPairwiseMenuItem
 708             .addActionListener(new java.awt.event.ActionListener()
 709             {
 710               public void actionPerformed(ActionEvent e)
 711               {
 712                 sortPairwiseMenuItem_actionPerformed(e);
 713               }
 714             });
 715     sortIDMenuItem.setText("by ID");
 716     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 717     {
 718       public void actionPerformed(ActionEvent e)
 719       {
 720         sortIDMenuItem_actionPerformed(e);
 721       }
 722     });
 723     sortLengthMenuItem.setText("By Length");
 724     sortLengthMenuItem
 725             .addActionListener(new java.awt.event.ActionListener()
 726             {
 727               public void actionPerformed(ActionEvent e)
 728               {
 729                 sortLengthMenuItem_actionPerformed(e);
 730               }
 731             });
 732     sortGroupMenuItem.setText("by Group");
 733     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 734     {
 735       public void actionPerformed(ActionEvent e)
 736       {
 737         sortGroupMenuItem_actionPerformed(e);
 738       }
 739     });
 740     removeRedundancyMenuItem.setText("Remove Redundancy...");
 741     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
 742             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
 743                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 744     removeRedundancyMenuItem
 745             .addActionListener(new java.awt.event.ActionListener()
 746             {
 747               public void actionPerformed(ActionEvent e)
 748               {
 749                 removeRedundancyMenuItem_actionPerformed(e);
 750               }
 751             });
 752     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
 753     pairwiseAlignmentMenuItem
 754             .addActionListener(new java.awt.event.ActionListener()
 755             {
 756               public void actionPerformed(ActionEvent e)
 757               {
 758                 pairwiseAlignmentMenuItem_actionPerformed(e);
 759               }
 760             });
 761     PCAMenuItem.setText("Principal Component Analysis");
 762     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 763     {
 764       public void actionPerformed(ActionEvent e)
 765       {
 766         PCAMenuItem_actionPerformed(e);
 767       }
 768     });
 769     averageDistanceTreeMenuItem
 770             .setText("Average Distance Using % Identity");
 771     averageDistanceTreeMenuItem
 772             .addActionListener(new java.awt.event.ActionListener()
 773             {
 774               public void actionPerformed(ActionEvent e)
 775               {
 776                 averageDistanceTreeMenuItem_actionPerformed(e);
 777               }
 778             });
 779     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
 780     neighbourTreeMenuItem
 781             .addActionListener(new java.awt.event.ActionListener()
 782             {
 783               public void actionPerformed(ActionEvent e)
 784               {
 785                 neighbourTreeMenuItem_actionPerformed(e);
 786               }
 787             });
 788     this.getContentPane().setLayout(borderLayout1);
 789     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 790     statusBar.setBackground(Color.white);
 791     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 792     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 793     statusBar.setText("Status bar");
 794     outputTextboxMenu.setText("Output to Textbox");
 795     clustalColour.setText("Clustalx");
 796
 797     clustalColour.addActionListener(new java.awt.event.ActionListener()
 798     {
 799       public void actionPerformed(ActionEvent e)
 800       {
 801         clustalColour_actionPerformed(e);
 802       }
 803     });
 804     zappoColour.setText("Zappo");
 805     zappoColour.addActionListener(new java.awt.event.ActionListener()
 806     {
 807       public void actionPerformed(ActionEvent e)
 808       {
 809         zappoColour_actionPerformed(e);
 810       }
 811     });
 812     taylorColour.setText("Taylor");
 813     taylorColour.addActionListener(new java.awt.event.ActionListener()
 814     {
 815       public void actionPerformed(ActionEvent e)
 816       {
 817         taylorColour_actionPerformed(e);
 818       }
 819     });
 820     hydrophobicityColour.setText("Hydrophobicity");
 821     hydrophobicityColour
 822             .addActionListener(new java.awt.event.ActionListener()
 823             {
 824               public void actionPerformed(ActionEvent e)
 825               {
 826                 hydrophobicityColour_actionPerformed(e);
 827               }
 828             });
 829     helixColour.setText("Helix Propensity");
 830     helixColour.addActionListener(new java.awt.event.ActionListener()
 831     {
 832       public void actionPerformed(ActionEvent e)
 833       {
 834         helixColour_actionPerformed(e);
 835       }
 836     });
 837     strandColour.setText("Strand Propensity");
 838     strandColour.addActionListener(new java.awt.event.ActionListener()
 839     {
 840       public void actionPerformed(ActionEvent e)
 841       {
 842         strandColour_actionPerformed(e);
 843       }
 844     });
 845     turnColour.setText("Turn Propensity");
 846     turnColour.addActionListener(new java.awt.event.ActionListener()
 847     {
 848       public void actionPerformed(ActionEvent e)
 849       {
 850         turnColour_actionPerformed(e);
 851       }
 852     });
 853     buriedColour.setText("Buried Index");
 854     buriedColour.addActionListener(new java.awt.event.ActionListener()
 855     {
 856       public void actionPerformed(ActionEvent e)
 857       {
 858         buriedColour_actionPerformed(e);
 859       }
 860     });
 861     userDefinedColour.setText("User Defined...");
 862     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 863     {
 864       public void actionPerformed(ActionEvent e)
 865       {
 866         userDefinedColour_actionPerformed(e);
 867       }
 868     });
 869     PIDColour.setText("Percentage Identity");
 870     PIDColour.addActionListener(new java.awt.event.ActionListener()
 871     {
 872       public void actionPerformed(ActionEvent e)
 873       {
 874         PIDColour_actionPerformed(e);
 875       }
 876     });
 877     BLOSUM62Colour.setText("BLOSUM62 Score");
 878     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 879     {
 880       public void actionPerformed(ActionEvent e)
 881       {
 882         BLOSUM62Colour_actionPerformed(e);
 883       }
 884     });
 885     avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
 886     avDistanceTreeBlosumMenuItem
 887             .addActionListener(new java.awt.event.ActionListener()
 888             {
 889               public void actionPerformed(ActionEvent e)
 890               {
 891                 avTreeBlosumMenuItem_actionPerformed(e);
 892               }
 893             });
 894     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
 895     njTreeBlosumMenuItem
 896             .addActionListener(new java.awt.event.ActionListener()
 897             {
 898               public void actionPerformed(ActionEvent e)
 899               {
 900                 njTreeBlosumMenuItem_actionPerformed(e);
 901               }
 902             });
 903     annotationPanelMenuItem.setActionCommand("");
 904     annotationPanelMenuItem.setText("Show Annotations");
 905     annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
 906             "SHOW_ANNOTATIONS", true));
 907     annotationPanelMenuItem
 908             .addActionListener(new java.awt.event.ActionListener()
 909             {
 910               public void actionPerformed(ActionEvent e)
 911               {
 912                 annotationPanelMenuItem_actionPerformed(e);
 913               }
 914             });
 915     colourTextMenuItem.setText("Colour Text");
 916     colourTextMenuItem
 917             .addActionListener(new java.awt.event.ActionListener()
 918             {
 919               public void actionPerformed(ActionEvent e)
 920               {
 921                 colourTextMenuItem_actionPerformed(e);
 922               }
 923             });
 924     htmlMenuItem.setText("HTML");
 925     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
 926     {
 927       public void actionPerformed(ActionEvent e)
 928       {
 929         htmlMenuItem_actionPerformed(e);
 930       }
 931     });
 932     overviewMenuItem.setText("Overview Window");
 933     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
 934     {
 935       public void actionPerformed(ActionEvent e)
 936       {
 937         overviewMenuItem_actionPerformed(e);
 938       }
 939     });
 940     undoMenuItem.setEnabled(false);
 941     undoMenuItem.setText("Undo");
 942     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 943             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
 944                     .getMenuShortcutKeyMask(), false));
 945     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
 946     {
 947       public void actionPerformed(ActionEvent e)
 948       {
 949         undoMenuItem_actionPerformed(e);
 950       }
 951     });
 952     redoMenuItem.setEnabled(false);
 953     redoMenuItem.setText("Redo");
 954     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 955             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
 956                     .getMenuShortcutKeyMask(), false));
 957     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
 958     {
 959       public void actionPerformed(ActionEvent e)
 960       {
 961         redoMenuItem_actionPerformed(e);
 962       }
 963     });
 964     conservationMenuItem.setText("By Conservation");
 965     conservationMenuItem
 966             .addActionListener(new java.awt.event.ActionListener()
 967             {
 968               public void actionPerformed(ActionEvent e)
 969               {
 970                 conservationMenuItem_actionPerformed(e);
 971               }
 972             });
 973     noColourmenuItem.setText("None");
 974     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 975     {
 976       public void actionPerformed(ActionEvent e)
 977       {
 978         noColourmenuItem_actionPerformed(e);
 979       }
 980     });
 981     wrapMenuItem.setText("Wrap");
 982     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
 983     {
 984       public void actionPerformed(ActionEvent e)
 985       {
 986         wrapMenuItem_actionPerformed(e);
 987       }
 988     });
 989     printMenuItem.setText("Print ...");
 990     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 991             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
 992                     .getMenuShortcutKeyMask(), false));
 993     printMenuItem.addActionListener(new java.awt.event.ActionListener()
 994     {
 995       public void actionPerformed(ActionEvent e)
 996       {
 997         printMenuItem_actionPerformed(e);
 998       }
 999     });
1000     renderGapsMenuItem.setText("Show Gaps");
1001     renderGapsMenuItem.setState(true);
1002     renderGapsMenuItem
1003             .addActionListener(new java.awt.event.ActionListener()
1004             {
1005               public void actionPerformed(ActionEvent e)
1006               {
1007                 renderGapsMenuItem_actionPerformed(e);
1008               }
1009             });
1010     findMenuItem.setText("Find...");
1011     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1012             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1013                     .getMenuShortcutKeyMask(), false));
1014     findMenuItem.addActionListener(new java.awt.event.ActionListener()
1015     {
1016       public void actionPerformed(ActionEvent e)
1017       {
1018         findMenuItem_actionPerformed(e);
1019       }
1020     });
1021     abovePIDThreshold.setText("Above Identity Threshold");
1022     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1023     {
1024       public void actionPerformed(ActionEvent e)
1025       {
1026         abovePIDThreshold_actionPerformed(e);
1027       }
1028     });
1029     showSeqFeatures.setText("Show Sequence Features");
1030     showSeqFeatures.addActionListener(new ActionListener()
1031     {
1032       public void actionPerformed(ActionEvent actionEvent)
1033       {
1034         showSeqFeatures_actionPerformed(actionEvent);
1035       }
1036     });
1037     /*
1038      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1039      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1040      * void actionPerformed(ActionEvent actionEvent) {
1041      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1042      */
1043     showDbRefsMenuitem.setText("Show Database Refs");
1044     showDbRefsMenuitem.addActionListener(new ActionListener()
1045     {
1046
1047       public void actionPerformed(ActionEvent e)
1048       {
1049         showDbRefs_actionPerformed(e);
1050       }
1051
1052     });
1053     showNpFeatsMenuitem.setText("Show Non-Positional Features");
1054     showNpFeatsMenuitem.addActionListener(new ActionListener()
1055     {
1056
1057       public void actionPerformed(ActionEvent e)
1058       {
1059         showNpFeats_actionPerformed(e);
1060       }
1061
1062     });
1063     showGroupConservation.setText("Group Conservation");
1064     showGroupConservation.addActionListener(new ActionListener()
1065     {
1066
1067       public void actionPerformed(ActionEvent e)
1068       {
1069         showGroupConservation_actionPerformed(e);
1070       }
1071
1072     });
1073
1074     showGroupConsensus.setText("Group Consensus");
1075     showGroupConsensus.addActionListener(new ActionListener()
1076     {
1077
1078       public void actionPerformed(ActionEvent e)
1079       {
1080         showGroupConsensus_actionPerformed(e);
1081       }
1082
1083     });
1084     showConsensusHistogram.setText("Show Consensus Histogram");
1085     showConsensusHistogram.addActionListener(new ActionListener()
1086     {
1087
1088       public void actionPerformed(ActionEvent e)
1089       {
1090         showConsensusHistogram_actionPerformed(e);
1091       }
1092
1093     });
1094     showSequenceLogo.setText("Show Consensus Logo");
1095     showSequenceLogo.addActionListener(new ActionListener()
1096     {
1097
1098       public void actionPerformed(ActionEvent e)
1099       {
1100         showSequenceLogo_actionPerformed(e);
1101       }
1102
1103     });
1104     applyAutoAnnotationSettings.setText("Apply to all groups");
1105     applyAutoAnnotationSettings.setState(false);
1106     applyAutoAnnotationSettings.setVisible(true);
1107     applyAutoAnnotationSettings.addActionListener(new ActionListener()
1108     {
1109
1110       public void actionPerformed(ActionEvent e)
1111       {
1112         applyAutoAnnotationSettings_actionPerformed(e);
1113       }
1114
1115     });
1116
1117     nucleotideColour.setText("Nucleotide");
1118     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1119     {
1120       public void actionPerformed(ActionEvent e)
1121       {
1122         nucleotideColour_actionPerformed(e);
1123       }
1124     });
1125
1126     tcoffeeColour.setText("T-Coffee scores");
1127     tcoffeeColour.setEnabled(false);
1128     tcoffeeColour.addActionListener( new ActionListener() {
1129
1130                 @Override
1131                 public void actionPerformed(ActionEvent e) {
1132                         tcoffeeColorScheme_actionPerformed(e);
1133                 }
1134         } );
1135
1136
1137     deleteGroups.setText("Undefine groups");
1138     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1139             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1140                     .getMenuShortcutKeyMask(), false));
1141     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1142     {
1143       public void actionPerformed(ActionEvent e)
1144       {
1145         deleteGroups_actionPerformed(e);
1146       }
1147     });
1148     copy.setText("Copy");
1149     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1150             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1151                     .getMenuShortcutKeyMask(), false));
1152
1153     copy.addActionListener(new java.awt.event.ActionListener()
1154     {
1155       public void actionPerformed(ActionEvent e)
1156       {
1157         copy_actionPerformed(e);
1158       }
1159     });
1160     cut.setText("Cut");
1161     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1162             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1163                     .getMenuShortcutKeyMask(), false));
1164     cut.addActionListener(new java.awt.event.ActionListener()
1165     {
1166       public void actionPerformed(ActionEvent e)
1167       {
1168         cut_actionPerformed(e);
1169       }
1170     });
1171     delete.setText("Delete");
1172     delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1173             java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1174     delete.addActionListener(new java.awt.event.ActionListener()
1175     {
1176       public void actionPerformed(ActionEvent e)
1177       {
1178         delete_actionPerformed(e);
1179       }
1180     });
1181     pasteMenu.setText("Paste");
1182     pasteNew.setText("To New Alignment");
1183     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1184             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1185                     .getMenuShortcutKeyMask()
1186                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1187     pasteNew.addActionListener(new java.awt.event.ActionListener()
1188     {
1189       public void actionPerformed(ActionEvent e)
1190       {
1191         pasteNew_actionPerformed(e);
1192       }
1193     });
1194     pasteThis.setText("Add To This Alignment");
1195     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1196             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1197                     .getMenuShortcutKeyMask(), false));
1198     pasteThis.addActionListener(new java.awt.event.ActionListener()
1199     {
1200       public void actionPerformed(ActionEvent e)
1201       {
1202         pasteThis_actionPerformed(e);
1203       }
1204     });
1205     applyToAllGroups.setText("Apply Colour To All Groups");
1206     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1207     {
1208       public void actionPerformed(ActionEvent e)
1209       {
1210         applyToAllGroups_actionPerformed(e);
1211       }
1212     });
1213     createPNG.addActionListener(new java.awt.event.ActionListener()
1214     {
1215       public void actionPerformed(ActionEvent e)
1216       {
1217         createPNG(null);
1218       }
1219     });
1220     createPNG.setActionCommand("Save As PNG Image");
1221     createPNG.setText("PNG");
1222     font.setText("Font...");
1223     font.addActionListener(new java.awt.event.ActionListener()
1224     {
1225       public void actionPerformed(ActionEvent e)
1226       {
1227         font_actionPerformed(e);
1228       }
1229     });
1230
1231     seqLimits.setText("Show Sequence Limits");
1232     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1233     seqLimits.addActionListener(new java.awt.event.ActionListener()
1234     {
1235       public void actionPerformed(ActionEvent e)
1236       {
1237         seqLimit_actionPerformed(e);
1238       }
1239     });
1240     epsFile.setText("EPS");
1241     epsFile.addActionListener(new java.awt.event.ActionListener()
1242     {
1243       public void actionPerformed(ActionEvent e)
1244       {
1245         createEPS(null);
1246       }
1247     });
1248     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1249     LoadtreeMenuItem.setText("Load Associated Tree");
1250     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1251     {
1252       public void actionPerformed(ActionEvent e)
1253       {
1254         LoadtreeMenuItem_actionPerformed(e);
1255       }
1256     });
1257
1258     loadScoresMenuItem.setActionCommand("Load T-Coffee scores");
1259     loadScoresMenuItem.setText("Load T-Coffee scores");
1260     loadScoresMenuItem.addActionListener(new ActionListener() {
1261
1262                 @Override
1263                 public void actionPerformed(ActionEvent e) {
1264                         loadScores_actionPerformed(e);
1265                 }
1266         });
1267
1268     scaleAbove.setVisible(false);
1269     scaleAbove.setText("Scale Above");
1270     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1271     {
1272       public void actionPerformed(ActionEvent e)
1273       {
1274         scaleAbove_actionPerformed(e);
1275       }
1276     });
1277     scaleLeft.setVisible(false);
1278     scaleLeft.setSelected(true);
1279     scaleLeft.setText("Scale Left");
1280     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1281     {
1282       public void actionPerformed(ActionEvent e)
1283       {
1284         scaleLeft_actionPerformed(e);
1285       }
1286     });
1287     scaleRight.setVisible(false);
1288     scaleRight.setSelected(true);
1289     scaleRight.setText("Scale Right");
1290     scaleRight.addActionListener(new java.awt.event.ActionListener()
1291     {
1292       public void actionPerformed(ActionEvent e)
1293       {
1294         scaleRight_actionPerformed(e);
1295       }
1296     });
1297     centreColumnLabelsMenuItem.setVisible(true);
1298     centreColumnLabelsMenuItem.setState(false);
1299     centreColumnLabelsMenuItem.setText("Centre Column Labels");
1300     centreColumnLabelsMenuItem
1301             .addActionListener(new java.awt.event.ActionListener()
1302             {
1303               public void actionPerformed(ActionEvent e)
1304               {
1305                 centreColumnLabels_actionPerformed(e);
1306               }
1307             });
1308     followHighlightMenuItem.setVisible(true);
1309     followHighlightMenuItem.setState(true);
1310     followHighlightMenuItem.setText("Automatic Scrolling");
1311     followHighlightMenuItem.addActionListener(new ActionListener()
1312     {
1313
1314       public void actionPerformed(ActionEvent e)
1315       {
1316         followHighlight_actionPerformed();
1317       }
1318
1319     });
1320
1321     modifyPID.setText("Modify Identity Threshold...");
1322     modifyPID.addActionListener(new java.awt.event.ActionListener()
1323     {
1324       public void actionPerformed(ActionEvent e)
1325       {
1326         modifyPID_actionPerformed(e);
1327       }
1328     });
1329     modifyConservation.setText("Modify Conservation Threshold...");
1330     modifyConservation
1331             .addActionListener(new java.awt.event.ActionListener()
1332             {
1333               public void actionPerformed(ActionEvent e)
1334               {
1335                 modifyConservation_actionPerformed(e);
1336               }
1337             });
1338     sortByTreeMenu.setText("By Tree Order");
1339     sort.setText("Sort");
1340     sort.addMenuListener(new MenuListener()
1341     {
1342       public void menuSelected(MenuEvent e)
1343       {
1344         buildTreeMenu();
1345       }
1346
1347       public void menuDeselected(MenuEvent e)
1348       {
1349       }
1350
1351       public void menuCanceled(MenuEvent e)
1352       {
1353       }
1354     });
1355     sortByAnnotScore.setText("by Score");
1356     sort.add(sortByAnnotScore);
1357     sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1358     {
1359
1360       public void menuCanceled(MenuEvent e)
1361       {
1362       }
1363
1364       public void menuDeselected(MenuEvent e)
1365       {
1366       }
1367
1368       public void menuSelected(MenuEvent e)
1369       {
1370         buildSortByAnnotationScoresMenu();
1371       }
1372     });
1373     sortByAnnotScore.setVisible(false);
1374
1375     calculateTree.setText("Calculate Tree");
1376
1377     jMenu2.setText("Export Image");
1378     padGapsMenuitem.setText("Pad Gaps");
1379     padGapsMenuitem.setState(jalview.bin.Cache
1380             .getDefault("PAD_GAPS", false));
1381     padGapsMenuitem.addActionListener(new ActionListener()
1382     {
1383       public void actionPerformed(ActionEvent e)
1384       {
1385         padGapsMenuitem_actionPerformed(e);
1386       }
1387     });
1388     vamsasStore.setVisible(false);
1389     vamsasStore.setText("VAMSAS store");
1390     vamsasStore.addActionListener(new ActionListener()
1391     {
1392       public void actionPerformed(ActionEvent e)
1393       {
1394         vamsasStore_actionPerformed(e);
1395       }
1396     });
1397     showTranslation.setText("Translate cDNA");
1398     showTranslation.addActionListener(new ActionListener()
1399     {
1400       public void actionPerformed(ActionEvent e)
1401       {
1402         showTranslation_actionPerformed(e);
1403       }
1404     });
1405     extractScores.setText("Extract Scores...");
1406     extractScores.addActionListener(new ActionListener()
1407     {
1408       public void actionPerformed(ActionEvent e)
1409       {
1410         extractScores_actionPerformed(e);
1411       }
1412     });
1413     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1414     // score extraction
1415     showProducts.setText("Get Cross References");
1416     /*
1417      * showProducts.addActionListener(new ActionListener() {
1418      *
1419      * public void actionPerformed(ActionEvent e) {
1420      * showProducts_actionPerformed(e); } });
1421      */
1422     featureSettings.setText("Feature Settings...");
1423     featureSettings.addActionListener(new ActionListener()
1424     {
1425       public void actionPerformed(ActionEvent e)
1426       {
1427         featureSettings_actionPerformed(e);
1428       }
1429     });
1430     fetchSequence.setText("Fetch Sequence(s)...");
1431     fetchSequence.addActionListener(new ActionListener()
1432     {
1433       public void actionPerformed(ActionEvent e)
1434       {
1435         fetchSequence_actionPerformed(e);
1436       }
1437     });
1438
1439     annotationColour.setText("By Annotation...");
1440     annotationColour.addActionListener(new ActionListener()
1441     {
1442       public void actionPerformed(ActionEvent e)
1443       {
1444         annotationColour_actionPerformed(e);
1445       }
1446     });
1447     associatedData.setText("Load Features / Annotations");
1448     associatedData.addActionListener(new ActionListener()
1449     {
1450       public void actionPerformed(ActionEvent e)
1451       {
1452         associatedData_actionPerformed(e);
1453       }
1454     });
1455     autoCalculate.setText("Autocalculate Consensus");
1456     autoCalculate.setState(jalview.bin.Cache.getDefault(
1457             "AUTO_CALC_CONSENSUS", true));
1458     autoCalculate.addActionListener(new ActionListener()
1459     {
1460       public void actionPerformed(ActionEvent e)
1461       {
1462         autoCalculate_actionPerformed(e);
1463       }
1464     });
1465     sortByTree.setText("Sort Alignment With New Tree");
1466     sortByTree.setToolTipText("<html>Enable this to automatically sort<br>the alignment when you open<br> a new tree.");
1467     sortByTree.setState(jalview.bin.Cache.getDefault(
1468             "SORT_BY_TREE", false));
1469     sortByTree.addActionListener(new ActionListener()
1470     {
1471       public void actionPerformed(ActionEvent e)
1472       {
1473         sortByTreeOption_actionPerformed(e);
1474       }
1475     });
1476
1477     listenToViewSelections.setText("Listen for selections");
1478     listenToViewSelections.setToolTipText("<html>When selected, selections in this view will mirror<br>selections made on the same sequences in other views.");
1479     listenToViewSelections.setState(false);
1480     listenToViewSelections.addActionListener(new ActionListener()
1481     {
1482       public void actionPerformed(ActionEvent e)
1483       {
1484         listenToViewSelections_actionPerformed(e);
1485       }
1486     });
1487
1488     addSequenceMenu.setText("Add Sequences");
1489     addFromFile.setText("From File");
1490     addFromFile.addActionListener(new ActionListener()
1491     {
1492       public void actionPerformed(ActionEvent e)
1493       {
1494         addFromFile_actionPerformed(e);
1495       }
1496     });
1497     addFromText.setText("From Textbox");
1498     addFromText.addActionListener(new ActionListener()
1499     {
1500       public void actionPerformed(ActionEvent e)
1501       {
1502         addFromText_actionPerformed(e);
1503       }
1504     });
1505     addFromURL.setText("From URL");
1506     addFromURL.addActionListener(new ActionListener()
1507     {
1508       public void actionPerformed(ActionEvent e)
1509       {
1510         addFromURL_actionPerformed(e);
1511       }
1512     });
1513     exportFeatures.setText("Export Features...");
1514     exportFeatures.addActionListener(new ActionListener()
1515     {
1516       public void actionPerformed(ActionEvent e)
1517       {
1518         exportFeatures_actionPerformed(e);
1519       }
1520     });
1521     exportAnnotations.setText("Export Annotations...");
1522     exportAnnotations.addActionListener(new ActionListener()
1523     {
1524       public void actionPerformed(ActionEvent e)
1525       {
1526         exportAnnotations_actionPerformed(e);
1527       }
1528     });
1529     statusPanel.setLayout(gridLayout1);
1530     jMenu3.setText("Show");
1531     showAllSeqs.setText("All Sequences");
1532     showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1533     showAllSeqs.addActionListener(new ActionListener()
1534     {
1535       public void actionPerformed(ActionEvent e)
1536       {
1537         showAllSeqs_actionPerformed(e);
1538       }
1539     });
1540     showAllColumns.setText("All Columns");
1541     showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1542     showAllColumns.addActionListener(new ActionListener()
1543     {
1544       public void actionPerformed(ActionEvent e)
1545       {
1546         showAllColumns_actionPerformed(e);
1547       }
1548     });
1549     hideMenu.setText("Hide");
1550     hideSelSequences.setText("Selected Sequences");
1551     hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1552     hideSelSequences.addActionListener(new ActionListener()
1553     {
1554       public void actionPerformed(ActionEvent e)
1555       {
1556         hideSelSequences_actionPerformed(e);
1557       }
1558     });
1559     hideSelColumns.setText("Selected Columns");
1560     hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1561     hideSelColumns.addActionListener(new ActionListener()
1562     {
1563       public void actionPerformed(ActionEvent e)
1564       {
1565         hideSelColumns_actionPerformed(e);
1566       }
1567     });
1568     hideAllSelection.setText("Selected Region");
1569     hideAllSelection.addActionListener(new ActionListener()
1570     {
1571       public void actionPerformed(ActionEvent e)
1572       {
1573         hideAllSelection_actionPerformed(e);
1574       }
1575     });
1576     // TODO: should be hidden if no selection exists.
1577     hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
1578     hideAllButSelection.addActionListener(new ActionListener()
1579     {
1580       public void actionPerformed(ActionEvent e)
1581       {
1582         hideAllButSelection_actionPerformed(e);
1583       }
1584     });
1585     showAllhidden.setText("All Sequences and Columns");
1586     showAllhidden
1587             .setToolTipText("H toggles visibility of hidden or selected regions.");
1588     showAllhidden.addActionListener(new ActionListener()
1589     {
1590       public void actionPerformed(ActionEvent e)
1591       {
1592         showAllhidden_actionPerformed(e);
1593       }
1594     });
1595
1596     hiddenMarkers.setText("Show Hidden Markers");
1597     hiddenMarkers.addActionListener(new ActionListener()
1598     {
1599       public void actionPerformed(ActionEvent e)
1600       {
1601         hiddenMarkers_actionPerformed(e);
1602       }
1603     });
1604     invertColSel.setText("Invert Column Selection");
1605     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1606             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1607                     .getMenuShortcutKeyMask()
1608                     | java.awt.event.KeyEvent.ALT_MASK, false));
1609     invertColSel.addActionListener(new ActionListener()
1610     {
1611       public void actionPerformed(ActionEvent e)
1612       {
1613         invertColSel_actionPerformed(e);
1614       }
1615     });
1616     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1617     {
1618       public void stateChanged(ChangeEvent evt)
1619       {
1620         JTabbedPane pane = (JTabbedPane) evt.getSource();
1621         int sel = pane.getSelectedIndex();
1622         tabSelectionChanged(sel);
1623       }
1624     });
1625     tabbedPane.addMouseListener(new MouseAdapter()
1626     {
1627       public void mousePressed(MouseEvent e)
1628       {
1629         tabbedPane_mousePressed(e);
1630       }
1631     });
1632     tabbedPane.addFocusListener(new FocusAdapter()
1633     {
1634       public void focusGained(FocusEvent e)
1635       {
1636         tabbedPane_focusGained(e);
1637       }
1638     });
1639     save.setText("Save");
1640     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1641             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1642                     .getMenuShortcutKeyMask(), false));
1643     save.addActionListener(new ActionListener()
1644     {
1645       public void actionPerformed(ActionEvent e)
1646       {
1647         save_actionPerformed(e);
1648       }
1649     });
1650     reload.setEnabled(false);
1651     reload.setText("Reload");
1652     reload.addActionListener(new ActionListener()
1653     {
1654       public void actionPerformed(ActionEvent e)
1655       {
1656         reload_actionPerformed(e);
1657       }
1658     });
1659     newView.setText("New View");
1660     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1661             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1662                     .getMenuShortcutKeyMask(), false));
1663     newView.addActionListener(new ActionListener()
1664     {
1665       public void actionPerformed(ActionEvent e)
1666       {
1667         newView_actionPerformed(e);
1668       }
1669     });
1670     tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1671             + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1672     textColour.setText("Colour Text ...");
1673     textColour.addActionListener(new ActionListener()
1674     {
1675       public void actionPerformed(ActionEvent e)
1676       {
1677         textColour_actionPerformed(e);
1678       }
1679     });
1680     formatMenu.setText("Format");
1681     selectMenu.setText("Select");
1682     idRightAlign.setText("Right Align Sequence Id");
1683     idRightAlign.addActionListener(new ActionListener()
1684     {
1685       public void actionPerformed(ActionEvent e)
1686       {
1687         idRightAlign_actionPerformed(e);
1688       }
1689     });
1690     gatherViews.setEnabled(false);
1691     gatherViews.setText("Gather Views");
1692     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1693             java.awt.event.KeyEvent.VK_G, 0, false));
1694     gatherViews.addActionListener(new ActionListener()
1695     {
1696       public void actionPerformed(ActionEvent e)
1697       {
1698         gatherViews_actionPerformed(e);
1699       }
1700     });
1701     expandViews.setEnabled(false);
1702     expandViews.setText("Expand Views");
1703     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1704             java.awt.event.KeyEvent.VK_X, 0, false));
1705     expandViews.addActionListener(new ActionListener()
1706     {
1707       public void actionPerformed(ActionEvent e)
1708       {
1709         expandViews_actionPerformed(e);
1710       }
1711     });
1712     pageSetup.setText("Page Setup ...");
1713     pageSetup.addActionListener(new ActionListener()
1714     {
1715       public void actionPerformed(ActionEvent e)
1716       {
1717         pageSetup_actionPerformed(e);
1718       }
1719     });
1720     alignmentProperties.setText("Alignment Properties...");
1721     alignmentProperties.addActionListener(new ActionListener()
1722     {
1723       public void actionPerformed(ActionEvent actionEvent)
1724       {
1725         alignmentProperties();
1726       }
1727     });
1728     tooltipSettingsMenu.setText("Sequence ID Tooltip");
1729     autoAnnMenu.setText("Autocalculated Annotation");
1730     alignFrameMenuBar.add(fileMenu);
1731     alignFrameMenuBar.add(editMenu);
1732     alignFrameMenuBar.add(selectMenu);
1733     alignFrameMenuBar.add(viewMenu);
1734     alignFrameMenuBar.add(formatMenu);
1735     alignFrameMenuBar.add(colourMenu);
1736     alignFrameMenuBar.add(calculateMenu);
1737     alignFrameMenuBar.add(webService);
1738     fileMenu.add(fetchSequence);
1739     fileMenu.add(addSequenceMenu);
1740     fileMenu.add(reload);
1741     fileMenu.addSeparator();
1742     fileMenu.add(vamsasStore);
1743     fileMenu.add(save);
1744     fileMenu.add(saveAs);
1745     fileMenu.add(outputTextboxMenu);
1746     fileMenu.add(pageSetup);
1747     fileMenu.add(printMenuItem);
1748     fileMenu.addSeparator();
1749     fileMenu.add(jMenu2);
1750     fileMenu.add(exportFeatures);
1751     fileMenu.add(exportAnnotations);
1752     fileMenu.add(LoadtreeMenuItem);
1753     fileMenu.add(associatedData);
1754     fileMenu.add(loadScoresMenuItem);
1755     fileMenu.addSeparator();
1756     fileMenu.add(closeMenuItem);
1757     editMenu.add(undoMenuItem);
1758     editMenu.add(redoMenuItem);
1759     editMenu.add(cut);
1760     editMenu.add(copy);
1761     editMenu.add(pasteMenu);
1762     editMenu.add(delete);
1763     editMenu.addSeparator();
1764     editMenu.add(remove2LeftMenuItem);
1765     editMenu.add(remove2RightMenuItem);
1766     editMenu.add(removeGappedColumnMenuItem);
1767     editMenu.add(removeAllGapsMenuItem);
1768     editMenu.add(removeRedundancyMenuItem);
1769     editMenu.addSeparator();
1770     // dont add these yet in the CVS build - they cannot be undone!
1771     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1772     // editMenu.add(justifyLeftMenuItem);
1773     // editMenu.add(justifyRightMenuItem);
1774     // editMenu.addSeparator();
1775     editMenu.add(padGapsMenuitem);
1776     viewMenu.add(newView);
1777     viewMenu.add(expandViews);
1778     viewMenu.add(gatherViews);
1779     viewMenu.addSeparator();
1780     viewMenu.add(jMenu3);
1781     viewMenu.add(hideMenu);
1782     viewMenu.addSeparator();
1783     viewMenu.add(followHighlightMenuItem);
1784     viewMenu.add(annotationPanelMenuItem);
1785     autoAnnMenu.add(applyAutoAnnotationSettings);
1786     autoAnnMenu.add(showConsensusHistogram);
1787     autoAnnMenu.add(showSequenceLogo);
1788     autoAnnMenu.addSeparator();
1789     autoAnnMenu.add(showGroupConservation);
1790     autoAnnMenu.add(showGroupConsensus);
1791     viewMenu.add(autoAnnMenu);
1792     viewMenu.addSeparator();
1793     viewMenu.add(showSeqFeatures);
1794     // viewMenu.add(showSeqFeaturesHeight);
1795
1796     viewMenu.add(featureSettings);
1797     tooltipSettingsMenu.add(showDbRefsMenuitem);
1798     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1799     viewMenu.add(tooltipSettingsMenu);
1800     viewMenu.addSeparator();
1801     viewMenu.add(alignmentProperties);
1802     viewMenu.addSeparator();
1803     viewMenu.add(overviewMenuItem);
1804     colourMenu.add(applyToAllGroups);
1805     colourMenu.add(textColour);
1806     colourMenu.addSeparator();
1807     colourMenu.add(noColourmenuItem);
1808     colourMenu.add(clustalColour);
1809     colourMenu.add(BLOSUM62Colour);
1810     colourMenu.add(PIDColour);
1811     colourMenu.add(zappoColour);
1812     colourMenu.add(taylorColour);
1813     colourMenu.add(hydrophobicityColour);
1814     colourMenu.add(helixColour);
1815     colourMenu.add(strandColour);
1816     colourMenu.add(turnColour);
1817     colourMenu.add(buriedColour);
1818     colourMenu.add(nucleotideColour);
1819     colourMenu.add(tcoffeeColour);
1820     colourMenu.add(userDefinedColour);
1821     colourMenu.addSeparator();
1822     colourMenu.add(conservationMenuItem);
1823     colourMenu.add(modifyConservation);
1824     colourMenu.add(abovePIDThreshold);
1825     colourMenu.add(modifyPID);
1826     colourMenu.add(annotationColour);
1827     calculateMenu.add(sort);
1828     calculateMenu.add(calculateTree);
1829     calculateMenu.addSeparator();
1830     calculateMenu.add(pairwiseAlignmentMenuItem);
1831     calculateMenu.add(PCAMenuItem);
1832     calculateMenu.addSeparator();
1833     calculateMenu.add(showTranslation);
1834     calculateMenu.add(showProducts);
1835     calculateMenu.add(autoCalculate);
1836     calculateMenu.add(sortByTree);
1837     calculateMenu.addSeparator();
1838     calculateMenu.add(extractScores);
1839     webServiceNoServices = new JMenuItem("<No Services>");
1840     webService.add(webServiceNoServices);
1841     pasteMenu.add(pasteNew);
1842     pasteMenu.add(pasteThis);
1843     sort.add(sortIDMenuItem);
1844     sort.add(sortLengthMenuItem);
1845     sort.add(sortGroupMenuItem);
1846     sort.add(sortPairwiseMenuItem);
1847     sort.add(sortByTreeMenu);
1848     calculateTree.add(averageDistanceTreeMenuItem);
1849     calculateTree.add(neighbourTreeMenuItem);
1850     calculateTree.add(avDistanceTreeBlosumMenuItem);
1851     calculateTree.add(njTreeBlosumMenuItem);
1852     jMenu2.add(htmlMenuItem);
1853     jMenu2.add(epsFile);
1854     jMenu2.add(createPNG);
1855     addSequenceMenu.add(addFromFile);
1856     addSequenceMenu.add(addFromText);
1857     addSequenceMenu.add(addFromURL);
1858     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1859     statusPanel.add(statusBar, null);
1860     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1861     jMenu3.add(showAllColumns);
1862     jMenu3.add(showAllSeqs);
1863     jMenu3.add(showAllhidden);
1864     hideMenu.add(hideSelColumns);
1865     hideMenu.add(hideSelSequences);
1866     hideMenu.add(hideAllSelection);
1867     hideMenu.add(hideAllButSelection);
1868
1869     formatMenu.add(font);
1870     formatMenu.addSeparator();
1871     formatMenu.add(wrapMenuItem);
1872     formatMenu.add(scaleAbove);
1873     formatMenu.add(scaleLeft);
1874     formatMenu.add(scaleRight);
1875     formatMenu.add(seqLimits);
1876     formatMenu.add(idRightAlign);
1877     formatMenu.add(hiddenMarkers);
1878     formatMenu.add(viewBoxesMenuItem);
1879     formatMenu.add(viewTextMenuItem);
1880     formatMenu.add(colourTextMenuItem);
1881     formatMenu.add(renderGapsMenuItem);
1882     formatMenu.add(centreColumnLabelsMenuItem);
1883     formatMenu.add(showNonconservedMenuItem);
1884     selectMenu.add(findMenuItem);
1885     selectMenu.addSeparator();
1886     selectMenu.add(selectAllSequenceMenuItem);
1887     selectMenu.add(deselectAllSequenceMenuItem);
1888     selectMenu.add(invertSequenceMenuItem);
1889     selectMenu.add(invertColSel);
1890     selectMenu.add(deleteGroups);
1891     selectMenu.add(grpsFromSelection);
1892     // TODO - determine if the listenToViewSelections button is needed : see bug JAL-574
1893     //selectMenu.addSeparator();
1894     //selectMenu.add(listenToViewSelections);
1895   }
1896
1897   protected void listenToViewSelections_actionPerformed(ActionEvent e)
1898   {
1899     // TODO Auto-generated method stub
1900
1901   }
1902
1903   protected void showAllhidden_actionPerformed(ActionEvent e)
1904   {
1905     // TODO Auto-generated method stub
1906
1907   }
1908
1909   protected void hideAllButSelection_actionPerformed(ActionEvent e)
1910   {
1911     // TODO Auto-generated method stub
1912
1913   }
1914
1915   protected void hideAllSelection_actionPerformed(ActionEvent e)
1916   {
1917     // TODO Auto-generated method stub
1918
1919   }
1920
1921   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
1922   {
1923     // TODO Auto-generated method stub
1924
1925   }
1926
1927   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
1928   {
1929     // TODO Auto-generated method stub
1930
1931   }
1932
1933   protected void showSequenceLogo_actionPerformed(ActionEvent e)
1934   {
1935     // TODO Auto-generated method stub
1936
1937   }
1938
1939   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
1940   {
1941     // TODO Auto-generated method stub
1942
1943   }
1944
1945   protected void showGroupConsensus_actionPerformed(ActionEvent e)
1946   {
1947     // TODO Auto-generated method stub
1948
1949   }
1950
1951   protected void showGroupConservation_actionPerformed(ActionEvent e)
1952   {
1953     // TODO Auto-generated method stub
1954
1955   }
1956
1957   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
1958   {
1959     // TODO Auto-generated method stub
1960
1961   }
1962
1963   protected void showSeqFeaturesHeight_actionPerformed(
1964           ActionEvent actionEvent)
1965   {
1966     // TODO Auto-generated method stub
1967
1968   }
1969
1970   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
1971   {
1972     // TODO Auto-generated method stub
1973
1974   }
1975
1976   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
1977   {
1978     // TODO Auto-generated method stub
1979
1980   }
1981
1982   protected void followHighlight_actionPerformed()
1983   {
1984     // TODO Auto-generated method stub
1985
1986   }
1987
1988   protected void showNpFeats_actionPerformed(ActionEvent e)
1989   {
1990     // TODO Auto-generated method stub
1991
1992   }
1993
1994   protected void showDbRefs_actionPerformed(ActionEvent e)
1995   {
1996     // TODO Auto-generated method stub
1997
1998   }
1999
2000   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2001   {
2002   }
2003
2004   protected void showProducts_actionPerformed(ActionEvent e)
2005   {
2006   }
2007
2008   protected void buildSortByAnnotationScoresMenu()
2009   {
2010   }
2011
2012   protected void extractScores_actionPerformed(ActionEvent e)
2013   {
2014   }
2015
2016   protected void outputText_actionPerformed(ActionEvent e)
2017   {
2018   }
2019
2020   public void addFromFile_actionPerformed(ActionEvent e)
2021   {
2022
2023   }
2024
2025   public void addFromText_actionPerformed(ActionEvent e)
2026   {
2027
2028   }
2029
2030   public void addFromURL_actionPerformed(ActionEvent e)
2031   {
2032
2033   }
2034
2035   public void exportFeatures_actionPerformed(ActionEvent e)
2036   {
2037
2038   }
2039
2040   public void exportAnnotations_actionPerformed(ActionEvent e)
2041   {
2042
2043   }
2044
2045   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2046   {
2047   }
2048
2049   protected void closeMenuItem_actionPerformed(boolean b)
2050   {
2051   }
2052
2053   protected void redoMenuItem_actionPerformed(ActionEvent e)
2054   {
2055   }
2056
2057   protected void undoMenuItem_actionPerformed(ActionEvent e)
2058   {
2059   }
2060
2061   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2062   {
2063   }
2064
2065   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2066   {
2067   }
2068
2069   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2070   {
2071   }
2072
2073   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2074   {
2075   }
2076
2077   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2078   {
2079   }
2080
2081   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2082   {
2083   }
2084
2085   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2086   {
2087   }
2088
2089   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2090   {
2091   }
2092
2093   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2094   {
2095   }
2096
2097   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2098   {
2099   }
2100
2101   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2102   {
2103   }
2104
2105   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2106   {
2107   }
2108
2109   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2110   {
2111   }
2112
2113   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2114   {
2115   }
2116
2117   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2118   {
2119   }
2120
2121   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2122   {
2123   }
2124
2125   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2126   {
2127   }
2128
2129   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2130   {
2131   }
2132
2133   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2134   {
2135   }
2136
2137   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2138   {
2139   }
2140
2141   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2142   {
2143   }
2144
2145   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2146   {
2147   }
2148
2149   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2150   {
2151   }
2152
2153   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2154   {
2155   }
2156
2157   protected void clustalColour_actionPerformed(ActionEvent e)
2158   {
2159   }
2160
2161   protected void zappoColour_actionPerformed(ActionEvent e)
2162   {
2163   }
2164
2165   protected void taylorColour_actionPerformed(ActionEvent e)
2166   {
2167   }
2168
2169   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2170   {
2171   }
2172
2173   protected void helixColour_actionPerformed(ActionEvent e)
2174   {
2175   }
2176
2177   protected void strandColour_actionPerformed(ActionEvent e)
2178   {
2179   }
2180
2181   protected void turnColour_actionPerformed(ActionEvent e)
2182   {
2183   }
2184
2185   protected void buriedColour_actionPerformed(ActionEvent e)
2186   {
2187   }
2188
2189   protected void userDefinedColour_actionPerformed(ActionEvent e)
2190   {
2191   }
2192
2193   protected void PIDColour_actionPerformed(ActionEvent e)
2194   {
2195   }
2196
2197   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2198   {
2199   }
2200
2201   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2202   {
2203   }
2204
2205   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2206   {
2207   }
2208
2209   protected void printMenuItem_actionPerformed(ActionEvent e)
2210   {
2211   }
2212
2213   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2214   {
2215   }
2216
2217   protected void findMenuItem_actionPerformed(ActionEvent e)
2218   {
2219   }
2220
2221   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2222   {
2223   }
2224
2225   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2226   {
2227   }
2228
2229   protected void nucleotideColour_actionPerformed(ActionEvent e)
2230   {
2231   }
2232
2233   protected void deleteGroups_actionPerformed(ActionEvent e)
2234   {
2235   }
2236
2237   protected void copy_actionPerformed(ActionEvent e)
2238   {
2239   }
2240
2241   protected void cut_actionPerformed(ActionEvent e)
2242   {
2243   }
2244
2245   protected void delete_actionPerformed(ActionEvent e)
2246   {
2247   }
2248
2249   protected void pasteNew_actionPerformed(ActionEvent e)
2250   {
2251   }
2252
2253   protected void pasteThis_actionPerformed(ActionEvent e)
2254   {
2255   }
2256
2257   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2258   {
2259   }
2260
2261   public void createPNG(java.io.File f)
2262   {
2263   }
2264
2265   protected void font_actionPerformed(ActionEvent e)
2266   {
2267   }
2268
2269   protected void seqLimit_actionPerformed(ActionEvent e)
2270   {
2271   }
2272
2273   public void seqDBRef_actionPerformed(ActionEvent e)
2274   {
2275
2276   }
2277
2278   public void createEPS(java.io.File f)
2279   {
2280   }
2281
2282   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2283   {
2284
2285   }
2286
2287   /**
2288    * Template method to handle the 'load T-Coffee scores' menu event.
2289    * <p>
2290    * Subclasses override this method to provide a custom action.
2291    *
2292    * @param event The raised event
2293    */
2294   protected void loadScores_actionPerformed(ActionEvent event) {
2295
2296   }
2297
2298
2299   /**
2300    * Template method to handle the 'Color T-Coffee scores' menu event.
2301    * <p>
2302    * Subclasses override this method to provide a custom action.
2303    *
2304    * @param event The raised event
2305    */
2306   protected void tcoffeeColorScheme_actionPerformed(ActionEvent event) {
2307
2308   }
2309
2310
2311   protected void jpred_actionPerformed(ActionEvent e)
2312   {
2313   }
2314
2315   protected void scaleAbove_actionPerformed(ActionEvent e)
2316   {
2317   }
2318
2319   protected void scaleLeft_actionPerformed(ActionEvent e)
2320   {
2321   }
2322
2323   protected void scaleRight_actionPerformed(ActionEvent e)
2324   {
2325   }
2326
2327   protected void modifyPID_actionPerformed(ActionEvent e)
2328   {
2329   }
2330
2331   protected void modifyConservation_actionPerformed(ActionEvent e)
2332   {
2333   }
2334
2335   protected void saveAs_actionPerformed(ActionEvent e)
2336   {
2337   }
2338
2339   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2340   {
2341   }
2342
2343   public void vamsasStore_actionPerformed(ActionEvent e)
2344   {
2345
2346   }
2347
2348   public void vamsasLoad_actionPerformed(ActionEvent e)
2349   {
2350
2351   }
2352
2353   public void showTranslation_actionPerformed(ActionEvent e)
2354   {
2355
2356   }
2357
2358   public void featureSettings_actionPerformed(ActionEvent e)
2359   {
2360
2361   }
2362
2363   public void fetchSequence_actionPerformed(ActionEvent e)
2364   {
2365
2366   }
2367
2368   public void smoothFont_actionPerformed(ActionEvent e)
2369   {
2370
2371   }
2372
2373   public void annotationColour_actionPerformed(ActionEvent e)
2374   {
2375
2376   }
2377
2378   public void associatedData_actionPerformed(ActionEvent e)
2379   {
2380
2381   }
2382
2383   public void autoCalculate_actionPerformed(ActionEvent e)
2384   {
2385
2386   }
2387
2388   public void sortByTreeOption_actionPerformed(ActionEvent e)
2389   {
2390
2391   }
2392
2393   public void showAllSeqs_actionPerformed(ActionEvent e)
2394   {
2395
2396   }
2397
2398   public void showAllColumns_actionPerformed(ActionEvent e)
2399   {
2400
2401   }
2402
2403   public void hideSelSequences_actionPerformed(ActionEvent e)
2404   {
2405
2406   }
2407
2408   public void hideSelColumns_actionPerformed(ActionEvent e)
2409   {
2410
2411   }
2412
2413   public void hiddenMarkers_actionPerformed(ActionEvent e)
2414   {
2415
2416   }
2417
2418   public void findPdbId_actionPerformed(ActionEvent e)
2419   {
2420
2421   }
2422
2423   public void enterPdbId_actionPerformed(ActionEvent e)
2424   {
2425
2426   }
2427
2428   public void pdbFile_actionPerformed(ActionEvent e)
2429   {
2430
2431   }
2432
2433   public void invertColSel_actionPerformed(ActionEvent e)
2434   {
2435
2436   }
2437
2438   public void tabSelectionChanged(int sel)
2439   {
2440
2441   }
2442
2443   public void tabbedPane_mousePressed(MouseEvent e)
2444   {
2445
2446   }
2447
2448   public void tabbedPane_focusGained(FocusEvent e)
2449   {
2450     requestFocus();
2451   }
2452
2453   public void save_actionPerformed(ActionEvent e)
2454   {
2455
2456   }
2457
2458   public void reload_actionPerformed(ActionEvent e)
2459   {
2460
2461   }
2462
2463   public void newView_actionPerformed(ActionEvent e)
2464   {
2465
2466   }
2467
2468   public void textColour_actionPerformed(ActionEvent e)
2469   {
2470
2471   }
2472
2473   public void idRightAlign_actionPerformed(ActionEvent e)
2474   {
2475
2476   }
2477
2478   public void expandViews_actionPerformed(ActionEvent e)
2479   {
2480
2481   }
2482
2483   public void gatherViews_actionPerformed(ActionEvent e)
2484   {
2485
2486   }
2487
2488   public void buildTreeMenu()
2489   {
2490
2491   }
2492
2493   public void pageSetup_actionPerformed(ActionEvent e)
2494   {
2495
2496   }
2497
2498   public void alignmentProperties()
2499   {
2500
2501   }
2502 }