src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   3  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 nucleotideColour = new JRadioButtonMenuItem();
 139
 140   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
 141
 142   protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
 143
 144   // protected JRadioButtonMenuItem covariationColour = new
 145   // JRadioButtonMenuItem();
 146
 147   protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
 148
 149   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 150
 151   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
 152
 153   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 154
 155   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 156
 157   public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
 158
 159   JMenuItem htmlMenuItem = new JMenuItem();
 160
 161   JMenuItem overviewMenuItem = new JMenuItem();
 162
 163   protected JMenuItem undoMenuItem = new JMenuItem();
 164
 165   protected JMenuItem redoMenuItem = new JMenuItem();
 166
 167   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 168
 169   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 170
 171   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 172
 173   JMenuItem printMenuItem = new JMenuItem();
 174
 175   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 176
 177   JMenuItem findMenuItem = new JMenuItem();
 178
 179   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 180
 181   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 182
 183   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 184
 185   JMenuItem deleteGroups = new JMenuItem();
 186
 187   JMenuItem delete = new JMenuItem();
 188
 189   JMenuItem copy = new JMenuItem();
 190
 191   JMenuItem cut = new JMenuItem();
 192
 193   JMenu pasteMenu = new JMenu();
 194
 195   JMenuItem pasteNew = new JMenuItem();
 196
 197   JMenuItem pasteThis = new JMenuItem();
 198
 199   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
 200
 201   JMenuItem createPNG = new JMenuItem();
 202
 203   protected JMenuItem font = new JMenuItem();
 204
 205   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 206
 207   JMenuItem epsFile = new JMenuItem();
 208
 209   JMenuItem LoadtreeMenuItem = new JMenuItem();
 210
 211   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 212
 213   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 214
 215   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 216
 217   protected JMenuItem modifyPID = new JMenuItem();
 218
 219   protected JMenuItem modifyConservation = new JMenuItem();
 220
 221   protected JMenu sortByTreeMenu = new JMenu();
 222
 223   protected JMenu sort = new JMenu();
 224
 225   protected JMenu calculateTree = new JMenu();
 226
 227   JMenu jMenu2 = new JMenu();
 228
 229   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 230
 231   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 232
 233   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 234
 235   protected ButtonGroup colours = new ButtonGroup();
 236
 237   JMenuItem vamsasStore = new JMenuItem();
 238
 239   protected JMenuItem showTranslation = new JMenuItem();
 240
 241   protected JMenuItem extractScores = new JMenuItem();
 242
 243   protected JMenu showProducts = new JMenu();
 244
 245   public JMenuItem openFeatureSettings = new JMenuItem();
 246
 247   JMenuItem fetchSequence = new JMenuItem();
 248
 249   JMenuItem annotationColour = new JMenuItem();
 250
 251   protected JMenuItem rnahelicesColour = new JMenuItem();
 252
 253   JMenuItem associatedData = new JMenuItem();
 254
 255   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 256
 257   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 258
 259   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 260
 261   JMenu addSequenceMenu = new JMenu();
 262
 263   JMenuItem addFromFile = new JMenuItem();
 264
 265   JMenuItem addFromText = new JMenuItem();
 266
 267   JMenuItem addFromURL = new JMenuItem();
 268
 269   JMenuItem exportAnnotations = new JMenuItem();
 270
 271   JMenuItem exportFeatures = new JMenuItem();
 272
 273   protected JPanel statusPanel = new JPanel();
 274
 275   GridLayout gridLayout1 = new GridLayout();
 276
 277   JMenu jMenu3 = new JMenu();
 278
 279   JMenuItem showAllSeqs = new JMenuItem();
 280
 281   JMenuItem showAllColumns = new JMenuItem();
 282
 283   JMenu hideMenu = new JMenu();
 284
 285   JMenuItem hideSelSequences = new JMenuItem();
 286
 287   JMenuItem hideSelColumns = new JMenuItem();
 288
 289   JMenuItem hideAllButSelection = new JMenuItem();
 290
 291   JMenuItem hideAllSelection = new JMenuItem();
 292
 293   JMenuItem showAllhidden = new JMenuItem();
 294
 295   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 296
 297   JMenuItem invertColSel = new JMenuItem();
 298
 299   protected JTabbedPane tabbedPane = new JTabbedPane();
 300
 301   JMenuItem save = new JMenuItem();
 302
 303   protected JMenuItem reload = new JMenuItem();
 304
 305   JMenuItem newView = new JMenuItem();
 306
 307   JMenuItem textColour = new JMenuItem();
 308
 309   JMenu formatMenu = new JMenu();
 310
 311   JMenu selectMenu = new JMenu();
 312
 313   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 314
 315   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 316
 317   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 318
 319   protected JMenuItem gatherViews = new JMenuItem();
 320
 321   protected JMenuItem expandViews = new JMenuItem();
 322
 323   JMenuItem pageSetup = new JMenuItem();
 324
 325   JMenuItem alignmentProperties = new JMenuItem();
 326
 327   JMenu tooltipSettingsMenu = new JMenu();
 328
 329   private JMenuItem justifyLeftMenuItem = new JMenuItem();
 330
 331   private JMenuItem justifyRightMenuItem = new JMenuItem();
 332
 333   JMenu autoAnnMenu = new JMenu();
 334
 335   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 336
 337   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 338
 339   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 340
 341   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 342
 343   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 344
 345   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 346
 347   private JMenuItem grpsFromSelection = new JMenuItem();
 348
 349   public GAlignFrame()
 350   {
 351     try
 352     {
 353       jbInit();
 354       setJMenuBar(alignFrameMenuBar);
 355
 356       // dynamically fill save as menu with available formats
 357       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 358       {
 359         JMenuItem item = new JMenuItem(
 360                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 361
 362         item.addActionListener(new java.awt.event.ActionListener()
 363         {
 364           public void actionPerformed(ActionEvent e)
 365           {
 366             outputText_actionPerformed(e);
 367           }
 368         });
 369
 370         outputTextboxMenu.add(item);
 371       }
 372     } catch (Exception e)
 373     {
 374     }
 375
 376     if (!new jalview.util.Platform().isAMac())
 377     {
 378       closeMenuItem.setMnemonic('C');
 379       outputTextboxMenu.setMnemonic('T');
 380       undoMenuItem.setMnemonic('Z');
 381       redoMenuItem.setMnemonic('0');
 382       copy.setMnemonic('C');
 383       cut.setMnemonic('U');
 384       pasteMenu.setMnemonic('P');
 385       reload.setMnemonic('R');
 386     }
 387
 388     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 389     {
 390       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 391               .getUserColourSchemes().keys();
 392
 393       while (userColours.hasMoreElements())
 394       {
 395         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 396                 userColours.nextElement().toString());
 397         radioItem.setName("USER_DEFINED");
 398         radioItem.addMouseListener(new MouseAdapter()
 399         {
 400           public void mousePressed(MouseEvent evt)
 401           {
 402             if (evt.isControlDown()
 403                     || SwingUtilities.isRightMouseButton(evt))
 404             {
 405               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 406
 407               int option = JOptionPane.showInternalConfirmDialog(
 408                       jalview.gui.Desktop.desktop,
 409                       "Remove from default list?",
 410                       "Remove user defined colour",
 411                       JOptionPane.YES_NO_OPTION);
 412               if (option == JOptionPane.YES_OPTION)
 413               {
 414                 jalview.gui.UserDefinedColours
 415                         .removeColourFromDefaults(radioItem.getText());
 416                 colourMenu.remove(radioItem);
 417               }
 418               else
 419               {
 420                 radioItem.addActionListener(new ActionListener()
 421                 {
 422                   public void actionPerformed(ActionEvent evt)
 423                   {
 424                     userDefinedColour_actionPerformed(evt);
 425                   }
 426                 });
 427               }
 428             }
 429           }
 430         });
 431         radioItem.addActionListener(new ActionListener()
 432         {
 433           public void actionPerformed(ActionEvent evt)
 434           {
 435             userDefinedColour_actionPerformed(evt);
 436           }
 437         });
 438         colourMenu.insert(radioItem, 15);
 439         colours.add(radioItem);
 440       }
 441     }
 442     colours.add(noColourmenuItem);
 443     colours.add(clustalColour);
 444     colours.add(zappoColour);
 445     colours.add(taylorColour);
 446     colours.add(hydrophobicityColour);
 447     colours.add(helixColour);
 448     colours.add(strandColour);
 449     colours.add(turnColour);
 450     colours.add(buriedColour);
 451     colours.add(userDefinedColour);
 452     colours.add(PIDColour);
 453     colours.add(BLOSUM62Colour);
 454     colours.add(nucleotideColour);
 455     colours.add(purinePyrimidineColour);
 456     // colours.add(covariationColour);
 457     colours.add(tcoffeeColour);
 458     colours.add(RNAInteractionColour);
 459     setColourSelected(jalview.bin.Cache
 460             .getDefault("DEFAULT_COLOUR", "None"));
 461
 462   }
 463
 464   public void setColourSelected(String defaultColour)
 465   {
 466
 467     if (defaultColour != null)
 468     {
 469       int index = ColourSchemeProperty
 470               .getColourIndexFromName(defaultColour);
 471
 472       switch (index)
 473       {
 474       case ColourSchemeProperty.CLUSTAL:
 475         clustalColour.setSelected(true);
 476
 477         break;
 478
 479       case ColourSchemeProperty.BLOSUM:
 480         BLOSUM62Colour.setSelected(true);
 481
 482         break;
 483
 484       case ColourSchemeProperty.PID:
 485         PIDColour.setSelected(true);
 486
 487         break;
 488
 489       case ColourSchemeProperty.ZAPPO:
 490         zappoColour.setSelected(true);
 491
 492         break;
 493
 494       case ColourSchemeProperty.TAYLOR:
 495         taylorColour.setSelected(true);
 496         break;
 497
 498       case ColourSchemeProperty.HYDROPHOBIC:
 499         hydrophobicityColour.setSelected(true);
 500
 501         break;
 502
 503       case ColourSchemeProperty.HELIX:
 504         helixColour.setSelected(true);
 505
 506         break;
 507
 508       case ColourSchemeProperty.STRAND:
 509         strandColour.setSelected(true);
 510
 511         break;
 512
 513       case ColourSchemeProperty.TURN:
 514         turnColour.setSelected(true);
 515
 516         break;
 517
 518       case ColourSchemeProperty.BURIED:
 519         buriedColour.setSelected(true);
 520
 521         break;
 522
 523       case ColourSchemeProperty.NUCLEOTIDE:
 524         nucleotideColour.setSelected(true);
 525
 526         break;
 527
 528       case ColourSchemeProperty.TCOFFEE:
 529         tcoffeeColour.setSelected(true);
 530         break;
 531
 532       case ColourSchemeProperty.PURINEPYRIMIDINE:
 533         purinePyrimidineColour.setSelected(true);
 534
 535         break;
 536
 537       case ColourSchemeProperty.RNAINTERACTION:
 538           RNAInteractionColour.setSelected(true);
 539
 540           break;
 541       /*
 542        * case ColourSchemeProperty.COVARIATION:
 543        * covariationColour.setSelected(true);
 544        *
 545        * break;
 546        */
 547       case ColourSchemeProperty.USER_DEFINED:
 548         userDefinedColour.setSelected(true);
 549
 550         break;
 551       case ColourSchemeProperty.NONE:
 552       default:
 553         noColourmenuItem.setSelected(true);
 554         break;
 555
 556       }
 557     }
 558
 559   }
 560
 561   private void jbInit() throws Exception
 562   {
 563     fileMenu.setText("File");
 564     saveAs.setText("Save As...");
 565     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 566             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
 567                     .getMenuShortcutKeyMask()
 568                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 569     saveAs.addActionListener(new ActionListener()
 570     {
 571       public void actionPerformed(ActionEvent e)
 572       {
 573         saveAs_actionPerformed(e);
 574       }
 575     });
 576     closeMenuItem.setText("Close");
 577     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 578             java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
 579                     .getMenuShortcutKeyMask(), false));
 580     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 581     {
 582       public void actionPerformed(ActionEvent e)
 583       {
 584         closeMenuItem_actionPerformed(false);
 585       }
 586     });
 587     editMenu.setText("Edit");
 588     viewMenu.setText("View");
 589     colourMenu.setText("Colour");
 590     calculateMenu.setText("Calculate");
 591     webService.setText("Web Service");
 592     selectAllSequenceMenuItem.setText("Select All");
 593     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 594             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
 595                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 596     selectAllSequenceMenuItem
 597             .addActionListener(new java.awt.event.ActionListener()
 598             {
 599               public void actionPerformed(ActionEvent e)
 600               {
 601                 selectAllSequenceMenuItem_actionPerformed(e);
 602               }
 603             });
 604     deselectAllSequenceMenuItem.setText("Deselect All");
 605     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 606             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 607     deselectAllSequenceMenuItem
 608             .addActionListener(new java.awt.event.ActionListener()
 609             {
 610               public void actionPerformed(ActionEvent e)
 611               {
 612                 deselectAllSequenceMenuItem_actionPerformed(e);
 613               }
 614             });
 615     invertSequenceMenuItem.setText("Invert Sequence Selection");
 616     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 617             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
 618                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 619     invertSequenceMenuItem
 620             .addActionListener(new java.awt.event.ActionListener()
 621             {
 622               public void actionPerformed(ActionEvent e)
 623               {
 624                 invertSequenceMenuItem_actionPerformed(e);
 625               }
 626             });
 627     grpsFromSelection.setText("Make Groups for selection");
 628     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
 629     {
 630       public void actionPerformed(ActionEvent e)
 631       {
 632         makeGrpsFromSelection_actionPerformed(e);
 633       }
 634     });
 635
 636     remove2LeftMenuItem.setText("Remove Left");
 637     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 638             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
 639                     .getMenuShortcutKeyMask(), false));
 640     remove2LeftMenuItem
 641             .addActionListener(new java.awt.event.ActionListener()
 642             {
 643               public void actionPerformed(ActionEvent e)
 644               {
 645                 remove2LeftMenuItem_actionPerformed(e);
 646               }
 647             });
 648     remove2RightMenuItem.setText("Remove Right");
 649     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 650             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
 651                     .getMenuShortcutKeyMask(), false));
 652     remove2RightMenuItem
 653             .addActionListener(new java.awt.event.ActionListener()
 654             {
 655               public void actionPerformed(ActionEvent e)
 656               {
 657                 remove2RightMenuItem_actionPerformed(e);
 658               }
 659             });
 660     removeGappedColumnMenuItem.setText("Remove Empty Columns");
 661     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
 662             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 663                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 664     removeGappedColumnMenuItem
 665             .addActionListener(new java.awt.event.ActionListener()
 666             {
 667               public void actionPerformed(ActionEvent e)
 668               {
 669                 removeGappedColumnMenuItem_actionPerformed(e);
 670               }
 671             });
 672     removeAllGapsMenuItem.setText("Remove All Gaps");
 673     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
 674             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 675                     .getDefaultToolkit().getMenuShortcutKeyMask()
 676                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 677     removeAllGapsMenuItem
 678             .addActionListener(new java.awt.event.ActionListener()
 679             {
 680               public void actionPerformed(ActionEvent e)
 681               {
 682                 removeAllGapsMenuItem_actionPerformed(e);
 683               }
 684             });
 685     justifyLeftMenuItem.setText("Left Justify Alignment");
 686     justifyLeftMenuItem
 687             .addActionListener(new java.awt.event.ActionListener()
 688             {
 689               public void actionPerformed(ActionEvent e)
 690               {
 691                 justifyLeftMenuItem_actionPerformed(e);
 692               }
 693             });
 694     justifyRightMenuItem.setText("Right Justify Alignment");
 695     justifyRightMenuItem
 696             .addActionListener(new java.awt.event.ActionListener()
 697             {
 698               public void actionPerformed(ActionEvent e)
 699               {
 700                 justifyRightMenuItem_actionPerformed(e);
 701               }
 702             });
 703     viewBoxesMenuItem.setText("Boxes");
 704     viewBoxesMenuItem.setState(true);
 705     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 706     {
 707       public void actionPerformed(ActionEvent e)
 708       {
 709         viewBoxesMenuItem_actionPerformed(e);
 710       }
 711     });
 712     viewTextMenuItem.setText("Text");
 713     viewTextMenuItem.setState(true);
 714     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 715     {
 716       public void actionPerformed(ActionEvent e)
 717       {
 718         viewTextMenuItem_actionPerformed(e);
 719       }
 720     });
 721     showNonconservedMenuItem.setText("Show nonconserved");
 722     showNonconservedMenuItem.setState(false);
 723     showNonconservedMenuItem
 724             .addActionListener(new java.awt.event.ActionListener()
 725             {
 726               public void actionPerformed(ActionEvent e)
 727               {
 728                 showUnconservedMenuItem_actionPerformed(e);
 729               }
 730             });
 731     sortPairwiseMenuItem.setText("by Pairwise Identity");
 732     sortPairwiseMenuItem
 733             .addActionListener(new java.awt.event.ActionListener()
 734             {
 735               public void actionPerformed(ActionEvent e)
 736               {
 737                 sortPairwiseMenuItem_actionPerformed(e);
 738               }
 739             });
 740     sortIDMenuItem.setText("by ID");
 741     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 742     {
 743       public void actionPerformed(ActionEvent e)
 744       {
 745         sortIDMenuItem_actionPerformed(e);
 746       }
 747     });
 748     sortLengthMenuItem.setText("By Length");
 749     sortLengthMenuItem
 750             .addActionListener(new java.awt.event.ActionListener()
 751             {
 752               public void actionPerformed(ActionEvent e)
 753               {
 754                 sortLengthMenuItem_actionPerformed(e);
 755               }
 756             });
 757     sortGroupMenuItem.setText("by Group");
 758     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 759     {
 760       public void actionPerformed(ActionEvent e)
 761       {
 762         sortGroupMenuItem_actionPerformed(e);
 763       }
 764     });
 765     removeRedundancyMenuItem.setText("Remove Redundancy...");
 766     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
 767             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
 768                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 769     removeRedundancyMenuItem
 770             .addActionListener(new java.awt.event.ActionListener()
 771             {
 772               public void actionPerformed(ActionEvent e)
 773               {
 774                 removeRedundancyMenuItem_actionPerformed(e);
 775               }
 776             });
 777     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
 778     pairwiseAlignmentMenuItem
 779             .addActionListener(new java.awt.event.ActionListener()
 780             {
 781               public void actionPerformed(ActionEvent e)
 782               {
 783                 pairwiseAlignmentMenuItem_actionPerformed(e);
 784               }
 785             });
 786     PCAMenuItem.setText("Principal Component Analysis");
 787     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 788     {
 789       public void actionPerformed(ActionEvent e)
 790       {
 791         PCAMenuItem_actionPerformed(e);
 792       }
 793     });
 794     averageDistanceTreeMenuItem
 795             .setText("Average Distance Using % Identity");
 796     averageDistanceTreeMenuItem
 797             .addActionListener(new java.awt.event.ActionListener()
 798             {
 799               public void actionPerformed(ActionEvent e)
 800               {
 801                 averageDistanceTreeMenuItem_actionPerformed(e);
 802               }
 803             });
 804     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
 805     neighbourTreeMenuItem
 806             .addActionListener(new java.awt.event.ActionListener()
 807             {
 808               public void actionPerformed(ActionEvent e)
 809               {
 810                 neighbourTreeMenuItem_actionPerformed(e);
 811               }
 812             });
 813     this.getContentPane().setLayout(borderLayout1);
 814     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 815     alignFrameMenuBar.setBackground(Color.lightGray);
 816     statusBar.setBackground(Color.white);
 817     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 818     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 819     statusBar.setText("Status bar");
 820     outputTextboxMenu.setText("Output to Textbox");
 821     clustalColour.setText("Clustalx");
 822
 823     clustalColour.addActionListener(new java.awt.event.ActionListener()
 824     {
 825       public void actionPerformed(ActionEvent e)
 826       {
 827         clustalColour_actionPerformed(e);
 828       }
 829     });
 830     zappoColour.setText("Zappo");
 831     zappoColour.addActionListener(new java.awt.event.ActionListener()
 832     {
 833       public void actionPerformed(ActionEvent e)
 834       {
 835         zappoColour_actionPerformed(e);
 836       }
 837     });
 838     taylorColour.setText("Taylor");
 839     taylorColour.addActionListener(new java.awt.event.ActionListener()
 840     {
 841       public void actionPerformed(ActionEvent e)
 842       {
 843         taylorColour_actionPerformed(e);
 844       }
 845     });
 846     hydrophobicityColour.setText("Hydrophobicity");
 847     hydrophobicityColour
 848             .addActionListener(new java.awt.event.ActionListener()
 849             {
 850               public void actionPerformed(ActionEvent e)
 851               {
 852                 hydrophobicityColour_actionPerformed(e);
 853               }
 854             });
 855     helixColour.setText("Helix Propensity");
 856     helixColour.addActionListener(new java.awt.event.ActionListener()
 857     {
 858       public void actionPerformed(ActionEvent e)
 859       {
 860         helixColour_actionPerformed(e);
 861       }
 862     });
 863     strandColour.setText("Strand Propensity");
 864     strandColour.addActionListener(new java.awt.event.ActionListener()
 865     {
 866       public void actionPerformed(ActionEvent e)
 867       {
 868         strandColour_actionPerformed(e);
 869       }
 870     });
 871     turnColour.setText("Turn Propensity");
 872     turnColour.addActionListener(new java.awt.event.ActionListener()
 873     {
 874       public void actionPerformed(ActionEvent e)
 875       {
 876         turnColour_actionPerformed(e);
 877       }
 878     });
 879     buriedColour.setText("Buried Index");
 880     buriedColour.addActionListener(new java.awt.event.ActionListener()
 881     {
 882       public void actionPerformed(ActionEvent e)
 883       {
 884         buriedColour_actionPerformed(e);
 885       }
 886     });
 887     userDefinedColour.setText("User Defined...");
 888     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 889     {
 890       public void actionPerformed(ActionEvent e)
 891       {
 892         userDefinedColour_actionPerformed(e);
 893       }
 894     });
 895     PIDColour.setText("Percentage Identity");
 896     PIDColour.addActionListener(new java.awt.event.ActionListener()
 897     {
 898       public void actionPerformed(ActionEvent e)
 899       {
 900         PIDColour_actionPerformed(e);
 901       }
 902     });
 903     BLOSUM62Colour.setText("BLOSUM62 Score");
 904     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 905     {
 906       public void actionPerformed(ActionEvent e)
 907       {
 908         BLOSUM62Colour_actionPerformed(e);
 909       }
 910     });
 911     nucleotideColour.setText("Nucleotide");
 912     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
 913     {
 914       public void actionPerformed(ActionEvent e)
 915       {
 916         nucleotideColour_actionPerformed(e);
 917       }
 918     });
 919
 920     purinePyrimidineColour.setText("Purine/Pyrimidine");
 921     purinePyrimidineColour.addActionListener(new java.awt.event.ActionListener()
 922             {
 923               public void actionPerformed(ActionEvent e)
 924               {
 925                 purinePyrimidineColour_actionPerformed(e);
 926               }
 927             });
 928
 929     RNAInteractionColour.setText("RNA Interaction type");
 930     RNAInteractionColour.addActionListener(new java.awt.event.ActionListener()
 931             {
 932               public void actionPerformed(ActionEvent e)
 933               {
 934                   RNAInteractionColour_actionPerformed(e);
 935               }
 936             });
 937     /*
 938      * covariationColour.setText("Covariation");
 939      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
 940      * public void actionPerformed(ActionEvent e) {
 941      * covariationColour_actionPerformed(e); } });
 942      */
 943
 944     avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
 945     avDistanceTreeBlosumMenuItem
 946             .addActionListener(new java.awt.event.ActionListener()
 947             {
 948               public void actionPerformed(ActionEvent e)
 949               {
 950                 avTreeBlosumMenuItem_actionPerformed(e);
 951               }
 952             });
 953     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
 954     njTreeBlosumMenuItem
 955             .addActionListener(new java.awt.event.ActionListener()
 956             {
 957               public void actionPerformed(ActionEvent e)
 958               {
 959                 njTreeBlosumMenuItem_actionPerformed(e);
 960               }
 961             });
 962     annotationPanelMenuItem.setActionCommand("");
 963     annotationPanelMenuItem.setText("Show Annotations");
 964     annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
 965             "SHOW_ANNOTATIONS", true));
 966     annotationPanelMenuItem
 967             .addActionListener(new java.awt.event.ActionListener()
 968             {
 969               public void actionPerformed(ActionEvent e)
 970               {
 971                 annotationPanelMenuItem_actionPerformed(e);
 972               }
 973             });
 974     colourTextMenuItem.setText("Colour Text");
 975     colourTextMenuItem
 976             .addActionListener(new java.awt.event.ActionListener()
 977             {
 978               public void actionPerformed(ActionEvent e)
 979               {
 980                 colourTextMenuItem_actionPerformed(e);
 981               }
 982             });
 983     htmlMenuItem.setText("HTML");
 984     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
 985     {
 986       public void actionPerformed(ActionEvent e)
 987       {
 988         htmlMenuItem_actionPerformed(e);
 989       }
 990     });
 991     overviewMenuItem.setText("Overview Window");
 992     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
 993     {
 994       public void actionPerformed(ActionEvent e)
 995       {
 996         overviewMenuItem_actionPerformed(e);
 997       }
 998     });
 999     undoMenuItem.setEnabled(false);
1000     undoMenuItem.setText("Undo");
1001     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1002             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1003                     .getMenuShortcutKeyMask(), false));
1004     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1005     {
1006       public void actionPerformed(ActionEvent e)
1007       {
1008         undoMenuItem_actionPerformed(e);
1009       }
1010     });
1011     redoMenuItem.setEnabled(false);
1012     redoMenuItem.setText("Redo");
1013     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1014             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1015                     .getMenuShortcutKeyMask(), false));
1016     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1017     {
1018       public void actionPerformed(ActionEvent e)
1019       {
1020         redoMenuItem_actionPerformed(e);
1021       }
1022     });
1023     conservationMenuItem.setText("By Conservation");
1024     conservationMenuItem
1025             .addActionListener(new java.awt.event.ActionListener()
1026             {
1027               public void actionPerformed(ActionEvent e)
1028               {
1029                 conservationMenuItem_actionPerformed(e);
1030               }
1031             });
1032     noColourmenuItem.setText("None");
1033     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1034     {
1035       public void actionPerformed(ActionEvent e)
1036       {
1037         noColourmenuItem_actionPerformed(e);
1038       }
1039     });
1040     wrapMenuItem.setText("Wrap");
1041     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1042     {
1043       public void actionPerformed(ActionEvent e)
1044       {
1045         wrapMenuItem_actionPerformed(e);
1046       }
1047     });
1048     printMenuItem.setText("Print ...");
1049     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1050             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1051                     .getMenuShortcutKeyMask(), false));
1052     printMenuItem.addActionListener(new java.awt.event.ActionListener()
1053     {
1054       public void actionPerformed(ActionEvent e)
1055       {
1056         printMenuItem_actionPerformed(e);
1057       }
1058     });
1059     renderGapsMenuItem.setText("Show Gaps");
1060     renderGapsMenuItem.setState(true);
1061     renderGapsMenuItem
1062             .addActionListener(new java.awt.event.ActionListener()
1063             {
1064               public void actionPerformed(ActionEvent e)
1065               {
1066                 renderGapsMenuItem_actionPerformed(e);
1067               }
1068             });
1069     findMenuItem.setText("Find...");
1070     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1071             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1072                     .getMenuShortcutKeyMask(), false));
1073     findMenuItem.addActionListener(new java.awt.event.ActionListener()
1074     {
1075       public void actionPerformed(ActionEvent e)
1076       {
1077         findMenuItem_actionPerformed(e);
1078       }
1079     });
1080     abovePIDThreshold.setText("Above Identity Threshold");
1081     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1082     {
1083       public void actionPerformed(ActionEvent e)
1084       {
1085         abovePIDThreshold_actionPerformed(e);
1086       }
1087     });
1088     showSeqFeatures.setText("Show Sequence Features");
1089     showSeqFeatures.addActionListener(new ActionListener()
1090     {
1091       public void actionPerformed(ActionEvent actionEvent)
1092       {
1093         showSeqFeatures_actionPerformed(actionEvent);
1094       }
1095     });
1096     /*
1097      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1098      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1099      * void actionPerformed(ActionEvent actionEvent) {
1100      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1101      */
1102     showDbRefsMenuitem.setText("Show Database Refs");
1103     showDbRefsMenuitem.addActionListener(new ActionListener()
1104     {
1105
1106       public void actionPerformed(ActionEvent e)
1107       {
1108         showDbRefs_actionPerformed(e);
1109       }
1110
1111     });
1112     showNpFeatsMenuitem.setText("Show Non-Positional Features");
1113     showNpFeatsMenuitem.addActionListener(new ActionListener()
1114     {
1115
1116       public void actionPerformed(ActionEvent e)
1117       {
1118         showNpFeats_actionPerformed(e);
1119       }
1120
1121     });
1122     showGroupConservation.setText("Group Conservation");
1123     showGroupConservation.addActionListener(new ActionListener()
1124     {
1125
1126       public void actionPerformed(ActionEvent e)
1127       {
1128         showGroupConservation_actionPerformed(e);
1129       }
1130
1131     });
1132
1133     showGroupConsensus.setText("Group Consensus");
1134     showGroupConsensus.addActionListener(new ActionListener()
1135     {
1136
1137       public void actionPerformed(ActionEvent e)
1138       {
1139         showGroupConsensus_actionPerformed(e);
1140       }
1141
1142     });
1143     showConsensusHistogram.setText("Show Consensus Histogram");
1144     showConsensusHistogram.addActionListener(new ActionListener()
1145     {
1146
1147       public void actionPerformed(ActionEvent e)
1148       {
1149         showConsensusHistogram_actionPerformed(e);
1150       }
1151
1152     });
1153     showSequenceLogo.setText("Show Consensus Logo");
1154     showSequenceLogo.addActionListener(new ActionListener()
1155     {
1156
1157       public void actionPerformed(ActionEvent e)
1158       {
1159         showSequenceLogo_actionPerformed(e);
1160       }
1161
1162     });
1163     normaliseSequenceLogo.setText("Normalise Consensus Logo");
1164     normaliseSequenceLogo.addActionListener(new ActionListener()
1165     {
1166
1167       public void actionPerformed(ActionEvent e)
1168       {
1169         normaliseSequenceLogo_actionPerformed(e);
1170       }
1171
1172     });
1173     applyAutoAnnotationSettings.setText("Apply to all groups");
1174     applyAutoAnnotationSettings.setState(false);
1175     applyAutoAnnotationSettings.setVisible(true);
1176     applyAutoAnnotationSettings.addActionListener(new ActionListener()
1177     {
1178
1179       public void actionPerformed(ActionEvent e)
1180       {
1181         applyAutoAnnotationSettings_actionPerformed(e);
1182       }
1183
1184     });
1185
1186     nucleotideColour.setText("Nucleotide");
1187     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1188     {
1189       public void actionPerformed(ActionEvent e)
1190       {
1191         nucleotideColour_actionPerformed(e);
1192       }
1193     });
1194
1195     tcoffeeColour.setText("T-Coffee scores");
1196     tcoffeeColour.setEnabled(false);
1197     tcoffeeColour.addActionListener(new ActionListener()
1198     {
1199
1200       @Override
1201       public void actionPerformed(ActionEvent e)
1202       {
1203         tcoffeeColorScheme_actionPerformed(e);
1204       }
1205     });
1206
1207     deleteGroups.setText("Undefine groups");
1208     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1209             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1210                     .getMenuShortcutKeyMask(), false));
1211     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1212     {
1213       public void actionPerformed(ActionEvent e)
1214       {
1215         deleteGroups_actionPerformed(e);
1216       }
1217     });
1218     copy.setText("Copy");
1219     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1220             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1221                     .getMenuShortcutKeyMask(), false));
1222
1223     copy.addActionListener(new java.awt.event.ActionListener()
1224     {
1225       public void actionPerformed(ActionEvent e)
1226       {
1227         copy_actionPerformed(e);
1228       }
1229     });
1230     cut.setText("Cut");
1231     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1232             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1233                     .getMenuShortcutKeyMask(), false));
1234     cut.addActionListener(new java.awt.event.ActionListener()
1235     {
1236       public void actionPerformed(ActionEvent e)
1237       {
1238         cut_actionPerformed(e);
1239       }
1240     });
1241     delete.setText("Delete");
1242     delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1243             java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1244     delete.addActionListener(new java.awt.event.ActionListener()
1245     {
1246       public void actionPerformed(ActionEvent e)
1247       {
1248         delete_actionPerformed(e);
1249       }
1250     });
1251     pasteMenu.setText("Paste");
1252     pasteNew.setText("To New Alignment");
1253     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1254             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1255                     .getMenuShortcutKeyMask()
1256                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1257     pasteNew.addActionListener(new java.awt.event.ActionListener()
1258     {
1259       public void actionPerformed(ActionEvent e)
1260       {
1261         pasteNew_actionPerformed(e);
1262       }
1263     });
1264     pasteThis.setText("Add To This Alignment");
1265     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1266             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1267                     .getMenuShortcutKeyMask(), false));
1268     pasteThis.addActionListener(new java.awt.event.ActionListener()
1269     {
1270       public void actionPerformed(ActionEvent e)
1271       {
1272         pasteThis_actionPerformed(e);
1273       }
1274     });
1275     applyToAllGroups.setText("Apply Colour To All Groups");
1276     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1277     {
1278       public void actionPerformed(ActionEvent e)
1279       {
1280         applyToAllGroups_actionPerformed(e);
1281       }
1282     });
1283     createPNG.addActionListener(new java.awt.event.ActionListener()
1284     {
1285       public void actionPerformed(ActionEvent e)
1286       {
1287         createPNG(null);
1288       }
1289     });
1290     createPNG.setActionCommand("Save As PNG Image");
1291     createPNG.setText("PNG");
1292     font.setText("Font...");
1293     font.addActionListener(new java.awt.event.ActionListener()
1294     {
1295       public void actionPerformed(ActionEvent e)
1296       {
1297         font_actionPerformed(e);
1298       }
1299     });
1300
1301     seqLimits.setText("Show Sequence Limits");
1302     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1303     seqLimits.addActionListener(new java.awt.event.ActionListener()
1304     {
1305       public void actionPerformed(ActionEvent e)
1306       {
1307         seqLimit_actionPerformed(e);
1308       }
1309     });
1310     epsFile.setText("EPS");
1311     epsFile.addActionListener(new java.awt.event.ActionListener()
1312     {
1313       public void actionPerformed(ActionEvent e)
1314       {
1315         createEPS(null);
1316       }
1317     });
1318     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1319     LoadtreeMenuItem.setText("Load Associated Tree");
1320     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1321     {
1322       public void actionPerformed(ActionEvent e)
1323       {
1324         LoadtreeMenuItem_actionPerformed(e);
1325       }
1326     });
1327
1328     scaleAbove.setVisible(false);
1329     scaleAbove.setText("Scale Above");
1330     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1331     {
1332       public void actionPerformed(ActionEvent e)
1333       {
1334         scaleAbove_actionPerformed(e);
1335       }
1336     });
1337     scaleLeft.setVisible(false);
1338     scaleLeft.setSelected(true);
1339     scaleLeft.setText("Scale Left");
1340     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1341     {
1342       public void actionPerformed(ActionEvent e)
1343       {
1344         scaleLeft_actionPerformed(e);
1345       }
1346     });
1347     scaleRight.setVisible(false);
1348     scaleRight.setSelected(true);
1349     scaleRight.setText("Scale Right");
1350     scaleRight.addActionListener(new java.awt.event.ActionListener()
1351     {
1352       public void actionPerformed(ActionEvent e)
1353       {
1354         scaleRight_actionPerformed(e);
1355       }
1356     });
1357     centreColumnLabelsMenuItem.setVisible(true);
1358     centreColumnLabelsMenuItem.setState(false);
1359     centreColumnLabelsMenuItem.setText("Centre Column Labels");
1360     centreColumnLabelsMenuItem
1361             .addActionListener(new java.awt.event.ActionListener()
1362             {
1363               public void actionPerformed(ActionEvent e)
1364               {
1365                 centreColumnLabels_actionPerformed(e);
1366               }
1367             });
1368     followHighlightMenuItem.setVisible(true);
1369     followHighlightMenuItem.setState(true);
1370     followHighlightMenuItem.setText("Automatic Scrolling");
1371     followHighlightMenuItem.addActionListener(new ActionListener()
1372     {
1373
1374       public void actionPerformed(ActionEvent e)
1375       {
1376         followHighlight_actionPerformed();
1377       }
1378
1379     });
1380
1381     modifyPID.setText("Modify Identity Threshold...");
1382     modifyPID.addActionListener(new java.awt.event.ActionListener()
1383     {
1384       public void actionPerformed(ActionEvent e)
1385       {
1386         modifyPID_actionPerformed(e);
1387       }
1388     });
1389     modifyConservation.setText("Modify Conservation Threshold...");
1390     modifyConservation
1391             .addActionListener(new java.awt.event.ActionListener()
1392             {
1393               public void actionPerformed(ActionEvent e)
1394               {
1395                 modifyConservation_actionPerformed(e);
1396               }
1397             });
1398     sortByTreeMenu.setText("By Tree Order");
1399     sort.setText("Sort");
1400     sort.addMenuListener(new MenuListener()
1401     {
1402       public void menuSelected(MenuEvent e)
1403       {
1404         buildTreeMenu();
1405       }
1406
1407       public void menuDeselected(MenuEvent e)
1408       {
1409       }
1410
1411       public void menuCanceled(MenuEvent e)
1412       {
1413       }
1414     });
1415     sortByAnnotScore.setText("by Score");
1416     sort.add(sortByAnnotScore);
1417     sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1418     {
1419
1420       public void menuCanceled(MenuEvent e)
1421       {
1422       }
1423
1424       public void menuDeselected(MenuEvent e)
1425       {
1426       }
1427
1428       public void menuSelected(MenuEvent e)
1429       {
1430         buildSortByAnnotationScoresMenu();
1431       }
1432     });
1433     sortByAnnotScore.setVisible(false);
1434
1435     calculateTree.setText("Calculate Tree");
1436
1437     jMenu2.setText("Export Image");
1438     padGapsMenuitem.setText("Pad Gaps");
1439     padGapsMenuitem.setState(jalview.bin.Cache
1440             .getDefault("PAD_GAPS", false));
1441     padGapsMenuitem.addActionListener(new ActionListener()
1442     {
1443       public void actionPerformed(ActionEvent e)
1444       {
1445         padGapsMenuitem_actionPerformed(e);
1446       }
1447     });
1448     vamsasStore.setVisible(false);
1449     vamsasStore.setText("VAMSAS store");
1450     vamsasStore.addActionListener(new ActionListener()
1451     {
1452       public void actionPerformed(ActionEvent e)
1453       {
1454         vamsasStore_actionPerformed(e);
1455       }
1456     });
1457     showTranslation.setText("Translate cDNA");
1458     showTranslation.addActionListener(new ActionListener()
1459     {
1460       public void actionPerformed(ActionEvent e)
1461       {
1462         showTranslation_actionPerformed(e);
1463       }
1464     });
1465     extractScores.setText("Extract Scores...");
1466     extractScores.addActionListener(new ActionListener()
1467     {
1468       public void actionPerformed(ActionEvent e)
1469       {
1470         extractScores_actionPerformed(e);
1471       }
1472     });
1473     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1474     // score extraction
1475     showProducts.setText("Get Cross References");
1476     /*
1477      * showProducts.addActionListener(new ActionListener() {
1478      *
1479      * public void actionPerformed(ActionEvent e) {
1480      * showProducts_actionPerformed(e); } });
1481      */
1482     openFeatureSettings.setText("Feature Settings...");
1483     openFeatureSettings.addActionListener(new ActionListener()
1484     {
1485       public void actionPerformed(ActionEvent e)
1486       {
1487         featureSettings_actionPerformed(e);
1488       }
1489     });
1490     fetchSequence.setText("Fetch Sequence(s)...");
1491     fetchSequence.addActionListener(new ActionListener()
1492     {
1493       public void actionPerformed(ActionEvent e)
1494       {
1495         fetchSequence_actionPerformed(e);
1496       }
1497     });
1498
1499     annotationColour.setText("By Annotation...");
1500     annotationColour.addActionListener(new ActionListener()
1501     {
1502       public void actionPerformed(ActionEvent e)
1503       {
1504         annotationColour_actionPerformed(e);
1505       }
1506     });
1507
1508     rnahelicesColour.setText("By RNA helices");
1509     rnahelicesColour.addActionListener(new ActionListener()
1510     {
1511       public void actionPerformed(ActionEvent e)
1512       {
1513         rnahelicesColour_actionPerformed(e);
1514       }
1515     });
1516
1517     associatedData.setText("Load Features / Annotations");
1518     associatedData.addActionListener(new ActionListener()
1519     {
1520       public void actionPerformed(ActionEvent e)
1521       {
1522         associatedData_actionPerformed(e);
1523       }
1524     });
1525     autoCalculate.setText("Autocalculate Consensus");
1526     autoCalculate.setState(jalview.bin.Cache.getDefault(
1527             "AUTO_CALC_CONSENSUS", true));
1528     autoCalculate.addActionListener(new ActionListener()
1529     {
1530       public void actionPerformed(ActionEvent e)
1531       {
1532         autoCalculate_actionPerformed(e);
1533       }
1534     });
1535     sortByTree.setText("Sort Alignment With New Tree");
1536     sortByTree
1537             .setToolTipText("<html>Enable this to automatically sort<br>the alignment when you open<br> a new tree.");
1538     sortByTree
1539             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1540     sortByTree.addActionListener(new ActionListener()
1541     {
1542       public void actionPerformed(ActionEvent e)
1543       {
1544         sortByTreeOption_actionPerformed(e);
1545       }
1546     });
1547
1548     listenToViewSelections.setText("Listen for selections");
1549     listenToViewSelections
1550             .setToolTipText("<html>When selected, selections in this view will mirror<br>selections made on the same sequences in other views.");
1551     listenToViewSelections.setState(false);
1552     listenToViewSelections.addActionListener(new ActionListener()
1553     {
1554       public void actionPerformed(ActionEvent e)
1555       {
1556         listenToViewSelections_actionPerformed(e);
1557       }
1558     });
1559
1560     addSequenceMenu.setText("Add Sequences");
1561     addFromFile.setText("From File");
1562     addFromFile.addActionListener(new ActionListener()
1563     {
1564       public void actionPerformed(ActionEvent e)
1565       {
1566         addFromFile_actionPerformed(e);
1567       }
1568     });
1569     addFromText.setText("From Textbox");
1570     addFromText.addActionListener(new ActionListener()
1571     {
1572       public void actionPerformed(ActionEvent e)
1573       {
1574         addFromText_actionPerformed(e);
1575       }
1576     });
1577     addFromURL.setText("From URL");
1578     addFromURL.addActionListener(new ActionListener()
1579     {
1580       public void actionPerformed(ActionEvent e)
1581       {
1582         addFromURL_actionPerformed(e);
1583       }
1584     });
1585     exportFeatures.setText("Export Features...");
1586     exportFeatures.addActionListener(new ActionListener()
1587     {
1588       public void actionPerformed(ActionEvent e)
1589       {
1590         exportFeatures_actionPerformed(e);
1591       }
1592     });
1593     exportAnnotations.setText("Export Annotations...");
1594     exportAnnotations.addActionListener(new ActionListener()
1595     {
1596       public void actionPerformed(ActionEvent e)
1597       {
1598         exportAnnotations_actionPerformed(e);
1599       }
1600     });
1601     statusPanel.setLayout(gridLayout1);
1602     jMenu3.setText("Show");
1603     showAllSeqs.setText("All Sequences");
1604     showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1605     showAllSeqs.addActionListener(new ActionListener()
1606     {
1607       public void actionPerformed(ActionEvent e)
1608       {
1609         showAllSeqs_actionPerformed(e);
1610       }
1611     });
1612     showAllColumns.setText("All Columns");
1613     showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1614     showAllColumns.addActionListener(new ActionListener()
1615     {
1616       public void actionPerformed(ActionEvent e)
1617       {
1618         showAllColumns_actionPerformed(e);
1619       }
1620     });
1621     hideMenu.setText("Hide");
1622     hideSelSequences.setText("Selected Sequences");
1623     hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1624     hideSelSequences.addActionListener(new ActionListener()
1625     {
1626       public void actionPerformed(ActionEvent e)
1627       {
1628         hideSelSequences_actionPerformed(e);
1629       }
1630     });
1631     hideSelColumns.setText("Selected Columns");
1632     hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1633     hideSelColumns.addActionListener(new ActionListener()
1634     {
1635       public void actionPerformed(ActionEvent e)
1636       {
1637         hideSelColumns_actionPerformed(e);
1638       }
1639     });
1640     hideAllSelection.setText("Selected Region");
1641     hideAllSelection.addActionListener(new ActionListener()
1642     {
1643       public void actionPerformed(ActionEvent e)
1644       {
1645         hideAllSelection_actionPerformed(e);
1646       }
1647     });
1648     // TODO: should be hidden if no selection exists.
1649     hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
1650     hideAllButSelection.addActionListener(new ActionListener()
1651     {
1652       public void actionPerformed(ActionEvent e)
1653       {
1654         hideAllButSelection_actionPerformed(e);
1655       }
1656     });
1657     showAllhidden.setText("All Sequences and Columns");
1658     showAllhidden
1659             .setToolTipText("H toggles visibility of hidden or selected regions.");
1660     showAllhidden.addActionListener(new ActionListener()
1661     {
1662       public void actionPerformed(ActionEvent e)
1663       {
1664         showAllhidden_actionPerformed(e);
1665       }
1666     });
1667
1668     hiddenMarkers.setText("Show Hidden Markers");
1669     hiddenMarkers.addActionListener(new ActionListener()
1670     {
1671       public void actionPerformed(ActionEvent e)
1672       {
1673         hiddenMarkers_actionPerformed(e);
1674       }
1675     });
1676     invertColSel.setText("Invert Column Selection");
1677     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1678             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1679                     .getMenuShortcutKeyMask()
1680                     | java.awt.event.KeyEvent.ALT_MASK, false));
1681     invertColSel.addActionListener(new ActionListener()
1682     {
1683       public void actionPerformed(ActionEvent e)
1684       {
1685         invertColSel_actionPerformed(e);
1686       }
1687     });
1688     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1689     {
1690       public void stateChanged(ChangeEvent evt)
1691       {
1692         JTabbedPane pane = (JTabbedPane) evt.getSource();
1693         int sel = pane.getSelectedIndex();
1694         tabSelectionChanged(sel);
1695       }
1696     });
1697     tabbedPane.addMouseListener(new MouseAdapter()
1698     {
1699       public void mousePressed(MouseEvent e)
1700       {
1701         tabbedPane_mousePressed(e);
1702       }
1703     });
1704     tabbedPane.addFocusListener(new FocusAdapter()
1705     {
1706       public void focusGained(FocusEvent e)
1707       {
1708         tabbedPane_focusGained(e);
1709       }
1710     });
1711     save.setText("Save");
1712     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1713             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1714                     .getMenuShortcutKeyMask(), false));
1715     save.addActionListener(new ActionListener()
1716     {
1717       public void actionPerformed(ActionEvent e)
1718       {
1719         save_actionPerformed(e);
1720       }
1721     });
1722     reload.setEnabled(false);
1723     reload.setText("Reload");
1724     reload.addActionListener(new ActionListener()
1725     {
1726       public void actionPerformed(ActionEvent e)
1727       {
1728         reload_actionPerformed(e);
1729       }
1730     });
1731     newView.setText("New View");
1732     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1733             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1734                     .getMenuShortcutKeyMask(), false));
1735     newView.addActionListener(new ActionListener()
1736     {
1737       public void actionPerformed(ActionEvent e)
1738       {
1739         newView_actionPerformed(e);
1740       }
1741     });
1742     tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1743             + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1744     textColour.setText("Colour Text ...");
1745     textColour.addActionListener(new ActionListener()
1746     {
1747       public void actionPerformed(ActionEvent e)
1748       {
1749         textColour_actionPerformed(e);
1750       }
1751     });
1752     formatMenu.setText("Format");
1753     selectMenu.setText("Select");
1754     idRightAlign.setText("Right Align Sequence Id");
1755     idRightAlign.addActionListener(new ActionListener()
1756     {
1757       public void actionPerformed(ActionEvent e)
1758       {
1759         idRightAlign_actionPerformed(e);
1760       }
1761     });
1762     gatherViews.setEnabled(false);
1763     gatherViews.setText("Gather Views");
1764     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1765             java.awt.event.KeyEvent.VK_G, 0, false));
1766     gatherViews.addActionListener(new ActionListener()
1767     {
1768       public void actionPerformed(ActionEvent e)
1769       {
1770         gatherViews_actionPerformed(e);
1771       }
1772     });
1773     expandViews.setEnabled(false);
1774     expandViews.setText("Expand Views");
1775     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1776             java.awt.event.KeyEvent.VK_X, 0, false));
1777     expandViews.addActionListener(new ActionListener()
1778     {
1779       public void actionPerformed(ActionEvent e)
1780       {
1781         expandViews_actionPerformed(e);
1782       }
1783     });
1784     pageSetup.setText("Page Setup ...");
1785     pageSetup.addActionListener(new ActionListener()
1786     {
1787       public void actionPerformed(ActionEvent e)
1788       {
1789         pageSetup_actionPerformed(e);
1790       }
1791     });
1792     alignmentProperties.setText("Alignment Properties...");
1793     alignmentProperties.addActionListener(new ActionListener()
1794     {
1795       public void actionPerformed(ActionEvent actionEvent)
1796       {
1797         alignmentProperties();
1798       }
1799     });
1800     tooltipSettingsMenu.setText("Sequence ID Tooltip");
1801     autoAnnMenu.setText("Autocalculated Annotation");
1802     alignFrameMenuBar.add(fileMenu);
1803     alignFrameMenuBar.add(editMenu);
1804     alignFrameMenuBar.add(selectMenu);
1805     alignFrameMenuBar.add(viewMenu);
1806     alignFrameMenuBar.add(formatMenu);
1807     alignFrameMenuBar.add(colourMenu);
1808     alignFrameMenuBar.add(calculateMenu);
1809     alignFrameMenuBar.add(webService);
1810     fileMenu.add(fetchSequence);
1811     fileMenu.add(addSequenceMenu);
1812     fileMenu.add(reload);
1813     fileMenu.addSeparator();
1814     fileMenu.add(vamsasStore);
1815     fileMenu.add(save);
1816     fileMenu.add(saveAs);
1817     fileMenu.add(outputTextboxMenu);
1818     fileMenu.add(pageSetup);
1819     fileMenu.add(printMenuItem);
1820     fileMenu.addSeparator();
1821     fileMenu.add(jMenu2);
1822     fileMenu.add(exportFeatures);
1823     fileMenu.add(exportAnnotations);
1824     fileMenu.add(LoadtreeMenuItem);
1825     fileMenu.add(associatedData);
1826     fileMenu.addSeparator();
1827     fileMenu.add(closeMenuItem);
1828     editMenu.add(undoMenuItem);
1829     editMenu.add(redoMenuItem);
1830     editMenu.add(cut);
1831     editMenu.add(copy);
1832     editMenu.add(pasteMenu);
1833     editMenu.add(delete);
1834     editMenu.addSeparator();
1835     editMenu.add(remove2LeftMenuItem);
1836     editMenu.add(remove2RightMenuItem);
1837     editMenu.add(removeGappedColumnMenuItem);
1838     editMenu.add(removeAllGapsMenuItem);
1839     editMenu.add(removeRedundancyMenuItem);
1840     editMenu.addSeparator();
1841     // dont add these yet in the CVS build - they cannot be undone!
1842     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1843     // editMenu.add(justifyLeftMenuItem);
1844     // editMenu.add(justifyRightMenuItem);
1845     // editMenu.addSeparator();
1846     editMenu.add(padGapsMenuitem);
1847     viewMenu.add(newView);
1848     viewMenu.add(expandViews);
1849     viewMenu.add(gatherViews);
1850     viewMenu.addSeparator();
1851     viewMenu.add(jMenu3);
1852     viewMenu.add(hideMenu);
1853     viewMenu.addSeparator();
1854     viewMenu.add(followHighlightMenuItem);
1855     viewMenu.add(annotationPanelMenuItem);
1856     autoAnnMenu.add(applyAutoAnnotationSettings);
1857     autoAnnMenu.add(showConsensusHistogram);
1858     autoAnnMenu.add(showSequenceLogo);
1859     autoAnnMenu.add(normaliseSequenceLogo);
1860     autoAnnMenu.addSeparator();
1861     autoAnnMenu.add(showGroupConservation);
1862     autoAnnMenu.add(showGroupConsensus);
1863     viewMenu.add(autoAnnMenu);
1864     viewMenu.addSeparator();
1865     viewMenu.add(showSeqFeatures);
1866     // viewMenu.add(showSeqFeaturesHeight);
1867
1868     viewMenu.add(openFeatureSettings);
1869     tooltipSettingsMenu.add(showDbRefsMenuitem);
1870     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1871     viewMenu.add(tooltipSettingsMenu);
1872     viewMenu.addSeparator();
1873     viewMenu.add(alignmentProperties);
1874     viewMenu.addSeparator();
1875     viewMenu.add(overviewMenuItem);
1876     colourMenu.add(applyToAllGroups);
1877     colourMenu.add(textColour);
1878     colourMenu.addSeparator();
1879     colourMenu.add(noColourmenuItem);
1880     colourMenu.add(clustalColour);
1881     colourMenu.add(BLOSUM62Colour);
1882     colourMenu.add(PIDColour);
1883     colourMenu.add(zappoColour);
1884     colourMenu.add(taylorColour);
1885     colourMenu.add(hydrophobicityColour);
1886     colourMenu.add(helixColour);
1887     colourMenu.add(strandColour);
1888     colourMenu.add(turnColour);
1889     colourMenu.add(buriedColour);
1890     colourMenu.add(nucleotideColour);
1891     colourMenu.add(purinePyrimidineColour);
1892     colourMenu.add(RNAInteractionColour);
1893     // colourMenu.add(covariationColour);
1894     colourMenu.add(tcoffeeColour);
1895     colourMenu.add(userDefinedColour);
1896     colourMenu.addSeparator();
1897     colourMenu.add(conservationMenuItem);
1898     colourMenu.add(modifyConservation);
1899     colourMenu.add(abovePIDThreshold);
1900     colourMenu.add(modifyPID);
1901     colourMenu.add(annotationColour);
1902     colourMenu.add(rnahelicesColour);
1903     calculateMenu.add(sort);
1904     calculateMenu.add(calculateTree);
1905     calculateMenu.addSeparator();
1906     calculateMenu.add(pairwiseAlignmentMenuItem);
1907     calculateMenu.add(PCAMenuItem);
1908     calculateMenu.addSeparator();
1909     calculateMenu.add(showTranslation);
1910     calculateMenu.add(showProducts);
1911     calculateMenu.add(autoCalculate);
1912     calculateMenu.add(sortByTree);
1913     calculateMenu.addSeparator();
1914     calculateMenu.add(extractScores);
1915     webServiceNoServices = new JMenuItem("<No Services>");
1916     webService.add(webServiceNoServices);
1917     pasteMenu.add(pasteNew);
1918     pasteMenu.add(pasteThis);
1919     sort.add(sortIDMenuItem);
1920     sort.add(sortLengthMenuItem);
1921     sort.add(sortGroupMenuItem);
1922     sort.add(sortPairwiseMenuItem);
1923     sort.add(sortByTreeMenu);
1924     calculateTree.add(averageDistanceTreeMenuItem);
1925     calculateTree.add(neighbourTreeMenuItem);
1926     calculateTree.add(avDistanceTreeBlosumMenuItem);
1927     calculateTree.add(njTreeBlosumMenuItem);
1928     jMenu2.add(htmlMenuItem);
1929     jMenu2.add(epsFile);
1930     jMenu2.add(createPNG);
1931     addSequenceMenu.add(addFromFile);
1932     addSequenceMenu.add(addFromText);
1933     addSequenceMenu.add(addFromURL);
1934     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1935     statusPanel.add(statusBar, null);
1936     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1937     jMenu3.add(showAllColumns);
1938     jMenu3.add(showAllSeqs);
1939     jMenu3.add(showAllhidden);
1940     hideMenu.add(hideSelColumns);
1941     hideMenu.add(hideSelSequences);
1942     hideMenu.add(hideAllSelection);
1943     hideMenu.add(hideAllButSelection);
1944
1945     formatMenu.add(font);
1946     formatMenu.addSeparator();
1947     formatMenu.add(wrapMenuItem);
1948     formatMenu.add(scaleAbove);
1949     formatMenu.add(scaleLeft);
1950     formatMenu.add(scaleRight);
1951     formatMenu.add(seqLimits);
1952     formatMenu.add(idRightAlign);
1953     formatMenu.add(hiddenMarkers);
1954     formatMenu.add(viewBoxesMenuItem);
1955     formatMenu.add(viewTextMenuItem);
1956     formatMenu.add(colourTextMenuItem);
1957     formatMenu.add(renderGapsMenuItem);
1958     formatMenu.add(centreColumnLabelsMenuItem);
1959     formatMenu.add(showNonconservedMenuItem);
1960     selectMenu.add(findMenuItem);
1961     selectMenu.addSeparator();
1962     selectMenu.add(selectAllSequenceMenuItem);
1963     selectMenu.add(deselectAllSequenceMenuItem);
1964     selectMenu.add(invertSequenceMenuItem);
1965     selectMenu.add(invertColSel);
1966     selectMenu.add(deleteGroups);
1967     selectMenu.add(grpsFromSelection);
1968     // TODO - determine if the listenToViewSelections button is needed : see bug
1969     // JAL-574
1970     // selectMenu.addSeparator();
1971     // selectMenu.add(listenToViewSelections);
1972   }
1973
1974   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
1975   {
1976     // TODO Auto-generated method stub
1977
1978   }
1979
1980   protected void listenToViewSelections_actionPerformed(ActionEvent e)
1981   {
1982     // TODO Auto-generated method stub
1983
1984   }
1985
1986   protected void showAllhidden_actionPerformed(ActionEvent e)
1987   {
1988     // TODO Auto-generated method stub
1989
1990   }
1991
1992   protected void hideAllButSelection_actionPerformed(ActionEvent e)
1993   {
1994     // TODO Auto-generated method stub
1995
1996   }
1997
1998   protected void hideAllSelection_actionPerformed(ActionEvent e)
1999   {
2000     // TODO Auto-generated method stub
2001
2002   }
2003
2004   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2005   {
2006     // TODO Auto-generated method stub
2007
2008   }
2009
2010   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2011   {
2012     // TODO Auto-generated method stub
2013
2014   }
2015
2016   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2017   {
2018     // TODO Auto-generated method stub
2019
2020   }
2021
2022   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2023   {
2024     // TODO Auto-generated method stub
2025
2026   }
2027
2028   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2029   {
2030     // TODO Auto-generated method stub
2031
2032   }
2033
2034   protected void showGroupConservation_actionPerformed(ActionEvent e)
2035   {
2036     // TODO Auto-generated method stub
2037
2038   }
2039
2040   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2041   {
2042     // TODO Auto-generated method stub
2043
2044   }
2045
2046   protected void showSeqFeaturesHeight_actionPerformed(
2047           ActionEvent actionEvent)
2048   {
2049     // TODO Auto-generated method stub
2050
2051   }
2052
2053   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2054   {
2055     // TODO Auto-generated method stub
2056
2057   }
2058
2059   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2060   {
2061     // TODO Auto-generated method stub
2062
2063   }
2064
2065   protected void followHighlight_actionPerformed()
2066   {
2067     // TODO Auto-generated method stub
2068
2069   }
2070
2071   protected void showNpFeats_actionPerformed(ActionEvent e)
2072   {
2073     // TODO Auto-generated method stub
2074
2075   }
2076
2077   protected void showDbRefs_actionPerformed(ActionEvent e)
2078   {
2079     // TODO Auto-generated method stub
2080
2081   }
2082
2083   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2084   {
2085   }
2086
2087   protected void showProducts_actionPerformed(ActionEvent e)
2088   {
2089   }
2090
2091   protected void buildSortByAnnotationScoresMenu()
2092   {
2093   }
2094
2095   protected void extractScores_actionPerformed(ActionEvent e)
2096   {
2097   }
2098
2099   protected void outputText_actionPerformed(ActionEvent e)
2100   {
2101   }
2102
2103   public void addFromFile_actionPerformed(ActionEvent e)
2104   {
2105
2106   }
2107
2108   public void addFromText_actionPerformed(ActionEvent e)
2109   {
2110
2111   }
2112
2113   public void addFromURL_actionPerformed(ActionEvent e)
2114   {
2115
2116   }
2117
2118   public void exportFeatures_actionPerformed(ActionEvent e)
2119   {
2120
2121   }
2122
2123   public void exportAnnotations_actionPerformed(ActionEvent e)
2124   {
2125
2126   }
2127
2128   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2129   {
2130   }
2131
2132   protected void closeMenuItem_actionPerformed(boolean b)
2133   {
2134   }
2135
2136   protected void redoMenuItem_actionPerformed(ActionEvent e)
2137   {
2138   }
2139
2140   protected void undoMenuItem_actionPerformed(ActionEvent e)
2141   {
2142   }
2143
2144   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2145   {
2146   }
2147
2148   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2149   {
2150   }
2151
2152   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2153   {
2154   }
2155
2156   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2157   {
2158   }
2159
2160   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2161   {
2162   }
2163
2164   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2165   {
2166   }
2167
2168   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2169   {
2170   }
2171
2172   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2173   {
2174   }
2175
2176   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2177   {
2178   }
2179
2180   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2181   {
2182   }
2183
2184   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2185   {
2186   }
2187
2188   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2189   {
2190   }
2191
2192   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2193   {
2194   }
2195
2196   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2197   {
2198   }
2199
2200   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2201   {
2202   }
2203
2204   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2205   {
2206   }
2207
2208   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2209   {
2210   }
2211
2212   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2213   {
2214   }
2215
2216   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2217   {
2218   }
2219
2220   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2221   {
2222   }
2223
2224   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2225   {
2226   }
2227
2228   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2229   {
2230   }
2231
2232   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2233   {
2234   }
2235
2236   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2237   {
2238   }
2239
2240   protected void clustalColour_actionPerformed(ActionEvent e)
2241   {
2242   }
2243
2244   protected void zappoColour_actionPerformed(ActionEvent e)
2245   {
2246   }
2247
2248   protected void taylorColour_actionPerformed(ActionEvent e)
2249   {
2250   }
2251
2252   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2253   {
2254   }
2255
2256   protected void helixColour_actionPerformed(ActionEvent e)
2257   {
2258   }
2259
2260   protected void strandColour_actionPerformed(ActionEvent e)
2261   {
2262   }
2263
2264   protected void turnColour_actionPerformed(ActionEvent e)
2265   {
2266   }
2267
2268   protected void buriedColour_actionPerformed(ActionEvent e)
2269   {
2270   }
2271
2272   protected void userDefinedColour_actionPerformed(ActionEvent e)
2273   {
2274   }
2275
2276   protected void PIDColour_actionPerformed(ActionEvent e)
2277   {
2278   }
2279
2280   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2281   {
2282   }
2283
2284   protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2285   {
2286   }
2287
2288   protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2289   {
2290   }
2291
2292
2293   /*
2294    * protected void covariationColour_actionPerformed(ActionEvent e) { }
2295    */
2296
2297   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2298   {
2299   }
2300
2301   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2302   {
2303   }
2304
2305   protected void printMenuItem_actionPerformed(ActionEvent e)
2306   {
2307   }
2308
2309   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2310   {
2311   }
2312
2313   protected void findMenuItem_actionPerformed(ActionEvent e)
2314   {
2315   }
2316
2317   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2318   {
2319   }
2320
2321   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2322   {
2323   }
2324
2325   protected void nucleotideColour_actionPerformed(ActionEvent e)
2326   {
2327   }
2328
2329   protected void deleteGroups_actionPerformed(ActionEvent e)
2330   {
2331   }
2332
2333   protected void copy_actionPerformed(ActionEvent e)
2334   {
2335   }
2336
2337   protected void cut_actionPerformed(ActionEvent e)
2338   {
2339   }
2340
2341   protected void delete_actionPerformed(ActionEvent e)
2342   {
2343   }
2344
2345   protected void pasteNew_actionPerformed(ActionEvent e)
2346   {
2347   }
2348
2349   protected void pasteThis_actionPerformed(ActionEvent e)
2350   {
2351   }
2352
2353   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2354   {
2355   }
2356
2357   public void createPNG(java.io.File f)
2358   {
2359   }
2360
2361   protected void font_actionPerformed(ActionEvent e)
2362   {
2363   }
2364
2365   protected void seqLimit_actionPerformed(ActionEvent e)
2366   {
2367   }
2368
2369   public void seqDBRef_actionPerformed(ActionEvent e)
2370   {
2371
2372   }
2373
2374   public void createEPS(java.io.File f)
2375   {
2376   }
2377
2378   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2379   {
2380
2381   }
2382
2383   /**
2384    * Template method to handle the 'load T-Coffee scores' menu event.
2385    * <p>
2386    * Subclasses override this method to provide a custom action.
2387    *
2388    * @param event
2389    *          The raised event
2390    */
2391   protected void loadScores_actionPerformed(ActionEvent event)
2392   {
2393
2394   }
2395
2396   /**
2397    * Template method to handle the 'Color T-Coffee scores' menu event.
2398    * <p>
2399    * Subclasses override this method to provide a custom action.
2400    *
2401    * @param event
2402    *          The raised event
2403    */
2404   protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2405   {
2406
2407   }
2408
2409   protected void jpred_actionPerformed(ActionEvent e)
2410   {
2411   }
2412
2413   protected void scaleAbove_actionPerformed(ActionEvent e)
2414   {
2415   }
2416
2417   protected void scaleLeft_actionPerformed(ActionEvent e)
2418   {
2419   }
2420
2421   protected void scaleRight_actionPerformed(ActionEvent e)
2422   {
2423   }
2424
2425   protected void modifyPID_actionPerformed(ActionEvent e)
2426   {
2427   }
2428
2429   protected void modifyConservation_actionPerformed(ActionEvent e)
2430   {
2431   }
2432
2433   protected void saveAs_actionPerformed(ActionEvent e)
2434   {
2435   }
2436
2437   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2438   {
2439   }
2440
2441   public void vamsasStore_actionPerformed(ActionEvent e)
2442   {
2443
2444   }
2445
2446   public void vamsasLoad_actionPerformed(ActionEvent e)
2447   {
2448
2449   }
2450
2451   public void showTranslation_actionPerformed(ActionEvent e)
2452   {
2453
2454   }
2455
2456   public void featureSettings_actionPerformed(ActionEvent e)
2457   {
2458
2459   }
2460
2461   public void fetchSequence_actionPerformed(ActionEvent e)
2462   {
2463
2464   }
2465
2466   public void smoothFont_actionPerformed(ActionEvent e)
2467   {
2468
2469   }
2470
2471   public void annotationColour_actionPerformed(ActionEvent e)
2472   {
2473
2474   }
2475
2476   public void rnahelicesColour_actionPerformed(ActionEvent e)
2477   {
2478
2479   }
2480
2481   public void associatedData_actionPerformed(ActionEvent e)
2482   {
2483
2484   }
2485
2486   public void autoCalculate_actionPerformed(ActionEvent e)
2487   {
2488
2489   }
2490
2491   public void sortByTreeOption_actionPerformed(ActionEvent e)
2492   {
2493
2494   }
2495
2496   public void showAllSeqs_actionPerformed(ActionEvent e)
2497   {
2498
2499   }
2500
2501   public void showAllColumns_actionPerformed(ActionEvent e)
2502   {
2503
2504   }
2505
2506   public void hideSelSequences_actionPerformed(ActionEvent e)
2507   {
2508
2509   }
2510
2511   public void hideSelColumns_actionPerformed(ActionEvent e)
2512   {
2513
2514   }
2515
2516   public void hiddenMarkers_actionPerformed(ActionEvent e)
2517   {
2518
2519   }
2520
2521   public void findPdbId_actionPerformed(ActionEvent e)
2522   {
2523
2524   }
2525
2526   public void enterPdbId_actionPerformed(ActionEvent e)
2527   {
2528
2529   }
2530
2531   public void pdbFile_actionPerformed(ActionEvent e)
2532   {
2533
2534   }
2535
2536   public void invertColSel_actionPerformed(ActionEvent e)
2537   {
2538
2539   }
2540
2541   public void tabSelectionChanged(int sel)
2542   {
2543
2544   }
2545
2546   public void tabbedPane_mousePressed(MouseEvent e)
2547   {
2548
2549   }
2550
2551   public void tabbedPane_focusGained(FocusEvent e)
2552   {
2553     requestFocus();
2554   }
2555
2556   public void save_actionPerformed(ActionEvent e)
2557   {
2558
2559   }
2560
2561   public void reload_actionPerformed(ActionEvent e)
2562   {
2563
2564   }
2565
2566   public void newView_actionPerformed(ActionEvent e)
2567   {
2568
2569   }
2570
2571   public void textColour_actionPerformed(ActionEvent e)
2572   {
2573
2574   }
2575
2576   public void idRightAlign_actionPerformed(ActionEvent e)
2577   {
2578
2579   }
2580
2581   public void expandViews_actionPerformed(ActionEvent e)
2582   {
2583
2584   }
2585
2586   public void gatherViews_actionPerformed(ActionEvent e)
2587   {
2588
2589   }
2590
2591   public void buildTreeMenu()
2592   {
2593
2594   }
2595
2596   public void pageSetup_actionPerformed(ActionEvent e)
2597   {
2598
2599   }
2600
2601   public void alignmentProperties()
2602   {
2603
2604   }
2605 }