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     statusBar.setBackground(Color.white);
 816     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 817     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 818     statusBar.setText("Status bar");
 819     outputTextboxMenu.setText("Output to Textbox");
 820     clustalColour.setText("Clustalx");
 821
 822     clustalColour.addActionListener(new java.awt.event.ActionListener()
 823     {
 824       public void actionPerformed(ActionEvent e)
 825       {
 826         clustalColour_actionPerformed(e);
 827       }
 828     });
 829     zappoColour.setText("Zappo");
 830     zappoColour.addActionListener(new java.awt.event.ActionListener()
 831     {
 832       public void actionPerformed(ActionEvent e)
 833       {
 834         zappoColour_actionPerformed(e);
 835       }
 836     });
 837     taylorColour.setText("Taylor");
 838     taylorColour.addActionListener(new java.awt.event.ActionListener()
 839     {
 840       public void actionPerformed(ActionEvent e)
 841       {
 842         taylorColour_actionPerformed(e);
 843       }
 844     });
 845     hydrophobicityColour.setText("Hydrophobicity");
 846     hydrophobicityColour
 847             .addActionListener(new java.awt.event.ActionListener()
 848             {
 849               public void actionPerformed(ActionEvent e)
 850               {
 851                 hydrophobicityColour_actionPerformed(e);
 852               }
 853             });
 854     helixColour.setText("Helix Propensity");
 855     helixColour.addActionListener(new java.awt.event.ActionListener()
 856     {
 857       public void actionPerformed(ActionEvent e)
 858       {
 859         helixColour_actionPerformed(e);
 860       }
 861     });
 862     strandColour.setText("Strand Propensity");
 863     strandColour.addActionListener(new java.awt.event.ActionListener()
 864     {
 865       public void actionPerformed(ActionEvent e)
 866       {
 867         strandColour_actionPerformed(e);
 868       }
 869     });
 870     turnColour.setText("Turn Propensity");
 871     turnColour.addActionListener(new java.awt.event.ActionListener()
 872     {
 873       public void actionPerformed(ActionEvent e)
 874       {
 875         turnColour_actionPerformed(e);
 876       }
 877     });
 878     buriedColour.setText("Buried Index");
 879     buriedColour.addActionListener(new java.awt.event.ActionListener()
 880     {
 881       public void actionPerformed(ActionEvent e)
 882       {
 883         buriedColour_actionPerformed(e);
 884       }
 885     });
 886     userDefinedColour.setText("User Defined...");
 887     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 888     {
 889       public void actionPerformed(ActionEvent e)
 890       {
 891         userDefinedColour_actionPerformed(e);
 892       }
 893     });
 894     PIDColour.setText("Percentage Identity");
 895     PIDColour.addActionListener(new java.awt.event.ActionListener()
 896     {
 897       public void actionPerformed(ActionEvent e)
 898       {
 899         PIDColour_actionPerformed(e);
 900       }
 901     });
 902     BLOSUM62Colour.setText("BLOSUM62 Score");
 903     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 904     {
 905       public void actionPerformed(ActionEvent e)
 906       {
 907         BLOSUM62Colour_actionPerformed(e);
 908       }
 909     });
 910     nucleotideColour.setText("Nucleotide");
 911     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
 912     {
 913       public void actionPerformed(ActionEvent e)
 914       {
 915         nucleotideColour_actionPerformed(e);
 916       }
 917     });
 918
 919     purinePyrimidineColour.setText("Purine/Pyrimidine");
 920     purinePyrimidineColour.addActionListener(new java.awt.event.ActionListener()
 921             {
 922               public void actionPerformed(ActionEvent e)
 923               {
 924                 purinePyrimidineColour_actionPerformed(e);
 925               }
 926             });
 927
 928     RNAInteractionColour.setText("RNA Interaction type");
 929     RNAInteractionColour.addActionListener(new java.awt.event.ActionListener()
 930             {
 931               public void actionPerformed(ActionEvent e)
 932               {
 933                   RNAInteractionColour_actionPerformed(e);
 934               }
 935             });
 936     /*
 937      * covariationColour.setText("Covariation");
 938      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
 939      * public void actionPerformed(ActionEvent e) {
 940      * covariationColour_actionPerformed(e); } });
 941      */
 942
 943     avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
 944     avDistanceTreeBlosumMenuItem
 945             .addActionListener(new java.awt.event.ActionListener()
 946             {
 947               public void actionPerformed(ActionEvent e)
 948               {
 949                 avTreeBlosumMenuItem_actionPerformed(e);
 950               }
 951             });
 952     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
 953     njTreeBlosumMenuItem
 954             .addActionListener(new java.awt.event.ActionListener()
 955             {
 956               public void actionPerformed(ActionEvent e)
 957               {
 958                 njTreeBlosumMenuItem_actionPerformed(e);
 959               }
 960             });
 961     annotationPanelMenuItem.setActionCommand("");
 962     annotationPanelMenuItem.setText("Show Annotations");
 963     annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
 964             "SHOW_ANNOTATIONS", true));
 965     annotationPanelMenuItem
 966             .addActionListener(new java.awt.event.ActionListener()
 967             {
 968               public void actionPerformed(ActionEvent e)
 969               {
 970                 annotationPanelMenuItem_actionPerformed(e);
 971               }
 972             });
 973     colourTextMenuItem.setText("Colour Text");
 974     colourTextMenuItem
 975             .addActionListener(new java.awt.event.ActionListener()
 976             {
 977               public void actionPerformed(ActionEvent e)
 978               {
 979                 colourTextMenuItem_actionPerformed(e);
 980               }
 981             });
 982     htmlMenuItem.setText("HTML");
 983     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
 984     {
 985       public void actionPerformed(ActionEvent e)
 986       {
 987         htmlMenuItem_actionPerformed(e);
 988       }
 989     });
 990     overviewMenuItem.setText("Overview Window");
 991     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
 992     {
 993       public void actionPerformed(ActionEvent e)
 994       {
 995         overviewMenuItem_actionPerformed(e);
 996       }
 997     });
 998     undoMenuItem.setEnabled(false);
 999     undoMenuItem.setText("Undo");
1000     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1001             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1002                     .getMenuShortcutKeyMask(), false));
1003     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1004     {
1005       public void actionPerformed(ActionEvent e)
1006       {
1007         undoMenuItem_actionPerformed(e);
1008       }
1009     });
1010     redoMenuItem.setEnabled(false);
1011     redoMenuItem.setText("Redo");
1012     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1013             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1014                     .getMenuShortcutKeyMask(), false));
1015     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1016     {
1017       public void actionPerformed(ActionEvent e)
1018       {
1019         redoMenuItem_actionPerformed(e);
1020       }
1021     });
1022     conservationMenuItem.setText("By Conservation");
1023     conservationMenuItem
1024             .addActionListener(new java.awt.event.ActionListener()
1025             {
1026               public void actionPerformed(ActionEvent e)
1027               {
1028                 conservationMenuItem_actionPerformed(e);
1029               }
1030             });
1031     noColourmenuItem.setText("None");
1032     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1033     {
1034       public void actionPerformed(ActionEvent e)
1035       {
1036         noColourmenuItem_actionPerformed(e);
1037       }
1038     });
1039     wrapMenuItem.setText("Wrap");
1040     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1041     {
1042       public void actionPerformed(ActionEvent e)
1043       {
1044         wrapMenuItem_actionPerformed(e);
1045       }
1046     });
1047     printMenuItem.setText("Print ...");
1048     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1049             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1050                     .getMenuShortcutKeyMask(), false));
1051     printMenuItem.addActionListener(new java.awt.event.ActionListener()
1052     {
1053       public void actionPerformed(ActionEvent e)
1054       {
1055         printMenuItem_actionPerformed(e);
1056       }
1057     });
1058     renderGapsMenuItem.setText("Show Gaps");
1059     renderGapsMenuItem.setState(true);
1060     renderGapsMenuItem
1061             .addActionListener(new java.awt.event.ActionListener()
1062             {
1063               public void actionPerformed(ActionEvent e)
1064               {
1065                 renderGapsMenuItem_actionPerformed(e);
1066               }
1067             });
1068     findMenuItem.setText("Find...");
1069     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1070             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1071                     .getMenuShortcutKeyMask(), false));
1072     findMenuItem.addActionListener(new java.awt.event.ActionListener()
1073     {
1074       public void actionPerformed(ActionEvent e)
1075       {
1076         findMenuItem_actionPerformed(e);
1077       }
1078     });
1079     abovePIDThreshold.setText("Above Identity Threshold");
1080     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1081     {
1082       public void actionPerformed(ActionEvent e)
1083       {
1084         abovePIDThreshold_actionPerformed(e);
1085       }
1086     });
1087     showSeqFeatures.setText("Show Sequence Features");
1088     showSeqFeatures.addActionListener(new ActionListener()
1089     {
1090       public void actionPerformed(ActionEvent actionEvent)
1091       {
1092         showSeqFeatures_actionPerformed(actionEvent);
1093       }
1094     });
1095     /*
1096      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1097      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1098      * void actionPerformed(ActionEvent actionEvent) {
1099      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1100      */
1101     showDbRefsMenuitem.setText("Show Database Refs");
1102     showDbRefsMenuitem.addActionListener(new ActionListener()
1103     {
1104
1105       public void actionPerformed(ActionEvent e)
1106       {
1107         showDbRefs_actionPerformed(e);
1108       }
1109
1110     });
1111     showNpFeatsMenuitem.setText("Show Non-Positional Features");
1112     showNpFeatsMenuitem.addActionListener(new ActionListener()
1113     {
1114
1115       public void actionPerformed(ActionEvent e)
1116       {
1117         showNpFeats_actionPerformed(e);
1118       }
1119
1120     });
1121     showGroupConservation.setText("Group Conservation");
1122     showGroupConservation.addActionListener(new ActionListener()
1123     {
1124
1125       public void actionPerformed(ActionEvent e)
1126       {
1127         showGroupConservation_actionPerformed(e);
1128       }
1129
1130     });
1131
1132     showGroupConsensus.setText("Group Consensus");
1133     showGroupConsensus.addActionListener(new ActionListener()
1134     {
1135
1136       public void actionPerformed(ActionEvent e)
1137       {
1138         showGroupConsensus_actionPerformed(e);
1139       }
1140
1141     });
1142     showConsensusHistogram.setText("Show Consensus Histogram");
1143     showConsensusHistogram.addActionListener(new ActionListener()
1144     {
1145
1146       public void actionPerformed(ActionEvent e)
1147       {
1148         showConsensusHistogram_actionPerformed(e);
1149       }
1150
1151     });
1152     showSequenceLogo.setText("Show Consensus Logo");
1153     showSequenceLogo.addActionListener(new ActionListener()
1154     {
1155
1156       public void actionPerformed(ActionEvent e)
1157       {
1158         showSequenceLogo_actionPerformed(e);
1159       }
1160
1161     });
1162     normaliseSequenceLogo.setText("Normalise Consensus Logo");
1163     normaliseSequenceLogo.addActionListener(new ActionListener()
1164     {
1165
1166       public void actionPerformed(ActionEvent e)
1167       {
1168         normaliseSequenceLogo_actionPerformed(e);
1169       }
1170
1171     });
1172     applyAutoAnnotationSettings.setText("Apply to all groups");
1173     applyAutoAnnotationSettings.setState(false);
1174     applyAutoAnnotationSettings.setVisible(true);
1175     applyAutoAnnotationSettings.addActionListener(new ActionListener()
1176     {
1177
1178       public void actionPerformed(ActionEvent e)
1179       {
1180         applyAutoAnnotationSettings_actionPerformed(e);
1181       }
1182
1183     });
1184
1185     nucleotideColour.setText("Nucleotide");
1186     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1187     {
1188       public void actionPerformed(ActionEvent e)
1189       {
1190         nucleotideColour_actionPerformed(e);
1191       }
1192     });
1193
1194     tcoffeeColour.setText("T-Coffee scores");
1195     tcoffeeColour.setEnabled(false);
1196     tcoffeeColour.addActionListener(new ActionListener()
1197     {
1198
1199       @Override
1200       public void actionPerformed(ActionEvent e)
1201       {
1202         tcoffeeColorScheme_actionPerformed(e);
1203       }
1204     });
1205
1206     deleteGroups.setText("Undefine groups");
1207     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1208             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1209                     .getMenuShortcutKeyMask(), false));
1210     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1211     {
1212       public void actionPerformed(ActionEvent e)
1213       {
1214         deleteGroups_actionPerformed(e);
1215       }
1216     });
1217     copy.setText("Copy");
1218     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1219             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1220                     .getMenuShortcutKeyMask(), false));
1221
1222     copy.addActionListener(new java.awt.event.ActionListener()
1223     {
1224       public void actionPerformed(ActionEvent e)
1225       {
1226         copy_actionPerformed(e);
1227       }
1228     });
1229     cut.setText("Cut");
1230     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1231             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1232                     .getMenuShortcutKeyMask(), false));
1233     cut.addActionListener(new java.awt.event.ActionListener()
1234     {
1235       public void actionPerformed(ActionEvent e)
1236       {
1237         cut_actionPerformed(e);
1238       }
1239     });
1240     delete.setText("Delete");
1241     delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1242             java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1243     delete.addActionListener(new java.awt.event.ActionListener()
1244     {
1245       public void actionPerformed(ActionEvent e)
1246       {
1247         delete_actionPerformed(e);
1248       }
1249     });
1250     pasteMenu.setText("Paste");
1251     pasteNew.setText("To New Alignment");
1252     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1253             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1254                     .getMenuShortcutKeyMask()
1255                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1256     pasteNew.addActionListener(new java.awt.event.ActionListener()
1257     {
1258       public void actionPerformed(ActionEvent e)
1259       {
1260         pasteNew_actionPerformed(e);
1261       }
1262     });
1263     pasteThis.setText("Add To This Alignment");
1264     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1265             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1266                     .getMenuShortcutKeyMask(), false));
1267     pasteThis.addActionListener(new java.awt.event.ActionListener()
1268     {
1269       public void actionPerformed(ActionEvent e)
1270       {
1271         pasteThis_actionPerformed(e);
1272       }
1273     });
1274     applyToAllGroups.setText("Apply Colour To All Groups");
1275     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1276     {
1277       public void actionPerformed(ActionEvent e)
1278       {
1279         applyToAllGroups_actionPerformed(e);
1280       }
1281     });
1282     createPNG.addActionListener(new java.awt.event.ActionListener()
1283     {
1284       public void actionPerformed(ActionEvent e)
1285       {
1286         createPNG(null);
1287       }
1288     });
1289     createPNG.setActionCommand("Save As PNG Image");
1290     createPNG.setText("PNG");
1291     font.setText("Font...");
1292     font.addActionListener(new java.awt.event.ActionListener()
1293     {
1294       public void actionPerformed(ActionEvent e)
1295       {
1296         font_actionPerformed(e);
1297       }
1298     });
1299
1300     seqLimits.setText("Show Sequence Limits");
1301     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1302     seqLimits.addActionListener(new java.awt.event.ActionListener()
1303     {
1304       public void actionPerformed(ActionEvent e)
1305       {
1306         seqLimit_actionPerformed(e);
1307       }
1308     });
1309     epsFile.setText("EPS");
1310     epsFile.addActionListener(new java.awt.event.ActionListener()
1311     {
1312       public void actionPerformed(ActionEvent e)
1313       {
1314         createEPS(null);
1315       }
1316     });
1317     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1318     LoadtreeMenuItem.setText("Load Associated Tree");
1319     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1320     {
1321       public void actionPerformed(ActionEvent e)
1322       {
1323         LoadtreeMenuItem_actionPerformed(e);
1324       }
1325     });
1326
1327     scaleAbove.setVisible(false);
1328     scaleAbove.setText("Scale Above");
1329     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1330     {
1331       public void actionPerformed(ActionEvent e)
1332       {
1333         scaleAbove_actionPerformed(e);
1334       }
1335     });
1336     scaleLeft.setVisible(false);
1337     scaleLeft.setSelected(true);
1338     scaleLeft.setText("Scale Left");
1339     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1340     {
1341       public void actionPerformed(ActionEvent e)
1342       {
1343         scaleLeft_actionPerformed(e);
1344       }
1345     });
1346     scaleRight.setVisible(false);
1347     scaleRight.setSelected(true);
1348     scaleRight.setText("Scale Right");
1349     scaleRight.addActionListener(new java.awt.event.ActionListener()
1350     {
1351       public void actionPerformed(ActionEvent e)
1352       {
1353         scaleRight_actionPerformed(e);
1354       }
1355     });
1356     centreColumnLabelsMenuItem.setVisible(true);
1357     centreColumnLabelsMenuItem.setState(false);
1358     centreColumnLabelsMenuItem.setText("Centre Column Labels");
1359     centreColumnLabelsMenuItem
1360             .addActionListener(new java.awt.event.ActionListener()
1361             {
1362               public void actionPerformed(ActionEvent e)
1363               {
1364                 centreColumnLabels_actionPerformed(e);
1365               }
1366             });
1367     followHighlightMenuItem.setVisible(true);
1368     followHighlightMenuItem.setState(true);
1369     followHighlightMenuItem.setText("Automatic Scrolling");
1370     followHighlightMenuItem.addActionListener(new ActionListener()
1371     {
1372
1373       public void actionPerformed(ActionEvent e)
1374       {
1375         followHighlight_actionPerformed();
1376       }
1377
1378     });
1379
1380     modifyPID.setText("Modify Identity Threshold...");
1381     modifyPID.addActionListener(new java.awt.event.ActionListener()
1382     {
1383       public void actionPerformed(ActionEvent e)
1384       {
1385         modifyPID_actionPerformed(e);
1386       }
1387     });
1388     modifyConservation.setText("Modify Conservation Threshold...");
1389     modifyConservation
1390             .addActionListener(new java.awt.event.ActionListener()
1391             {
1392               public void actionPerformed(ActionEvent e)
1393               {
1394                 modifyConservation_actionPerformed(e);
1395               }
1396             });
1397     sortByTreeMenu.setText("By Tree Order");
1398     sort.setText("Sort");
1399     sort.addMenuListener(new MenuListener()
1400     {
1401       public void menuSelected(MenuEvent e)
1402       {
1403         buildTreeMenu();
1404       }
1405
1406       public void menuDeselected(MenuEvent e)
1407       {
1408       }
1409
1410       public void menuCanceled(MenuEvent e)
1411       {
1412       }
1413     });
1414     sortByAnnotScore.setText("by Score");
1415     sort.add(sortByAnnotScore);
1416     sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1417     {
1418
1419       public void menuCanceled(MenuEvent e)
1420       {
1421       }
1422
1423       public void menuDeselected(MenuEvent e)
1424       {
1425       }
1426
1427       public void menuSelected(MenuEvent e)
1428       {
1429         buildSortByAnnotationScoresMenu();
1430       }
1431     });
1432     sortByAnnotScore.setVisible(false);
1433
1434     calculateTree.setText("Calculate Tree");
1435
1436     jMenu2.setText("Export Image");
1437     padGapsMenuitem.setText("Pad Gaps");
1438     padGapsMenuitem.setState(jalview.bin.Cache
1439             .getDefault("PAD_GAPS", false));
1440     padGapsMenuitem.addActionListener(new ActionListener()
1441     {
1442       public void actionPerformed(ActionEvent e)
1443       {
1444         padGapsMenuitem_actionPerformed(e);
1445       }
1446     });
1447     vamsasStore.setVisible(false);
1448     vamsasStore.setText("VAMSAS store");
1449     vamsasStore.addActionListener(new ActionListener()
1450     {
1451       public void actionPerformed(ActionEvent e)
1452       {
1453         vamsasStore_actionPerformed(e);
1454       }
1455     });
1456     showTranslation.setText("Translate cDNA");
1457     showTranslation.addActionListener(new ActionListener()
1458     {
1459       public void actionPerformed(ActionEvent e)
1460       {
1461         showTranslation_actionPerformed(e);
1462       }
1463     });
1464     extractScores.setText("Extract Scores...");
1465     extractScores.addActionListener(new ActionListener()
1466     {
1467       public void actionPerformed(ActionEvent e)
1468       {
1469         extractScores_actionPerformed(e);
1470       }
1471     });
1472     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1473     // score extraction
1474     showProducts.setText("Get Cross References");
1475     /*
1476      * showProducts.addActionListener(new ActionListener() {
1477      *
1478      * public void actionPerformed(ActionEvent e) {
1479      * showProducts_actionPerformed(e); } });
1480      */
1481     openFeatureSettings.setText("Feature Settings...");
1482     openFeatureSettings.addActionListener(new ActionListener()
1483     {
1484       public void actionPerformed(ActionEvent e)
1485       {
1486         featureSettings_actionPerformed(e);
1487       }
1488     });
1489     fetchSequence.setText("Fetch Sequence(s)...");
1490     fetchSequence.addActionListener(new ActionListener()
1491     {
1492       public void actionPerformed(ActionEvent e)
1493       {
1494         fetchSequence_actionPerformed(e);
1495       }
1496     });
1497
1498     annotationColour.setText("By Annotation...");
1499     annotationColour.addActionListener(new ActionListener()
1500     {
1501       public void actionPerformed(ActionEvent e)
1502       {
1503         annotationColour_actionPerformed(e);
1504       }
1505     });
1506
1507     rnahelicesColour.setText("By RNA helices");
1508     rnahelicesColour.addActionListener(new ActionListener()
1509     {
1510       public void actionPerformed(ActionEvent e)
1511       {
1512         rnahelicesColour_actionPerformed(e);
1513       }
1514     });
1515
1516     associatedData.setText("Load Features / Annotations");
1517     associatedData.addActionListener(new ActionListener()
1518     {
1519       public void actionPerformed(ActionEvent e)
1520       {
1521         associatedData_actionPerformed(e);
1522       }
1523     });
1524     autoCalculate.setText("Autocalculate Consensus");
1525     autoCalculate.setState(jalview.bin.Cache.getDefault(
1526             "AUTO_CALC_CONSENSUS", true));
1527     autoCalculate.addActionListener(new ActionListener()
1528     {
1529       public void actionPerformed(ActionEvent e)
1530       {
1531         autoCalculate_actionPerformed(e);
1532       }
1533     });
1534     sortByTree.setText("Sort Alignment With New Tree");
1535     sortByTree
1536             .setToolTipText("<html>Enable this to automatically sort<br>the alignment when you open<br> a new tree.");
1537     sortByTree
1538             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1539     sortByTree.addActionListener(new ActionListener()
1540     {
1541       public void actionPerformed(ActionEvent e)
1542       {
1543         sortByTreeOption_actionPerformed(e);
1544       }
1545     });
1546
1547     listenToViewSelections.setText("Listen for selections");
1548     listenToViewSelections
1549             .setToolTipText("<html>When selected, selections in this view will mirror<br>selections made on the same sequences in other views.");
1550     listenToViewSelections.setState(false);
1551     listenToViewSelections.addActionListener(new ActionListener()
1552     {
1553       public void actionPerformed(ActionEvent e)
1554       {
1555         listenToViewSelections_actionPerformed(e);
1556       }
1557     });
1558
1559     addSequenceMenu.setText("Add Sequences");
1560     addFromFile.setText("From File");
1561     addFromFile.addActionListener(new ActionListener()
1562     {
1563       public void actionPerformed(ActionEvent e)
1564       {
1565         addFromFile_actionPerformed(e);
1566       }
1567     });
1568     addFromText.setText("From Textbox");
1569     addFromText.addActionListener(new ActionListener()
1570     {
1571       public void actionPerformed(ActionEvent e)
1572       {
1573         addFromText_actionPerformed(e);
1574       }
1575     });
1576     addFromURL.setText("From URL");
1577     addFromURL.addActionListener(new ActionListener()
1578     {
1579       public void actionPerformed(ActionEvent e)
1580       {
1581         addFromURL_actionPerformed(e);
1582       }
1583     });
1584     exportFeatures.setText("Export Features...");
1585     exportFeatures.addActionListener(new ActionListener()
1586     {
1587       public void actionPerformed(ActionEvent e)
1588       {
1589         exportFeatures_actionPerformed(e);
1590       }
1591     });
1592     exportAnnotations.setText("Export Annotations...");
1593     exportAnnotations.addActionListener(new ActionListener()
1594     {
1595       public void actionPerformed(ActionEvent e)
1596       {
1597         exportAnnotations_actionPerformed(e);
1598       }
1599     });
1600     statusPanel.setLayout(gridLayout1);
1601     jMenu3.setText("Show");
1602     showAllSeqs.setText("All Sequences");
1603     showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1604     showAllSeqs.addActionListener(new ActionListener()
1605     {
1606       public void actionPerformed(ActionEvent e)
1607       {
1608         showAllSeqs_actionPerformed(e);
1609       }
1610     });
1611     showAllColumns.setText("All Columns");
1612     showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1613     showAllColumns.addActionListener(new ActionListener()
1614     {
1615       public void actionPerformed(ActionEvent e)
1616       {
1617         showAllColumns_actionPerformed(e);
1618       }
1619     });
1620     hideMenu.setText("Hide");
1621     hideSelSequences.setText("Selected Sequences");
1622     hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1623     hideSelSequences.addActionListener(new ActionListener()
1624     {
1625       public void actionPerformed(ActionEvent e)
1626       {
1627         hideSelSequences_actionPerformed(e);
1628       }
1629     });
1630     hideSelColumns.setText("Selected Columns");
1631     hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1632     hideSelColumns.addActionListener(new ActionListener()
1633     {
1634       public void actionPerformed(ActionEvent e)
1635       {
1636         hideSelColumns_actionPerformed(e);
1637       }
1638     });
1639     hideAllSelection.setText("Selected Region");
1640     hideAllSelection.addActionListener(new ActionListener()
1641     {
1642       public void actionPerformed(ActionEvent e)
1643       {
1644         hideAllSelection_actionPerformed(e);
1645       }
1646     });
1647     // TODO: should be hidden if no selection exists.
1648     hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
1649     hideAllButSelection.addActionListener(new ActionListener()
1650     {
1651       public void actionPerformed(ActionEvent e)
1652       {
1653         hideAllButSelection_actionPerformed(e);
1654       }
1655     });
1656     showAllhidden.setText("All Sequences and Columns");
1657     showAllhidden
1658             .setToolTipText("H toggles visibility of hidden or selected regions.");
1659     showAllhidden.addActionListener(new ActionListener()
1660     {
1661       public void actionPerformed(ActionEvent e)
1662       {
1663         showAllhidden_actionPerformed(e);
1664       }
1665     });
1666
1667     hiddenMarkers.setText("Show Hidden Markers");
1668     hiddenMarkers.addActionListener(new ActionListener()
1669     {
1670       public void actionPerformed(ActionEvent e)
1671       {
1672         hiddenMarkers_actionPerformed(e);
1673       }
1674     });
1675     invertColSel.setText("Invert Column Selection");
1676     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1677             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1678                     .getMenuShortcutKeyMask()
1679                     | java.awt.event.KeyEvent.ALT_MASK, false));
1680     invertColSel.addActionListener(new ActionListener()
1681     {
1682       public void actionPerformed(ActionEvent e)
1683       {
1684         invertColSel_actionPerformed(e);
1685       }
1686     });
1687     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1688     {
1689       public void stateChanged(ChangeEvent evt)
1690       {
1691         JTabbedPane pane = (JTabbedPane) evt.getSource();
1692         int sel = pane.getSelectedIndex();
1693         tabSelectionChanged(sel);
1694       }
1695     });
1696     tabbedPane.addMouseListener(new MouseAdapter()
1697     {
1698       public void mousePressed(MouseEvent e)
1699       {
1700         tabbedPane_mousePressed(e);
1701       }
1702     });
1703     tabbedPane.addFocusListener(new FocusAdapter()
1704     {
1705       public void focusGained(FocusEvent e)
1706       {
1707         tabbedPane_focusGained(e);
1708       }
1709     });
1710     save.setText("Save");
1711     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1712             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1713                     .getMenuShortcutKeyMask(), false));
1714     save.addActionListener(new ActionListener()
1715     {
1716       public void actionPerformed(ActionEvent e)
1717       {
1718         save_actionPerformed(e);
1719       }
1720     });
1721     reload.setEnabled(false);
1722     reload.setText("Reload");
1723     reload.addActionListener(new ActionListener()
1724     {
1725       public void actionPerformed(ActionEvent e)
1726       {
1727         reload_actionPerformed(e);
1728       }
1729     });
1730     newView.setText("New View");
1731     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1732             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1733                     .getMenuShortcutKeyMask(), false));
1734     newView.addActionListener(new ActionListener()
1735     {
1736       public void actionPerformed(ActionEvent e)
1737       {
1738         newView_actionPerformed(e);
1739       }
1740     });
1741     tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1742             + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1743     textColour.setText("Colour Text ...");
1744     textColour.addActionListener(new ActionListener()
1745     {
1746       public void actionPerformed(ActionEvent e)
1747       {
1748         textColour_actionPerformed(e);
1749       }
1750     });
1751     formatMenu.setText("Format");
1752     selectMenu.setText("Select");
1753     idRightAlign.setText("Right Align Sequence Id");
1754     idRightAlign.addActionListener(new ActionListener()
1755     {
1756       public void actionPerformed(ActionEvent e)
1757       {
1758         idRightAlign_actionPerformed(e);
1759       }
1760     });
1761     gatherViews.setEnabled(false);
1762     gatherViews.setText("Gather Views");
1763     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1764             java.awt.event.KeyEvent.VK_G, 0, false));
1765     gatherViews.addActionListener(new ActionListener()
1766     {
1767       public void actionPerformed(ActionEvent e)
1768       {
1769         gatherViews_actionPerformed(e);
1770       }
1771     });
1772     expandViews.setEnabled(false);
1773     expandViews.setText("Expand Views");
1774     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1775             java.awt.event.KeyEvent.VK_X, 0, false));
1776     expandViews.addActionListener(new ActionListener()
1777     {
1778       public void actionPerformed(ActionEvent e)
1779       {
1780         expandViews_actionPerformed(e);
1781       }
1782     });
1783     pageSetup.setText("Page Setup ...");
1784     pageSetup.addActionListener(new ActionListener()
1785     {
1786       public void actionPerformed(ActionEvent e)
1787       {
1788         pageSetup_actionPerformed(e);
1789       }
1790     });
1791     alignmentProperties.setText("Alignment Properties...");
1792     alignmentProperties.addActionListener(new ActionListener()
1793     {
1794       public void actionPerformed(ActionEvent actionEvent)
1795       {
1796         alignmentProperties();
1797       }
1798     });
1799     tooltipSettingsMenu.setText("Sequence ID Tooltip");
1800     autoAnnMenu.setText("Autocalculated Annotation");
1801     alignFrameMenuBar.add(fileMenu);
1802     alignFrameMenuBar.add(editMenu);
1803     alignFrameMenuBar.add(selectMenu);
1804     alignFrameMenuBar.add(viewMenu);
1805     alignFrameMenuBar.add(formatMenu);
1806     alignFrameMenuBar.add(colourMenu);
1807     alignFrameMenuBar.add(calculateMenu);
1808     alignFrameMenuBar.add(webService);
1809     fileMenu.add(fetchSequence);
1810     fileMenu.add(addSequenceMenu);
1811     fileMenu.add(reload);
1812     fileMenu.addSeparator();
1813     fileMenu.add(vamsasStore);
1814     fileMenu.add(save);
1815     fileMenu.add(saveAs);
1816     fileMenu.add(outputTextboxMenu);
1817     fileMenu.add(pageSetup);
1818     fileMenu.add(printMenuItem);
1819     fileMenu.addSeparator();
1820     fileMenu.add(jMenu2);
1821     fileMenu.add(exportFeatures);
1822     fileMenu.add(exportAnnotations);
1823     fileMenu.add(LoadtreeMenuItem);
1824     fileMenu.add(associatedData);
1825     fileMenu.addSeparator();
1826     fileMenu.add(closeMenuItem);
1827     editMenu.add(undoMenuItem);
1828     editMenu.add(redoMenuItem);
1829     editMenu.add(cut);
1830     editMenu.add(copy);
1831     editMenu.add(pasteMenu);
1832     editMenu.add(delete);
1833     editMenu.addSeparator();
1834     editMenu.add(remove2LeftMenuItem);
1835     editMenu.add(remove2RightMenuItem);
1836     editMenu.add(removeGappedColumnMenuItem);
1837     editMenu.add(removeAllGapsMenuItem);
1838     editMenu.add(removeRedundancyMenuItem);
1839     editMenu.addSeparator();
1840     // dont add these yet in the CVS build - they cannot be undone!
1841     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1842     // editMenu.add(justifyLeftMenuItem);
1843     // editMenu.add(justifyRightMenuItem);
1844     // editMenu.addSeparator();
1845     editMenu.add(padGapsMenuitem);
1846     viewMenu.add(newView);
1847     viewMenu.add(expandViews);
1848     viewMenu.add(gatherViews);
1849     viewMenu.addSeparator();
1850     viewMenu.add(jMenu3);
1851     viewMenu.add(hideMenu);
1852     viewMenu.addSeparator();
1853     viewMenu.add(followHighlightMenuItem);
1854     viewMenu.add(annotationPanelMenuItem);
1855     autoAnnMenu.add(applyAutoAnnotationSettings);
1856     autoAnnMenu.add(showConsensusHistogram);
1857     autoAnnMenu.add(showSequenceLogo);
1858     autoAnnMenu.add(normaliseSequenceLogo);
1859     autoAnnMenu.addSeparator();
1860     autoAnnMenu.add(showGroupConservation);
1861     autoAnnMenu.add(showGroupConsensus);
1862     viewMenu.add(autoAnnMenu);
1863     viewMenu.addSeparator();
1864     viewMenu.add(showSeqFeatures);
1865     // viewMenu.add(showSeqFeaturesHeight);
1866
1867     viewMenu.add(openFeatureSettings);
1868     tooltipSettingsMenu.add(showDbRefsMenuitem);
1869     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1870     viewMenu.add(tooltipSettingsMenu);
1871     viewMenu.addSeparator();
1872     viewMenu.add(alignmentProperties);
1873     viewMenu.addSeparator();
1874     viewMenu.add(overviewMenuItem);
1875     colourMenu.add(applyToAllGroups);
1876     colourMenu.add(textColour);
1877     colourMenu.addSeparator();
1878     colourMenu.add(noColourmenuItem);
1879     colourMenu.add(clustalColour);
1880     colourMenu.add(BLOSUM62Colour);
1881     colourMenu.add(PIDColour);
1882     colourMenu.add(zappoColour);
1883     colourMenu.add(taylorColour);
1884     colourMenu.add(hydrophobicityColour);
1885     colourMenu.add(helixColour);
1886     colourMenu.add(strandColour);
1887     colourMenu.add(turnColour);
1888     colourMenu.add(buriedColour);
1889     colourMenu.add(nucleotideColour);
1890     colourMenu.add(purinePyrimidineColour);
1891     colourMenu.add(RNAInteractionColour);
1892     // colourMenu.add(covariationColour);
1893     colourMenu.add(tcoffeeColour);
1894     colourMenu.add(userDefinedColour);
1895     colourMenu.addSeparator();
1896     colourMenu.add(conservationMenuItem);
1897     colourMenu.add(modifyConservation);
1898     colourMenu.add(abovePIDThreshold);
1899     colourMenu.add(modifyPID);
1900     colourMenu.add(annotationColour);
1901     colourMenu.add(rnahelicesColour);
1902     calculateMenu.add(sort);
1903     calculateMenu.add(calculateTree);
1904     calculateMenu.addSeparator();
1905     calculateMenu.add(pairwiseAlignmentMenuItem);
1906     calculateMenu.add(PCAMenuItem);
1907     calculateMenu.addSeparator();
1908     calculateMenu.add(showTranslation);
1909     calculateMenu.add(showProducts);
1910     calculateMenu.add(autoCalculate);
1911     calculateMenu.add(sortByTree);
1912     calculateMenu.addSeparator();
1913     calculateMenu.add(extractScores);
1914     webServiceNoServices = new JMenuItem("<No Services>");
1915     webService.add(webServiceNoServices);
1916     pasteMenu.add(pasteNew);
1917     pasteMenu.add(pasteThis);
1918     sort.add(sortIDMenuItem);
1919     sort.add(sortLengthMenuItem);
1920     sort.add(sortGroupMenuItem);
1921     sort.add(sortPairwiseMenuItem);
1922     sort.add(sortByTreeMenu);
1923     calculateTree.add(averageDistanceTreeMenuItem);
1924     calculateTree.add(neighbourTreeMenuItem);
1925     calculateTree.add(avDistanceTreeBlosumMenuItem);
1926     calculateTree.add(njTreeBlosumMenuItem);
1927     jMenu2.add(htmlMenuItem);
1928     jMenu2.add(epsFile);
1929     jMenu2.add(createPNG);
1930     addSequenceMenu.add(addFromFile);
1931     addSequenceMenu.add(addFromText);
1932     addSequenceMenu.add(addFromURL);
1933     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1934     statusPanel.add(statusBar, null);
1935     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1936     jMenu3.add(showAllColumns);
1937     jMenu3.add(showAllSeqs);
1938     jMenu3.add(showAllhidden);
1939     hideMenu.add(hideSelColumns);
1940     hideMenu.add(hideSelSequences);
1941     hideMenu.add(hideAllSelection);
1942     hideMenu.add(hideAllButSelection);
1943
1944     formatMenu.add(font);
1945     formatMenu.addSeparator();
1946     formatMenu.add(wrapMenuItem);
1947     formatMenu.add(scaleAbove);
1948     formatMenu.add(scaleLeft);
1949     formatMenu.add(scaleRight);
1950     formatMenu.add(seqLimits);
1951     formatMenu.add(idRightAlign);
1952     formatMenu.add(hiddenMarkers);
1953     formatMenu.add(viewBoxesMenuItem);
1954     formatMenu.add(viewTextMenuItem);
1955     formatMenu.add(colourTextMenuItem);
1956     formatMenu.add(renderGapsMenuItem);
1957     formatMenu.add(centreColumnLabelsMenuItem);
1958     formatMenu.add(showNonconservedMenuItem);
1959     selectMenu.add(findMenuItem);
1960     selectMenu.addSeparator();
1961     selectMenu.add(selectAllSequenceMenuItem);
1962     selectMenu.add(deselectAllSequenceMenuItem);
1963     selectMenu.add(invertSequenceMenuItem);
1964     selectMenu.add(invertColSel);
1965     selectMenu.add(deleteGroups);
1966     selectMenu.add(grpsFromSelection);
1967     // TODO - determine if the listenToViewSelections button is needed : see bug
1968     // JAL-574
1969     // selectMenu.addSeparator();
1970     // selectMenu.add(listenToViewSelections);
1971   }
1972
1973   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
1974   {
1975     // TODO Auto-generated method stub
1976
1977   }
1978
1979   protected void listenToViewSelections_actionPerformed(ActionEvent e)
1980   {
1981     // TODO Auto-generated method stub
1982
1983   }
1984
1985   protected void showAllhidden_actionPerformed(ActionEvent e)
1986   {
1987     // TODO Auto-generated method stub
1988
1989   }
1990
1991   protected void hideAllButSelection_actionPerformed(ActionEvent e)
1992   {
1993     // TODO Auto-generated method stub
1994
1995   }
1996
1997   protected void hideAllSelection_actionPerformed(ActionEvent e)
1998   {
1999     // TODO Auto-generated method stub
2000
2001   }
2002
2003   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2004   {
2005     // TODO Auto-generated method stub
2006
2007   }
2008
2009   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2010   {
2011     // TODO Auto-generated method stub
2012
2013   }
2014
2015   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2016   {
2017     // TODO Auto-generated method stub
2018
2019   }
2020
2021   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2022   {
2023     // TODO Auto-generated method stub
2024
2025   }
2026
2027   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2028   {
2029     // TODO Auto-generated method stub
2030
2031   }
2032
2033   protected void showGroupConservation_actionPerformed(ActionEvent e)
2034   {
2035     // TODO Auto-generated method stub
2036
2037   }
2038
2039   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2040   {
2041     // TODO Auto-generated method stub
2042
2043   }
2044
2045   protected void showSeqFeaturesHeight_actionPerformed(
2046           ActionEvent actionEvent)
2047   {
2048     // TODO Auto-generated method stub
2049
2050   }
2051
2052   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2053   {
2054     // TODO Auto-generated method stub
2055
2056   }
2057
2058   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2059   {
2060     // TODO Auto-generated method stub
2061
2062   }
2063
2064   protected void followHighlight_actionPerformed()
2065   {
2066     // TODO Auto-generated method stub
2067
2068   }
2069
2070   protected void showNpFeats_actionPerformed(ActionEvent e)
2071   {
2072     // TODO Auto-generated method stub
2073
2074   }
2075
2076   protected void showDbRefs_actionPerformed(ActionEvent e)
2077   {
2078     // TODO Auto-generated method stub
2079
2080   }
2081
2082   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2083   {
2084   }
2085
2086   protected void showProducts_actionPerformed(ActionEvent e)
2087   {
2088   }
2089
2090   protected void buildSortByAnnotationScoresMenu()
2091   {
2092   }
2093
2094   protected void extractScores_actionPerformed(ActionEvent e)
2095   {
2096   }
2097
2098   protected void outputText_actionPerformed(ActionEvent e)
2099   {
2100   }
2101
2102   public void addFromFile_actionPerformed(ActionEvent e)
2103   {
2104
2105   }
2106
2107   public void addFromText_actionPerformed(ActionEvent e)
2108   {
2109
2110   }
2111
2112   public void addFromURL_actionPerformed(ActionEvent e)
2113   {
2114
2115   }
2116
2117   public void exportFeatures_actionPerformed(ActionEvent e)
2118   {
2119
2120   }
2121
2122   public void exportAnnotations_actionPerformed(ActionEvent e)
2123   {
2124
2125   }
2126
2127   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2128   {
2129   }
2130
2131   protected void closeMenuItem_actionPerformed(boolean b)
2132   {
2133   }
2134
2135   protected void redoMenuItem_actionPerformed(ActionEvent e)
2136   {
2137   }
2138
2139   protected void undoMenuItem_actionPerformed(ActionEvent e)
2140   {
2141   }
2142
2143   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2144   {
2145   }
2146
2147   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2148   {
2149   }
2150
2151   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2152   {
2153   }
2154
2155   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2156   {
2157   }
2158
2159   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2160   {
2161   }
2162
2163   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2164   {
2165   }
2166
2167   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2168   {
2169   }
2170
2171   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2172   {
2173   }
2174
2175   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2176   {
2177   }
2178
2179   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2180   {
2181   }
2182
2183   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2184   {
2185   }
2186
2187   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2188   {
2189   }
2190
2191   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2192   {
2193   }
2194
2195   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2196   {
2197   }
2198
2199   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2200   {
2201   }
2202
2203   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2204   {
2205   }
2206
2207   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2208   {
2209   }
2210
2211   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2212   {
2213   }
2214
2215   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2216   {
2217   }
2218
2219   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2220   {
2221   }
2222
2223   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2224   {
2225   }
2226
2227   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2228   {
2229   }
2230
2231   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2232   {
2233   }
2234
2235   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2236   {
2237   }
2238
2239   protected void clustalColour_actionPerformed(ActionEvent e)
2240   {
2241   }
2242
2243   protected void zappoColour_actionPerformed(ActionEvent e)
2244   {
2245   }
2246
2247   protected void taylorColour_actionPerformed(ActionEvent e)
2248   {
2249   }
2250
2251   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2252   {
2253   }
2254
2255   protected void helixColour_actionPerformed(ActionEvent e)
2256   {
2257   }
2258
2259   protected void strandColour_actionPerformed(ActionEvent e)
2260   {
2261   }
2262
2263   protected void turnColour_actionPerformed(ActionEvent e)
2264   {
2265   }
2266
2267   protected void buriedColour_actionPerformed(ActionEvent e)
2268   {
2269   }
2270
2271   protected void userDefinedColour_actionPerformed(ActionEvent e)
2272   {
2273   }
2274
2275   protected void PIDColour_actionPerformed(ActionEvent e)
2276   {
2277   }
2278
2279   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2280   {
2281   }
2282
2283   protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2284   {
2285   }
2286
2287   protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2288   {
2289   }
2290
2291
2292   /*
2293    * protected void covariationColour_actionPerformed(ActionEvent e) { }
2294    */
2295
2296   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2297   {
2298   }
2299
2300   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2301   {
2302   }
2303
2304   protected void printMenuItem_actionPerformed(ActionEvent e)
2305   {
2306   }
2307
2308   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2309   {
2310   }
2311
2312   protected void findMenuItem_actionPerformed(ActionEvent e)
2313   {
2314   }
2315
2316   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2317   {
2318   }
2319
2320   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2321   {
2322   }
2323
2324   protected void nucleotideColour_actionPerformed(ActionEvent e)
2325   {
2326   }
2327
2328   protected void deleteGroups_actionPerformed(ActionEvent e)
2329   {
2330   }
2331
2332   protected void copy_actionPerformed(ActionEvent e)
2333   {
2334   }
2335
2336   protected void cut_actionPerformed(ActionEvent e)
2337   {
2338   }
2339
2340   protected void delete_actionPerformed(ActionEvent e)
2341   {
2342   }
2343
2344   protected void pasteNew_actionPerformed(ActionEvent e)
2345   {
2346   }
2347
2348   protected void pasteThis_actionPerformed(ActionEvent e)
2349   {
2350   }
2351
2352   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2353   {
2354   }
2355
2356   public void createPNG(java.io.File f)
2357   {
2358   }
2359
2360   protected void font_actionPerformed(ActionEvent e)
2361   {
2362   }
2363
2364   protected void seqLimit_actionPerformed(ActionEvent e)
2365   {
2366   }
2367
2368   public void seqDBRef_actionPerformed(ActionEvent e)
2369   {
2370
2371   }
2372
2373   public void createEPS(java.io.File f)
2374   {
2375   }
2376
2377   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2378   {
2379
2380   }
2381
2382   /**
2383    * Template method to handle the 'load T-Coffee scores' menu event.
2384    * <p>
2385    * Subclasses override this method to provide a custom action.
2386    *
2387    * @param event
2388    *          The raised event
2389    */
2390   protected void loadScores_actionPerformed(ActionEvent event)
2391   {
2392
2393   }
2394
2395   /**
2396    * Template method to handle the 'Color T-Coffee scores' menu event.
2397    * <p>
2398    * Subclasses override this method to provide a custom action.
2399    *
2400    * @param event
2401    *          The raised event
2402    */
2403   protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2404   {
2405
2406   }
2407
2408   protected void jpred_actionPerformed(ActionEvent e)
2409   {
2410   }
2411
2412   protected void scaleAbove_actionPerformed(ActionEvent e)
2413   {
2414   }
2415
2416   protected void scaleLeft_actionPerformed(ActionEvent e)
2417   {
2418   }
2419
2420   protected void scaleRight_actionPerformed(ActionEvent e)
2421   {
2422   }
2423
2424   protected void modifyPID_actionPerformed(ActionEvent e)
2425   {
2426   }
2427
2428   protected void modifyConservation_actionPerformed(ActionEvent e)
2429   {
2430   }
2431
2432   protected void saveAs_actionPerformed(ActionEvent e)
2433   {
2434   }
2435
2436   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2437   {
2438   }
2439
2440   public void vamsasStore_actionPerformed(ActionEvent e)
2441   {
2442
2443   }
2444
2445   public void vamsasLoad_actionPerformed(ActionEvent e)
2446   {
2447
2448   }
2449
2450   public void showTranslation_actionPerformed(ActionEvent e)
2451   {
2452
2453   }
2454
2455   public void featureSettings_actionPerformed(ActionEvent e)
2456   {
2457
2458   }
2459
2460   public void fetchSequence_actionPerformed(ActionEvent e)
2461   {
2462
2463   }
2464
2465   public void smoothFont_actionPerformed(ActionEvent e)
2466   {
2467
2468   }
2469
2470   public void annotationColour_actionPerformed(ActionEvent e)
2471   {
2472
2473   }
2474
2475   public void rnahelicesColour_actionPerformed(ActionEvent e)
2476   {
2477
2478   }
2479
2480   public void associatedData_actionPerformed(ActionEvent e)
2481   {
2482
2483   }
2484
2485   public void autoCalculate_actionPerformed(ActionEvent e)
2486   {
2487
2488   }
2489
2490   public void sortByTreeOption_actionPerformed(ActionEvent e)
2491   {
2492
2493   }
2494
2495   public void showAllSeqs_actionPerformed(ActionEvent e)
2496   {
2497
2498   }
2499
2500   public void showAllColumns_actionPerformed(ActionEvent e)
2501   {
2502
2503   }
2504
2505   public void hideSelSequences_actionPerformed(ActionEvent e)
2506   {
2507
2508   }
2509
2510   public void hideSelColumns_actionPerformed(ActionEvent e)
2511   {
2512
2513   }
2514
2515   public void hiddenMarkers_actionPerformed(ActionEvent e)
2516   {
2517
2518   }
2519
2520   public void findPdbId_actionPerformed(ActionEvent e)
2521   {
2522
2523   }
2524
2525   public void enterPdbId_actionPerformed(ActionEvent e)
2526   {
2527
2528   }
2529
2530   public void pdbFile_actionPerformed(ActionEvent e)
2531   {
2532
2533   }
2534
2535   public void invertColSel_actionPerformed(ActionEvent e)
2536   {
2537
2538   }
2539
2540   public void tabSelectionChanged(int sel)
2541   {
2542
2543   }
2544
2545   public void tabbedPane_mousePressed(MouseEvent e)
2546   {
2547
2548   }
2549
2550   public void tabbedPane_focusGained(FocusEvent e)
2551   {
2552     requestFocus();
2553   }
2554
2555   public void save_actionPerformed(ActionEvent e)
2556   {
2557
2558   }
2559
2560   public void reload_actionPerformed(ActionEvent e)
2561   {
2562
2563   }
2564
2565   public void newView_actionPerformed(ActionEvent e)
2566   {
2567
2568   }
2569
2570   public void textColour_actionPerformed(ActionEvent e)
2571   {
2572
2573   }
2574
2575   public void idRightAlign_actionPerformed(ActionEvent e)
2576   {
2577
2578   }
2579
2580   public void expandViews_actionPerformed(ActionEvent e)
2581   {
2582
2583   }
2584
2585   public void gatherViews_actionPerformed(ActionEvent e)
2586   {
2587
2588   }
2589
2590   public void buildTreeMenu()
2591   {
2592
2593   }
2594
2595   public void pageSetup_actionPerformed(ActionEvent e)
2596   {
2597
2598   }
2599
2600   public void alignmentProperties()
2601   {
2602
2603   }
2604 }